bluuebunny/crossref_metadata_2025 huggingface dataset:
Treatment Outcomes of Third-line Antiretroviral Regimens in HIV-infected Thai Adolescents
Authors: Prasitsuebsai Wasana , Sophonphan Jiratchaya , Chokephaibulkit Kulkanya , Wongsawat Jurai , Kanjanavanit Suparat , Kosalaraksa Pope , Ngampiyakul Chaiwat , Sangkla Pakarat , Hansudewechakul Rawiwan , Kerr Stephen J. , Puthanakit Thanyawee , Ananworanich Jintanat
Published: May 2017

Background:

Efficacy and safety data of third-line antiretroviral (ARV) regimens in adolescents are limited.

Methodology:

This study enrolled HIV-infected Thais who were treated with third-line regimens consisting of darunavir/ritonavir (DRV/r), etravirine (ETR), tipranavir/ritonavir or raltegravir.

Results:

Fifty-four adolescents 2–17 years of age were enrolled from 8 sites and followed for 48 weeks. Reasons for switch were second-line failure (n = 44) and toxicity to second-line regimens (n = 10). At switching to third-line ARV, the median age (interquartile range) was 14.3 (12.4–15.4) years. Genotypes at time of second-line failure (n = 44) were M184V (77%), ≥4 thymidine analogue mutations (25%), non-nucleoside reverse transcriptase inhibitor–resistant associated mutation (RAM) (80%), ETR-RAM score ≥4 (14%), any lopinavir-RAM (59%) and ≥1 major DRV-RAM (41%). The third-line regimens had a median of 4 (min–max, 4–6) drugs and included ETR/DRV/r (43%), DRV/r (33%), ETR (17%), tipranavir/ritonavir (2%) or raltegravir/DRV/r/ (4%). The median CD4 (interquartile range) increased from 16% (12–21) at third-line switch to 21% (18–25) and 410 (172–682) to 607 (428–742) cells/mm3 at 48 weeks (P < 0.001). HIV RNA declined from 3.9 (2.9–4.9) to 1.6 (1.6–3.0) log10 copies/mL (P < 0.001) and 33/50 (66%) had levels <50 copies/mL at 48 weeks. Seventeen (31%) had HIV-RNA ≥1000 copies/mL; about half due to poor adherence; genotyping in 13 of these adolescents revealed ETR-RAM score ≥4 in 2 (15%) and ≥1 major DRV-RAM in 7 (54%).

Conclusions:

Third-line ARV therapy was well tolerated and resulted in virologic suppression in 70% of adolescents at 1 year. Poor adherence and limited ARV options are major problems in the long-term management of adolescents with HIV.
Coalescent Processes with Skewed Offspring Distributions and non-Equilibrium Demography
Authors: Matuszewski Sebastian , Hildebrandt Marcel E. , Achaz Guillaume , Jensen Jeffrey D.
Published: May 2017

Non-equilibrium demography impacts coalescent genealogies leaving detectable, well-studied signatures of variation. However, similar genomic footprints are also expected under models of large reproductive skew, posing a serious problem when trying to make inference. Furthermore, current approaches consider only one of the two processes at a time, neglecting any genomic signal that could arise from their simultaneous effects, pre-venting the possibility of jointly inferring parameters relating to both offspring distribution and population history. Here, we develop an extended Moran model with exponential population growth, and demonstrate that the underlying ancestral process converges to a time-inhomogeneous psi-coalescent. However, by applying a non-linear change of time scale – analogous to the Kingman coalescent – we find that the ancestral process can be rescaled to its time-homogeneous analogue, allowing the process to be simulated quickly and efficiently. Furthermore, we derive analytical expressions for the expected site-frequency spectrum under the time-inhomogeneous psi-coalescent and develop an approximate-likelihood framework for the joint estimation of the coalescent and growth parameters. By means of extensive simulation, we demonstrate that both can be estimated accurately from whole-genome data. In addition, not accounting for demography can lead to serious biases in the inferred coalescent model, with broad implications for genomic studies ranging from ecology to conservation biology. Finally, we use our method to analyze sequence data from Japanese sardine populations and find evidence of high variation in individual reproductive success, but few signs of a recent demographic expansion.
Agonist-Dependent And -Independent Kappa Opioid Receptor Phosphorylation Showed Distinct Phosphorylation Patterns And Resulted In Different Cellular Outcomes
Authors: Chiu Yi-Ting , Chen Chongguang , Schulz Stefan , Liu-Chen Lee-Yuan
Published: May 2017

We reported previously that the selective agonist U50,488H promoted phosphorylation of the mouse kappa opioid receptor (KOPR) at residues S356, T357, T363 and S369. Here, we found that agonist (U50,488H)-dependent KOPR phosphorylation at all the residues were mediated by Gi/oα proteins and multiple protein kinases [GRKs2, 3, 5 and 6 and protein kinase C (PKC)]. In addition, PKC activation by phorbol ester induced agonist-independent KOPR phosphorylation. Compared with U50,488H, PKC activation promoted much higher S356/T357 phosphorylation, much lower T363 phosphorylation and similar levels of S369 phosphorylation. Following U50,488H, GRKs, but not PKC, were involved in agonist-induced KOPR internalization. In contrast, PKC activation caused a lower level of agonist-independent KOPR internalization, compared to U50,488H. U50,488H-induced activation of extracellular signal regulated kinase 1/2 (ERK1/2) was G protein-, but not β-arrestin-, dependent. After U50,488H, GRK-mediated, but not PKC-mediated, KOPR phosphorylation followed by β-arrestin recruitment desensitized U50,488H-induced ERK1/2 response. Therefore, agonist-dependent (GRK- and PKC-mediated) and agonist-independent (PKC-promoted) KOPR phosphorylations show distinct phosphorylation patterns, leading to diverse cellular outcomes.
Responses to mechanically and visually cued water waves in the nervous system of the medicinal leech
Authors: Lehmkuhl Andrew M. , Muthusamy Arunkumar , Wagenaar Daniel A.
Published: May 2017

Summary statement

Cues from water movement help aquatic predators find their prey. We study how the nervous system of the medicinal leech processes visual and mechanical information derived from surface waves.

Sensitivity to water waves is a key modality by which aquatic predators can detect and localize their prey. For one such predator, the medicinal leech,Hirudo verbana, behavioral responses to visual and mechanical cues from water waves are well documented. Here, we quantitatively characterized the response patterns of a multisensory interneuron, the S cell, to mechanically and visually cued water waves. The frequency dependence of the S-cell response matched the behavioral response well, in that sensitivity was higher for low frequencies in the visual modality and for high frequencies in the mechanical modality. We demonstrated that neither the cephalic ganglia nor the tail brain is required for the S cell to respond to visually cued water waves. The direction of spike propagation within the S- cell system did follow the direction of wave propagation under certain circumstances, but it is unlikely that downstream neuronal targets can use this information. In terms of overall firing rate, the S cell response was not direction selective. Accordingly we propose a role for the S cell in the detection of waves but not in the localization of their source.
Integrated Computing and Tracking System for Centralized High-Throughput Genetic Analysis: a Case Study
Authors: Stilp Adrienne M. , Gogarten Stephanie M. , Laurie Cathy C. , Sofer Tamar
Published: May 2017

The Genetic Analysis Center (GAC) of the Hispanic Community Health Study/Study of Latinos (HCHS/SOL) developed an Integrated Computing and Tracking system (ICT) in order to perform genome-wide and other genetic association studies automatically and efficiently, while documenting all analysis specifications. This system provides easy-to-use analysis set-up and computing procedures, automatic reports, and analysis search functionality due to integration with an on-site database. In this paper we describe the ICT and demonstrate how it satisfies key principles of reproducible research, while respecting constraints and challenges arising from using very large, restricted access, human-subjects data. This case study may benefit other groups that have similar requirements for high-throughput analysis execution and management.
Role of the membrane cholesterol-glycosphingolipid complex as a ‘transistor’ to regulate GSL receptor function and signaling of both lipids
Authors: Novak Anton , Lingwood Clifford
Published: May 2017

Cholesterol and glycosphingolipids (GSL) are the major species that accumulate in plasma membrane lipid rafts. These complexes imbue the membrane with increased order, which in turn, plays a central role in the transmembrane signaling foci lipid rafts provide. In addition, both GSL and cholesterol binding can mediate (separate) signal pathways. We have shown that cholesterol and GSLs however, form a complex in which the GSL sugar is reoriented from a membrane perpendicular to parallel format, becoming largely unavailable for exogenous ligand binding. Similarly, the steroid hydroxyl is masked, restricting access of cholesterol ligands. This was observed in model and cell membranes and in human tumour frozen tissue sections. We now show the order of exogenous ligand binding plays a significant role to determine the extent of GSL or cholesterol receptor activity. Ligand binding to cholesterol enhances subsequent GSL recognition and vice versa, suggesting that ligand binding to “free” receptor (membrane perpendicular GSL carbohydrate, nonmasked cholesterol) can result in partial dissociation of the GSL/cholesterol complex to allow additional GSL ligand and cholesterol ligand binding. Since many GSLs can complex with membrane cholesterol, the binding of a single cholesterol ligand may unmask cholesterol-complexed GSL for increased binding of both a single or multiple GSL-specific ligands. We show that multiple cholesterol-masked GSLs can be coincident in tissues. This provides a mechanism for GSL-dependent signal amplification and diversification, representing a biological ‘transistor’, regulating amplitude and potentially, diversity of GSL signaling. The process represents a new mechanism of ‘cross-talk’ between GSL and cholesterol signaling. This is of clinical importance since we have found cholesterol/GSL masking applies to monoclonal anti GSL antibodies in development and in current use as antineoplastic therapeutics.
A model for adult organ resizing demonstrates stem cell scaling through a tunable commitment rate
Authors: Du XinXin , O’Brien Lucy Erin , Riedel-Kruse Ingmar
Published: May 2017

Many adult organs grow or shrink to accommodate different physiological demands. Often, as total cell number changes, stem cell number changes proportionally in a phenomenon called ‘stem cell scaling’. The cellular behaviors that give rise to scaling are unknown. Here we study two complementary theoretical models of the adult Drosophila midgut, a stem cell-based organ with known resizing dynamics. First, we derive a differential equations model of midgut resizing and show that the in vivo kinetics of growth can be recapitulated if the rate of fate commitment depends on the tissue’s stem cell proportion. Second, we develop a twodimensional simulation of the midgut and find that proportion-dependent commitment rate and stem cell scaling can arise phenomenologically from the stem cells’ exploration of physical tissue space during its lifetime. Together, these models provide a biophysical understanding of how stem cell scaling is maintained during organ growth and shrinkage.
Quantitative Models Identify Histone Signatures of Poised Genes Prior to Cellular Differentiation
Authors: Tian Rui
Published: May 2017

Background

Recent studies have shown that histone marks are involved in pre-programming gene fates during cellular differentiation. Bivalent domains (marked by both H3K4me3 and H3K27me3) have been proposed to act in the histone pre-patterning of poised genes; however, bivalent genes could also resolve into monovalent silenced states during differentiation. Thus, the histone signatures of poised genes need to be more precisely characterized.

Results

Using a support vector machine (SVM), we show that the collective histone modification data from human blood hematopoietic cells (HSCs) could predict poised genes with fairly high predictive accuracy within the model of directed erythrocyte differentiation from HSCs. Surprisingly, models with single histone marks (e.g., H3K4me3 or H2A.Z) could reach comparable predictive powers to the full model built with all of the nine histone marks. We also derived an H2A.Z and H3K9me3-based Naive Bayesian model for inferring poised genes, and the validity of this model was supported by data from several other pluripotent/multipotent cells (including mouse ES cells).

Conclusion

Our work represents a systematic quantitative study that verified that histone marks play a role in pre-programming the activation or repression of specific genes during cellular differentiation. Our results suggest that the relative quantities of H2A.Z modification and H3K9me3 modification are important in determining a corresponding gene’s fate during cellular differentiation.
Role of competition in the strain structure of rotavirus under invasion and reassortment
Authors: Zinder Daniel , Riolo Maria A , Woods Robert J. , Pascual Mercedes
Published: May 2017

The role of competitive interactions in the formation and coexistence of viral strains remains unresolved. Neglected aspects of existing strain theory are that viral pathogens are repeatedly introduced from animal sources and readily exchange their genes. The combined effect of introduction and reassortment opposes strain structure, in particular the predicted stable coexistence of antigenically differentiated strains under strong frequency-dependent selection mediated by cross-immunity. Here we use a stochastic model motivated by rotavirus, the most common cause of childhood diarrheal mortality, to investigate serotype structure under these conditions. We describe a regime in which the transient coexistence of distinct strains emerges despite only weak cross-immunity, but is disturbed by invasions of new antigenic segments that reassort into existing backgrounds. We find support for this behavior in global rotavirus sequence data and present evidence for the displacement of new strains towards open antigenic niches. Our work extends previous work to bacterial and viral pathogens that share these rotavirus-like characteristics, with important implications for the effects of interventions such as vaccination on strain composition, and for the understanding of the factors promoting emergence of new subtypes.
A gated relaxation oscillator controls morphogenetic movements in bacteria
Authors: Guzzo Mathilde , Murray Seán M. , Martineau Eugénie , Lhospice Sébastien , Baronian Grégory , My Laetitia , Zhang Yong , Espinosa Leon , Vincentelli Renaud , Bratton Benjamin P. , Shaevitz Joshua W. , Molle Virginie , Howard Martin , Mignot Tâm
Published: May 2017

Dynamic control of cell polarity is of critical importance for many aspects of cellular development and motility. InMyxococcus xanthus, a G-protein and its cognate GTPase-activating protein establish a polarity axis that defines the direction of movement of the cell and which can be rapidly inverted by the Frz chemosensory system. Although vital for collective cell behaviours, how Frz triggers this switch has remained unknown. Here, we use genetics, imaging and mathematical modelling to show that Frz controls polarity reversals via a gated relaxation oscillator. FrzX, which we newly identify as the primary Frz output, provides the gating and thus acts as the trigger for reversals. Slow relocalisation of the polarity protein RomR then creates a refractory period during which another switch cannot be triggered. A secondary Frz output, FrzZ, decreases this delay allowing rapid reversals when required. This architecture thus results in a highly tunable switch that allows a wide range of motility responses.
Experimental Evolution of Insect Immune Memory VS. Pathogen Resistance
Authors: Khan Imroze , Prakash Arun , Agashe Deepa
Published: May 2017

Under strong pathogen pressure, insects often evolve resistance to infection. Many insects are also protected via immune memory (‘immune priming’), whereby sub-lethal exposure to a pathogen enhances survival after secondary infection. To understand the evolution and consequences of these immune responses, we imposed strong pathogen selection on flour beetles (Tribolium castaneum), infecting them withBacillus thuringiensis(Bt) for 11 generations. Populations injected first with heat-killed and then live Bt each generation evolved high basal resistance against multiple Bt strains. In contrast, all populations injected only with a high dose of live Bt evolved less effective but strain-specific priming response. Control populations injected with heat-killed Bt did not evolve priming; and in the ancestor, priming was effective only against a low Bt dose. Thus, pathogens can select for rapid modulation of insect priming ability, leading to divergent immune strategies (generalized resistance vs. specific immune priming) with distinct mechanisms and adaptive benefits.
The condensin complex is a mechanochemical motor that translocates along DNA
Authors: Terekawa Tsuyoshi , Bisht Shveta , Eeftens Jorine M. , Dekker Cees , Haering Christian H. , Greene Eric C.
Published: May 2017

One Sentence Summary

Single-molecule imaging reveals that eukaryotic condensin is a highly processive DNA-translocating motor complex.

Condensin plays crucial roles in chromosome organization and compaction, but the mechanistic basis for its functions remains obscure. Here, we use single-molecule imaging to demonstrate that Saccharomyces cerevisiae condensin is a molecular motor capable of ATP hydrolysis-dependent translocation along double-stranded DNA. Condensin’s translocation activity is rapid and highly processive, with individual complexes traveling an average distance of ≥10 kilobases at a velocity of ∼60 base pairs per second. Our results suggest that condensin may take steps comparable in length to its ∼50-nanometer coiled-coil subunits, suggestive of a translocation mechanism that is distinct from any reported DNA motor protein. The finding that condensin is a mechanochemical motor has important implications for understanding the mechanisms of chromosome organization and condensation.
Tacrolimus rescues endothelial ALK1 loss-of-function signaling and improves HHT vascular pathology
Authors: Ruiz Santiago , Chandakkar Pallavi , Zhao Haitian , Papoin Julien , Chatterjee Prodyot K. , Christen Erica , Metz Christine N. , Blanc Lionel , Campagne Fabien , Marambaud Philippe
Published: May 2017

Hereditary hemorrhagic telangiectasia (HHT) is a genetic vascular disorder arising from endothelial cell (EC) proliferation and hypervascularization, for which no cure exists. Because HHT is caused by loss-of-function mutations in BMP9-ALK1-Smad1/5/8 signaling, interventions aimed at activating this pathway are of therapeutic value. By screening FDA-approved drug libraries, we identified tacrolimus (FK-506) as a potent activator of Smad1/5/8 in BMP9-challenged reporter cells. In primary ECs, tacrolimus activated Smad1/5/8 to oppose the pro-angiogenic gene expression signature associated with ALK1 loss-of-function, by notably reducing Dll4 expression. In these cells, tacrolimus also inhibited Akt and p38 stimulation by VEGF. In the BMP9/10-immunodepleted postnatal retina—a mouse model of HHT vascular pathology—tacrolimus activated endothelial Smad1/5/8 and prevented the Dll4 overexpression and hypervascularization associated with this model. Finally, tacrolimus stimulated Smad1/5/8 in cells transfected with BMP9-unresponsive ALK1 HHT mutants and in HHT patient blood outgrowth ECs. We propose that tacrolimus repurposing has therapeutic potential in HHT.
Physiological assembly of functionally active 30S ribosomal subunits fromin vitrosynthesized parts
Authors: Li Jun , Wassie Brook , Church George M.
Published: May 2017

Synthetic ribosomesin vitrocan facilitate engineering translation of novel polymers, identifying ribosome biogenesis central components, and paving the road to constructing replicating systems from defined biochemical components. Here, we report functional syntheticEscherichia coli30S ribosomal subunits constructed using a defined, purified cell free system under physiological conditions. We test hypotheses about key components of natural ribosome biogenesis pathway as required for efficient function – including integration of 16S rRNA modification, cofactors facilitated ribosome assembly and protein synthesis in the same compartmentin vitro. We observe ~17% efficiency for fully synthetic 30S and ~70% efficiency fromin vitrotranscribed 16S rRNA assembled with natural proteins. We observe up to 5 fold improvement over previous crude extracts. We suggest extending the minimal list of components required for central-dogma replication from the 151 gene products previously reported to at least 180 to allow the speed and accuracy of macromolecular synthesis to approach nativeE. colivalues.
Functional types in the Bromeliaceae: relationships with drought‐resistance traits and bioclimatic distributions
Authors: Males Jamie , Griffiths Howard
Published: May 2017

Neotropical Bromeliaceae occupy an exceptional diversity of habitats. The five principal functional types, which are defined by innovations such as Crassulacean acid metabolism (CAM), epiphytism, the tank growth form and neoteny, display distinct ecological water‐use strategies.

The contribution of putative drought‐resistance traits to the ecological differentiation of functional types has not previously been assessed, despite growing interest in the importance of these traits in other plant groups.

We formulated a set of hypotheses to be tested through a major survey of 376 bromeliad species (over 10% of the entire family) representing different functional types and ecologies. We quantified four drought‐resistance traits: osmotic potential at full turgor (πo), saturated water content (SWC), water mass per unit area (WMA) and dry leaf mass per unit area (LMA). For a subset of 308 species, relationships between drought‐resistance traits and species bioclimatic envelopes were also analysed.

Saturated water content, WMA and LMA were closely inter‐correlated, and there was weaker coordination with πo, but the four traits differed significantly between functional types. Species of different functional types occupied distinct areas of bioclimatic space, and the relationships mapping drought‐resistance trait values into bioclimatic space also varied between functional types.

We conclude that divergences in drought‐resistance trait values form an integral part of the evolution of functional type distinctiveness and climatic niche differentiation in this megadiverse tropical plant family.

This study demonstrates how rapid, taxonomically extensive quantification of plant functional traits can provide important insights into the evolution of ecological diversity.

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Optimal running speeds when there is a trade‐off between speed and the probability of mistakes
Authors: Amir Abdul Nasir Ami Fadhillah , Clemente Christofer J. , Wynn Melissa L. , Wilson Robbie S.
Published: May 2017

Do prey run as fast as they can to avoid capture? This is a common assumption in studies of animal performance, yet a recent mathematical model (Wheatley et al. Integrative and Comparative Biology, 55, 1166–1175; ) of escape behaviour predicts that animals should instead use speeds below their maximum capabilities even when running from predators. Fast speeds may compromise motor control and accuracy of limb placement, particularly as the animal runs along narrow structures like beams or branches. Mistakes decrease speed and increase the probability of capture.

We tested several key assumptions and predictions of Wheatley et al.'s () model using wild‐caught northern quolls (Dasyurus hallucatus), a squirrel‐sized marsupial carnivore. We quantified the speeds of quolls as they traversed beams of differing width and expected animals should balance the benefits of higher speeds against the increased probability of mistakes when selecting speeds.

We first explored whether the probability of mistakes when running along a beam increased at faster running speeds (speed‐accuracy trade‐off) and when the difficulty of a task was greater (narrower beam). In addition, we quantified the costs of locomotor mistakes to test the assumption that mistakes decreased overall running speed. Finally, we tested whether individual northern quolls modulated their running speeds when moving on narrow beams, which would decrease the probability of making catastrophic mistakes.

We found quolls were more likely to make mistakes when running faster and on the narrower beam. Locomotor mistakes increased the total time needed to traverse the entire beam, and each mistake decreased average escape speed by around 50%, representing a substantial cost for slips or trips. To circumvent the costs of these mistakes, quolls voluntarily reduced speeds in situations when they are more likely to make a mistake (i.e. narrower beams), thereby allowing them to decrease the total time it took to traverse the beam.

Our data provide support for the assumptions and predictions of Wheatley et al.'s () model of optimal escape speeds, and suggest that animals optimize rather than simply maximize speeds when running along challenging substrates. Our work provides a foundation for understanding the movement behaviour of animals when their objective is to escape predatory attacks, and demonstrates that animals should select their escape strategy based on how both the speed of movement and motor control affect task success.

A lay summary is available for this article.
Conspecific and not performance‐based attraction on immigrants drives colony growth in a waterbird
Authors: Tenan Simone , Fasola Mauro , Volponi Stefano , Tavecchia Giacomo
Published: May 2017

Local recruitment and immigration play an important part in the dynamics and growth of animal populations. However, their estimation and incorporation into open population models is, in most cases, problematic. We studied factors affecting the growth of a recently established colony of Eurasian spoonbill (Platalea leucorodia) and assessed the contribution of local recruits, i.e. birds born in the colony, and immigrants, i.e. birds of unknown origin, to colony growth.

We applied an integrated population model that accounts for uncertainty in breeding state assignment and merges population surveys, local fecundity and individual longitudinal data of breeding and non‐breeding birds, to estimate demographic rates and the relative role of recruitment and immigration in driving the local dynamics. We also used this analytical framework to assess the degree of support for the ‘performance‐based’ and ‘conspecific attraction’ hypotheses as possible mechanisms of colony growth.

Among the demographic rates, only immigration was positively and significantly correlated with population growth rate. In addition, the number of immigrants settling in the colony was positively correlated with colony size in the previous and current year, but was not correlated with fecundity of the previous year.

Our results suggest that the variation in immigration affected colony dynamics and that conspecific attraction likely triggered the relevant role of immigration in the growth of a recently formed waterbird colony, supporting the need of including immigration in population analysis.
Reproductive performance of resident and migrant males, females and pairs in a partially migratory bird
Authors: Grist Hannah , Daunt Francis , Wanless Sarah , Burthe Sarah J. , Newell Mark A. , Harris Mike P. , Reid Jane M.
Published: May 2017

Quantifying among‐individual variation in life‐history strategies, and associated variation in reproductive performance and resulting demographic structure, is key to understanding and predicting population dynamics and life‐history evolution. Partial migration, where populations comprise a mixture of resident and seasonally migrant individuals, constitutes a dimension of life‐history variation that could be associated with substantial variation in reproductive performance. However, such variation has rarely been quantified due to the challenge of measuring reproduction and migration across a sufficient number of seasonally mobile males and females.

We used intensive winter (non‐breeding season) resightings of colour‐ringed adult European shags (Phalacrocorax aristotelis) from a known breeding colony to identify resident and migrant individuals. We tested whether two aspects of annual reproductive performance, brood hatch date and breeding success, differed between resident and migrant males, females and breeding pairs observed across three consecutive winters and breeding seasons.

The sex ratios of observed resident and migrant shags did not significantly differ from each other or from 1:1, suggesting that both sexes are partially migratory and that migration was not sex‐biased across surveyed areas.

Individual resident males and females hatched their broods 6 days earlier and fledged 0.2 more chicks per year than migrant males and females on average. Resident individuals of both sexes therefore had higher breeding success than migrants.

Hatch date and breeding success also varied with a pair's joint migratory strategy such that resident–resident pairs hatched their broods 12 days earlier than migrant–migrant pairs, and fledged 0.7 more chicks per year on average. However, there was no evidence of assortative pairing with respect to migratory strategy: observed frequencies of migrant–migrant and resident–resident pairs did not differ from those expected given random pairing.

These data demonstrate substantial variation in two key aspects of reproductive performance associated with the migratory strategies of males, females and breeding pairs within a partially migratory population. These patterns could reflect direct and/or indirect mechanisms, but imply that individual variation in migratory strategy and variation in pairing among residents and migrants could influence selection on migration and drive complex population and evolutionary dynamics.
Gut microbial communities of American pikas (Ochotona princeps): Evidence for phylosymbiosis and adaptations to novel diets
Authors: Kohl Kevin D. , Varner Johanna , Wilkening Jennifer L. , Dearing M. Denise
Published: May 2017

Gut microbial communities provide many physiological functions to their hosts, especially in herbivorous animals. We still lack an understanding of how these microbial communities are structured across hosts in nature, especially within a given host species. Studies on laboratory mice have demonstrated that host genetics can influence microbial community structure, but that diet can overwhelm these genetic effects.

We aimed to test these ideas in a natural system, the American pika (Ochotona princeps). First, pikas are high‐elevation specialists with significant population structure across various mountain ranges in the USA, allowing us to investigate whether similarities in microbial communities match host genetic differences. Additionally, pikas are herbivorous, with some populations exhibiting remarkable dietary plasticity and consuming high levels of moss, which is exceptionally high in fibre and low in protein. This allows us to investigate adaptations to an herbivorous diet, as well as to the especially challenging diet of moss.

Here, we inventoried the microbial communities of pika caecal pellets from various populations using 16S rRNA sequencing to investigate structuring of microbial communities across various populations with different natural diets.

Microbial communities varied significantly across populations, and differences in microbial community structure were congruent with genetic differences in host population structure, a pattern known as “phylosymbiosis.”

Several microbial members (Ruminococcus, Prevotella, Oxalobacter and Coprococcus) were detected across all samples, and thus likely represent a “core microbiome.” These genera are known to perform a number of services for herbivorous hosts such as fibre fermentation and the degradation of plant defensive compounds, and thus are likely important for herbivory in pikas. Moreover, pikas that feed on moss harboured microbial communities highly enriched in Melainabacteria. This uncultivable candidate phylum has been proposed to ferment fibre for herbivores, and thus may contribute to the ability of some pika populations to consume high amounts of moss.

These findings demonstrate that both host genetics and diet can influence the microbial communities of the American pika. These animals may be novel sources of fibre‐degrading microbes. Last, we discuss the implications of population‐specific microbial communities for conservation efforts in this species.
The role of rare morph advantage and conspicuousness in the stable gold‐dark colour polymorphism of a crater lake Midas cichlid fish
Authors: Torres‐Dowdall Julián , Golcher‐Benavides Jimena , Machado‐Schiaffino Gonzalo , Meyer Axel
Published: May 2017

Genetically based stable colour polymorphisms provide a unique opportunity to study the evolutionary processes that preserve genetic variability in the wild. Different mechanisms are proposed to promote the stability of polymorphisms, but only few empirical examples have been documented, resulting in an incomplete understanding of these mechanisms.

A remarkable genetically determined stable colour polymorphism is found in the Nicaraguan Midas cichlid species complex (Amphilophus cf. citrinellus). All Midas cichlids start their life with a dark‐grey coloration (dark morph), but individuals carrying the dominant “gold” allele (c. 10%) lose their melanophores later in life, revealing the underlying orange coloration (gold morph). How this polymorphism is maintained remains unclear. Two main hypotheses have been proposed, both suggesting differential predation upon colour morphs as the proximate mechanism. One predicts that the conspicuous gold morph is more likely to be preyed upon, but this disadvantage is balanced by their competitive dominance over the dark morph. The second hypothesis suggests a rare morph advantage where the rarer gold morph experiences less predation. Empirical evidence for either of these mechanisms is still circumstantial and inconclusive.

We conducted two field experiments in a Nicaraguan crater lake using wax models simulating both morphs to determine predation pressure upon Midas cichlid colour morphs. First, we tested the interaction of coloration and depth on attack rate. Second, we tested the interaction of fish size and coloration. We contrasted the pattern of attacks from these experiments to the predicted predation patterns from the hypotheses proposed to explain the colour polymorphism's stability.

Large models imitating colour morphs were attacked at similar rates irrespectively of their position in the water column. Yet, attacks upon small models resembling juveniles were directed mainly towards dark models. This resulted in a significant size‐by‐colour interaction.

We suggest that gold Midas cichlids experience a rare morph advantage as juveniles when individuals of this morph are extremely uncommon. But this effect is reduced or disappears among adults, where gold individuals are relatively more common. Thus, the interaction of rare morph advantage and conspicuousness, rather than either of those factors alone, is a likely mechanism resulting in the stability of the colour polymorphism in Midas cichlids.
Desynchronizations in bee–plant interactions cause severe fitness losses in solitary bees
Authors: Schenk Mariela , Krauss Jochen , Holzschuh Andrea
Published: May 2017

Global warming can disrupt mutualistic interactions between solitary bees and plants when increasing temperature differentially changes the timing of interacting partners. One possible scenario is for insect phenology to advance more rapidly than plant phenology.

However, empirical evidence for fitness consequences due to temporal mismatches is lacking for pollinators and it remains unknown if bees have developed strategies to mitigate fitness losses following temporal mismatches.

We tested the effect of temporal mismatches on the fitness of three spring‐emerging solitary bee species, including one pollen specialist. Using flight cages, we simulated (i) a perfect synchronization (from a bee perspective): bees and flowers occur simultaneously, (ii) a mismatch of 3 days and (iii) a mismatch of 6 days, with bees occurring earlier than flowers in the latter two cases.

A mismatch of 6 days caused severe fitness losses in all three bee species, as few bees survived without flowers. Females showed strongly reduced activity and reproductive output compared to synchronized bees. Fitness consequences of a 3‐day mismatch were species‐specific. Both the early‐spring species Osmia cornuta and the mid‐spring species Osmia bicornis produced the same number of brood cells after a mismatch of 3 days as under perfect synchronization. However, O. cornuta decreased the number of female offspring, whereas O. bicornis spread the brood cells over fewer nests, which may increase offspring mortality, e.g. due to parasitoids. The late‐spring specialist Osmia brevicornis produced fewer brood cells even after a mismatch of 3 days. Additionally, our results suggest that fitness losses after temporal mismatches are higher during warm than cold springs, as the naturally occurring temperature variability revealed that warm temperatures during starvation decreased the survival rate of O. bicornis.

We conclude that short temporal mismatches can cause clear fitness losses in solitary bees. Although our results suggest that bees have evolved species‐specific strategies to mitigate fitness losses after temporal mismatches, the bees were not able to completely compensate for impacts on their fitness after temporal mismatches with their food resources.
Towards a mechanistic understanding of the effect that different species of large grazers have on grassland soil N availability
Authors: Liu Chen , Wang Ling , Song Xuxin , Chang Qing , Frank Douglas A. , Wang Deli , Li Jing , Lin Haijiao , Du Feiyue
Published: May 2017

Herbivore grazing has major effects on soil nutrient dynamics in a variety of grassland ecosystems. Previous studies have examined how large herbivores as a group affect nutrient cycling, but little information is available on how assemblages of different herbivore species may influence nutrient cycling, and whether herbivore assemblage effects are influenced by plant community characteristics (e.g. composition, diversity) of the grazed grassland.

We conducted a 5‐year, replicated grazing experiment to test the effects of different large herbivore assemblages (cattle grazing, sheep grazing, combined cattle and sheep grazing, no grazing) under moderate grazing intensity on soil nitrogen (N) mineralization rate in two types of grassland communities (high forbs/high diversity and low forbs/low diversity) in meadow steppe habitat of northeast China. Moreover, we examined two distinctly different pathways that herbivores could influence soil N availability: directly through urine and dung deposition and indirectly by shifting grassland species composition (i.e. the grass: forb ratio), thereby the quality of plant litter available to soil decomposers.

We found that grazer effects on soil N availability (indexed with anion and cation adsorption strips) depended on herbivore assemblage, and the herbivore assemblage effects varied in the two types of grasslands. In one type of grassland characterized by low diversity, grazing by each of the herbivore assemblages enhanced soil N availability compared to the ungrazed plots, and mixed species (cattle and sheep) grazing had a greater effect than single species grazing. In high diversity grassland, single species herbivore grazing significantly increased soil N availability, but mixed grazing had no effect.

Mixed linear modelling revealed that soil N availability was facilitated primarily by excreta additions to the soil and secondarily by the abundance of grasses.

Synthesis. Grazers increased soil N availability directly by adding readily accessible N in urine and dung to the soil. Herbivores indirectly influenced soil N availability by altering the plant composition (grass: forb cover). Both mechanisms contributed to the variation in how different herbivore assemblages affected soil N availability in the two grassland types.
The ‘golden kelp’ Laminaria ochroleuca under global change: Integrating multiple eco‐physiological responses with species distribution models
Authors: Franco João N. , Tuya Fernando , Bertocci Iacopo , Rodríguez Laura , Martínez Brezo , Sousa‐Pinto Isabel , Arenas Francisco
Published: May 2017

The loss of marine foundation species, in particular kelps at temperate latitudes, has been linked to climatic drivers and co‐occurring human perturbations. Ocean temperature and nutrients typically covary over local and regional scales and play a crucial role on kelp dynamics. Examining their independent and interactive effects on kelp physiological performance is essential to understand and predict patterns of kelp distribution, particularly under scenarios of global change.

Crossed combinations of ocean temperatures and availability of nutrients were experimentally tested on juveniles of the ‘golden kelp’, Laminaria ochroleuca, from the northwestern Iberian Peninsula. Eco‐physiological responses included: survival, growth and total N content. Results were embedded into a Species Distribution Model (SDM), which relates presence records and climatic and non‐climatic data to forecast distribution patterns of L. ochroleuca under different climate change scenarios.

Temperatures above 24.6°C were lethal irrespective of nutrients. Optimal growth of juvenile sporophytes occurred between 12 and 18°C and no nutrient limitation. The SDM, where ocean temperature was the main predictor of kelp distribution in line with temperature thresholds given by eco‐physiological responses, suggests a future expansion towards northern latitudes and a retreat from the southern limit/boundary of the current distribution.

Synthesis. Range‐shifting of the golden kelp can have severe ecological impacts at regional and local scales. The expansion or retraction of the species along the European coast seems to be modulated mainly by temperature, but nutrient availability would be a key to maintain optimal physiological performance. Our work highlights that the combination of empirical and modelling approaches is accessible to researchers and crucial to building more robust predictions of ecological and biogeographic responses of habitat‐forming species to forecasted environmental change.
Difference in shade tolerance drives the mixture effect on oak productivity
Authors: Toïgo Maude , Perot Thomas , Courbaud Benoit , Castagneyrol Bastien , Gégout Jean‐Claude , Longuetaud Fleur , Jactel Hervé , Vallet Patrick
Published: May 2017

Assessing how species productivity in mixtures is influenced by species shade tolerance (ST) and phylogeny would be helpful to improve our general understanding of the relationship between tree species diversity and productivity in forests.

We investigated the effects of differences in ST and phylogenetic distances (PDs) between pairs of species on the productivity of Quercus petraea growing in 18 mixtures in lowland temperate forests. We calculated the mixture effect as the difference in productivity of Q. petraea in mixed vs. pure stands. Our analyses were based on data from seven annual campaigns of the French National Forest Inventory covering 1,573 plots.

The mixture effect on Q. petraea productivity increased when the ST of the companion species decreased. Compared to its productivity in pure stands, Q. petraea productivity in mixed coniferous stands varied from −14.6% up to +39.6% as the ST of the companion species inversely varied from highest to lowest. With broadleaved companion species, the mixture effect varied from −10% up to +13.9% with decreasing ST. We found no effect of PD between Q. petraea and the companion species on the mixture effect.

Synthesis. Our results confirm that shade tolerance is an important driver of the diversity effect on productivity at species level in temperate forests and that phylogenetic distance is not a relevant proxy for species functional dissimilarity.
Reduced platelet aggregation in women after intercourse: a possible role for the cyclooxygenase pathway
Authors: Mayoral‐Andrade Gabriel , Pérez‐Campos‐Mayoral Laura , Majluf‐Cruz Abraham , Perez‐Campos Mayoral Eduardo , Perez campos Mayoral Carlos , Rocha‐Núñez Ana , Martinez Margarito , Zenteno Edgar , Hernandez‐Gonzalez Leticia , López Juan María Guadalupe , Pérez‐Santiago Alma Dolores , Pérez‐Campos Eduardo
Published: May 2017

We hypothesise that molecules in the cyclooxygenase pathway affect platelet activity when seminal fluid (SF) is present. We considered the influence of SF on platelet aggregation in women, and believe that the prostanoids in SF signalling are significant. Thirty‐one female subjects were studied, 20 of whom were sexually active. Male partners were given either aspirin or indomethacin to inhibit cyclooxygenase. The 6‐keto prostaglandin F1α (6‐keto PGF1α) and prostaglandin E metabolite (PGE‐M) in SF were measured by competitive assay. Platelets and prostanoids were evaluated in women, periodically, before and after intercourse. The platelets were tested with adenosine diphosphate (ADP) and arachidonic acid (AA). To block the interaction between the uterus and SF, some couples used condoms. We found that the 6‐keto prostaglandin F1α in urine at 2 hours post‐intercourse (1418.75 pg/mL, Std 688.39) was greater than pre‐intercourse (772.68 pg/mL, Std 116.54). Post‐intercourse, a transient decrease in platelet aggregation was observed in women whose partners did not use condoms. Averages for platelet aggregation were 20.16% with ADP, and more significantly, 37.79% with AA after 2 hours. In contrast, couples using condoms showed no changes, averaging 64.02% with ADP and 72.06% with AA. Women whose partners were taking aspirin or indomethacin also showed no changes. SF from men taking aspirin or indomethacin led to no reduction in platelet aggregometry in their partners. These results indicate that in cases of exposure to SF, the transient change in women's platelet activity could be related to the cyclooxygenase pathway.
Dissimilarity‐overlap analysis of community dynamics: Opportunities and pitfalls
Authors: Kalyuzhny Michael , Shnerb Nadav M.
Published: May 2017

Do multiple different communities have similar dynamics? This novel question was recently addressed with the development of the dissimilarity–overlap curve (DOC) method, designed to identify sets of communities with similar (‘universal’) dynamics using pairwise comparison of communities’ composition. However, the theoretical properties of the method were tested using very restrictive and, in some cases, unrealistic assumptions.

We test the ability of the DOC method to discriminate universal from non‐universal dynamics in more realistic scenarios—under various levels and regimes of stochasticity and sampling errors, in cases where species respond to environmental gradients or geographical axes and in cases when only a fraction of the communities have universal dynamics. We also examine the ability of the method to test the Neutral Theory of Biodiversity.

We found that multiple factors and processes that produce variability among observed communities lead in general to a spurious detection of universal dynamics. In particular, sets of communities subject to environmental gradients, differences in stochasticity and in sampling quality among communities, and cases in which only a small fraction of the communities are similar, may be detected as having universal dynamics. We suggest the DOC method as a potential for testing the symmetric interactions assumption of neutral or symmetric theories, superior to the common techniques which are based on species abundance statistics.

Despite the promise of the DOC method, interpreting its results may be challenging and further developments are needed to address the question of similarity in dynamics.