bluuebunny/crossref_metadata_2025_split huggingface dataset:
Parseq: reconstruction of microbial transcription landscape from RNA-Seq read counts using state-space models
Authors: Mirauta Bogdan , Nicolas Pierre , Richard Hugues 
Published: January 2014

AbstractMotivation: The most common RNA-Seq strategy consists of random shearing, amplification and high-throughput sequencing of the RNA fraction. Methods to analyze transcription level variations along the genome from the read count profiles generated by the RNA-Seq protocol are needed.Results: We developed a statistical approach to estimate the local transcription levels and to identify transcript borders. This transcriptional landscape reconstruction relies on a state-space model to describe transcription level variations in terms of abrupt shifts and more progressive drifts. A new emission model is introduced to capture not only the read count variance inside a transcript but also its short-range autocorrelation and the fraction of positions with zero counts. The estimation relies on a particle Gibbs algorithm whose running time makes it more suited to microbial genomes. The approach outperformed read-overlapping strategies on synthetic and real microbial datasets.Availability: A program named Parseq is available at: http://www.lgm.upmc.fr/parseq/.Contact: bodgan.mirauta@upmc.frSupplementary information: Supplementary data are available at Bioinformatics online.
The RSC chromatin remodeling complex has a crucial role in the complete remodeler set for yeast PHO5 promoter opening
Authors: Musladin Sanja , Krietenstein Nils , Korber Philipp , Barbaric Slobodan 
Published: January 2014

Abstract
Although yeast PHO5 promoter chromatin opening is a founding model for chromatin remodeling, the complete set of involved remodelers remained unknown for a long time. The SWI/SNF and INO80 remodelers cooperate here, but nonessentially, and none of the many tested single or combined remodeler gene mutations could prevent PHO5 promoter opening. RSC, the most abundant and only remodeler essential for viability, was a controversial candidate for the unrecognized remodeling activity but unassessed in vivo. Now we show that remodels the structure of chromatin (RSC) is crucially involved in PHO5 promoter opening. Further, the isw1 chd1 double deletion also delayed chromatin remodeling. Strikingly, combined absence of RSC and Isw1/Chd1 or Snf2 abolished for the first time promoter opening on otherwise sufficient induction in vivo. Together with previous findings, we recognize now a surprisingly complex network of five remodelers (RSC, SWI/SNF, INO80, Isw1 and Chd1) from four subfamilies (SWI/SNF, INO80, ISWI and CHD) as involved in PHO5 promoter chromatin remodeling. This is likely the first described complete remodeler set for a physiological chromatin transition. RSC was hardly involved at the coregulated PHO8 or PHO84 promoters despite cofactor recruitment by the same transactivator and RSC’s presence at all three promoters. Therefore, promoter-specific chromatin rather than transactivators determine remodeler requirements.
Large-scale reconstruction of 3D structures of human chromosomes from chromosomal contact data
Authors: Trieu Tuan , Cheng Jianlin 
Published: January 2014

Abstract
Chromosomes are not positioned randomly within a nucleus, but instead, they adopt preferred spatial conformations to facilitate necessary long-range gene–gene interactions and regulations. Thus, obtaining the 3D shape of chromosomes of a genome is critical for understanding how the genome folds, functions and how its genes interact and are regulated. Here, we describe a method to reconstruct preferred 3D structures of individual chromosomes of the human genome from chromosomal contact data generated by the Hi-C chromosome conformation capturing technique. A novel parameterized objective function was designed for modeling chromosome structures, which was optimized by a gradient descent method to generate chromosomal structural models that could satisfy as many intra-chromosomal contacts as possible. We applied the objective function and the corresponding optimization method to two Hi-C chromosomal data sets of both a healthy and a cancerous human B-cell to construct 3D models of individual chromosomes at resolutions of 1 MB and 200 KB, respectively. The parameters used with the method were calibrated according to an independent fluorescence in situ hybridization experimental data. The structural models generated by our method could satisfy a high percentage of contacts (pairs of loci in interaction) and non-contacts (pairs of loci not in interaction) and were compatible with the known two-compartment organization of human chromatin structures. Furthermore, structural models generated at different resolutions and from randomly permuted data sets were consistent.
A widespread bacteriophage abortive infection system functions through a Type IV toxin–antitoxin mechanism
Authors: Dy Ron L. , Przybilski Rita , Semeijn Koen , Salmond George P.C. , Fineran Peter C. 
Published: January 2014

Abstract
Bacterial abortive infection (Abi) systems are ‘altruistic’ cell death systems that are activated by phage infection and limit viral replication, thereby providing protection to the bacterial population. Here, we have used a novel approach of screening Abi systems as a tool to identify and characterize toxin–antitoxin (TA)-acting Abi systems. We show that AbiE systems are encoded by bicistronic operons and function via a non-interacting (Type IV) bacteriostatic TA mechanism. The abiE operon was negatively autoregulated by the antitoxin, AbiEi, a member of a widespread family of putative transcriptional regulators. AbiEi has an N-terminal winged-helix-turn-helix domain that is required for repression of abiE transcription, and an uncharacterized bi-functional C-terminal domain, which is necessary for transcriptional repression and sufficient for toxin neutralization. The cognate toxin, AbiEii, is a predicted nucleotidyltransferase (NTase) and member of the DNA polymerase β family. AbiEii specifically bound GTP, and mutations in conserved NTase motifs (I-III) and a newly identified motif (IV), abolished GTP binding and subsequent toxicity. The AbiE systems can provide phage resistance and enable stabilization of mobile genetic elements, such as plasmids. Our study reveals molecular insights into the regulation and function of the widespread bi-functional AbiE Abi-TA systems and the biochemical properties of both toxin and antitoxin proteins.
The hematopoietic regulator TAL1 is required for chromatin looping between the β-globin LCR and human γ-globin genes to activate transcription
Authors: Yun Won Ju , Kim Yea Woon , Kang Yujin , Lee Jungbae , Dean Ann , Kim AeRi 
Published: January 2014

Abstract
TAL1 is a key hematopoietic transcription factor that binds to regulatory regions of a large cohort of erythroid genes as part of a complex with GATA-1, LMO2 and Ldb1. The complex mediates long-range interaction between the β-globin locus control region (LCR) and active globin genes, and although TAL1 is one of the two DNA-binding complex members, its role is unclear. To explore the role of TAL1 in transcription activation of the human γ-globin genes, we reduced the expression of TAL1 in erythroid K562 cells using lentiviral short hairpin RNA, compromising its association in the β-globin locus. In the TAL1 knockdown cells, the γ-globin transcription was reduced to 35% and chromatin looping of the Gγ-globin gene with the LCR was disrupted with decreased occupancy of the complex member Ldb1 and LMO2 in the locus. However, GATA-1 binding, DNase I hypersensitive site formation and several histone modifications were largely maintained across the β-globin locus. In addition, overexpression of TAL1 increased the γ-globin transcription and increased interaction frequency between the Gγ-globin gene and LCR. These results indicate that TAL1 plays a critical role in chromatin loop formation between the γ-globin genes and LCR, which is a critical step for the transcription of the γ-globin genes.
Functional signature for the recognition of specific target mRNAs by human Staufen1 protein
Authors: de Lucas Susana , Oliveros Juan Carlos , Chagoyen Mónica , Ortín Juan 
Published: January 2014

AbstractCellular messenger RNAs (mRNAs) are associated to proteins in the form of ribonucleoprotein particles. The double-stranded RNA-binding (DRB) proteins play important roles in mRNA synthesis, modification, activity and decay. Staufen is a DRB protein involved in the localized translation of specific mRNAs during Drosophila early development. The human Staufen1 (hStau1) forms RNA granules that contain translation regulation proteins as well as cytoskeleton and motor proteins to allow the movement of the granule on microtubules, but the mechanisms of hStau1-RNA recognition are still unclear. Here we used a combination of affinity chromatography, RNAse-protection, deep-sequencing and bioinformatic analyses to identify mRNAs differentially associated to hStau1 or a mutant protein unable to bind RNA and, in this way, defined a collection of mRNAs specifically associated to wt hStau1. A common sequence signature consisting of two opposite-polarity Alu motifs was present in the hStau1-associated mRNAs and was shown to be sufficient for binding to hStau1 and hStau1-dependent stimulation of protein expression. Our results unravel how hStau1 identifies a wide spectrum of cellular target mRNAs to control their localization, expression and fate.
Bayesian Energy Landscape Tilting: Towards Concordant Models of Molecular Ensembles
Authors: Beauchamp Kyle A. , Pande Vijay S. , Das Rhiju 
Published: January 2014

AbstractPredicting biological structure has remained challenging for systems such as disordered proteins that take on myriad conformations. Hybrid simulation/experiment strategies have been undermined by difficulties in evaluating errors from computa- tional model inaccuracies and data uncertainties. Building on recent proposals from maximum entropy theory and nonequilibrium thermodynamics, we address these issues through a Bayesian Energy Landscape Tilting (BELT) scheme for computing Bayesian “hyperensembles” over conformational ensembles. BELT uses Markov chain Monte Carlo to directly sample maximum-entropy conformational ensembles consistent with a set of input experimental observables. To test this framework, we apply BELT to model trialanine, starting from disagreeing simulations with the force fields ff96, ff99, ff99sbnmr-ildn, CHARMM27, and OPLS-AA. BELT incorporation of limited chemical shift and3Jmeasurements gives convergent values of the peptide’sα,β, andPPIIconformational populations in all cases. As a test of predictive power, all five BELT hyperensembles recover set-aside measurements not used in the fitting and report accu- rate errors, even when starting from highly inaccurate simulations. BELT’s principled fxramework thus enables practical predictions for complex biomolecular systems from discordant simulations and sparse data.
Holsteins Favor Heifers, Not Bulls: Biased Milk Production Programmed during Pregnancy as a Function of Fetal Sex
Authors: Katie Hinde , Abigail J. Carpenter , John S. Clay , Barry J. Bradford 
Published: January 2014

ABSTRACTMammalian females pay high energetic costs for reproduction, the greatest of which is imposed by lactation. The synthesis of milk requires, in part, the mobilization of bodily reserves to nourish developing young. Numerous hypotheses have been advanced to predict how mothers will differentially invest in sons and daughters, however few studies have addressed sex-biased milk synthesis. Here we leverage the dairy cow model to investigate such phenomena. Using 2.39 million lactation records from 1.49 million dairy cows, we demonstrate that the sex of the fetus influences the capacity of the mammary gland to synthesize milk during lactation. Cows favor daughters, producing significantly more milk for daughters than for sons across lactation. Using a sub-sample of this dataset (N = 113,750 subjects) we further demonstrate that the effects of fetal sex interact dynamically across parities, whereby the sex of the fetus being gestated can enhance or diminish the production of milk during an established lactation. Moreover the sex of the fetus gestated on the first parity has persistent consequences for milk synthesis on the subsequent parity. Specifically, gestation of a daughter on the first parity increases milk production by ∼445 kg over the first two lactations. Our results identify a dramatic and sustained programming of mammary function by offspringin utero. Nutritional and endocrine conditionsin uteroare known to have pronounced and long-term effects on progeny, but the ways in which the progeny has sustained physiological effects on the dam have received little attention to date.
Serosurvey of Rickettsia typhi and Rickettsia felis in HIV‐infected patients
Authors: Nogueras María Mercedes , Pons Immaculada , Sanfeliu Isabel , Sala Montserrat , Segura Ferran 
Published: January 2014

ABSTRACTConsistent with the effects of HIV on cell‐mediated immunity, an increased susceptibility to intracellular microorganisms has been observed. Rickettsiae are obligate intracellular microorganisms. The aim of this study was to examine Rickettsia typhi and Rickettsia felis infections in HIV+ population. Sera of 341 HIV+ patients were evaluated by indirect immunofluorescent assay. Age, sex, residential locality, risk behavior, stage according to criteria of the Center for Disease Control and Prevention, CD4+/CD8+ T cells, Hepatitis B antigen, and Hepatitis C serology were surveyed. Seroprevalences of R. typhi and R. felis infection were 7.6% and 4.4%, respectively. No associations were found between seropositivities and the assessed variables. Findings were similar to those obtained in healthy subjects from the same region.
Rapid acclimation to cold allows the cane toad to invade montane areas within its Australian range
Authors: McCann Samantha , Greenlees Matthew J. , Newell David , Shine Richard 
Published: January 2014

Summary

The cane toad (Rhinella marina) invasion of Australia has now reached areas much colder than most of its native range in tropical America. Understanding the toad's ability to function in such conditions can clarify its potential for further spread.

In northeastern New South Wales (NSW), cane toads have been recorded up to 1100 m above sea level (asl). Our monitoring over summer 2012–2013 confirmed that ground temperatures were lower at three high‐elevation (750–1010 m asl) sites than at two nearby lower (100–210 m asl) sites (by day, 18°C vs. 25°C; at night, 17–18°C vs. 20–25°C, respectively).

Critical thermal minima (CTmins) of field‐collected toads (loss of the righting reflex) were lower for high‐elevation than low‐elevation toads (5·5°C vs. 7·5°C), but laboratory acclimation abolished this difference. A toad's CTmin was not affected by site of collection, nor by 1 month's exposure to warm (24°C) or cool (12°C) conditions; instead, a toad's CTmin was determined by its thermal exposure over the previous 12 h. Locomotor ability was affected by test temperature, by elevation and by acclimation. Toads from high elevations exhibited equal endurance at cold and warm test temperatures after month‐long acclimation to cold conditions, whereas toads from low elevations performed better at high temperatures regardless of previous temperature treatments.

Cane toads at the southern edge of their expanding Australian range can function under cool conditions by adjusting their thermal tolerance within a few hours of encountering low temperatures.

The toads' ability for rapid thermal acclimation suggests that current models underestimate the potential range of abiotic conditions accessible to this invading species.
Variation in elemental stoichiometry and RNA:DNA in four phyla of benthic organisms from coral reefs
Authors: Lovelock Catherine E. , Reef Ruth , Pandolfi John M. 
Published: January 2014

Summary

The elemental composition of organisms has been linked to traits such as growth rates, through investment of phosphorus (P) in RNA (called the Growth Rate Hypothesis) and through ecological processes such as susceptibility to predation and herbivory.

To test the predictions of the Growth Rate Hypothesis, we assessed the elemental composition and RNA of four phyla of common, co‐occurring benthic coral reef organisms, corals, and green, brown and red macroalgae, whose patterns of dominance are predicted to be strongly influenced by differences in growth and herbivory and thus elemental stoichiometry. We assessed the importance of phylogeny and functional form, two important attributes for predicting the composition of macroalgal communities, on the variation in elemental composition.

Over these widely divergent taxonomic groups of organisms, we found support for links between elemental composition and RNA in tissues. The RNA:DNA in corals was positively correlated with % nitrogen (N) and negatively correlated with carbon (C):N ratios of tissues while RNA:DNA and RNA concentrations in macroalgae were positively correlated with %N, N:P ratios and negatively correlated with C:N ratios. Corals had higher concentrations of P and lower C:P ratios than macroalgae. Among the macroalgal lineages, C:P was higher in the brown algae than in red and green algae. Overall, the variation in elemental composition of macroalgae was relatively low compared with the variation reported for terrestrial plants and similar to that in corals.

Analysis of phylogenetic sources of variation (family and genus) in elemental composition and RNA found that genus accounted for a significant proportion of variation in both corals and macroalgae (15–47%), but the largest source of variation (50–97%) was unexplained by our statistical model and thus likely attributable to species and environmental factors. Although elemental composition of macroalgae did not vary in a way that was consistent with functional form models, genera with larger thalli had higher tissue N than smaller forms and more lineages with greater complexity of form had lower C:P ratios than less complex brown algal lineages.

Our data indicate that the despite relatively low levels of variation in elemental composition compared with terrestrial organisms, elemental stoichiometry varied significantly among coral reef taxa and with the structure of organisms and thus may have potential for predicting variation in growth rates and patterns of consumption on coral reefs.
Community assembly and functional diversity along succession post‐management
Authors: Bhaskar Radika , Dawson Todd E. , Balvanera Patricia 
Published: January 2014

Summary

Despite extensive development of successional theory, few empirical studies have evaluated whether existing models are applicable to human‐modified landscapes. Seasonally dry tropical forests are experiencing widespread transformation, and represent a critical system to assess in a successional framework to infer the mechanisms that shape assembly of secondary forests post‐management.

We used a functional trait‐based approach to assess changes in community assembly mechanisms along a successional gradient in secondary dry forests of varying stages following abandonment of cattle activity. Nearby old‐growth forests served as an undisturbed comparison. We evaluated whether re‐assembly proceeded consistent with existing theory, in early successional stages via habitat filtering, leading to reduced trait range, and via competitive exclusion in later stages, leading to increased trait evenness. Using three orthogonal traits and two functional diversity indices we tested for evidence of assembly mechanisms along resource axes that may be particularly important to dry forest systems, dynamic changes in habitat filtering and competitive exclusion, and potential legacy effects of management.

We found little support of a progression from habitat filtering to competitive exclusion, with the exception of dispersion patterns for specific leaf area and multi‐variate functional richness. Water availability may underlie species sorting in most stages, as evidenced by range reduction in wood density, and might be a resource particularly important to dry forest assembly. Early successional stages displayed an unexpected pattern of low evenness, which may be due to initial stand composition including remnants and resprouts, a regeneration strategy typical to dry forest species. Beyond influencing initial conditions, management legacy was apparent in advanced secondary forests, which differed in range, even dispersion, and functional richness from old‐growth forests, suggesting the operation of different assembly mechanisms.

The departures from expectations suggest the need to re‐assess successional models to include effects of management legacies on the operation of community assembly mechanisms in human‐modified landscapes, as well as characteristics that distinguish wet and dry forest dynamics.
Linking phenological shifts to species interactions through size‐mediated priority effects
Authors: Rasmussen Nick L. , Van Allen Benjamin G. , Rudolf Volker H. W. 
Published: January 2014

Summary

Interannual variation in seasonal weather patterns causes shifts in the relative timing of phenological events of species within communities, but we currently lack a mechanistic understanding of how these phenological shifts affect species interactions. Identifying these mechanisms is critical to predicting how interannual variation affects populations and communities.

Species' phenologies, particularly the timing of offspring arrival, play an important role in the annual cycles of community assembly. We hypothesize that shifts in relative arrival of offspring can alter interspecific interactions through a mechanism called size‐mediated priority effects (SMPE), in which individuals that arrive earlier can grow to achieve a body size advantage over those that arrive later.

In this study, we used an experimental approach to isolate and quantify the importance of SMPE for species interactions. Specifically, we simulated shifts in relative arrival of the nymphs of two dragonfly species to determine the consequences for their interactions as intraguild predators.

We found that shifts in relative arrival altered not only predation strength but also the nature of predator–prey interactions. When arrival differences were great, SMPE allowed the early arriver to prey intensely upon the late arriver, causing exclusion of the late arriver from nearly all habitats. As arrival differences decreased, the early arriver's size advantage also decreased. When arrival differences were smallest, there was mutual predation, and the two species coexisted in similar abundances across habitats. Importantly, we also found a nonlinear scaling relationship between shifts in relative arrival and predation strength. Specifically, small shifts in relative arrival caused large changes in predation strength while subsequent changes had relatively minor effects.

These results demonstrate that SMPE can alter not only the outcome of interactions but also the demographic rates of species and the structure of communities. Elucidating the mechanisms that link phenological shifts to species interactions is crucial for understanding the dynamics of seasonal communities as well as for predicting the effects of climate change on these communities.