bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification of microsporidia host-exposed proteins reveals a repertoire of large paralogous gene families and rapidly evolving proteins
Authors: Reinke Aaron W. , Balla Keir M. , Bennett Eric J. , Troemel Emily R. 
Published: June 2016

AbstractPathogens use a variety of secreted and surface proteins to interact with and manipulate their hosts, but a systematic approach for identifying such proteins has been lacking. To identify these ‘host-exposed’ proteins, we used spatially restricted enzymatic tagging followed by mass spectrometry analysis ofC. elegansinfected with two species ofNematocidamicrosporidia. We identified 82 microsporidia proteins inside of intestinal cells, including several pathogen proteins in the nucleus. These microsporidia proteins are enriched in targeting signals, are rapidly evolving, and belong to large,Nematocida-specific gene families. We also find that large, species-specific families are common throughout microsporidia species. Our data suggest that the use of a large number of rapidly evolving species-specific proteins represents a common strategy for these intracellular pathogens to interact with their hosts. The unbiased method described here for identifying potential pathogen effectors represents a powerful approach for the study of a broad range of pathogens.
The evolutionary basis of premature migration in Pacific salmon highlights the utility of genomics for informing conservation
Authors: Prince Daniel J. , O’Rourke Sean M. , Thompson Tasha Q. , Ali Omar A. , Lyman Hannah S. , Saglam Ismail K. , Hotaling Thomas J. , Spidle Adrian P. , Miller Michael R. 
Published: June 2016

AbstractThe delineation of conservation units (CUs) is a challenging issue that has profound implications for minimizing the loss of biodiversity and ecosystem services. CU delineation typically seeks to prioritize evolutionary significance and genetic methods play a pivotal role in the delineation process by quantifying overall differentiation between populations. While CUs that primarily reflect overall genetic differentiation do protect adaptive differences between distant populations, they do not necessarily protect adaptive variation within highly connected populations. Advances in genomic methodology facilitate the characterization of adaptive genetic variation, but the potential utility of this information for CU delineation is unclear. Here we use genomic methods to investigate the evolutionary basis of premature migration in Pacific salmon, a complex behavioral and physiological adaptation that exists within highly-connected populations and has experienced severe declines. Strikingly, we find that premature migration is associated with the same single locus across multiple populations in each of two different species. Patterns of variation at this locus suggest that the premature migration alleles arose from a single evolutionary event within each species and were subsequently spread to distant populations through straying and positive selection. Our results reveal that complex adaptive variation can depend on rare mutational events at a single locus, demonstrate that CUs reflecting overall genetic differentiation can fail to protect evolutionarily significant variation that has substantial ecological and societal benefits, and suggest that a supplemental framework for protecting specific adaptive variation will sometimes be necessary to prevent the loss of significant biodiversity and ecosystem services.
Predicting future learning from baseline network architecture
Authors: Mattar Marcelo G. , Wymbs Nicholas F. , Bock Andrew S. , Aguirre Geoffrey K. , Grafton Scott T. , Bassett Danielle S. 
Published: June 2016

AbstractHuman behavior and cognition result from a complex pattern of interactions between brain regions. The flexible reconfiguration of these patterns enables behavioral adaptation, such as the acquisition of a new motor skill. Yet, the degree to which these reconfigurations depend on the brain’s baseline sensorimotor integration is far from understood. Here, we asked whether spontaneous fluctuations in sensorimotor networks at baseline were predictive of individual differences in future learning. We analyzed functional MRI data from 19 participants prior to six weeks of training on a new motor skill. We found that visual-motor connectivity was inversely related to learning rate: sensorimotor autonomy at baseline corresponded to faster learning in the future. Using three additional scans, we found that visual-motor connectivity at baseline is a relatively stable individual trait. These results suggest that individual differences in motor skill learning can be predicted from sensorimotor autonomy at baseline prior to task execution.HighlightsSensorimotor autonomy at rest predicts faster motor learning in the future.Connection between calcarine and superior precentral sulci form strongest predictor.Sensorimotor autonomy is a relatively stable individual trait.
Phased Diploid Genome Assembly with Single Molecule Real-Time Sequencing
Authors: Chin Chen-Shan , Peluso Paul , Sedlazeck Fritz J. , Nattestad Maria , Concepcion Gregory T. , Clum Alicia , Dunn Christopher , O'Malley Ronan , Figueroa-Balderas Rosa , Morales-Cruz Abraham , Cramer Grant R. , Delledonne Massimo , Luo Chongyuan , Ecker Joseph R. , Cantu Dario , Rank David R. , Schatz Michael C. 
Published: June 2016

AbstractWhile genome assembly projects have been successful in a number of haploid or inbred species, one of the current main challenges is assembling non-inbred or rearranged heterozygous genomes. To address this critical need, we introduce the open-source FALCON and FALCON-Unzip algorithms (https://github.com/PacificBiosciences/FALCON/) to assemble Single Molecule Real-Time (SMRT®) Sequencing data into highly accurate, contiguous, and correctly phased diploid genomes. We demonstrate the quality of this approach by assembling new reference sequences for three heterozygous samples, including an F1 hybrid of the model speciesArabidopsis thaliana, the widely cultivatedV. viniferacv. Cabernet Sauvignon, and the coral fungusClavicorona pyxidatathat have challenged short-read assembly approaches. The FALCON-based assemblies were substantially more contiguous and complete than alternate short or long-read approaches. The phased diploid assembly enabled the study of haplotype structures and heterozygosities between the homologous chromosomes, including identifying widespread heterozygous structural variations within the coding sequences.
First evidence of a menstruating rodent: the spiny mouse (Acomys cahirinus)
Authors: Bellofiore N. , Ellery S. , Mamrot J. , Walker D. , Temple-Smith P. , Dickinson H. 
Published: June 2016

ABSTRACTBackgroundAdvances in research relating to menstruation and associated disorders (such as endometriosis and pre-menstrual syndrome) have been hindered by the lack of an appropriate animal model. Thus, many aspects of this phenomenon remain poorly understood limiting the development of efficacious treatment for women. Menstruating species account for only 1.5% of mammals, and less than 0.09% of these are non-primates. Menstruation occurs as a consequence of progesterone priming of the endometrial stroma and a spontaneous decidual reaction. At the end of each infertile cycle as progesterone levels decline the uterus is unable to maintain this terminally differentiated stroma and the superficial endometrium is shed. True menstruation has never been reported in rodents.ObjectiveHere we describe the first observation of menstruation in a rodent, the spiny mouse (Acomys cahirinus).Study DesignVirgin female spiny mice (n=14) aged 12-16 weeks were sampled through daily vaginal lavage for 2 complete reproductive cycles in our in-house colony at Monash Medical Centre, Clayton, Australia. Stage-specific collection of reproductive tissue and plasma was used for histology, prolactin immunohistochemistry, and ELISA assay of progesterone (n=5 / stage of the menstrual cycle). Normally distributed data are reported as the mean ± standard error and significant differences calculated using a one-way ANOVA. Non-normal data are displayed as the median values of replicates (with interquartile range) and significant differences calculated using Kruskal-Wallis test.ResultsMean cycle length was 8.7 ± 0.4 days with red blood cells observed in the lavages over 3.0 ± 0.2 days. Cyclic endometrial shedding and blood in the vaginal canal concluding with each infertile cycle was confirmed in all virgin females. The endometrium was thickest during the luteal phase, when plasma progesterone peaked at ~102.1 ng/mL and the optical density for prolactin immunoreactivity was strongest. The spiny mouse undergoes spontaneous decidualisation, demonstrating for the first time menstruation in a rodent.ConclusionThe spiny mouse is the first rodent species known to menstruate and provides an unprecedented natural non-primate model to study the mechanisms of menstrual shedding and repair, and may be useful in furthering our understanding of human specific menstrual and pregnancy associated diseases.
High habitat-specificity in fungal communities of an oligo-mesotrophic, temperate lake
Authors: Wurzbacher Christian , Warthmann Norman , Bourne Elizabeth , Attermeyer Katrin , Allgaier Martin , Powell Jeff R. , Detering Harald , Mbedi Susan , Grossart Hans-Peter , Monaghan Michael T. 
Published: June 2016

AbstractFreshwater fungi are a poorly studied paraphyletic group that include a high diversity of phyla. Most studies of aquatic fungal diversity have focussed on single habitats, thus the linkage between habitat heterogeneity and fungal diversity remains largely unexplored. We took 216 samples from 54 locations representing eight different habitats in meso-oligotrophic, temperate Lake Stechlin in northern Germany, including the pelagic and littoral water column, sediments, and biotic substrates. We pyrosequenced with an universal eukaryotic marker within the ribosomal large subunit (LSU) in order to compare fungal diversity, community structure, and species turnover among habitats. Our analysis recovered 1024 fungal OTUs (97% criterion). Diversity was highest in the sediment, biofilms, and benthic samples (293-428 OTUs), intermediate in water and reed samples (36-64 OTUs), and lowest in plankton (8 OTUs) samples. NMDS clustering clearly grouped the eight studied habitats into six clusters, indicating that total diversity was strongly influenced by turnover among habitats. Fungal communities exhibited pronounced changes at the levels of phylum and order along a gradient from littoral to pelagic habitats. The large majority of OTUs could not be classified below the order level due to the lack of aquatic fungal entries in taxonomic databases. Our study provides a first estimate of lake-wide fungal diversity and highlights the important contribution of habitat-specificity to total fungal diversity. This remarkable diversity is probably an underestimate, because most lakes undergo seasonal changes and previous studies have uncovered differences in fungal communities among lakes.
Controlling Noise in the Timing of Intracellular Events: A First-Passage Time Approach
Authors: Ghusinga Khem Raj , Dennehy John J. , Singh Abhyudai 
Published: June 2016

AbstractIn the noisy cellular environment, gene products are subject to inherent random fluctuations in copy numbers over time. How cells ensure precision in the timing of key intracellular events, in spite of such stochasticity is an intriguing fundamental problem. We formulate event timing as a first-passage time problem, where an event is triggered when the level of a protein crosses a critical threshold for the first time. Novel analytical calculations are preformed for the first-passage time distribution in stochastic models of gene expression, including models with feedback regulation. Derivation of these formulas motivates an interesting question: is there an optimal feedback strategy to regulate the synthesis of a protein to ensure that an event will occur at a precise time, while minimizing deviations or noise about the mean. Counter-intuitively, results show that for a stable long-lived protein, the optimal strategy is to express the protein at a constant rate without any feedback regulation, and any form of feedback (positive, negative or any combination of them) will always amplify noise in event timing. In contrast, a positive feedback mechanism provides the highest precision in timing for an unstable protein. These theoretical results explain recent experimental observations of single-cell lysis times in bacteriophageλ. Here, lysis of an infected bacterial cell is orchestrated by the expression and accumulation of a stableλprotein up to a threshold, and precision in timing is achieved via feedforward, rather than feedback control. Our results have broad implications for diverse cellular processes that rely on precise temporal triggering of events.
Acoustic-based model estimation of snapping shrimp populations and the effects of a sponge die-off
Authors: Butler Jack , Butler Mark J , Gaff Holly 
Published: June 2016

ABSTRACTHuman use of the ocean and its ecosystems continues to degrade coastal habitats around the world. Assessing anthropogenic impacts on these environments can be cost and manpower intensive; thus, developing rapid, remote techniques to assess habitat quality has become increasingly important. We employed autonomous hydrophone receivers to record the soundscapes of healthy hard-bottom habitat in Florida Bay, Florida (USA) and hard-bottom areas impacted by sponge die-offs. We also recorded sounds emanating from individual sponges of three species that were isolated in underwater sound booths, and then enumerated the invertebrates (mostly snapping shrimp) dwelling within the canals of each sponge. From these recordings, a modified cylindrical sound propagation model was used to estimate distances to snapping shrimp snaps. Using the programDistance, which applies distance sampling theory to cue count surveys, we estimated snapping shrimp population density and abundance within both habitat types. More snapping shrimp snaps per unit time were recorded in healthy hard-bottom areas as compared to degraded hard-bottom areas. In addition, the average distance to a snap source was greater within degraded hard-bottom areas than within healthy hard-bottom areas. As a consequence, the estimated density and abundance of snapping shrimp were one to two orders of magnitude greater within healthy habitat than within degraded habitat. This study demonstrates the feasibility of using acoustic sampling and modeling to rapidly assess populations of soniferous benthic indicator species, whose vocalizations may yield indirect estimates of habitat quality.
Female-female aggression in a sexual/unisexual species complex over resources
Authors: Makowicz Amber , Moore Tana , Schlupp Ingo 
Published: June 2016

AbstractKin selection theory predicts that closely related individuals should be more altruistic and less antagonistic towards one another. In addition, it would predict that the higher the relatedness value (R) between individuals, such as in clonal organisms, the more likely kin selection is to evolve. One benefit of kin selection is a reduction in aggression towards kininvarious social contexts, such as foraging. In the gynogenetic Amazon molly,Poecilia formosa,females have been shown to differentiate between clone types, preferring to associate with clonal sisters to non-sisters, and regulate their aggressive behaviors accordingly. We ask ifAmazon mollies in resource-limited environments: 1) still maintain the ability to regulate aggressive behaviors according to relatedness (heterospecific females, clonal sisters or non-sisters), and 2) how their aggressivebehaviors change relative to a female’s social partner? Using a repeated-measures design, we found that focal females regulated their aggressive behaviors depending on partner type (i.e., a heterospecific female, clonal sister, or non-sister). Heterospecific females and the non-sister clones spent more time behaving aggressively towards the focal females, and these females also received significantly more bites from heterospecific females. Interestingly, the clonal sisters, when compared to the other two female types, performed significantly more tail beats towards focal females.We are able to confirm that females do show more aggression towards heterospecific females and non-sister clones in a food-limited environment, andthat their aggression scales with relatedness (R).Lay SummaryKin recognition allows individuals to adjust costly behaviors, such as aggression, according to the degree of genetic relatedness. We show that in a food-limited environment, a clonal species of fish, the Amazon molly, females regulate aggressive behaviors depending on how closely related they are to the recipient female, behaving more aggressively to both heterospecific females and non-sister clones. The ability to regulate costly behaviors under variable socialconditions is advantageous, especially when resources are limited.
Within-patient mutation frequencies reveal fitness costs of CpG dinucleotides and drastic amino acid changes in HIV
Authors: Theys Kristof , Feder Alison F. , Gelbart Maoz , Hartl Marion , Stern Adi , Pennings Pleuni S. 
Published: June 2016

AbstractHIV has a high mutation rate, which contributes to its ability to evolve quickly. However, we know little about the fitness costs of individual HIV mutationsin vivo, their distribution and the different factors shaping the viral fitness landscape. We calculated the mean frequency of transition mutations at 870 sites of thepolgene in 160 patients, allowing us to determine the cost of these mutations. As expected, we found high costs for non-synonymous and nonsense mutations as compared to synonymous mutations. In addition, we found that non-synonymous mutations that lead to drastic amino acid changes are twice as costly as those that do not and mutations that create new CpG dinucleotides are also twice as costly as those that do not. We also found that G→A and C→T mutations are more costly than A→G mutations. We anticipate that our newin vivofrequency-based approach will provide insights into the fitness landscape and evolvability of not only HIV, but a variety of microbes.Author summaryHIV’s high mutation rate allows it to evolve quickly. However, most mutations probably reduce the virus’ ability to replicate – they are costly to the virus. Until now, the actual cost of mutations is not well understood. We used within-patient mutation frequencies to estimate the cost of 870 HIV mutationsin vivo. As expected, we found high costs for non-synonymous and nonsense mutations. In addition, we found surprisingly high costs for mutations that lead to drastic amino acid changes, mutations that create new CpG sites (possibly because they trigger the host’s immune system), and G→A and C→T mutations. Our results demonstrate the power of analyzing mutant frequencies fromin vivoviral populations to study costs of mutations. A better understanding of fitness costs will help to predict the evolution of HIV.
The PAS domain-containing protein HeuR regulates heme uptake inCampylobacter jejuni
Authors: Johnson Jeremiah G. , Gaddy Jennifer A. , DiRita Victor J. 
Published: June 2016

AbstractCampylobacter jejuniis a leading cause of bacterial-derived gastroenteritis. A previous mutant screen demonstrated that the heme uptake system (Chu) is required for full colonization of the chicken gastrointestinal tract. Subsequent work found identified a PAS domain-containing regulator, termed HeuR, as required for chicken colonization. Here we confirmthat both the heme uptake system and HeuR are required for full chicken gastrointestinal tract colonization, with theheuRmutant being particularlyaffected during competition with wild-typeC. jejuni.Transcriptomic analysis identified the chu genes-and those encoding other iron uptake systems-as likely regulatory targets of HeuR. Purified HeuR specifically bound thechuZApromoter region in electrophoretic mobility shift assays. Consistentwith a role forHeuR inchuexpression,heuRmutants wereunable to efficiently use heme asa source of iron in iron-limitingconditions and, mutants exhibited decreased levels of cell-associated ironby massspectrometry.Finally, we demonstrate that a heuR mutant ofC. jejuniisresistant to hydrogen peroxide, and that this resistance correlates to elevated levels ofcatalase activity.Author SummaryCampylobacter jejunicauses millions of gastrointestinal infection every year. This is primarily due to the its ability to reside in the gastrointestinal tract of chickens.C.jejunicontaminates chicken meat during harvesting and processing. Following consumption of undercooked chicken or uncooked food that was contaminated with raw chicken juice, humans develop a debilitating illness that is characterized by diarrhea and abdominal cramps. As chickens are the source of most human infections, there is a need to understand howC. jejunicolonizes chickens so we can develop ways to reduce its presence in chickens and thereby improve food safety. Most organisms require iron to thrive and that some bacteria steal iron from host molecules, including hemoglobin. Here we demonstrate thatC. jejunimay need to get iron from hemoglobin in order to colonize the chicken and that aregulatory protein, HeuR, controls the ability ofthe bacteria to do this. If we can understand how this protein works, we may be able to develop ways to inhibit its function and reduce the ability ofC. jejunito get iron during chicken colonization. This would limit theamount ofC. jejuniin the chicken and make food safer.
A rare variant in CYP27A1 and its association with atopic dermatitis with high serum total IgE
Authors: Suzuki H. , Makino Y. , Nagata M. , Furuta J. , Enomoto H. , Hirota T. , Tamari M. , Noguchi E. 
Published: June 2016

AbstractThis study investigated rare variants associated with atopic dermatitis. We performed exome analyses on 37 patients who were diagnosed with atopic dermatitis by board‐certified dermatologists and had total serum IgE levels greater than 1000 IU/ml. The exome analysis identified seven variants with <1% allele frequency in Asian (ASN) population of 1000 Genomes Project phase 1 data and >5% allele frequency in the atopic dermatitis exome samples. We then conducted a replication study using 469 atopic dermatitis patients with total serum IgE ≥1000 IU/ml and 935 Japanese controls to assess the presence of these 7 candidate variants. The replication study confirmed that CYP27A1 rs199691576 (A/G) was associated with atopic dermatitis with high serum IgE levels (P = 0.012, odds ratio = 2.1). CYP27A1 is involved in the metabolism of vitamin D3, which plays important roles in modulating immune function. Previous studies have reported polymorphisms in vitamin D pathway genes that are associated with allergy‐related phenotypes. Our data confirm the importance of genes regulating the vitamin D pathway in the development of atopic dermatitis.