About | BLOGS | Portfolio | Misc | Recommended | What's New | What's Hot

About | BLOGS | Portfolio | Misc | Recommended | What's New | What's Hot


Bibliography Options Menu

19 Nov 2018 at 01:32
Hide Abstracts   |   Hide Additional Links
Long bibliographies are displayed in blocks of 100 citations at a time. At the end of each block there is an option to load the next block.

Bibliography on: Current Literature — Recent Full Contents


Robert J. Robbins is a biologist, an educator, a science administrator, a publisher, an information technologist, and an IT leader and manager who specializes in advancing biomedical knowledge and supporting education through the application of information technology. More About:  RJR | OUR TEAM | OUR SERVICES | THIS WEBSITE

RJR: Recommended Bibliography 19 Nov 2018 at 01:32 Created: 

Current Literature — Recent Full Contents

Current Literature: Full, recent table-of-contents listings for a few selected journals.

Created with PubMed® Query: 2018[PDAT] AND ( 0003-0147[issn] or 0006-3568[issn] or 0006-8977[issn] or 0012-1606[issn] or 0014-3820[issn] or 0022-0930[issn] or 0022-2844[issn] or 0025-9241[issn] or 0028-0836[issn] or 0031-8248[issn] or 0033-5770[issn] or 0039-3681[issn] or 0047-2484[issn] or 0066-4154[issn] or 0066-4162[issn] or 0066-4197[issn] or 0066-4227[issn] or 0068-6735[issn] or 0071-3260[issn] or 0085-0748[issn] or 0090-4996[issn] or 0095-134x[issn] or 0165-0157[issn] or 0168-6445[issn] or 0168-6496[issn] or 0168-9525[issn] or 0169-3867[issn] or 0169-5347[issn] or 0169-6149[issn] or 0269-7653[issn] or 0343-8651[issn] or 0346-8313[issn] or 0378-2697[issn] or 0393-9375[issn] or 0394-9370[issn] or 0737-4038[issn] or 0743-4634[issn] or 0923-2508[issn] or 0947-5745[issn] or 0949-944x[issn] or 0960-8788[issn] or 0962-8436[issn] or 0966-842x[issn] or 0967-3849[issn] or 0972-7736[issn] or 0972-8422[issn] or 1010-061x[issn] or 1055-7903[issn] or 1060-1538[issn] or 1061-4036[issn] or 1064-7554[issn] or 1081-0706[issn] or 1090-5138[issn] or 1091-6490[issn] or 1095-9203[issn] or 1121-7138[issn] or 1176-9343[issn] or 1369-5274[issn] or 1369-8486[issn] or 1399-560x[issn] or 1433-8319[issn] or 1439-6092[issn] or 1462-2912[issn] or 1464-7931[issn] or 1466-5026[issn] or 1471-0056[issn] or 1471-2091[issn] or 1471-2105[issn] or 1471-2121[issn] or 1471-213x[issn] or 1471-2148[issn] or 1471-2156[issn] or 1471-2164[issn] or 1471-2180[issn] or 1471-2199[issn] or 1471-2229[issn] or 1471-4922[issn] or 1472-6785[issn] or 1474-7049[issn] or 1520-541x[issn] or 1522-0613[issn] or 1527-8204[issn] or 1543-5008[issn] or 1543-592x[issn] or 1552-4884[issn] or 1552-5007[issn] or 1661-5425[issn] or 1674-4918[issn] or 1740-1526[issn] or 1741-7007[issn] or 1752-0509[issn] or 1752-4571[issn] or 1753-6561[issn] or 1756-0500[issn] or 1758-2229[issn] or 1759-6653[issn] or 1933-5377[issn] or 1935-7877[issn] or 1936-6426[issn] or 1941-1405[issn] or 1943-0264[issn] or 1944-3277[issn] or 2036-2641[issn] or 2041-210x[issn] or 2045-7758[issn] or 2049-2618[issn] or 2050-6201[issn] or 2058-5276[issn] or 2090-8032[issn] or 2163-9434[issn] or 2165-3402[issn] or 2210-6502[issn] or 2296-701x[issn] or 2326-8298[issn] or 2329-9002[issn] or 2333-9683[issn] or 2397-334x[issn] or freeble ) NOT pmcbook NOT ispreviousversion

Citations The Papers (from PubMed®)

RevDate: 2018-11-18

Edme A, Zobač P, Korsten P, et al (2018)

Moderate heritability and low evolvability of sperm morphology in a species with high risk of sperm competition, the collared flycatcher Ficedula albicollis.

Journal of evolutionary biology [Epub ahead of print].

Spermatozoa represent the morphologically most diverse type of animal cells and show remarkable variation in size across and also within species. To understand the evolution of this diversity, it is important to reveal to what degree this variation is genetic or environmental in origin and whether this depends on species' life-histories. Here we applied quantitative genetic methods to a pedigreed multigenerational data set of the collared flycatcher Ficedula albicollis, a passerine bird with high levels of extra-pair paternity, to partition genetic and environmental sources of phenotypic variation in sperm dimensions for the first time in a natural population. Narrow-sense heritability (h2) of total sperm length amounted to 0.44±0.14 SE while the corresponding figure for evolvability (estimated as coefficient of additive genetic variation, CVa) was 0.02±0.003 SE. We also found an increase in total sperm length within individual males between the arrival and nestling period. This seasonal variation may reflect constraints in the production of fully elongated spermatozoa shortly after arrival at the breeding grounds. There was no evidence of an effect of male age on sperm dimensions. In many previous studies on laboratory populations of several insect, mammal and avian species, heritabilities of sperm morphology were higher while evolvabilities were similar. Explanations for the differences in heritability may include variation in the environment (laboratory vs. wild), intensity of sexual selection via sperm competition (high vs. low) and genetic architecture that involves unusual linkage disequilibrium coupled with overdominance in one of the studied species. This article is protected by copyright. All rights reserved.

RevDate: 2018-11-18

Gmiter D, Czerwonka G, Drewnowska JM, et al (2018)

Draft Genome Sequences of Proteus mirabilis K1609 and K670: A Model Strains for Territoriality Examination.

Current microbiology pii:10.1007/s00284-018-1598-6 [Epub ahead of print].

Proteus mirabilis is a pathogenic Gram-negative bacterium characterized by its ability to swarm across surfaces, which frequently leads to colonization of the urinary tract and causes severe infections. P. mirabilis strains are also well known from their self-recognition phenomenon, referred to as Dienes phenomenon. In this study, we present novel aspect of self-recognition, which is a hierarchy in terms of strains territoriality. We report the draft genome sequences of P. mirabilis K1609 and K670 strains exhibiting the strongest and the weakest territoriality, respectively. Our results indicated that K1609 is closely related to strain BB2000, a model system for self-recognition, comparing with the K670. We annotated genes associated with recognition of kin and swarming initiation control and indicated polymorphisms by which observed differences in territoriality might results from. The phenotypic and genomic features of both strains reveal their application as a model organisms for studying not only the mechanisms of kin-recognition but also strains territoriality, thus providing new approach to the phenomenon. Availability of these genome sequences may facilitate understanding of the interactions between P. mirabilis strains.

RevDate: 2018-11-18

Du Toit A (2018)

Growth capacity and cell size.

Nature reviews. Microbiology pii:10.1038/s41579-018-0124-y [Epub ahead of print].

RevDate: 2018-11-18

Du Toit A (2018)

Decomposition responses to climate.

Nature reviews. Microbiology pii:10.1038/s41579-018-0123-z [Epub ahead of print].

RevDate: 2018-11-18

Du Toit A (2018)

Let's get moving.

Nature reviews. Microbiology pii:10.1038/s41579-018-0122-0 [Epub ahead of print].

RevDate: 2018-11-18

Qi Y, C Dong (2018)

Incorrect policy interpretation affects conclusion on SO2 emissions by coal-fired power plants in China.

RevDate: 2018-11-18

Jena MK, Jaswal S, Kumar S, et al (2018)

Molecular Mechanism of Mammary Gland Involution: An Update.

Developmental biology pii:S0012-1606(18)30267-7 [Epub ahead of print].

The mammary gland (MG) is a unique organ responsible for milk synthesis, secretion, and involution to prepare the gland for subsequent lactation. The mammary epithelial cells (MECs), which are the milk synthesizing units of the MG, proliferate, differentiate, undergo apoptosis and regenerate following a cyclic pathway of lactation - involution - lactation, fine-tuning these molecular events through hormones, growth factors and other regulatory molecules. The developmental stages of the MG are embryonic, prepubertal, pubertal, pregnancy, lactation and involution, with major developmental processes occurring after puberty. The involution stage includes interesting physiological processes such as MEC apoptosis, matrix remodeling, and the generation of cells regaining the shape of a virgin MG. Signal transducer and activator of transcription 3 (STAT3) is the established master regulator of this process and aberrant expression of STAT3 leads to subnormal involution and may induce neoplasia. Several studies have reported on the molecular mechanism of MG involution with substantial knowledge being gained about this process; however, a deep understanding of this phenomenon has yet to be attained. This review focuses deeply on the molecular details of post-lactational regression, the signaling pathways involved in the lactation-involution cycle, and the latest developments in STAT3-associated MG neoplasia. Deep insight into the involution process will pave the way towards understanding the biology, apoptosis, and oncogenesis of the MG.

RevDate: 2018-11-18

Simkin JE, Zhang D, Stamp LA, et al (2018)

Fine scale differences within the vagal neural crest for enteric nervous system formation.

Developmental biology pii:S0012-1606(18)30721-8 [Epub ahead of print].

The enteric nervous system is mostly derived from vagal neural crest (NC) cells adjacent to somites (s)1-7. We used in ovo focal fluorescent vital dyes and focal electroporation of fluorophore-encoding plasmids in quail embryos to investigate NC cell migration to the foregut initially and later throughout the entire gut. NC cells of different somite-level origins were largely separate until reaching the foregut at about QE2.5, when all routes converged. By QE3.5, NC cells of different somite-levels became mixed, although s1-s2 NC cells were mainly confined to rostral foregut. Mid-vagal NC-derived cells (s3 and s4 level) arrived earliest at the foregut, and occurred in greatest number. By QE6.5 ENS was present from foregut to hindgut. Mid-vagal NC-derived cells occurred in greatest numbers from foregut to distal hindgut. NC-derived cells of s2, s5, and s6 levels were fewer and were widely distributed but were never observed in the distal hindgut. Rostro-vagal (s1) and caudo-vagal (s7) levels were few and restricted to the foregut. Single somite levels of quail neural tube/NC from s1 to s8 were combined with chick aneural ChE4.5 midgut and hindgut and the ensemble was grown on the chorio-allantoic membrane for 6 days. This tests ENS-forming competence in the absence of intra-segmental competition between NC cells, of differential influences of segmental paraxial tissues, and of positional advantage. All vagal NC-levels, but not s8 level, furnished enteric plexuses in the recipient gut, but the density of both ENS cells in total and neurons was highest from mid-vagal level donors, as was the length colonised. We conclude that the fate and competence for ENS formation of vagal NC sub-levels is not uniform over the vagal level but is biased to favour mid-vagal levels. Overviewing this and prior studies suggests the vagal region is, as in its traditional sense, a natural unit but with complex sub-divisions.

RevDate: 2018-11-18

Prasetyoputri A, Jarrad AM, Cooper MA, et al (2018)

The Eagle Effect and Antibiotic-Induced Persistence: Two Sides of the Same Coin?.

Trends in microbiology pii:S0966-842X(18)30230-0 [Epub ahead of print].

The Eagle effect describes a phenomenon in which bacteria or fungi exposed to concentrations of antibiotic higher than an optimal bactericidal concentration (OBC) have paradoxically improved levels of survival than at the OBC due to a decreased net rate of cell death. Despite extensive observational reports of this effect in different microorganisms, its underlying mode of action is not well understood. Although aspects of the Eagle effect resemble persistence, there is strong evidence that these phenomena are substantially different phenotypic responses to antibiotic treatment. We present an overview of the microorganism and antimicrobial combinations in which the Eagle effect has been observed. Proposed underlying mechanism(s) are assessed, and the Eagle effect and microbial persistence are compared and contrasted. The clinical relevance of the Eagle effect is reviewed, incorporating evidence from experimental in vitro and in vivo studies, as well as clinical reports.

RevDate: 2018-11-18

Gillson L, Biggs H, Smit IPJ, et al (2018)

Finding Common Ground between Adaptive Management and Evidence-Based Approaches to Biodiversity Conservation.

Trends in ecology & evolution pii:S0169-5347(18)30248-9 [Epub ahead of print].

Adaptive management (AM) and evidence-based conservation (EBC) have emerged as major decision-making frameworks for conservation management. AM deals with complexity and the importance of local context in making conservation decisions under conditions of high variability, uncertainty, and rapid environmental and social change. EBC seeks for generality from empirical data and aims to develop and enhance best practice. The goal of this review is to explore opportunities for finding common ground between AM and EBC. We propose a framework for distinguishing the subset of conservation problems that are amenable to an evidence-based approach, based on levels of uncertainty, complexity, and social agreement. We then suggest ways for combining multiple lines of evidence and developing greater opportunities for iteration and co-learning in EBC.

RevDate: 2018-11-18

Fajardo A, McIntire EJB, ME Olson (2018)

When Short Stature Is an Asset in Trees.

Trends in ecology & evolution pii:S0169-5347(18)30268-4 [Epub ahead of print].

With their imposing grandeur, the small number of very tall tree species attract a disproportionate amount of scientific study. We right this bias by focusing here on the shorter trees, which often grow in the shade of the giants and many other places besides. That tall trees are so restricted in distribution indicates that there are far more habitats available for small trees. We discuss some leading candidates for the mechanisms that limit maximum plant height in any given habitat, as well as why every habitat has a range of plant sizes. At least two attributes - greater adaptation capacity and higher drought resistance - suggest that the forests of the future belong to short trees.

RevDate: 2018-11-17

Li R, Helbig L, Fu J, et al (2018)

Expressing Cytotoxic Compounds in Escherichia coli Nissle 1917 for Tumor-targeting Therapy.

Research in microbiology pii:S0923-2508(18)30147-5 [Epub ahead of print].

Abnormal blood vessels and hypoxic and necrotic regions are common features of solid tumors and related to the malignant phenotype and therapy resistance. Certain obligate or facultative anaerobic bacteria exhibit inherent ability to colonize and proliferate within solid tumors in vivo. Escherichia coli Nissle 1917 (EcN), a non-pathogenic probiotic in European markets, has been known to proliferate selectively in the interface between the viable and necrotic regions of solid tumors. The objective of this study was to establish a tumor-targeting therapy system using the genetically engineered EcN for targeted delivery of cytotoxic compounds, including colibactin, glidobactin and luminmide. Biosynthetic gene clusters of these cytotoxic compounds were introduced into EcN and the corresponding compounds were detected in the resultant recombinant EcN strains. The recombinant EcN showed significant cytotoxic activity in vitro and in vivo as well, and significantly suppressed the tumor growth. Together, this study confirmed efficient tumor-targeting colonization of EcN and demonstrated its potentiality in the tumor-specific delivery of cytotoxic compounds as a new tumor-targeting therapy system.

RevDate: 2018-11-17

Kelu JJ, Webb SE, Galione A, et al (2018)

Characterization of ADP-ribosyl cyclase 1-like (ARC1-like) activity and NAADP signaling during slow muscle cell development in zebrafish embryos.

Developmental biology pii:S0012-1606(18)30508-6 [Epub ahead of print].

We recently demonstrated the requirement of two-pore channel type 2 (TPC2)-mediated Ca2+ release during slow muscle cell differentiation and motor circuit maturation in intact zebrafish embryos. However, the upstream trigger of TPC2/Ca2+ signaling during these developmental processes remains unclear. Nicotinic acid adenine dinucleotide phosphate (NAADP) is a potent Ca2+ mobilizing messenger, which is suggested to target TPC2 in mediating the release of Ca2+ from acidic vesicles. Here, we report the molecular cloning of the zebrafish ADP ribosyl cyclase (ARC) homolog (i.e., ARC1-like), which is the putative enzyme for generating NAADP. We characterized the expression of the arc1-like transcript and the NAADP level between ~16hours post-fertilization (hpf) and ~48 hpf in whole zebrafish embryos. We showed that when ARC1-like was fused with either EGFP or tdTomato, it was localized in the plasma membrane, and associated with intracellular organelles, such as the acidic vesicles, Golgi complex and sarcoplasmic reticulum, in primary muscle cell cultures. Morpholino (MO)-mediated knockdown of arc1-like or pharmacological inhibition of ARC1 (via treatment with nicotinamide), led to an attenuation of Ca2+ signaling and disruption of slow muscle cell development. In addition, the injection of arc1-like mRNA into ARC1-like morphants partially rescued the Ca2+ signals and slow muscle cell development. Together, our data might suggest a link between ARC1-like, NAADP, TPC2 and Ca2+ signaling during zebrafish myogenesis.

RevDate: 2018-11-17

Morris VB, Kable E, Koop D, et al (2018)

Early development of the feeding larva of the sea urchin Heliocidaris tuberculata: role of the small micromeres.

Development genes and evolution pii:10.1007/s00427-018-0622-y [Epub ahead of print].

The two modes of development in sea urchins are direct development, in which the adult develops directly from the gastrula to the adult and does not feed, and indirect development, in which the adult develops indirectly through a feeding larva. In this account of the indirect, feeding larva of Heliocidaris tuberculata, the question raised is whether an evolutionary difference of unequal cell divisions contributes to the development of feeding structures in the indirect larva. In indirect development, the cell divisions at the fourth and fifth cell cycles of the zygote are unequal, with four small micromeres formed at the vegetal pole at the fifth cell division. In direct development, these cell divisions are not unequal. From their position at the head of the archenteron, the small micromeres are strategically located to contribute to the feeding tissues of the larva and the adult of H. tuberculata.

RevDate: 2018-11-17

Ten LN, Li W, Lee SY, et al (2018)

Hymenobacter pomorum sp. nov., Isolated from Apple Orchard Soil.

Current microbiology pii:10.1007/s00284-018-1595-9 [Epub ahead of print].

A Gram-stain-negative, non-motile, rod-shaped bacterial strain, designated 9-2-1-1T, was isolated from apple orchard soil in Daegu, Republic of Korea. Comparative 16S rRNA gene sequence analysis showed that the isolate belongs to the family Cytophagaceae, Bacteroidetes and it is most closely related to Hymenobacter metalli A2-91T (97.8% similarity) and Hymenobacter marinus KJ035T (96.6%). Growth of strain 9-2-1-1T was observed at 4-30 °C, pH 6-8, and in the presence of 0-1.0% NaCl. The G+C content of the genomic DNA was 62.0 mol%. The predominant respiratory quinone of the isolate was MK-7; the major fatty acids were C15:0 iso (29.3%), C16:1 ω5c (15.4%), C15:0 anteiso (12.5%), summed feature 3 (C16:1 ω7c/C16:1 ω6c; 12.3%), and C16:0 (10.6%); and the major polar lipid was phosphatidylethanolamine. The phenotypic and chemotaxonomic data supported the affiliation of strain 9-2-1-1T with the genus Hymenobacter. However, the DNA-DNA relatedness between the isolate and H. metalli and H. marinus were 31.3% and 24.7%, respectively. The DNA-DNA hybridization result and the differentiating phenotypic properties clearly indicate that strain 9-2-1-1T is the representative of a novel species in the genus Hymenobacter, for which the name Hymenobacter pomorum sp. nov. is proposed. The type strain is 9-2-1-1T (=KCTC 52740T = JCM 32193T).

RevDate: 2018-11-17

Cloney R (2018)

The oracle of inDelphi predicts Cas9 repair outcomes.

Nature reviews. Genetics pii:10.1038/s41576-018-0077-z [Epub ahead of print].

RevDate: 2018-11-17

Ozata DM, Gainetdinov I, Zoch A, et al (2018)

PIWI-interacting RNAs: small RNAs with big functions.

Nature reviews. Genetics pii:10.1038/s41576-018-0073-3 [Epub ahead of print].

In animals, PIWI-interacting RNAs (piRNAs) of 21-35 nucleotides in length silence transposable elements, regulate gene expression and fight viral infection. piRNAs guide PIWI proteins to cleave target RNA, promote heterochromatin assembly and methylate DNA. The architecture of the piRNA pathway allows it both to provide adaptive, sequence-based immunity to rapidly evolving viruses and transposons and to regulate conserved host genes. piRNAs silence transposons in the germ line of most animals, whereas somatic piRNA functions have been lost, gained and lost again across evolution. Moreover, most piRNA pathway proteins are deeply conserved, but different animals employ remarkably divergent strategies to produce piRNA precursor transcripts. Here, we discuss how a common piRNA pathway allows animals to recognize diverse targets, ranging from selfish genetic elements to genes essential for gametogenesis.

RevDate: 2018-11-17

Baker J (2018)

The Doctor Who theme and beyond: female pioneers of electronic music.

Nature, 563(7732):470-471.

RevDate: 2018-11-17

Koch C (2018)

Paul G. Allen (1953-2018).

Nature, 563(7732):474.

RevDate: 2018-11-17

Yan X, H Akiyama (2018)

Overestimation of N2O mitigation potential by water management in rice paddy fields.

RevDate: 2018-11-17

Kritee K, Rudek J, Hamburg SP, et al (2018)

Reply to Yan and Akiyama: Nitrous oxide emissions from rice and their mitigation potential depend on the nature of intermittent flooding.

Proceedings of the National Academy of Sciences of the United States of America pii:1816677115 [Epub ahead of print].

RevDate: 2018-11-17

Einsle JF, Eggeman AS, Martineau BH, et al (2018)

Nanomagnetic properties of the meteorite cloudy zone.

Proceedings of the National Academy of Sciences of the United States of America pii:1809378115 [Epub ahead of print].

Meteorites contain a record of their thermal and magnetic history, written in the intergrowths of iron-rich and nickel-rich phases that formed during slow cooling. Of intense interest from a magnetic perspective is the "cloudy zone," a nanoscale intergrowth containing tetrataenite-a naturally occurring hard ferromagnetic mineral that has potential applications as a sustainable alternative to rare-earth permanent magnets. Here we use a combination of high-resolution electron diffraction, electron tomography, atom probe tomography (APT), and micromagnetic simulations to reveal the 3D architecture of the cloudy zone with subnanometer spatial resolution and model the mechanism of remanence acquisition during slow cooling on the meteorite parent body. Isolated islands of tetrataenite are embedded in a matrix of an ordered superstructure. The islands are arranged in clusters of three crystallographic variants, which control how magnetic information is encoded into the nanostructure. The cloudy zone acquires paleomagnetic remanence via a sequence of magnetic domain state transformations (vortex to two domain to single domain), driven by Fe-Ni ordering at 320 ○C. Rather than remanence being recorded at different times at different positions throughout the cloudy zone, each subregion of the cloudy zone records a coherent snapshot of the magnetic field that was present at 320 ○C. Only the coarse and intermediate regions of the cloudy zone are found to be suitable for paleomagnetic applications. The fine regions, on the other hand, have properties similar to those of rare-earth permanent magnets, providing potential routes to synthetic tetrataenite-based magnetic materials.

RevDate: 2018-11-17

Romney ALT, Davis EM, Corona MM, et al (2018)

Temperature-dependent vitamin D signaling regulates developmental trajectory associated with diapause in an annual killifish.

Proceedings of the National Academy of Sciences of the United States of America pii:1804590115 [Epub ahead of print].

The mechanisms that integrate environmental signals into developmental programs remain largely uncharacterized. Nuclear receptors (NRs) are ligand-regulated transcription factors that orchestrate the expression of complex phenotypes. The vitamin D receptor (VDR) is an NR activated by 1α,25-dihydroxyvitamin D3 [1,25(OH)2D3], a hormone derived from 7-dehydrocholesterol (7-DHC). VDR signaling is best known for regulating calcium homeostasis in mammals, but recent evidence suggests a diversity of uncharacterized roles. In response to incubation temperature, embryos of the annual killifish Austrofundulus limnaeus can develop along two alternative trajectories: active development and diapause. These trajectories diverge early in development, from a biochemical, morphological, and physiological perspective. We manipulated incubation temperature to induce the two trajectories and profiled changes in gene expression using RNA sequencing and weighted gene coexpression network analysis. We report that transcripts involved in 1,25(OH)2D3 synthesis and signaling are expressed in a trajectory-specific manner. Furthermore, exposure of embryos to vitamin D3 analogs and Δ4-dafachronic acid directs continuous development under diapause-inducing conditions. Conversely, blocking synthesis of 1,25(OH)2D3 induces diapause in A. limnaeus and a diapause-like state in zebrafish, suggesting vitamin D signaling is critical for normal vertebrate development. These data support vitamin D signaling as a molecular pathway that can regulate developmental trajectory and metabolic dormancy in a vertebrate. Interestingly, the VDR is homologous to the daf-12 and ecdysone NRs that regulate dormancy in Caenorhabditis elegans and Drosophila We suggest that 7-DHC-derived hormones and their associated NRs represent a conserved pathway for the integration of environmental information into developmental programs associated with life history transitions in animals.

RevDate: 2018-11-17

Wang Q, Li Y, Ishikawa K, et al (2018)

Resistance protein Pit interacts with the GEF OsSPK1 to activate OsRac1 and trigger rice immunity.

Proceedings of the National Academy of Sciences of the United States of America pii:1813058115 [Epub ahead of print].

Resistance (R) genes encode intracellular nucleotide-binding/leucine-rich repeat-containing (NLR) family proteins that serve as critical plant immune receptors to induce effector-triggered immunity (ETI). NLR proteins possess a tripartite domain architecture consisting of an N-terminal variable region, a central nucleotide-binding domain, and a C-terminal leucine-rich repeat. N-terminal coiled-coil (CC) or Toll-interleukin 1 receptor (TIR) domains of R proteins appear to serve as platforms to trigger immune responses, because overexpression of the CC or TIR domain of some R proteins is sufficient to induce an immune response. Because direct downstream signaling molecules of R proteins remain obscure, the molecular mechanisms by which R proteins regulate downstream signaling are largely unknown. We reported previously that a rice R protein named Pit triggers ETI through a small GTPase, OsRac1, although how Pit activates OsRac1 is unclear. Here, we identified OsSPK1, a DOCK family guanine nucleotide exchange factor, as an interactor of Pit and activator for OsRac1. OsSPK1 contributes to signaling by two disease-resistance genes, Pit and Pia, against the rice blast fungus Magnaporthe oryzae and facilitates OsRac1 activation in vitro and in vivo. The CC domain of Pit is required for its binding to OsSPK1, OsRac1 activation, and the induction of cell death. Overall, we conclude that OsSPK1 is a direct and key signaling target of Pit-mediated immunity. Our results shed light on how R proteins trigger ETI through direct downstream molecules.

RevDate: 2018-11-17

Cory S (2018)

Phosphatidylserine hide-and-seek.

Proceedings of the National Academy of Sciences of the United States of America pii:1817485115 [Epub ahead of print].

RevDate: 2018-11-17

Ramsbottom SA, Molinari E, Srivastava S, et al (2018)

Targeted exon skipping of a CEP290 mutation rescues Joubert syndrome phenotypes in vitro and in a murine model.

Proceedings of the National Academy of Sciences of the United States of America pii:1809432115 [Epub ahead of print].

Genetic treatments of renal ciliopathies leading to cystic kidney disease would provide a real advance in current therapies. Mutations in CEP290 underlie a ciliopathy called Joubert syndrome (JBTS). Human disease phenotypes include cerebral, retinal, and renal disease, which typically progresses to end stage renal failure (ESRF) within the first two decades of life. While currently incurable, there is often a period of years between diagnosis and ESRF that provides a potential window for therapeutic intervention. By studying patient biopsies, patient-derived kidney cells, and a mouse model, we identify abnormal elongation of primary cilia as a key pathophysiological feature of CEP290-associated JBTS and show that antisense oligonucleotide (ASO)-induced splicing of the mutated exon (41, G1890*) restores protein expression in patient cells. We demonstrate that ASO-induced splicing leading to exon skipping is tolerated, resulting in correct localization of CEP290 protein to the ciliary transition zone, and restoration of normal cilia length in patient kidney cells. Using a gene trap Cep290 mouse model of JBTS, we show that systemic ASO treatment can reduce the cystic burden of diseased kidneys in vivo. These findings indicate that ASO treatment may represent a promising therapeutic approach for kidney disease in CEP290-associated ciliopathy syndromes.

RevDate: 2018-11-17

Coppock A, Leeper TJ, KJ Mullinix (2018)

Generalizability of heterogeneous treatment effect estimates across samples.

Proceedings of the National Academy of Sciences of the United States of America pii:1808083115 [Epub ahead of print].

The extent to which survey experiments conducted with nonrepresentative convenience samples are generalizable to target populations depends critically on the degree of treatment effect heterogeneity. Recent inquiries have found a strong correspondence between sample average treatment effects estimated in nationally representative experiments and in replication studies conducted with convenience samples. We consider here two possible explanations: low levels of effect heterogeneity or high levels of effect heterogeneity that are unrelated to selection into the convenience sample. We analyze subgroup conditional average treatment effects using 27 original-replication study pairs (encompassing 101,745 individual survey responses) to assess the extent to which subgroup effect estimates generalize. While there are exceptions, the overwhelming pattern that emerges is one of treatment effect homogeneity, providing a partial explanation for strong correspondence across both unconditional and conditional average treatment effect estimates.

RevDate: 2018-11-17

Chouinard-Watkins R, RP Bazinet (2018)

ACSL6 is critical for maintaining brain DHA levels.

Proceedings of the National Academy of Sciences of the United States of America pii:1817557115 [Epub ahead of print].

RevDate: 2018-11-17

Camac JS, Condit R, FitzJohn RG, et al (2018)

Partitioning mortality into growth-dependent and growth-independent hazards across 203 tropical tree species.

Proceedings of the National Academy of Sciences of the United States of America pii:1721040115 [Epub ahead of print].

Tree death drives population dynamics, nutrient cycling, and evolution within plant communities. Mortality variation across species is thought to be influenced by different factors relative to variation within species. The unified model provided here separates mortality rates into growth-dependent and growth-independent hazards. This model creates the opportunity to simultaneously estimate these hazards both across and within species. Moreover, it provides the ability to examine how species traits affect growth-dependent and growth-independent hazards. We derive this unified mortality model using cross-validated Bayesian methods coupled with mortality data collected over three census intervals for 203 tropical rainforest tree species at Barro Colorado Island (BCI), Panama. We found that growth-independent mortality tended to be higher in species with lower wood density, higher light requirements, and smaller maximum diameter at breast height (dbh). Mortality due to marginal carbon budget as measured by near-zero growth rate tended to be higher in species with lower wood density and higher light demand. The total mortality variation attributable to differences among species was large relative to variation explained by these traits, emphasizing that much remains to be understood. This additive hazards model strengthens our capacity to parse and understand individual-level mortality in highly diverse tropical forests and hence to predict its consequences.

RevDate: 2018-11-17

Czajka JJ, Abernathy MH, Benites VT, et al (2018)

Model metabolic strategy for heterotrophic bacteria in the cold ocean based on Colwellia psychrerythraea 34H.

Proceedings of the National Academy of Sciences of the United States of America pii:1807804115 [Epub ahead of print].

Colwellia psychrerythraea 34H is a model psychrophilic bacterium found in the cold ocean-polar sediments, sea ice, and the deep sea. Although the genomes of such psychrophiles have been sequenced, their metabolic strategies at low temperature have not been quantified. We measured the metabolic fluxes and gene expression of 34H at 4 °C (the mean global-ocean temperature and a normal-growth temperature for 34H), making comparative analyses at room temperature (above its upper-growth temperature of 18 °C) and with mesophilic Escherichia coli When grown at 4 °C, 34H utilized multiple carbon substrates without catabolite repression or overflow byproducts; its anaplerotic pathways increased flux network flexibility and enabled CO2 fixation. In glucose-only medium, the Entner-Doudoroff (ED) pathway was the primary glycolytic route; in lactate-only medium, gluconeogenesis and the glyoxylate shunt became active. In comparison, E. coli, cold stressed at 4 °C, had rapid glycolytic fluxes but no biomass synthesis. At their respective normal-growth temperatures, intracellular concentrations of TCA cycle metabolites (α-ketoglutarate, succinate, malate) were 4-17 times higher in 34H than in E. coli, while levels of energy molecules (ATP, NADH, NADPH) were 10- to 100-fold lower. Experiments with E. coli mutants supported the thermodynamic advantage of the ED pathway at cold temperature. Heat-stressed 34H at room temperature (2 hours) revealed significant down-regulation of genes associated with glycolytic enzymes and flagella, while 24 hours at room temperature caused irreversible cellular damage. We suggest that marine heterotrophic bacteria in general may rely upon simplified metabolic strategies to overcome thermodynamic constraints and thrive in the cold ocean.

RevDate: 2018-11-17

Karplus VJ, Zhang S, D Almond (2018)

Reply to Qi and Dong: Policy clarification and robustness of effects.

Proceedings of the National Academy of Sciences of the United States of America pii:1815003115 [Epub ahead of print].

RevDate: 2018-11-17

Polishchuk LV, JL Blanchard (2018)

Uniting Discoveries of Abundance-Size Distributions from Soils and Seas.

Trends in ecology & evolution pii:S0169-5347(18)30264-7 [Epub ahead of print].

Science is a search for patterns but there are few cross-habitat patterns in ecology. We propose key questions following the findings of consistent scaling of abundance versus body mass from bacteria to earthworms and whales, based on an almost forgotten study of soils and a well-known one from the open ocean.

RevDate: 2018-11-17

Amodio P, Boeckle M, Schnell AK, et al (2018)

Grow Smart and Die Young: Why Did Cephalopods Evolve Intelligence?.

Trends in ecology & evolution pii:S0169-5347(18)30267-2 [Epub ahead of print].

Intelligence in large-brained vertebrates might have evolved through independent, yet similar processes based on comparable socioecological pressures and slow life histories. This convergent evolutionary route, however, cannot explain why cephalopods developed large brains and flexible behavioural repertoires: cephalopods have fast life histories and live in simple social environments. Here, we suggest that the loss of the external shell in cephalopods (i) caused a dramatic increase in predatory pressure, which in turn prevented the emergence of slow life histories, and (ii) allowed the exploitation of novel challenging niches, thus favouring the emergence of intelligence. By highlighting convergent and divergent aspects between cephalopods and large-brained vertebrates we illustrate how the evolution of intelligence might not be constrained to a single evolutionary route.

RevDate: 2018-11-17

Fouet C, C Kamdem (2018)

Integrated Mosquito Management: Is Precision Control a Luxury or Necessity?.

Trends in parasitology pii:S1471-4922(18)30224-1 [Epub ahead of print].

The versatility of mosquito species that spread emerging arthropod-borne viruses such as Zika has highlighted the urgent need to re-evaluate mosquito-control standards. The prospect of using precise knowledge of the geographic distribution and vector status of local populations to guide targeted interventions has gained renewed attention, but the feasibility and utility of such an approach remain to be investigated. Using the example of mosquito management in the USA, we present ideas for designing, monitoring, and assessing precision vector control tailored to different environmental and epidemiological settings. We emphasize the technical adjustments that could be implemented in mosquito-control districts to enable targeted control while strengthening traditional management.

RevDate: 2018-11-17

Kenmoe S, Tagnouokam PAN, Nde CK, et al (2018)

Using dried blood spot for the detection of HBsAg and anti-HCV antibodies in Cameroon.

BMC research notes, 11(1):818 pii:10.1186/s13104-018-3931-3.

OBJECTIVE: Dried blood spots (DBS) offer multiple benefits for collecting, storing and shipping whole blood samples. Our objective was to compare, for the first time in Africa, the performance of DBS with respect to plasma in the detection of Hepatitis B surface antigen (HBsAg) and antibodies to Hepatitis C Virus (anti-HCV) using Architect, Abbott Diagnostics.

RESULTS: DBS had a sensitivity of 99%, a specificity of 100%, a positive predictive value of 99%, a negative predictive value of 100% and a kappa index of 0.99 for the detection of HBsAg. For anti-HCV detection, the sensitivity, specificity, positive predictive value, negative predictive value and kappa index were 99%, 98%, 98%, 99%, and 0.97, respectively. This study confirms that DBS may be a reliable alternative specimen type for HBV and HCV diagnosis.

RevDate: 2018-11-17

Schmutz C, D Mäusezahl (2018)

The burden of gastroenteritis in Switzerland (BUGS) study: a research proposal for a 1-year, prospective cohort study.

BMC research notes, 11(1):816 pii:10.1186/s13104-018-3916-2.

OBJECTIVES: Acute gastroenteritis (AG) is a usually self-limiting, but common disease worldwide. In Europe, incidence estimates range from 0.3-1.5 AG episodes/person-year. For Switzerland, available information on AG is restricted to notifiable foodborne diseases and findings from research studies starting at primary care level. The aims of this 1-year, population-based prospective cohort study are to assess the incidence, burden of disease, aetiology and socio-economic impact of AG in the Swiss general population. Additionally, the prevalence of bacterial gastrointestinal pathogens and bacteria harbouring antimicrobial resistances in the asymptomatic population shall be assessed.

RESULTS: Weekly follow-up of the cohort consisting of 3000 participants will provide incidence estimates of AG. Furthermore, information collected will be used to assess risk factors for experiencing an episode of AG, to explore determinants for help seeking, and to characterise the socio-economic impact of AG including absence from work and inability to perform daily activities. Aetiology of AG is determined by investigating stool samples from symptomatic participants. Finally, stool samples from participants collected during an asymptomatic period will be used to assess the prevalence of enterohaemorrhagic E. coli, Campylobacter spp., Salmonella spp. and Shigella spp. as well as of resistance to different antibiotics (extended-spectrum beta-lactamase-, fluoroquinolone- and carbapenemase-resistance).

RevDate: 2018-11-17

Al Bahhawi T, Doweri AA, Sawadi RM, et al (2018)

Consumption habits of pregnant women in the Jazan region, Saudi Arabia: a descriptive study.

BMC research notes, 11(1):817 pii:10.1186/s13104-018-3921-5.

OBJECTIVE: Maternal nutritional habits are critical for the health of both mother and offspring. Postpartum outcomes for mother and infant are strongly influenced by the mother's nutritional status. Information about consumption habits among pregnant women in Saudi Arabia is scarce. Thus, this study aims to describe the consumption habits of pregnant women in the Jazan region, Saudi Arabia.

RESULTS: Meat, fish, and fruits were consumed by 97%, 86%, and 90% of the sample. Sugary desserts, fast food, and canned food were consumed by 90%, 81%, and 71% of the sample. Caffeine, juices, and milk were consumed by 75%, 92%, and 81% of the sample. Previous percentages show general higher consumption habits of food and beverages. Over-the-counter medication was used by only 17%. Folic acid, iron, and calcium use by 77%, 64%, and 58% of the sample, respectively. These percentage shows conservative use of Over-the-counter medication and sub-optimal use of important dietary supplements. Moreover, there was a positive association between caffeine intake and trimesters. Furthermore, there was negative association between education level and fish intake. Finally, canned foods consumption was higher among low income pregnant women.

RevDate: 2018-11-17

Ayalew TW, AM Nigatu (2018)

Focused antenatal care utilization and associated factors in Debre Tabor Town, northwest Ethiopia, 2017.

BMC research notes, 11(1):819 pii:10.1186/s13104-018-3928-y.

OBJECTIVE: Attending antenatal care helps to reduce the occurrence of maternal morbidity and mortality by providing chances for health promotion and information about danger signs, birth preparedness and where to seek care for pregnancy complications. Therefore identifying factors affecting the utilization of focused ANC service is of supreme importance.

RESULTS: A total of 317 mothers who had a history of antenatal care for their last birth during the previous 6 months were included in the study from which 112 (35.3%, 95% CI 30.6, 40.4) of mothers attended focused antenatal care services. Age of mother [AOR = 4.7, 95% CI 1.87, 11.88], Educational status [AOR = 2.5, 95% CI 1.00, 6.19], history of still birth [AOR = 13.1, 95% CI 2.14, 80.20] and planned pregnancy [AOR = 3.7, 95% CI 1.23, 11.12] were found to be major predictors for focused ANC service utilization. Proportion of focused antenatal care was low (35.3%). Age of mother, education, history of stillbirth and planned pregnancy were identified as predictors affecting focused antenatal care service utilization. Encouraging women's educational status, behavioral change communication at grass root level and improving the capacity and quality of ANC service are some of the recommendations forwarded.

RevDate: 2018-11-17

Kondhare KR, Malankar NN, Devani RS, et al (2018)

Genome-wide transcriptome analysis reveals small RNA profiles involved in early stages of stolon-to-tuber transitions in potato under photoperiodic conditions.

BMC plant biology, 18(1):284 pii:10.1186/s12870-018-1501-4.

BACKGROUND: Small RNAs (sRNAs), especially miRNAs, act as crucial regulators of plant growth and development. Two other sRNA groups, trans-acting short-interfering RNAs (tasiRNAs) or phased siRNAs (phasiRNAs), are also emerging as potential regulators of plant development. Stolon-to-tuber transition in potato is an important developmental phase governed by many environmental, biochemical and hormonal cues. Among different environmental factors, photoperiod has a major influence on tuberization. Several mobile signals, mRNAs, proteins and transcription factors have been widely studied for their role in tuber formation in potato, however, no information is yet available that describes the molecular signals governing the early stages of stolon transitions or cell-fate changes at the stolon tip before it matures to potato. Stolon could be an interesting model for studying below ground organ development and we hypothesize that small RNAs might be involved in regulation of stolon-to-tuber transition process in potato. Also, there is no literature that describes the phased siRNAs in potato development.

RESULTS: We performed sRNA profiling of early stolon stages (4, 7 and 10 d) under long-day (LD; 16 h light, 8 h dark) and short-day (SD; 8 h light, 16 h dark) photoperiodic conditions. Altogether, 7 (out of 324) conserved and 12 (out of 311) novel miRNAs showed differential expression in early stolon stages under SD vs LD photoperiodic conditions. Key target genes (StGRAS, StTCP2/4 and StPTB6) exhibited differential expression in early stolon stages under SD vs LD photoperiodic conditions, indicative of their potential role in tuberization. Out of 830 TAS-like loci identified, 24 were cleaved by miRNAs to generate 190 phased siRNAs. Some of them targeted crucial tuberization genes such as StPTB1, POTH1 and StCDPKs. Two conserved TAS loci, referred as StTAS3 and StTAS5, which share close conservation with members of the Solanaceae family, were identified in our analysis. One TAS-like locus (StTm2) was validated for phased siRNA generation and one of its siRNA was predicted to cleave an important tuber marker gene StGA2ox1.

CONCLUSION: Our study suggests that sRNAs and their selective target genes could be associated with the regulation of early stages of stolon-to-tuber transitions in a photoperiod-dependent manner in potato.

RevDate: 2018-11-17

Guo DL, Li Q, Lv WQ, et al (2018)

MicroRNA profiling analysis of developing berries for 'Kyoho' and its early-ripening mutant during berry ripening.

BMC plant biology, 18(1):285 pii:10.1186/s12870-018-1516-x.

BACKGROUND: 'Fengzao' is an early-ripening bud mutant of 'Kyoho', which matures nearly 30 days earlier than 'Kyoho'. To gain a better understanding of the regulatory role of miRNAs in early-ripening of grape berry, high-throughput sequencing approach and quantitative RT-PCR validation were employed to identify miRNAs at the genome-wide level and profile the expression patterns of the miRNAs during berry development in 'Kyho' and 'Fengzao', respectively.

RESULTS: Nine independent small RNA libraries were constructed and sequenced in two varieties from key berry development stages. A total of 108 known miRNAs and 61 novel miRNAs were identified. Among that, 159 miRNAs identified in 'Fengzao' all completely expressed in 'Kyoho' and there were 10 miRNAs specifically expressed in 'Kyoho'. The expression profiles of known and novel miRNAs were quite similar between two varieties. As the major differentially expressed miRNAs, novel_144, vvi-miR3626-3p and vvi-miR3626-5p only expressed in 'Kyoho', vvi-miR399b and vvi-miR399e were down-regulated in 'Fengzao', while vvi-miR477b-3p up-regulated in 'Fengzao'. According to the expression analysis and previous reports, miR169-NF-Y subunit, miR398-CSD, miR3626-RNA helicase, miR399- phosphate transporter and miR477-GRAS transcription factor were selected as the candidates for further investigations of miRNA regulation role in the early-ripening of grape. The qRT-PCR analyses validated the contrasting expression patterns for these miRNAs and their target genes.

CONCLUSIONS: The miRNAome of the grape berry development of 'Kyoho', and its early-ripening bud mutant, 'Fengzao' were compared by high-throughput sequencing. The expression pattern of several key miRNAs and their target genes during grape berry development and ripening stages was examined. Our results provide valuable basis towards understanding the regulatory mechanisms of early-ripening of grape berry.

RevDate: 2018-11-17

Wakita Y, Shimomura Y, Kitada Y, et al (2018)

Taxonomic classification for microbiome analysis, which correlates well with the metabolite milieu of the gut.

BMC microbiology, 18(1):188 pii:10.1186/s12866-018-1311-8.

BACKGROUND: 16S rRNA gene amplicon sequencing analysis (16S amplicon sequencing) has provided considerable information regarding the ecology of the intestinal microbiome. Recently, metabolomics has been used for investigating the crosstalk between the intestinal microbiome and the host via metabolites. In the present study, we determined the accuracy with which 16S rRNA gene data at different classification levels correspond to the metabolome data for an in-depth understanding of the intestinal environment.

RESULTS: Over 200 metabolites were identified using capillary electrophoresis and time-of-flight mass spectrometry (CE-TOFMS)-based metabolomics in the feces of antibiotic-treated and untreated mice. 16S amplicon sequencing, followed by principal component analysis (PCA) of the intestinal microbiome at each taxonomic rank, revealed differences between the antibiotic-treated and untreated groups in the first principal component in the family-, genus, and species-level analyses. These differences were similar to those observed in the PCA of the metabolome. Furthermore, a strong correlation between principal component (PC) scores of the metabolome and microbiome was observed in family-, genus-, and species-level analyses.

CONCLUSIONS: Lower taxonomic ranks such as family, genus, or species are preferable for 16S amplicon sequencing to investigate the correlation between the microbiome and metabolome. The correlation of PC scores between the microbiome and metabolome at lower taxonomic levels yield a simple method of integrating different "-omics" data, which provides insights regarding crosstalk between the intestinal microbiome and the host.

RevDate: 2018-11-17

Garapati HS, K Mishra (2018)

Comparative genomics of nuclear envelope proteins.

BMC genomics, 19(1):823 pii:10.1186/s12864-018-5218-4.

BACKGROUND: The nuclear envelope (NE) that encapsulates the nuclear genome is a double lipid bilayer with several integral and peripherally associated proteins. It is a characteristic feature of the eukaryotes and acts as a hub for a number of important nuclear events including transcription, repair, and regulated gene expression. The proteins associated with the nuclear envelope mediate the NE functions and maintain its structural integrity, which is crucial for survival. In spite of the importance of this structure, knowledge of the protein composition of the nuclear envelope and their function, are limited to very few organisms belonging to Opisthokonta and Archaeplastida supergroups. The NE composition is largely unknown in organisms outside these two supergroups.

RESULTS: In this study, we have taken a comparative sequence analysis approach to identify the NE proteome that is present across all five eukaryotic supergroups. We identified 22 proteins involved in various nuclear functions to be part of the core NE proteome. The presence of these proteins across eukaryotes, suggests that they are traceable to the Last Eukaryotic Common Ancestor (LECA). Additionally, we also identified the NE proteins that have evolved in a lineage specific manner and those that have been preserved only in a subset of organisms.

CONCLUSIONS: Our study identifies the conserved features of the nuclear envelope across eukaryotes and provides insights into the potential composition and the functionalities that were constituents of the LECA NE.

RevDate: 2018-11-17

de Verdal H, Vandeputte M, Mekkawy W, et al (2018)

Quantifying the genetic parameters of feed efficiency in juvenile Nile tilapia Oreochromis niloticus.

BMC genetics, 19(1):105 pii:10.1186/s12863-018-0691-y.

BACKGROUND: Improving feed efficiency in fish is crucial at the economic, social and environmental levels with respect to developing a more sustainable aquaculture. The important contribution of genetic improvement to achieve this goal has been hampered by the lack of accurate basic information on the genetic parameters of feed efficiency in fish. We used video assessment of feed intake on individual fish reared in groups to estimate the genetic parameters of six growth traits, feed intake, feed conversion ratio (FCR) and residual feed intake in 40 pedigreed families of the GIFT strain of Nile tilapia, Oreochromis niloticus. Feed intake and growth were measured on juvenile fish (22.4 g mean body weight) during 13 consecutive meals, representing 7 days of measurements. We used these data to estimate the FCR response to different selection criteria to assess the potential of genetics as a means of increasing FCR in tilapia.

RESULTS: Our results demonstrate genetic control for FCR in tilapia, with a heritability estimate of 0.32 ± 0.11. Response to selection estimates showed FCR could be efficiently improved by selective breeding. Due to low genetic correlations, selection for growth traits would not improve FCR. However, weight loss at fasting has a high genetic correlation with FCR (0.80 ± 0.25) and a moderate heritability (0.23), and could be an easy to measure and efficient criterion to improve FCR by selective breeding in tilapia.

CONCLUSION: At this age, FCR is genetically determined in Nile tilapia. A selective breeding program could be possible and could help enabling the development of a more sustainable aquaculture production.

RevDate: 2018-11-17

Jones KE, Benitez L, Angielczyk KD, et al (2018)

Adaptation and constraint in the evolution of the mammalian backbone.

BMC evolutionary biology, 18(1):172 pii:10.1186/s12862-018-1282-2.

BACKGROUND: The axial skeleton consists of repeating units (vertebrae) that are integrated through their development and evolution. Unlike most tetrapods, vertebrae in the mammalian trunk are subdivided into distinct thoracic and lumbar modules, resulting in a system that is constrained in terms of count but highly variable in morphology. This study asks how thoracolumbar regionalization has impacted adaptation and evolvability across mammals. Using geometric morphometrics, we examine evolutionary patterns in five vertebral positions from diverse mammal species encompassing a broad range of locomotor ecologies. We quantitatively compare the effects of phylogenetic and allometric constraints, and ecological adaptation between regions, and examine their impact on evolvability (disparity and evolutionary rate) of serially-homologous vertebrae.

RESULTS: Although phylogenetic signal and allometry are evident throughout the trunk, the effect of locomotor ecology is partitioned between vertebral positions. Lumbar vertebral shape correlates most strongly with ecology, differentiating taxa based on their use of asymmetric gaits. Similarly, disparity and evolutionary rates are also elevated posteriorly, indicating a link between the lumbar region, locomotor adaptation, and evolvability.

CONCLUSION: Vertebral regionalization in mammals has facilitated rapid evolution of the posterior trunk in response to selection for locomotion and static body support.

RevDate: 2018-11-17

Shen Y, Kubben N, Candia J, et al (2018)

RefCell: multi-dimensional analysis of image-based high-throughput screens based on 'typical cells'.

BMC bioinformatics, 19(1):427 pii:10.1186/s12859-018-2454-1.

BACKGROUND: Image-based high-throughput screening (HTS) reveals a high level of heterogeneity in single cells and multiple cellular states may be observed within a single population. Currently available high-dimensional analysis methods are successful in characterizing cellular heterogeneity, but suffer from the "curse of dimensionality" and non-standardized outputs.

RESULTS: Here we introduce RefCell, a multi-dimensional analysis pipeline for image-based HTS that reproducibly captures cells with typical combinations of features in reference states and uses these "typical cells" as a reference for classification and weighting of metrics. RefCell quantitatively assesses heterogeneous deviations from typical behavior for each analyzed perturbation or sample.

CONCLUSIONS: We apply RefCell to the analysis of data from a high-throughput imaging screen of a library of 320 ubiquitin-targeted siRNAs selected to gain insights into the mechanisms of premature aging (progeria). RefCell yields results comparable to a more complex clustering-based single-cell analysis method; both methods reveal more potential hits than a conventional analysis based on averages.

RevDate: 2018-11-17

Tekle YI, FC Wood (2018)

A practical implementation of large transcriptomic data analysis to resolve cryptic species diversity problems in microbial eukaryotes.

BMC evolutionary biology, 18(1):170 pii:10.1186/s12862-018-1283-1.

BACKGROUND: Transcriptome sequencing has become a method of choice for evolutionary studies in microbial eukaryotes due to low cost and minimal sample requirements. Transcriptome data has been extensively used in phylogenomic studies to infer ancient evolutionary histories. However, its utility in studying cryptic species diversity is not well explored. An empirical investigation was conducted to test the applicability of transcriptome data in resolving two major types of discordances at lower taxonomic levels. These include cases where species have the same morphology but different genetics (cryptic species) and species of different morphologies but have the same genetics. We built a species comparison bioinformatic pipeline that takes into account the nature of transcriptome data in amoeboid microbes exemplifying such discordances.

RESULT: Our analyses of known or suspected cryptic species yielded consistent results regardless of the methods of culturing, RNA collection or sequencing. Over 95% of the single copy genes analyzed in samples of the same species sequenced using different methods and cryptic species had intra- and interspecific divergences below 2%. Only a minority of groups (2.91-4.87%) had high distances exceeding 2% in these taxa, which was likely caused by low data quality. This pattern was also observed in suspected genetically similar species with different morphologies. Transcriptome data consistently delineated all taxa above species level, including cryptically diverse species. Using our approach we were able to resolve cryptic species problems, uncover misidentification and discover new species. We also identified several potential barcode markers with varying evolutionary rates that can be used in lineages with different evolutionary histories.

CONCLUSION: Our findings demonstrate that transcriptome data is appropriate for understanding cryptic species diversity in microbial eukaryotes.

RevDate: 2018-11-17

Mohapatra S, JC Weisshaar (2018)

Modified Pearson correlation coefficient for two-color imaging in spherocylindrical cells.

BMC bioinformatics, 19(1):428 pii:10.1186/s12859-018-2444-3.

The revolution in fluorescence microscopy enables sub-diffraction-limit ("superresolution") localization of hundreds or thousands of copies of two differently labeled proteins in the same live cell. In typical experiments, fluorescence from the entire three-dimensional (3D) cell body is projected along the z-axis of the microscope to form a 2D image at the camera plane. For imaging of two different species, here denoted "red" and "green", a significant biological question is the extent to which the red and green spatial distributions are positively correlated, anti-correlated, or uncorrelated. A commonly used statistic for assessing the degree of linear correlation between two image matrices R and G is the Pearson Correlation Coefficient (PCC). PCC should vary from - 1 (perfect anti-correlation) to 0 (no linear correlation) to + 1 (perfect positive correlation). However, in the special case of spherocylindrical bacterial cells such as E. coli or B. subtilis, we show that the PCC fails both qualitatively and quantitatively. PCC returns the same + 1 value for 2D projections of distributions that are either perfectly correlated in 3D or completely uncorrelated in 3D. The PCC also systematically underestimates the degree of anti-correlation between the projections of two perfectly anti-correlated 3D distributions. The problem is that the projection of a random spatial distribution within the 3D spherocylinder is non-random in 2D, whereas PCC compares every matrix element of R or G with the constant mean value [Formula: see text] or [Formula: see text]. We propose a modified Pearson Correlation Coefficient (MPCC) that corrects this problem for spherocylindrical cell geometry by using the proper reference matrix for comparison with R and G. Correct behavior of MPCC is confirmed for a variety of numerical simulations and on experimental distributions of HU and RNA polymerase in live E. coli cells. The MPCC concept should be generalizable to other cell shapes.

RevDate: 2018-11-17

Iqbal M, Dubey M, Gudmundsson M, et al (2018)

Comparative evolutionary histories of fungal proteases reveal gene gains in the mycoparasitic and nematode-parasitic fungus Clonostachys rosea.

BMC evolutionary biology, 18(1):171 pii:10.1186/s12862-018-1291-1.

BACKGROUND: The ascomycete fungus Clonostachys rosea (order Hypocreales) can control several important plant diseases caused by plant pathogenic fungi and nematodes. Subtilisin-like serine proteases are considered to play an important role in pathogenesis in entomopathogenic, mycoparasitic, and nematophagous fungi used for biological control. In this study, we analysed the evolutionary histories of protease gene families, and investigated sequence divergence and regulation of serine protease genes in C. rosea.

RESULTS: Proteases of selected hypocrealean fungal species were classified into families based on the MEROPS peptidase database. The highest number of protease genes (590) was found in Fusarium solani, followed by C. rosea with 576 genes. Analysis of gene family evolution identified non-random changes in gene copy numbers in the five serine protease gene families S1A, S8A, S9X, S12 and S33. Four families, S1A, S8A, S9X, and S33, displayed gene gains in C. rosea. A gene-tree / species-tree reconciliation analysis of the S8A family revealed that the gene copy number increase in C. rosea was primarily associated with the S08.054 (proteinase K) subgroup. In addition, regulatory and predicted structural differences, including twelve sites evolving under positive selection, among eighteen C. rosea S8A serine protease paralog genes were also observed. The C. rosea S8A serine protease gene prs6 was induced during interaction with the plant pathogenic species F. graminearum.

CONCLUSIONS: Non-random increases in S8A, S9X and S33 serine protease gene numbers in the mycoparasitic species C. rosea, Trichoderma atroviride and T. virens suggests an involvement in fungal-fungal interactions. Regulatory and predicted structural differences between C. rosea S8A paralogs indicate that functional diversification is driving the observed increase in gene copy numbers. The induction of prs6 expression in C. rosea during confrontation with F. graminearum suggests an involvement of the corresponding protease in fungal-fungal interactions. The results pinpoint the importance of serine proteases for ecological niche adaptation in C. rosea, including a potential role in the mycoparasitic attack on fungal prey.

RevDate: 2018-11-16

Li C, Sun X, Conover JL, et al (2018)

Cytonuclear coevolution following homoploid hybrid speciation in Aegilops tauschii.

Molecular biology and evolution pii:5184915 [Epub ahead of print].

The diploid D-genome lineage of the Triticum/Aegilops complex has an evolutionary history involving genomic contributions from ancient A- and B/S-genome species. We explored here the possible cytonuclear evolutionary responses to this history of hybridization. Phylogenetic analysis of chloroplast DNAs indicate that the D-genome lineage has a maternal origin of the A-genome or some other closely allied lineage. Analyses of the nuclear genome in the D-genome species Aegilops tauschii indicate that accompanying and/or following this ancient hybridization, there has been biased maintenance of maternal A-genome ancestry in nuclear genes encoding cytonuclear enzyme complexes (CECs). Our study provides insights into mechanisms of cytonuclear coevolution accompanying the evolution and eventual stabilization of homoploid hybrid species. We suggest that this coevolutionary process includes likely rapid fixation of A-genome CEC orthologs as well as biased retention of A-genome nucleotides in CEC homologs following population level recombination during the initial generations.

RevDate: 2018-11-16

Chen H, Xia Q, Yang T, et al (2018)

The soil microbial community of turf: linear and nonlinear changes of taxa and N-cycle gene abundances over a century long turf development.

FEMS microbiology ecology pii:5184450 [Epub ahead of print].

Turf, consisting of closely-spaced grasses and the subtending soil, is a unique ecosystem subject to intense management. Yet, soil organic matter accumulates quickly and reaches equilibrium after 20 to 50 years. Resource availability is an important driver of species richness and theoretically their relationship is expected to be unimodal. In this work, we examined the effects of turf development (i.e. 1, 15, 20, and 109 year-old chronosequence) on microbial taxon richness, community composition, and abundances of genes putatively involved in N cycling through 16S rRNA gene and ITS region amplicon sequencing. Microbial alpha-diversity remained relatively stable although soil organic C and N increased up to 3 folds over a century long turf development. However, both bacterial and fungal community compositions changed substantially from those in the previous land use, pine stands and along turf development. Youngest turf was closer to the oldest turf than to middle-aged ones, specifically for bacterial community. Microbial changes to resource availability were also taxonomically specific. The relative abundance of Proteobacteria was independent of resource availability; Nitrospirae increased monotonically, and Bacteroidetes, Actinobacteria, and Glomeromycota varied curvilinearly. However, abundances of most taxa from the phylum to OTU level and N-cycle genes varied nonlinearly with turf development.

RevDate: 2018-11-16

Teufel AI, Johnson MM, Laurent JM, et al (2018)

The many nuanced evolutionary consequences of duplicated genes.

Molecular biology and evolution pii:5184914 [Epub ahead of print].

Gene duplication is seen as a major source of structural and functional divergence in genome evolution. Under the conventional models of sub- or neofunctionalizaton, functional changes arise in one of the duplicates after duplication. However, we suggest here that the presence of a duplicated gene can result in functional changes to its interacting partners. We explore this hypothesis by in-silico evolution of a heterodimer when one member of the interacting pair is duplicated. We examine how a range of selection pressures and protein structures leads to differential patterns of evolutionary divergence. We find that a surprising number of distinct evolutionary trajectories can be observed even in a simple three member system. Further, we observe that selection to correct dosage imbalance can affect the evolution of the initial function in several unexpected ways. For example, if a duplicate is under selective pressure to avoid binding its original binding partner, this can lead to changes in the binding interface of a non-duplicated interacting partner to exclude the duplicate. Hence, independent of the fate of the duplicate, its presence can impact how the original function operates. Additionally, we introduce a conceptual framework to describe how interacting partners cope with dosage imbalance after duplication. Contextualizing our results within this framework reveals that the evolutionary path taken by a duplicate's interacting partners is highly stochastic in nature. Consequently, the fate of duplicate genes may not only be controlled by their own ability to accumulate mutations but also by how interacting partners cope with them.

RevDate: 2018-11-16

Zeibich L, Schmidt O, HL Drake (2018)

Fermenters in the Earthworm Gut: Do Transients Matter?.

FEMS microbiology ecology pii:5185111 [Epub ahead of print].

Earthworms have profound impact on soil-based ecosystems. Although theoretical considerations suggest that most microbes in the earthworm gut are likely ingested and transient, the non-responsiveness of soil microbes to a specific high value gut nutrient and anoxia has made it difficult to demonstrate that responsive gut fermenters are derived from soil. Therefore, soil and gut content of the model earthworm Lumbricus terrestris were examined for their fermentative capabilities. In unsupplemented anoxic microcosms, fermentation was negligible with soil but rapid with gut content. However, both soil and gut content facilitated robust fermentations when challenged with complex nutrients indicative of those released from gizzard-disrupted cells. Based on the relative abundances of 16S rRNA and 16S rRNA gene sequences, the responsive fermentative taxa in unsupplemented gut content treatments were negligible in unsupplemented soil treatments. In contrast, the responsive fermentative taxa in soil and gut content treatments supplemented with complex nutrients displayed marked similarities, with numerous Proteobacteria- and Firmicutes-affiliated phylotypes being dominant. These findings indicated that detectable differences between the fermentative taxa in soil and gut contents are due in part to the nutrient-dependent metabolic status of community members and reinforce the likelihood that ingested transient microbes contribute to fermentation in the alimentary canal.

RevDate: 2018-11-16

Jones JM, Heath KD, Ferrer A, et al (2018)

Wood decomposition in aquatic and terrestrial ecosystems in the tropics: contrasting biotic and abiotic processes.

FEMS microbiology ecology pii:5184448 [Epub ahead of print].

Wood decomposition, a critical process in carbon and nutrient cycles, is influenced by environmental conditions, decomposer communities, and substrate composition. While these factors differ between land and stream habitats, across-habitat comparisons of wood decay processes are rare, limiting our ability to evaluate the context dependency of the drivers of decay. Here we tracked wood decomposition of three tree species placed in stream and terrestrial habitats in a lowland tropical forest in Panama. At 3 mo. and 11 mo. we measured mass loss, wood nitrogen, and wood polymer concentrations, and sampled wood associated fungal and bacterial communities. After 11 mo. of decay we found that mass loss occurred 9% faster in streams than on land, but loss of cellulose, hemicellulose, and lignin did not differ between habitats. We also observed large differences in microbial decomposer communities between habitats. Overall, we found faster mass loss of wood in water, but no differences in biotic decay processes between habitats despite distinct microbial communities in streams and on land. Our research challenges the assumption that wood decays relatively slowly in water reflecting unfavorable environmental conditions and a limited capacity of aquatic microbial communities to effectively degrade wood polymers.

RevDate: 2018-11-16

Hu XJ, Yang J, Xie XL, et al (2018)

The genome landscape of Tibetan sheep reveals adaptive introgression from argali and the history of early human settlements on the Qinghai-Tibetan Plateau.

Molecular biology and evolution pii:5184913 [Epub ahead of print].

Tibetan sheep are the most common and widespread domesticated animals on the Qinghai-Tibetan Plateau (QTP), and have played an essential role in the permanent human occupation of this high-altitude region. However, the precise timing, route and process of sheep pastoralism in the QTP region remain poorly established, and little is known about the underlying genomic changes that occurred during the process. Here, we investigate the genomic variation in Tibetan sheep using whole-genome sequences, SNP arrays, mitochondrial DNA and Y-chromosomal variants in 986 samples throughout their distribution range. We detect strong signatures of selection in genes involved in the hypoxia and ultraviolet signaling pathways (e.g., HIF-1 pathway and HBB and MITF genes) and in genes associated with morphological traits such as horn size and shape (e.g., RXFP2). We identify clear signals of argali (Ovis ammon) introgression into sympatric Tibetan sheep, covering 5.23% - 5.79% of their genomes. The introgressed genomic regions are enriched in genes related to oxygen transportation system, sensory perception and morphological phenotypes, in particular the genes HBB and RXFP2 with strong signs of adaptive introgression. The spatial distribution of genomic diversity and demographic reconstruction of the history of Tibetan sheep shows a stepwise pattern of colonization with their initial spread onto the QTP from its northeastern part c. 3,100 years ago, followed by further southwest expansion to the central QTP c. 1,300 years ago. Together with archeological evidence, the date and route reveals the history of human expansions on the QTP by the Tang-Bo Ancient Road during the late-Holocene. Our findings contribute to a depth understanding of early pastoralism and the local adaptation of Tibetan sheep as well as the late-Holocene human occupation of the QTP.

RevDate: 2018-11-16

Shekhar Saxena A, Salomon MP, Matsuba C, et al (2018)

Evolution of the mutational process under relaxed selection in Caenorhabditis elegans.

Molecular biology and evolution pii:5184273 [Epub ahead of print].

The mutational process varies at many levels, from within genomes to among taxa. Many mechanisms have been linked to variation in mutation, but understanding of the evolution of the mutational process is rudimentary. Physiological condition is often implicated as a source of variation in microbial mutation rate and may contribute to mutation rate variation in multicellular organisms.Deleterious mutations are a ubiquitous source of variation in condition. We test the hypothesis that the mutational process depends on the underlying mutation load in two groups of Caenorhabditis elegans mutation accumulation (MA) lines that differ in their starting mutation loads. "First-Order MA" (O1MA) lines maintained under minimal selection for ∼250 generations were divided into high-fitness and low-fitness groups and sets of "second-order MA" (O2MA) lines derived from each O1MA line were maintained for ∼150 additional generations. Genomes of 48 O2MA lines and their progenitors were sequenced. There is significant variation among O2MA lines in base-substitution rate (µbs), but no effect of initial fitness; the indel rate is greater in high-fitness O2MA lines. Overall, µbs is positively correlated with recombination and proximity to short tandem repeats and negatively correlated with 10 bp and 1 Kb GC content. However, probability of mutation is sufficiently predicted by the three-nucleotide motif alone. ∼90% of the variance in standing nucleotide variation is explained by mutability. Total mutation rate increased in the O2MA lines, as predicted by the "drift barrier" model of mutation rate evolution. These data, combined with experimental estimates of fitness, suggest that epistasis is synergistic.

RevDate: 2018-11-16

Parker DJ, Bast J, Jalvingh K, et al (2018)

Repeated evolution of asexuality involves convergent gene expression changes.

Molecular biology and evolution pii:5184916 [Epub ahead of print].

Asexual reproduction has evolved repeatedly from sexual ancestors across a wide range of taxa. While the costs and benefits associated with asexuality have received considerable attention, the molecular changes underpinning the evolution of asexual reproduction remain relatively unexplored. In particular, it is completely unknown whether the repeated evolution of asexual phenotypes involves similar molecular changes, as previous studies have focused on changes occurring in single lineages. Here we investigate the extent of convergent gene expression changes across five independent transitions to asexuality in stick insects. We compared gene expression of asexual females to females of close sexual relatives in whole-bodies, reproductive tracts, and legs. We identified a striking amount of convergent gene expression change (up to 8% of genes), greatly exceeding that expected by chance. Convergent changes were also tissue-specific, and most likely driven by selection for functional changes. Genes showing convergent changes in the reproductive tract were associated with meiotic spindle formation and centrosome organization. These genes are particularly interesting as they can influence the production of unreduced eggs, a key barrier to asexual reproduction. Changes in legs and whole-bodies were likely involved in female sexual trait decay, with enrichment in terms such as sperm-storage and pigmentation. By identifying changes occurring across multiple independent transitions to asexuality, our results provide a rare insight into the molecular basis of asexual phenotypes and suggest that the evolutionary path to asexuality is highly constrained, requiring repeated changes to the same key genes.

RevDate: 2018-11-16

Holt S, Miks MH, de Carvalho BT, et al (2018)

The molecular biology of fruity and floral aromas in beer and other alcoholic beverages.

FEMS microbiology reviews pii:5184464 [Epub ahead of print].

Aroma compounds provide attractiveness and variety to alcoholic beverages. We discuss the molecular biology of a major subset of beer aroma volatiles, fruity and floral compounds, originating from raw materials (malt and hops), or formed by yeast during fermentation. We introduce aroma perception, describe the most aroma-active, fruity and floral compounds in fruits and their presence and origin in beer. They are classified into categories based on their functional groups and biosynthesis pathways: 1) Higher alcohols and esters, 2) Polyfunctional thiols, 3) Lactones and furanones, and 4) Terpenoids. Yeast and hops are the main sources of fruity and flowery aroma compounds in beer. For yeast, the focus is on higher alcohols and esters, and particularly the complex regulation of the alcohol acetyl transferase ATF1 gene. We discuss the release of polyfunctional thiols and monoterpenoids from cysteine- and glutathione-S-conjugated compounds and glucosides, respectively, the primary biological functions of the yeast enzymes involved, their mode of action and mechanisms of regulation that control aroma compound production. Furthermore, we discuss biochemistry and genetics of terpenoid production and formation of non-volatile precursors in Humulus lupulus (hops). Insight in these pathways provides a toolbox for creating innovative products with a diversity of pleasant aromas.

RevDate: 2018-11-16

Philips J, Monballyu E, Georg S, et al (2018)

An Acetobacterium strain isolated with metallic iron as electron donor enhances iron corrosion by a similar mechanism as Sporomusa sphaeroides.

FEMS microbiology ecology pii:5184449 [Epub ahead of print].

Sporomusa sphaeroides related strains are to date the only homoacetogens known to increase metallic iron corrosion. The goal of this work was to isolate additional homoacetogenic bacteria capable of using Fe(0) as electron donor and to explore their extracellular electron transfer mechanism. Enrichments were started from anoxic corrosion products and yielded Acetobacterium as main homoacetogenic genus. Isolations were performed with a new procedure using plates with a Fe(0) powder top layer. An Acetobacterium strain, closely related to A. malicum and A. wieringae, was isolated, in addition to a S. sphaeroides strain. The Acetobacterium isolate significantly increased Fe(0) corrosion ((1.44 ± 0.16)-fold) compared to abiotic controls. The increase of corrosion by type strains ranged from (1.28 ± 0.13)-fold for A. woodii to (2.03 ± 0.22)-fold for S. sphaeroides. Hydrogen mediated the electron uptake from Fe(0) by the acetogenic isolates and tested type strains. Exchange of the medium and SEM imaging suggested that cells were attached to Fe(0). The corrosion enhancement mechanism is for all tested strains likely related to free extracellular components catalyzing hydrogen formation on the Fe(0) surface, or to the maintenance of low hydrogen concentrations on the Fe(0) surface by attached cells thereby thermodynamically favoring hydrogen formation.

RevDate: 2018-11-16

Planques A, Malem J, Parapar J, et al (2018)

Morphological, cellular and molecular characterization of posterior regeneration in the marine annelid Platynereis dumerilii.

Developmental biology pii:S0012-1606(18)30453-6 [Epub ahead of print].

Regeneration, the ability to restore body parts after an injury or an amputation, is a widespread but highly variable and complex phenomenon in animals. While having fascinated scientists for centuries, fundamental questions about the cellular basis of animal regeneration as well as its evolutionary history remain largely unanswered. Here, we present a study of regeneration of the marine annelid Platynereis dumerilii, an emerging comparative developmental biology model, which, like many other annelids, displays important regenerative abilities. When P. dumerilii worms are amputated, they are able to regenerate the posteriormost differentiated part of their body and a stem cell-rich growth zone that allows the production of new segments replacing the amputated ones. We show that posterior regeneration is a rapid process that follows a well reproducible path and timeline, going through specific stages that we thoroughly defined. Wound healing is achieved one day after amputation and a regeneration blastema forms one day later. At this time point, some tissue specification already occurs, and a functional posterior growth zone is re-established as early as three days after amputation. Regeneration timing is only influenced, in a minor manner, by worm size. Comparable regenerative abilities are found for amputations performed at different positions along the antero-posterior axis of the worm, except when amputation planes are very close to the pharynx. Regenerative abilities persist upon repeated amputations without important alterations of the process. We also show that intense cell proliferation occurs during regeneration and that cell divisions are required for regeneration to proceed normally. Finally, 5-ethynyl-2'-deoxyuridine (EdU) pulse and chase experiments suggest that blastemal cells mostly derive from the segment immediately abutting the amputation plane. The detailed characterization of P. dumerilii posterior body regeneration presented in this article provides the foundation for future mechanistic and comparative studies of regeneration in this species.

RevDate: 2018-11-16

Mullon C, L Lehmann (2018)

Eco-Evolutionary Dynamics in Metacommunities: Ecological Inheritance, Helping within Species, and Harming between Species.

The American naturalist, 192(6):664-686.

Understanding selection on intra- and interspecific interactions that take place in dispersal-limited communities is a challenge for ecology and evolutionary biology. The problem is that local demographic stochasticity generates eco-evolutionary dynamics that are generally too complicated to make tractable analytical investigations. Here we circumvent this problem by approximating the selection gradient on a quantitative trait that influences local community dynamics, assuming that such dynamics are deterministic with a stable fixed point. The model nonetheless captures unavoidable kin selection effects arising from demographic stochasticity. Our approximation reveals that selection depends on how an individual expressing a trait change influences (1) its own fitness and the fitness of its current relatives and (2) the fitness of its downstream relatives through modifications of local ecological conditions (i.e., through ecological inheritance). Mathematically, the effects of ecological inheritance on selection are captured by dispersal-limited versions of press perturbations of community ecology. We use our approximation to investigate the evolution of helping within species and harming between species when these behaviors influence demography. We find that altruistic helping evolves more readily when intraspecific competition is for material resources rather than for space, because in this case the costs of kin competition tend to be paid by downstream relatives. Similarly, altruistic harming between species evolves when it alleviates downstream relatives from interspecific competition. Beyond these examples, our approximation can help better understand the influence of ecological inheritance on a variety of eco-evolutionary dynamics in metacommunities, from consumer-resource and predator-prey coevolution to selection on mating systems with demographic feedbacks.

RevDate: 2018-11-16

Holding T, Valletta JJ, M Recker (2018)

Multiscale Immune Selection and the Transmission-Diversity Feedback in Antigenically Diverse Pathogen Systems.

The American naturalist, 192(6):E189-E201.

Antigenic diversity is commonly used by pathogens to enhance their transmission success. Within-host clonal antigenic variation helps to maintain long infectious periods, whereas high levels of allelic diversity at the population level significantly expand the pool of susceptible individuals. Diversity, however, is not necessarily a static property of a pathogen population but in many cases is generated by the very act of infection and transmission, and it is therefore expected to respond dynamically to changes in transmission and immune selection. We hypothesized that this coupling creates a positive feedback whereby infection and disease transmission promote the generation of diversity, which itself facilitates immune evasion and further infections. To investigate this link in more detail, we considered the human malaria parasite Plasmodium falciparum, one of the most important antigenically diverse pathogens. We developed an individual-based model in which antigenic diversity emerges as a dynamic property from the underlying transmission processes. Our results show that the balance between stochastic extinction and the generation of new antigenic variants is intrinsically linked to within-host and between-host immune selection. This in turn determines the level of diversity that can be maintained in a given population. Furthermore, the transmission-diversity feedback can lead to temporal lags in the response to natural or intervention-induced perturbations in transmission rates. Our results therefore have important implications for monitoring and assessing the effectiveness of disease control efforts.

RevDate: 2018-11-16

Rohner PT, WU Blanckenhorn (2018)

A Comparative Study of the Role of Sex-Specific Condition Dependence in the Evolution of Sexually Dimorphic Traits.

The American naturalist, 192(6):E202-E215.

Sexual selection can displace traits acting as ornaments or armaments from their viability optimum in one sex, ultimately giving rise to sexual dimorphism. The degree of dimorphism should not only mirror the strength of sexual selection but also the net viability costs of trait maintenance at equilibrium. As the ability of organisms to bear exaggerated traits will depend on their condition, more sexually dimorphic traits should also exhibit greater sex differences in condition dependence. While this has been demonstrated among traits within species, similar patterns are expected across the phylogeny. We investigated this prediction within and across 11 (sub)species of sepsid flies with varying mating systems. When estimating condition dependence for seven sexual and nonsexual traits that vary in their sexual dimorphism, we not only found a positive relationship between the sex difference in allometric slopes (our measure of condition dependence) and relative trait exaggeration within species but also across species for those traits expected to be under sexual selection. Species with more pronounced male aggression further had relatively larger and more condition-dependent male fore- and midlegs. Our comparative study suggests a common genetic/developmental basis of sexual dimorphism and sex-specific plasticity that evolves across the phylogeny-and that the evolution of size consistently alters scaling relationships and thus contributes to the allometric variation of sexual armaments or ornaments in animals.

RevDate: 2018-11-16

Rebolleda-Gómez M, M Travisano (2018)

The Cost of Being Big: Local Competition, Importance of Dispersal, and Experimental Evolution of Reversal to Unicellularity.

The American naturalist, 192(6):731-744.

Multicellularity provides multiple benefits. Nonetheless, unicellularity is ubiquitous, and there have been multiple cases of evolutionary reversal to a unicellular organization. In this article, we explore some of the costs of multicellularity as well as the possibility and dynamics of evolutionary reversals to unicellularity. We hypothesize that recently evolved multicellular organisms would face a high cost of increased competition for local resources in spatially structured environments because of larger size and increased cell densities. To test this hypothesis we conducted competition assays, computer simulations, and selection experiments using isolates of Saccharomyces cerevisiae that recently evolved multicellularity. In well-mixed environments, multicellular isolates had lower growth rates relative to their unicellular ancestor because of limitations of space and resource acquisition. In structured environments with localized resources, cells in both multicellular and unicellular isolates grew at a similar rate. Despite similar growth, higher local density of cells in multicellular groups led to increased competition and higher fitness costs in spatially structured environments. In structured environments all of the multicellular isolates rapidly evolved a predominantly unicellular life cycle, while in well-mixed environments reversal was more gradual. Taken together, these results suggest that a lack of dispersal, leading to higher local competition, might have been one of the main constraints in the evolution of early multicellular forms.

RevDate: 2018-11-16

Wadgymar SM, Mactavish RM, JT Anderson (2018)

Transgenerational and Within-Generation Plasticity in Response to Climate Change: Insights from a Manipulative Field Experiment across an Elevational Gradient.

The American naturalist, 192(6):698-714.

Parental environmental effects-or transgenerational plasticity-can influence an individual's phenotype or fitness yet remain underexplored in the context of global change. Using the perennial self-pollinating plant Boechera stricta, we explored the effects of climate change on transgenerational and within-generation plasticity in dormancy, germination, growth, and survival. We first conducted a snow removal experiment in the field, in which we transplanted 16 families of known origin into three common gardens at different elevations and exposed half of the siblings to contemporary snow dynamics and half to early snow removal. We planted the offspring of these individuals in a factorial manipulation of temperature and water level in the growth chamber and reciprocally transplanted them across all parental environments in the field. The growth chamber experiment revealed that the effects of transgenerational plasticity persist in traits expressed after establishment, even when accounting for parental effects on seed mass. The field experiment showed that transgenerational and within-generation plasticity can interact and that plasticity varies clinally in populations distributed across elevations. These findings demonstrate that transgenerational plasticity can influence fitness-related traits and should be incorporated in studies of biological responses to climate change.

RevDate: 2018-11-16

Sparks AM, Watt K, Sinclair R, et al (2018)

Natural Selection on Antihelminth Antibodies in a Wild Mammal Population.

The American naturalist, 192(6):745-760.

An effective immune response is expected to confer fitness benefits through improved resistance to parasites but also incur energetic costs that negatively impact fitness-related traits, such as reproduction. The fitness costs and benefits of an immune response are likely to depend on host age, sex, and levels of parasite exposure. Few studies have examined the full extent to which patterns of natural selection on immune phenotypes vary across demographic groups and environments in the wild. Here, we assessed natural selection on plasma levels of three functionally distinct isotypes (IgA, IgE, and IgG) of antibodies against a prevalent nematode parasite measured in a wild Soay sheep population over 26 years. We found little support for environment-dependent selection or reproductive costs. However, antibody levels were negatively associated with parasite egg counts and positively associated with subsequent survival, albeit in a highly age- and isotype-dependent manner. Raised levels of antiparasite IgA best predicted reduced egg counts, but this did not predict survival in lambs. In adults increased antiparasite IgG predicted reduced egg counts, and in adult females IgG levels also positively predicted overwinter survival. Our results highlight the potential importance of age- and sex-dependent selection on immune phenotypes in nature and show that patterns of selection can vary even among functionally related immune markers.

RevDate: 2018-11-16

Bernhardt JR, Sunday JM, MI O'Connor (2018)

Metabolic Theory and the Temperature-Size Rule Explain the Temperature Dependence of Population Carrying Capacity.

The American naturalist, 192(6):687-697.

The temperature dependence of highly conserved subcellular metabolic systems affects ecological patterns and processes across scales, from organisms to ecosystems. Population density at carrying capacity plays an important role in evolutionary processes, biodiversity, and ecosystem function, yet how it varies with temperature-dependent metabolism remains unclear. Though the exponential effect of temperature on intrinsic population growth rate, r, is well known, we still lack clear evidence that population density at carrying capacity, K, declines with increasing per capita metabolic rate, as predicted by the metabolic theory of ecology (MTE). We experimentally tested whether temperature effects on photosynthesis propagate directly to population carrying capacity in a model species, the mobile phytoplankton Tetraselmis tetrahele. After maintaining populations at a fixed resource supply and fixed temperatures for 43 days, we found that carrying capacity declined with increasing temperature. This decline was predicted quantitatively when models included temperature-dependent metabolic rates and temperature-associated body-size shifts. Our results demonstrate that warming reduces carrying capacity and that temperature effects on body size and metabolic rate interact to determine how temperature affects population dynamics. These findings bolster efforts to relate metabolic temperature dependence to population and ecosystem patterns via MTE.

RevDate: 2018-11-16

Simms E, C Caruso (2018)

Treasurer's Report, 2017: Statement of Activities For the year ending December 31, 2017.

The American naturalist, 192(6):786-787.

RevDate: 2018-11-16

Brengdahl M, Kimber CM, Maguire-Baxter J, et al (2018)

Genetic Quality Affects the Rate of Male and Female Reproductive Aging Differently in Drosophila melanogaster.

The American naturalist, 192(6):761-772.

Males and females often maximize fitness by pursuing different reproductive strategies, with males commonly assumed to benefit more from increased resource allocation into current reproduction. Such investment should trade off with somatic maintenance and may explain why males frequently live shorter than females. It also predicts that males should experience faster reproductive aging. Here we investigate whether reproductive aging and life span respond to condition differently in male and female Drosophila melanogaster, as predicted if sexual selection has shaped male and female resource-allocation patterns. We manipulate condition through genetic quality by comparing individuals inbred or outbred for a major autosome. While genetic quality had a similar effect on condition in both sexes, condition had a much larger general effect on male reproductive output than on female reproductive output, as expected when sexual selection on vigor acts more strongly on males. We find no differences in reproductive aging between the sexes in low condition, but in high condition reproductive aging is relatively faster in males. No corresponding sex-specific change was found for life span. The sex difference in reproductive aging appearing in high condition was specifically due to a decreased aging rate in females rather than any change in males. Our results suggest that females age slower than males in high condition primarily because sexual selection has favored sex differences in resource allocation under high condition, with females allocating relatively more toward somatic maintenance than males.

RevDate: 2018-11-16

Tinghitella RM, Broder ED, Gurule-Small GA, et al (2018)

Purring Crickets: The Evolution of a Novel Sexual Signal.

The American naturalist, 192(6):773-782.

Opportunities to observe contemporary signal change are incredibly rare but critical for understanding how diversity is created and maintained. We discovered a population of the Pacific field cricket (Teleogryllus oceanicus) with a newly evolved song (purring), different from any known cricket. Male crickets use song to attract females from afar and to court females once near. Teleogryllus oceanicus is well known for sexual signal evolution, as exemplified by a recent signal loss. In this study, we characterized the new purring sound and investigated the role of the purr in long-distance and short-distance communication. The purring sound differed from typical ancestral calls in peak frequency, amplitude, and bandwidth. Further, the long-distance purring song facilitated mate location, though the role of courtship purring song is less clear. Our discovery of purring male crickets is an unprecedented opportunity to watch the emergence of a newly evolved sexual signal unfold in real time and has potential to illuminate the mechanisms by which evolutionary novelties arise and coevolve between the sexes.

RevDate: 2018-11-16

Bronstein JL, DI Bolnick (2018)

"Her Joyous Enthusiasm for Her Life-Work …": Early Women Authors in The American Naturalist.

The American naturalist, 192(6):655-663.

Women have long been underrepresented in the natural sciences, and although great progress has been made in recent decades, many subtle and not-so-subtle barriers persist. In this context, it is easy to get the impression that the early history of ecology and evolutionary biology was exclusively the domain of male researchers. In fact, a number of women made very substantial contributions to The American Naturalist in its first decades. In a follow-up to a series of retrospective essays celebrating 150 years of this journal, we highlight the scientific contributions of the women published in it during its first 50 years (1867-1916). We also discuss the diverse paths that their scientific careers took and the barriers they faced along the way.

RevDate: 2018-11-16

Lau J (2018)

Secretary's Report, 2018: American Society of Naturalists.

The American naturalist, 192(6):783-785.

RevDate: 2018-11-16

O'Brien AM, Sawers RJH, Ross-Ibarra J, et al (2018)

Evolutionary Responses to Conditionality in Species Interactions across Environmental Gradients.

The American naturalist, 192(6):715-730.

The outcomes of many species interactions are conditional on the environments in which they occur. Often, interactions grade from being more positive under stressful or low-resource conditions to more antagonistic or neutral under benign conditions. Here, we take predictions about two well-supported ecological theories on conditionality-limiting resource models and the stress-gradient hypothesis-and combine them with those from the geographic mosaic theory of coevolution (GMTC) to generate predictions for systematic patterns of adaptation and coadaptation between partners along abiotic gradients. When interactions become more positive in stressful environments, mutations that increase fitness in one partner may also increase fitness in the other; because fitnesses are aligned, selection should favor greater mutualistic adaptation and coadaptation between interacting species in stressful ends of environmental gradients. As a corollary, in benign environments antagonistic coadaptation could result in Red Queen or arms-race dynamics or the reduction of antagonism through character displacement and niche partitioning. Here, we distinguish between generally mutualistic or antagonistic adaptation (i.e., mutations in one partner that have similar effects across multiple populations of the other) and specific adaptations to sympatric partners (local adaptation), which can occur either alone or simultaneously. We then outline the kinds of data required to test these predictions, develop experimental designs and statistical methods, and demonstrate these using simulations based on GMTC models. Our methods can be applied to a range of conditional outcomes and may also be useful in assisted translocation approaches in the face of climate change.

RevDate: 2018-11-16

Zeder MA (2018)

Why evolutionary biology needs anthropology: Evaluating core assumptions of the extended evolutionary synthesis.

Evolutionary anthropology [Epub ahead of print].

Anthropologists have a long history of applying concepts from evolutionary biology to cultural evolution. Evolutionary biologists, however, have been slow to turn to anthropology for insights about evolution. Recently, evolutionary biology has been engaged in a debate over the need to revise evolutionary theory to account for developments made in 60 years since the Modern Synthesis, the standard evolutionary paradigm, was framed. Revision proponents maintain these developments challenge central tenets of standard theory that can only be accounted for in an extended evolutionary synthesis (EES). Anthropology has much to offer to this debate. One important transition in human cultural evolution, the domestication of plants and animals, provides an ideal model system assessing core EES assumptions about directionality, causality, targets of selection, modes of inheritance, and pace of evolution. In so doing, anthropologists contribute to an overarching framework that brings together cultural and biological evolution.

RevDate: 2018-11-16

Sun Y, Jiang ZM, Zhao LL, et al (2018)

Allorhizocola rhizosphaerae gen. nov., sp. nov., a new member of Micromonosporaceae isolated from rhizosphere soil of the plant Calligonum mongolicum.

International journal of systematic and evolutionary microbiology [Epub ahead of print].

The taxonomic position of an actinobacterium, designated CPCC 204380T, which was isolated from a rhizosphere soil sample of the plant Calligonum mongolicum collected from Xinjiang Province, China, was established using a polyphasic approach. Vegetative hyphae developed well and globose bodies formed from aged hyphae. Spore chains that differentiated from the vegetative hyphae contained non-motile rod-shaped spores. The peptidoglycan contained meso-diaminopimelic acid and 3-hydroxydiaminopimelic acid as the diagnostic amino acids. The acyl type of the peptidoglycan was glycolyl. Glucose, mannose, ribose and xylose were detected in whole-cell hydrolysates. The predominant menaquinone was MK-10(H8), followed by MK-10(H6) and MK-10(H4). The polar lipid profile consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol and phosphatidylinositol mannoside. The major fatty acids were iso-C15 : 0, iso-C16 : 0 and C17 : 1ω9c. The genomic G+C content was 64.9 mol%. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain CPCC 204380T should be placed in the family Micromonosporaceae, in which it formed a distinct lineage next to the genera Rhizocola, Catellatospora, Catelliglobosispora, Hamadaea and Allocatelliglobosispora. It shared the highest 16S rRNA gene sequence similarities with Rhizocola hellebori K12-0602T (96.1 %), Catellatospora chokoriensis 2-25/1T (95.9 %), Catelliglobosispora koreensis DSM 44566T (95.9 %), Hamadaea tsunoensis DSM 44101T (95.3 %) and Allocatelliglobosispora scoriae Sco-B14 T (94.2 %), and less than 94.0 % sequence similarity with other validly described species. The combination of phylogenetic analysis and phenotypic characteristics supported the proposal of strain CPCC 204380T as representing a novel species of a new genus in the family Micromonosporaceae, for which the name Allorhizocola rhizosphaerae gen. nov., sp. nov. is proposed. CPCC 204380T (=DSM 102292T=KCTC 39746 T) is the type strain of the type species.

RevDate: 2018-11-16

Trujillo ME, Oren A, GM Garrity (2018)

Preparation of the Validation Lists and the role of the List Editors.

International journal of systematic and evolutionary microbiology [Epub ahead of print].

Recently a number of queries were received about the ways in which requests for validation of names of taxa effectively published in journals other than the IJSEM are approved or denied and about the criteria used by the List Editors of the journal when deciding whether or not a validation request can be approved. As this process may be unclear to some authors of proposals, we would like to clarify the nature of the validation process and the role of the List Editors.

RevDate: 2018-11-16

Duangupama T, Pittayakhajonwut P, C Thawai (2018)

Thermocatellispora soli sp. nov., isolated from hot spring soil.

International journal of systematic and evolutionary microbiology [Epub ahead of print].

An aerobic, spore-forming, actinomycete, designated strain CHM3-46T, was isolated from soil in a hot spring pond located in Chiangmai province, Thailand. The strain exhibited taxonomic characteristics consistent with the genus Thermocatellispora. Strain CHM3-46T produced short, straight chains of warty spores on aerial mycelia. The presence of meso-diaminopimelic acid was observed in the cell-wall peptidoglycan. The whole-cell reducing sugars were glucose, mannose, galacose and ribose. The phospholipids comprised phosphatidylmethylethanolamine, hydroxyphosphatidylmethylethanolamine, phosphatidylethanolamine, hydroxyphosphatidylethanolamine, diphosphatidylglycerol, phosphatidylinositol, four phosphoglycolipids and three unidentified phospholipids. The predominant menaquinones were MK-9(H4), MK-9(H6) and MK-9(H8). 10-methyl C17 : 0, C16 : 0, C17 : 0 and iso-C16 : 0 were identified as the main cellular fatty acids. The G+C content of the genomic DNA was 73.2 mol%. Analysis of the 16S rRNA gene sequence showed that strain CHM3-46T belonged to the genus Thermocatellispora, exhibiting the highest similarity to Thermocatellispora tengchongensis YIM 77521T (98.5 %). Furthermore, a low DNA relatedness value (23.4 %±0.8) and several physiological and biochemical characteristic differences were detected between strain CHM3-46T and its closest relative. Based on the taxonomic data, strain CHM3-46T could be readily distinguished from its closest phylogenetic relative and represents a novel species, for which the name Thermocatellisporasoli sp. nov. is proposed. The type strain is CHM3-46T (=TBRC 7649T=NBRC 113148T).

RevDate: 2018-11-16

Lemskaya NA, Kulemzina AI, Beklemisheva VR, et al (2018)

A combined banding method that allows the reliable identification of chromosomes as well as differentiation of AT- and GC-rich heterochromatin.

Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology pii:10.1007/s10577-018-9589-9 [Epub ahead of print].

Сonstitutive heterochromatin areas are revealed by differential staining as C-positive chromosomal regions. These C-positive bands may greatly vary by location, size, and nucleotide composition. CBG-banding is the most commonly used method to detect structural heterochromatin in animals. The difficulty in identification of individual chromosomes represents an unresolved problem of this method as the body of the chromosome is stained uniformly and does not have banding pattern beyond C-bands. Here, we present the method that we called CDAG for sequential heterochromatin staining after differential GTG-banding. The method uses G-banding followed by heat denaturation in the presence of formamide with consecutive fluorochrome staining. The new technique is valid for the concurrent revealing of heterochromatin position due to differential banding of chromosomes and heterochromatin composition (AT-/GC-rich) in animal karyotyping.

RevDate: 2018-11-16

Song W, Wang S, Shen J, et al (2018)

Complete Genome Sequence of Massilia oculi sp. nov. CCUG 43427T (=DSM 26321T), the Type Strain of M. oculi, and Comparison with Genome Sequences of Other Massilia Strains.

Massilia oculi sp. nov. of type strain CCUG 43427T is a Gram-negative, rod-shaped, nonspore-forming bacterium, which was recently isolated from the eye of a patient suffering from endophthalmitis and was described as novel species in Massilia genus. In this study, we present the complete genome sequence of this strain by using Pacbio SMRT cell platform and compare this sequence with the genomes of 30 Massilia representative strains. Also, a comprehensive search was conducted for genes and proteins involved in antibiotic resistance and pathogenicity. The genome of CCUG 43427T is 5,844,653 bp with 65.55% GC content. This genome contains four prophages and four genomic islands (GIs). The cobalt/zinc/cadmium transporter locus CzcABCD is included in these GIs. This GI was predicted to play important role in bacterial heavy-metal tolerance. The in silico genome analysis also revealed that this strain contains a lot of antibiotic resistance and pathogenicity related genes. This result suggested that this strain may has evolved a wide arsenal of weapons for pathogenicity and survival. Genome comparison among CCUG 43427T and other 30 Massilia strains revealed that more than 400 genes are unique in CCUG 43427T. Among these, one gene cluster, which was annotated to be important for LOS biosynthesis, catalytic mechanism and the substrate specificity of the enzyme, was predicted to be horizontally transferred by using phylogenies and biased GC content.

RevDate: 2018-11-16

Kalthoff DC, JL Green (2018)

Feeding Ecology in Oligocene Mylodontoid Sloths (Mammalia, Xenarthra) as Revealed by Orthodentine Microwear Analysis.

Journal of mammalian evolution, 25(4):551-564.

Recently, dental microwear analysis has been successfully employed to xenarthran teeth. Here, we present new data on use wear features on 16 molariforms of Orophodon hapaloides and Octodontotherium grande. These taxa count among the earliest sloths and are known from the Deseadan SALMA (late Oligocene). Modern phylogenetic analyses classify Octodontotherium and Orophodon within Mylodontoidea with whom they share lobate cheek teeth with an outer layer of cementum and a thick layer of orthodentine. Similar target areas of 100μm2 were analyzed on the orthodentine surface of each tooth by stereomicroscopic microwear and by SEM microwear. Results were unlike those of extant sloths (stereomicroscopic microwear: Bradypus, Choloepus) and published data from fossil sloths (SEM microwear: Acratocnus, Megalonyx, Megatherium, Thinobadistes); thus, both approaches independently indicate a different feeding ecology for the Oligocene taxa. The unique microwear results suggest that both taxa fed on plant material with low to moderate intrinsic toughness (foliage, twigs) but also proposes intake of tougher food items (e.g., seeds). Frequent gouging of the tooth surfaces can be explained by exogenous influence on microwear, such as possible intake of abrasive grit. We suggest an unspecialized herbivorous diet for Octodontotherium and Orophodon utilizing diverse food resources of their habitat. These interpretations support the reconstruction of (1) Deseadan environments as open habitats with spreading savannas/grasslands and (2) both taxa as wide-muzzled bulk feeders at ground level.

RevDate: 2018-11-16

Wrighton KH (2018)

Personalized DNA methylomics.

Nature reviews. Genetics pii:10.1038/s41576-018-0076-0 [Epub ahead of print].

RevDate: 2018-11-17

Du Toit A (2018)

Well-timed toxin export.

Nature reviews. Microbiology pii:10.1038/s41579-018-0119-8 [Epub ahead of print].

RevDate: 2018-11-16

Nilsson RH, Anslan S, Bahram M, et al (2018)

Mycobiome diversity: high-throughput sequencing and identification of fungi.

Nature reviews. Microbiology pii:10.1038/s41579-018-0116-y [Epub ahead of print].

Fungi are major ecological players in both terrestrial and aquatic environments by cycling organic matter and channelling nutrients across trophic levels. High-throughput sequencing (HTS) studies of fungal communities are redrawing the map of the fungal kingdom by hinting at its enormous - and largely uncharted - taxonomic and functional diversity. However, HTS approaches come with a range of pitfalls and potential biases, cautioning against unwary application and interpretation of HTS technologies and results. In this Review, we provide an overview and practical recommendations for aspects of HTS studies ranging from sampling and laboratory practices to data processing and analysis. We also discuss upcoming trends and techniques in the field and summarize recent and noteworthy results from HTS studies targeting fungal communities and guilds. Our Review highlights the need for reproducibility and public data availability in the study of fungal communities. If the associated challenges and conceptual barriers are overcome, HTS offers immense possibilities in mycology and elsewhere.

RevDate: 2018-11-16

Marchio E (2018)

Climbing out of the bottle.

Science (New York, N.Y.), 362(6416):862.

RevDate: 2018-11-16

Visnes T, Cázares-Körner A, Hao W, et al (2018)

Small-molecule inhibitor of OGG1 suppresses proinflammatory gene expression and inflammation.

Science (New York, N.Y.), 362(6416):834-839.

The onset of inflammation is associated with reactive oxygen species and oxidative damage to macromolecules like 7,8-dihydro-8-oxoguanine (8-oxoG) in DNA. Because 8-oxoguanine DNA glycosylase 1 (OGG1) binds 8-oxoG and because Ogg1-deficient mice are resistant to acute and systemic inflammation, we hypothesized that OGG1 inhibition may represent a strategy for the prevention and treatment of inflammation. We developed TH5487, a selective active-site inhibitor of OGG1, which hampers OGG1 binding to and repair of 8-oxoG and which is well tolerated by mice. TH5487 prevents tumor necrosis factor-α-induced OGG1-DNA interactions at guanine-rich promoters of proinflammatory genes. This, in turn, decreases DNA occupancy of nuclear factor κB and proinflammatory gene expression, resulting in decreased immune cell recruitment to mouse lungs. Thus, we present a proof of concept that targeting oxidative DNA repair can alleviate inflammatory conditions in vivo.

RevDate: 2018-11-16

Chorev DS, Baker LA, Wu D, et al (2018)

Protein assemblies ejected directly from native membranes yield complexes for mass spectrometry.

Science (New York, N.Y.), 362(6416):829-834.

Membrane proteins reside in lipid bilayers and are typically extracted from this environment for study, which often compromises their integrity. In this work, we ejected intact assemblies from membranes, without chemical disruption, and used mass spectrometry to define their composition. From Escherichia coli outer membranes, we identified a chaperone-porin association and lipid interactions in the β-barrel assembly machinery. We observed efflux pumps bridging inner and outer membranes, and from inner membranes we identified a pentameric pore of TonB, as well as the protein-conducting channel SecYEG in association with F1FO adenosine triphosphate (ATP) synthase. Intact mitochondrial membranes from Bos taurus yielded respiratory complexes and fatty acid-bound dimers of the ADP (adenosine diphosphate)/ATP translocase (ANT-1). These results highlight the importance of native membrane environments for retaining small-molecule binding, subunit interactions, and associated chaperones of the membrane proteome.

RevDate: 2018-11-16

Nicholson CW, Lücke A, Schmidt WG, et al (2018)

Beyond the molecular movie: Dynamics of bands and bonds during a photoinduced phase transition.

Science (New York, N.Y.), 362(6416):821-825.

Ultrafast nonequilibrium dynamics offer a route to study the microscopic interactions that govern macroscopic behavior. In particular, photoinduced phase transitions (PIPTs) in solids provide a test case for how forces, and the resulting atomic motion along a reaction coordinate, originate from a nonequilibrium population of excited electronic states. Using femtosecond photoemission, we obtain access to the transient electronic structure during an ultrafast PIPT in a model system: indium nanowires on a silicon(111) surface. We uncover a detailed reaction pathway, allowing a direct comparison with the dynamics predicted by ab initio simulations. This further reveals the crucial role played by localized photoholes in shaping the potential energy landscape and enables a combined momentum- and real-space description of PIPTs, including the ultrafast formation of chemical bonds.

RevDate: 2018-11-16

Lee JS, Choi SH, Yun SJ, et al (2018)

Wafer-scale single-crystal hexagonal boron nitride film via self-collimated grain formation.

Science (New York, N.Y.), 362(6416):817-821.

Although polycrystalline hexagonal boron nitride (PC-hBN) has been realized, defects and grain boundaries still cause charge scatterings and trap sites, impeding high-performance electronics. Here, we report a method of synthesizing wafer-scale single-crystalline hBN (SC-hBN) monolayer films by chemical vapor deposition. The limited solubility of boron (B) and nitrogen (N) atoms in liquid gold promotes high diffusion of adatoms on the surface of liquid at high temperature to provoke the circular hBN grains. These further evolve into closely packed unimodal grains by means of self-collimation of B and N edges inherited by electrostatic interaction between grains, eventually forming an SC-hBN film on a wafer scale. This SC-hBN film also allows for the synthesis of wafer-scale graphene/hBN heterostructure and single-crystalline tungsten disulfide.

RevDate: 2018-11-16

Guo J, Suástegui M, Sakimoto KK, et al (2018)

Light-driven fine chemical production in yeast biohybrids.

Science (New York, N.Y.), 362(6416):813-816.

Inorganic-biological hybrid systems have potential to be sustainable, efficient, and versatile chemical synthesis platforms by integrating the light-harvesting properties of semiconductors with the synthetic potential of biological cells. We have developed a modular bioinorganic hybrid platform that consists of highly efficient light-harvesting indium phosphide nanoparticles and genetically engineered Saccharomyces cerevisiae, a workhorse microorganism in biomanufacturing. The yeast harvests photogenerated electrons from the illuminated nanoparticles and uses them for the cytosolic regeneration of redox cofactors. This process enables the decoupling of biosynthesis and cofactor regeneration, facilitating a carbon- and energy-efficient production of the metabolite shikimic acid, a common precursor for several drugs and fine chemicals. Our work provides a platform for the rational design of biohybrids for efficient biomanufacturing processes with higher complexity and functionality.

RevDate: 2018-11-16

Cheng KCK, Bedolla-Pantoja MA, Kim YK, et al (2018)

Templated nanofiber synthesis via chemical vapor polymerization into liquid crystalline films.

Science (New York, N.Y.), 362(6416):804-808.

Extrusion, electrospinning, and microdrawing are widely used to create fibrous polymer mats, but these approaches offer limited access to oriented arrays of nanometer-scale fibers with controlled size, shape, and lateral organization. We show that chemical vapor polymerization can be performed on surfaces coated with thin films of liquid crystals to synthesize organized assemblies of end-attached polymer nanofibers. The process uses low concentrations of radical monomers formed initially in the vapor phase and then diffused into the liquid-crystal template. This minimizes monomer-induced changes to the liquid-crystal phase and enables access to nanofiber arrays with complex yet precisely defined structures and compositions. The nanofiber arrays permit tailoring of a wide range of functional properties, including adhesion that depends on nanofiber chirality.

RevDate: 2018-11-16

Hilton MC, Zhang X, Boyle BT, et al (2018)

Heterobiaryl synthesis by contractive C-C coupling via P(V) intermediates.

Science (New York, N.Y.), 362(6416):799-804.

Heterobiaryls composed of pyridine and diazine rings are key components of pharmaceuticals and are often central to pharmacological function. We present an alternative approach to metal-catalyzed cross-coupling to make heterobiaryls using contractive phosphorus C-C couplings, also termed phosphorus ligand coupling reactions. The process starts by regioselective phosphorus substitution of the C-H bonds para to nitrogen in two successive heterocycles; ligand coupling is then triggered via acidic alcohol solutions to form the heterobiaryl bond. Mechanistic studies imply that ligand coupling is an asynchronous process involving migration of one heterocycle to the ipso position of the other around a central pentacoordinate P(V) atom. The strategy can be applied to complex drug-like molecules containing multiple reactive sites and polar functional groups, and also enables convergent coupling of drug fragments and late-stage heteroarylation of pharmaceuticals.

RevDate: 2018-11-16

Burke LM, JA Hawley (2018)

Swifter, higher, stronger: What's on the menu?.

Science (New York, N.Y.), 362(6416):781-787.

The exploits of elite athletes delight, frustrate, and confound us as they strive to reach their physiological, psychological, and biomechanical limits. We dissect nutritional approaches to optimal performance, showcasing the contribution of modern sports science to gold medals and world titles. Despite an enduring belief in a single, superior "athletic diet," diversity in sports nutrition practices among successful athletes arises from the specificity of the metabolic demands of different sports and the periodization of training and competition goals. Pragmatic implementation of nutrition strategies in real-world scenarios and the prioritization of important strategies when nutrition themes are in conflict add to this variation. Lastly, differences in athlete practices both promote and reflect areas of controversy and disagreement among sports nutrition experts.

RevDate: 2018-11-16

Gentile CL, TL Weir (2018)

The gut microbiota at the intersection of diet and human health.

Science (New York, N.Y.), 362(6416):776-780.

Diet affects multiple facets of human health and is inextricably linked to chronic metabolic conditions such as obesity, type 2 diabetes, and cardiovascular disease. Dietary nutrients are essential not only for human health but also for the health and survival of the trillions of microbes that reside within the human intestines. Diet is a key component of the relationship between humans and their microbial residents; gut microbes use ingested nutrients for fundamental biological processes, and the metabolic outputs of those processes may have important impacts on human physiology. Studies in humans and animal models are beginning to unravel the underpinnings of this relationship, and increasing evidence suggests that it may underlie some of the broader effects of diet on human health and disease.

RevDate: 2018-11-16

Di Francesco A, Di Germanio C, Bernier M, et al (2018)

A time to fast.

Science (New York, N.Y.), 362(6416):770-775.

Nutrient composition and caloric intake have traditionally been used to devise optimized diets for various phases of life. Adjustment of meal size and frequency have emerged as powerful tools to ameliorate and postpone the onset of disease and delay aging, whereas periods of fasting, with or without reduced energy intake, can have profound health benefits. The underlying physiological processes involve periodic shifts of metabolic fuel sources, promotion of repair mechanisms, and the optimization of energy utilization for cellular and organismal health. Future research endeavors should be directed to the integration of a balanced nutritious diet with controlled meal size and patterns and periods of fasting to develop better strategies to prevent, postpone, and treat the socioeconomical burden of chronic diseases associated with aging.

RevDate: 2018-11-16

Ludwig DS, Willett WC, Volek JS, et al (2018)

Dietary fat: From foe to friend?.

Science (New York, N.Y.), 362(6416):764-770.

For decades, dietary advice was based on the premise that high intakes of fat cause obesity, diabetes, heart disease, and possibly cancer. Recently, evidence for the adverse metabolic effects of processed carbohydrate has led to a resurgence in interest in lower-carbohydrate and ketogenic diets with high fat content. However, some argue that the relative quantity of dietary fat and carbohydrate has little relevance to health and that focus should instead be placed on which particular fat or carbohydrate sources are consumed. This review, by nutrition scientists with widely varying perspectives, summarizes existing evidence to identify areas of broad consensus amid ongoing controversy regarding macronutrients and chronic disease.

RevDate: 2018-11-16

Ray LB (2018)

Optimizing the diet.

Science (New York, N.Y.), 362(6416):762-763.

RevDate: 2018-11-16

Anonymous (2018)

NextGen VOICES: Transition challenges.

Science (New York, N.Y.), 362(6416):760.

RevDate: 2018-11-16

Botkin JR, Appelbaum PS, Bakken S, et al (2018)

Standardizing return of participant results.

Science (New York, N.Y.), 362(6416):759-760.

RevDate: 2018-11-16

Valdés-Sosa MJ, KR Foster (2018)

Halt speculation on U.S. embassy in Cuba.

Science (New York, N.Y.), 362(6416):758-759.

RevDate: 2018-11-16

Klein T, H Hartmann (2018)

Climate change drives tree mortality.

Science (New York, N.Y.), 362(6416):758.

RevDate: 2018-11-16

Crowley M, Shang L, M Dando (2018)

Preventing chemical weapons as sciences converge.

Science (New York, N.Y.), 362(6416):753-755.


RJR Experience and Expertise


Robbins holds BS, MS, and PhD degrees in the life sciences. He served as a tenured faculty member in the Zoology and Biological Science departments at Michigan State University. He is currently exploring the intersection between genomics, microbial ecology, and biodiversity — an area that promises to transform our understanding of the biosphere.


Robbins has extensive experience in college-level education: At MSU he taught introductory biology, genetics, and population genetics. At JHU, he was an instructor for a special course on biological database design. At FHCRC, he team-taught a graduate-level course on the history of genetics. At Bellevue College he taught medical informatics.


Robbins has been involved in science administration at both the federal and the institutional levels. At NSF he was a program officer for database activities in the life sciences, at DOE he was a program officer for information infrastructure in the human genome project. At the Fred Hutchinson Cancer Research Center, he served as a vice president for fifteen years.


Robbins has been involved with information technology since writing his first Fortran program as a college student. At NSF he was the first program officer for database activities in the life sciences. At JHU he held an appointment in the CS department and served as director of the informatics core for the Genome Data Base. At the FHCRC he was VP for Information Technology.


While still at Michigan State, Robbins started his first publishing venture, founding a small company that addressed the short-run publishing needs of instructors in very large undergraduate classes. For more than 20 years, Robbins has been operating The Electronic Scholarly Publishing Project, a web site dedicated to the digital publishing of critical works in science, especially classical genetics.


Robbins is well-known for his speaking abilities and is often called upon to provide keynote or plenary addresses at international meetings. For example, in July, 2012, he gave a well-received keynote address at the Global Biodiversity Informatics Congress, sponsored by GBIF and held in Copenhagen. The slides from that talk can be seen HERE.


Robbins is a skilled meeting facilitator. He prefers a participatory approach, with part of the meeting involving dynamic breakout groups, created by the participants in real time: (1) individuals propose breakout groups; (2) everyone signs up for one (or more) groups; (3) the groups with the most interested parties then meet, with reports from each group presented and discussed in a subsequent plenary session.


Robbins has been engaged with photography and design since the 1960s, when he worked for a professional photography laboratory. He now prefers digital photography and tools for their precision and reproducibility. He designed his first web site more than 20 years ago and he personally designed and implemented this web site. He engages in graphic design as a hobby.

21454 NE 143rd Street
Woodinville, WA 98077


E-mail: RJR8222@gmail.com

Collection of publications by R J Robbins

Reprints and preprints of publications, slide presentations, instructional materials, and data compilations written or prepared by Robert Robbins. Most papers deal with computational biology, genome informatics, using information technology to support biomedical research, and related matters.

Research Gate page for R J Robbins

ResearchGate is a social networking site for scientists and researchers to share papers, ask and answer questions, and find collaborators. According to a study by Nature and an article in Times Higher Education , it is the largest academic social network in terms of active users.

Curriculum Vitae for R J Robbins

short personal version

Curriculum Vitae for R J Robbins

long standard version

RJR Picks from Around the Web (updated 11 MAY 2018 )