bluuebunny/crossref_metadata_2025 huggingface dataset:
Deciphering the unique SNPs among leading Indian Tomato Cultivars using Double Digestion Restriction Associated DNA sequencing
Authors: Bodanapu Reddaiah , Vasudevan Sreehari V , Lekkala Sivarama Prasad , Chakravartty Navajeet , Lalam Krishna , Kuriakose Boney , Bhanot Chetan , Morey Pallavi Namdeo , Katta A. V. S. Krishna Mohan , Thomas George , Gupta Saurabh , Lachagari V B Reddy
Published: February 2019

World-wide grown and consumed tomato (Solanum lycopersicum) crop used as model system for new cultivar and fruit development. Genetic and genomic research of Indian tomato cultivars will provide an insight to develop new breeding strategies and crop improvement. The present study aimed to identify the high quality common and unique single nucleotide polymorphisms (SNPs), present in 9 different Indian tomato cultivars using double digestion restriction associated DNA sequencing (ddRAD-seq). Total of 36,847,092 raw reads (3.68 GB) were generated for all samples and 3,329,625 of high-quality reads were aligned uniquely to the reference tomato genome. Using stringent filtering, a total of 1,165 SNPs and 69 INDELs were found in genic regions, along with the unique variants to each cultivar was observed. Similarly, 7 and 33 variants were identified in chloroplast and mitochondrial genome of tomato. In addition, the population structure and genetic relationship among these cultivars suggested 4 well-differentiated sub-populations. Functional annotation of SNP/INDLEs associated with flanking sequences along with gene ontology and pathway analysis was performed. Identified SNPs/INDELs could be useful as markers for variety identification for genetic purity analysis. Findings from this work will be useful to plant breeders and research community to deepen their understanding and enhance tomato breeding programs.
The mechanistic basis for chromatin invasion and remodeling by the yeast pioneer transcription factor Rap1
Authors: Mivelaz Maxime , Cao Anne-Marinette , Kubik Slawomir , Zencir Sevil , Hovius Ruud , Boichenko Iuliia , Stachowicz Anna Maria , Kurat Christoph F. , Shore David , Fierz Beat
Published: February 2019

Pioneer transcription factors (pTFs) bind to target sites within compact chromatin initiating chromatin remodeling and controlling the recruitment of downstream factors. The mechanisms by which pTFs overcome the chromatin barrier are not well understood. Here we reveal, using single-molecule fluorescence approaches, how the yeast transcription factor Rap1 invades and remodels chromatin. Using a reconstituted chromatin system replicating yeast promoter architecture we demonstrate that Rap1 can bind nucleosomal DNA within a chromatin fiber, but with shortened dwell times compared to naked DNA. Moreover, we show that Rap1 binding opens chromatin fiber structure by inhibiting nucleosome-nucleosome contacts. Finally, we reveal that Rap1 collaborates with the chromatin remodeler RSC to destabilize promoter nucleosomes, paving the way to form long-lived bound states on now exposed DNA. Together, our results provide a mechanistic view of how Rap1 gains access and opens chromatin, thereby establishing an active promoter architecture and controlling gene expression.
Molecular mechanism of the chitinolytic monocopper peroxygenase reaction
Authors: Bissaro Bastien , Streit Bennett , Isaksen Ingvild , Eijsink Vincent G.H. , Beckham Gregg T. , DuBois Jennifer , Røhr Åsmund K.
Published: February 2019

Lytic polysaccharide monooxygenases (LPMOs) are a recently discovered class of monocopper enzymes, broadly distributed across the Tree of Life. We recently reported that LPMOs can use H2O2 as an oxidant, revealing a novel reaction pathway. Here, we aimed to elucidate the H2O2-mediated reaction mechanism with experimental and computational approaches. In silico studies suggest that a network of hydrogen bonds, involving both the enzyme and the substrate, brings H2O2 into a strained reactive conformation, and guides the derived hydroxyl radical towards formation of a copper-oxyl intermediate. The initial H2O2 homolytic cleavage and subsequent hydrogen atom abstraction from chitin by the copper-oxyl intermediate are suggested to be the main energy barriers. Under single turnover conditions, stopped-flow fluorimetry demonstrates that LPMO-Cu(II) reduction to Cu(I) is a fast process compared to the re-oxidation reactions. We found that re-oxidation of LPMO-Cu(I) is 2000-fold faster with H2O2 than with O2, the latter being several orders of magnitude slower than rates reported for other monooxygenases. In agreement with the notion of ternary complex formation, when chitin is added, re-oxidation by H2O2 is accelerated whereas that by O2 slows. Simulations indicated that Glu60, a highly-conserved residue, gates the access to the confined active site and constrains H2O2 during catalysis, and Glu60 mutations significantly decreased the enzyme performance. By providing molecular and kinetic insights into the peroxygenase activity of chitinolytic LPMOs, this study will aid the development of applications of enzymatic and synthetic copper catalysis and contribute to understanding pathogenesis, notably chitinolytic plant defenses against fungi and insects.
Trypanosoma bruceiribonuclease H2A is an essential enzyme that resolves R-loops associated with transcription initiation and antigenic variation
Authors: Briggs Emma , Crouch Kathryn , Lemgruber Leandro , Hamilton Graham , Lapsley Craig , McCulloch Richard
Published: February 2019

In every cell ribonucleotides represent a threat to the stability and transmission of the DNA genome. Two types of Ribonuclease H (RNase H) tackle such ribonucleotides, either by excision when they form part of the DNA strand, or by hydrolysing RNA when it base-pairs with DNA, in structures termed R-loops. Loss of either RNase H is lethal in mammals, whereas yeast can prosper in the absence of both enzymes. Removal of RNase H1 is tolerated by the parasiteTrypanosoma bruceibut no work has examined the function of RNase H2. Here we show that loss of the catalytic subunit ofT. bruceiRNase H2 (TbRH2A) leads to growth and cell cycle arrest that is concomitant with accumulation of nuclear damage at sites of RNA polymerase (Pol) II transcription initiation, revealing a novel and critical role for RNase H2. In addition, differential gene expression of both RNA Pol I and II transcribed genes occurs after TbRH2A loss, including patterns that may relate to cytosolic DNA accumulation in humans with autoimmune disease. Finally, we show that TbRH2A loss causes R-loop and DNA damage accumulation in telomeric RNA Pol I transcription sites, leading to altered variant surface glycoprotein expression. Thus, we demonstrate a separation of function between the two nuclearT. bruceiRNase H enzymes during RNA Pol II transcription, but overlap in function during RNA Pol I-mediated gene expression during host immune evasion.
The effect of stimulus envelope shape on the auditory steady-state response
Authors: Van Canneyt Jana , Hofmann Michael , Wouters Jan , Francart Tom
Published: February 2019

Auditory steady-state responses (ASSRs) are auditory evoked potentials that reflect phase-locked neural activity to periodic stimuli. ASSRs are often evoked by tones with a modulated envelope, with sinusoidal envelopes being most common. However, it is unclear if and how the shape of the envelope affects ASSR responses. In this study, we used various trapezoidal modulated tones to evoke ASSRs (modulation frequency = 40 Hz) and studied the effect of four envelope parameters: attack time, hold time, decay time and off time. ASSR measurements in 20 normal hearing subjects showed that envelope shape significantly influenced responses: increased off time and/or increased decay time led to responses with a larger signal-to-noise-ratio (SNR). Response phase delay was significantly influenced by attack time and to a lesser degree by off time. We also simulated neural population responses that approximate ASSRs with a model of the auditory periphery (Bruce et al. 2018). The modulation depth of the simulated responses, i.e. the difference between maximum and minimum firing rate, correlated highly with the response SNRs found in the ASSR measurements. Longer decay time and off time enhanced the modulation depth both by decreasing the minimum firing rate and by increasing the maximum firing rate. In conclusion, custom envelopes with long decay and off time provide larger response SNRs and the benefit over the commonly used sinusoidal envelope was in the range of several dB.
Comparative transcriptome analysis of Powdery mildew Resistance between two Melon (Cucumis melo L) with Different Thickness Peel
Authors: Hong Cheng , Wei-ping Kong , Jun-Feng Lü
Published: February 2019

Melon (Cucumis melo L.) is wildly planted in the world and China is a major producer of muskmelon. Powdery mildew is one of the most common fungal diseases in the world and this disease frequently affects melon (Cucumis melo L.) and due to the reduction of melon yield. In this study, one material GanTianmi with thin peel and another material XueLianHua with thick peel were selected. After inoculating the powdery mildew, both materials were used to do the RNA-Seq. In total two RNA-seq libraries were constructed and sequenced separately. The reads per kilobase per Million mapped reads (RPKM) values of all the genes in the two materials were calculated and there were 13828 genes were expressed in the material G and 13944 genes were expressed in the material S (RPKM>1). The differentially expression gene (DEG) analysis result suggested that total 769 the DEGs between the two materials were identified. All the DEGs were annotated with several database and the transcript factors (TFs) that related to disease resistance such as MYB, ERF and WRKY among the DEGs were also identified. This research could not only provide the information about understanding the mechanism of powdery mildew infection but also help researchers breed the varieties with powdery mildew resistance.
The landscape of the alternatively spliced transcriptome remains stable during aging across different species and tissues
Authors: Sieber Patricia , Barth Emanuel , Marz Manja
Published: February 2019

Aging is characterized by a decline of cellular homeostasis over time, leading to various severe disorders and death. Alternative splicing is an important regulatory level of gene expression and thus takes on a key role in the maintenance of accurate cell and tissue function. Missplicing of certain genes has already been linked to several age-associated diseases, such as progeria, Alzheimer’s disease, Parkinson’s disease and cancer. Nevertheless, many studies focus only on transcriptional variations of single genes or the expression changes of spliceosomal genes, coding for the proteins that aggregate to the spliceosomal machinery. Little is known on the general change of present and switching isoforms in different tissues over time. In this descriptive RNA-Seq study, we report differences and commonalities of isoform usage during aging among different tissues within one species and compare changes of alternative splicing among different, evolutionarily distinct species. Although we identified a multitude of differntially spliced genes among different time points, we observed little to no general changes in the transcriptomic landscape of the investigated samples. Although there is undoubtedly considerable influence of specifically spliced genes on certain age-associated processes, this work shows that alternative splicing remains stable for the majority of genes with aging.
Contextual effects on binocular matching are evident in primary visual cortex
Authors: Rideaux Reuben , Welchman Andrew E
Published: February 2019

Global context can dramatically influence local visual perception. This phenomenon is well-documented for monocular features, e.g., the Kanizsa triangle. It has been demonstrated for binocular matching: the disambiguation of the Wallpaper Illusion (Brewster, 1844) via the luminance of the background (Anderson & Nakayama, 1994). For monocular features, there is evidence that global context can influence neuronal responses as early as V1 (Muckli et al., 2015). However, for binocular matching, the activity in this area of the visual cortex is thought to represent local processing, suggesting that the influence of global context may occur at later stages of cortical processing. Here we sought to test if binocular matching is influenced by contextual effects in V1, using fMRI to measure brain activity while participants viewed perceptually ambiguous “wallpaper” stereograms whose depth was disambiguated by the luminance of the surrounding region. We localized voxels in V1 corresponding to the ambiguous region of the pattern, i.e., where the signal received from the eyes was not predictive of depth, and despite the ambiguity of the input signal, using multi-voxel pattern analysis we were able to reliably decode perceived (near/far) depth from the activity of these voxels. These findings indicate that stereoscopic related neural activity is influenced by global context as early as V1.
Ligand dependent gene regulation by transient ERα clustered enhancers
Authors: Saravanan Bharath , Soota Deepanshu , Islam Zubairul , Jayani Ranveer , Mann Rajat , Farooq Umer , Meel Sweety , Walavalkar Kaivalya , Gayen Srimonta , Singh Anurag Kumar , Hannenhalli Sridhar , Notani Dimple
Published: February 2019

Unliganded nuclear receptors have been implicated in ligand-dependent gene regulation. However, the underlying mechanisms are not fully understood. Here we demonstrate that unliganded ERα binds to specific sites in the genome thereby pre-marking them as future functional enhancers. Upon ligand exposure, ERα binds to several EREs relatively proximal to the pre-marked, or persistent, ERα-bound sites. Interestingly, the persistent sites interact extensively, via chromatin looping, with the proximal transiently bound sites forming ERα clustered enhancers in 3D. CRISPR-based deletion of TFF1 persistent site disrupts the formation of its clustered enhancer resulting in the loss of E2-dependent induced expression of TFF1 and its neighboring genes within the same cluster. The clustered enhancers overlap with nuclear ERα puncta that coalesce in a ligand-dependent manner. Furthermore, formation of clustered enhancers, as well as puncta, coincide with the active phase of signaling and their later disappearance results in the loss of gene expression even though persistent sites remain bound by ERα. Our results establish the role of persistent unliganded ERα binding in priming enhancer clusters in 3D that drive transient, but robust, gene expression in a ligand-dependent fashion.
The functional landscape of the human phosphoproteome
Authors: Ochoa David , Jarnuczak Andrew F. , Gehre Maja , Soucheray Margaret , Kleefeldt Askar A. , Viéitez Cristina , Hill Anthony , Garcia-Alonso Luz , Swaney Danielle L. , Vizcaíno Juan Antonio , Noh Kyung-Min , Beltrao Pedro
Published: February 2019

Protein phosphorylation is a key post-translational modification regulating protein function in almost all cellular processes. While tens of thousands of phosphorylation sites have been identified in human cells to date, the extent and functional importance of the phosphoproteome remains largely unknown. Here, we have analyzed 6,801 publicly available phospho-enriched mass spectrometry proteomics experiments, creating a state-of-the-art phosphoproteome containing 119,809 human phosphosites. To prioritize functional sites, 59 features indicative of proteomic, structural, regulatory or evolutionary relevance were integrated into a single functional score using machine learning. We demonstrate how this prioritization identifies regulatory phosphosites across different molecular mechanisms and pinpoint genetic susceptibilities at a genomic scale. Several novel regulatory phosphosites were experimentally validated including a role in neuronal differentiation for phosphosites present in the SWI/SNF SMARCC2 complex member. The scored reference phosphoproteome and its annotations identify the most relevant phosphorylations for a given process or disease addressing a major bottleneck in cell signaling studies.
Manganese-induced Parkinsonism in mice is reduced using a novel contaminated water sediment exposure model
Authors: Freeman Dana M. , O’Neal Rachel , Zhang Qiang , Bouwer Edward J. , Wang Zhibin
Published: February 2019

The effects of heavy metals on human health have become an important area of study. For instance, acute manganese toxicity is known to induce Parkinsonism. Heavy metals including manganese enter the aquatic environment from both anthropogenic and natural processes. These metals accumulate within water sediments and their behavior is then dependent upon the sediment composition and phase. These metal-sediment interactions remain to be explored within in-vivo animal studies. To study the effect of these interactions, herein we successfully developed an exposure model in mice that encapsulates the aquatic microenvironment of heavy metals before exposure. Male and female C57/BL6 mice were exposed to manganese contaminated sediment via their drinking water (Sed_Mn) or to manganese placed directly into their drinking water with no prior sediment interaction (Mn) for six weeks. Sediment interaction did not alter total manganese in drinking water (mg/L) or weekly manganese consumption (mg) in males (54.9±1.5 mg) or females (44.6±1.0 mg) over the six-week exposure period. We analyzed motor impairment, a common feature in Parkinson’s disease, using the beam traversal, cylinder, and accelerating rotarod behavioral tests. We observed Parkinson’s like deficits in motor control in both treatment groups as early as four weeks of exposure in males but not in females. Intriguingly, mice given water incubated with manganese spiked sediment (Sed_Mn) performed better overall compared to mice given manganese directly in water (Mn) despite having similar exposure in males and females. Male Sed_Mn mice compared to Mn mice had a 146% reduction in time to cross the beam traversal test (p<0.05), a 10% increase in rearing activity in the cylinder test (p<0.05), and a 14% increase in time remaining on the rotarod (not significant). Female Sed_Mn mice compared to Mn mice had no change in the time to cross the beam traversal test, a 36% increase in rearing activity in the cylinder test (p<0.05), and a 35% increase in time on the rotarod (p<0.05). Our study indicates that metal-sediment interactions may alter metal toxicity in mammals and introduces a new exposure model to test the toxicity of metal contaminants of drinking water.
Steroid hormones sulfatase inactivation extends lifespan and ameliorates age-related diseases
Authors: Pérez-Jiménez Mercedes M. , Sansigre Paula , Valladares Amador , Venegas-Calerón Mónica , Sánchez-García Alicia , Monje José M. , Esteban-García Sara , Suarez-Pereira Irene , Vitorica Javier , Ríos José J , Artal-Sanz Marta , Carrión Ángel M. , Muñoz Manuel J.
Published: February 2019

Aging and fertility are two interconnected processes. From invertebrates to mammals, absence of the germline increases longevity by a still not fully understood mechanism. We find that loss of function of sul-2, the Caenorhabditis elegans steroid sulfatase (STS), raises the pool of sulfated steroid hormones and increases longevity. This increased longevity requires factors involved in germline-mediated longevity (daf-16, daf-12, kri-1, tcer-1 and daf-36 genes) and is not additive to the longevity of germline-less mutants. Noteworthy, sul-2 mutations do not affect fertility. Thus, STS inactivation affects the germline signalling process regulating longevity. Interestingly, sul-2 is only expressed in sensory neurons, suggesting a regulation of germline longevity by environmental cues. We also demonstrate that treatment with the specific STS inhibitor STX64, reproduces the longevity phenotype of sul-2 mutants. Remarkably, STS inhibition by either mutation or drug treatment ameliorates protein aggregation diseases in C. elegans models of Parkinson, Huntington and Alzheimer, as well as Alzheimer disease in a mammalian model. These results open the possibility of reallocating steroid sulfatase inhibitors for the treatment of aging and aging related diseases.
Characterization of the workplace chemical exposome using untargeted LC-MS/MS: a case study
Authors: McCall Laura-Isobel , Anderson Victoria M. , Fogle Robert S. , Haffner Jacob J. , Hossain Ekram , Liu Renmeng , Ly Anita H. , Ma Hongyan , Nadeem Maham , Yao Songyuan
Published: February 2019

Western people now spend close to 90% of their time indoors, one-quarter of which occurs at their place of employment. As such, interactions between employees and the workplace built environment have significant potential impact on employee health and safety. However, the range of workers’ daily chemical exposures is still poorly understood. Likewise, the influence of workers themselves and of worker behavior on the chemical composition of the workplace is still unknown. In this case study, we used untargeted liquid chromatography-tandem mass spectrometry (LC-MS/MS) to compare the chemical signatures of three different types of workplaces: scientific research buildings, office buildings, and one mixed-purpose building. Our results identified differential signatures of public building surfaces based on building purpose, sampling location and surface materials. Overall, these results are helping define the influence of human behavior on the workplace chemical environment and identify the chemical hazards to which people are exposed throughout their workday.

Highlights

Implementation of untargeted liquid chromatography-tandem mass spectrometry to study workplace chemical exposures.

Shared chemical signatures were identified based on building purpose.

Differential chemical signatures were identified based on surface material and sampling location.

Annotated molecules include pharmaceuticals, illicit drugs, food chemicals, constituents of paints and stains, and cleaning products.
SNIPE score can capture prodromal Alzheimer’s in cognitively normal subjects
Authors: Zandifar Azar , Fonov Vladimir , Potvin Olivier , Duchesne Simon , Collins D. Louis ,   for the Alzheimer’s Disease Neuroimaging Initiative
Published: February 2019

Capturing early changes in the brain related to Alzheimer’s disease may lead to models that successfully predict cognitive decline and the eventual onset of dementia, well ahead of onset of clinical symptoms. In this study we used both hippocampal volume and our hippocampal driven SNIPE score to show which marker better captures Alzheimer’s related changes in a large dataset of normal controls (N=515) from the ADNI study, comparing controls that remain cognitively stable and controls that progress to either MCI or Alzheimer’s dementia during 10 years of follow-up (median follow-up: 30 months). We measured hippocampal volume and SNIPE score and found that the effect size to differentiate between stable and progressor groups was significantly larger for SNIPE score than for volume. Our results also show that there is a significant age-related difference between groups for both markers, and the difference is greater with the SNIPE score. Our experiments show that considering high sensitivity of our SNIPE score regarding to early AD-related brain changes, this marker is a better candidate in comparison to hippocampal volume for predicting the future onset of dementia.
Emergence of stable coexistence in a complex microbial community through metabolic cooperation and spatio-temporal niche partitioning
Authors: Blasche Sonja , Kim Yongkyu , Mars Ruben , Kafkia Eleni , Maansson Maria , Machado Daniel , Teusink Bas , Nielsen Jens , Benes Vladimir , Neves Rute , Sauer Uwe , Patil Kiran Raosaheb
Published: February 2019

Microbial communities in nature often feature complex compositional dynamics yet also stable coexistence of diverse species. The mechanistic underpinnings of such dynamic stability remain unclear as system-wide studies have been limited to small engineered communities or synthetic assemblies. Here we show how kefir, a natural milk-fermenting community, realizes stable coexistence through spatio-temporal orchestration of species and metabolite dynamics. During milk fermentation, kefir grains (a polysaccharide matrix synthesized by kefir microbes) grow in mass but remain unchanged in composition. In contrast, the milk is colonized in a dynamic fashion with early members opening metabolic niches for the followers. Through large-scale mapping of metabolic preferences and inter-species interactions, we show how microbes poorly suited for milk survive in, and even dominate, the community through metabolic cooperation and uneven partitioning between the grain and the liquid phase. Overall, our findings reveal how spatio-temporal dynamics promote stable coexistence and have implications for deciphering and modulating complex microbial ecosystems.
From expression footprints to causal pathways: contextualizing large signaling networks with CARNIVAL
Authors: Liu Anika , Trairatphisan Panuwat , Gjerga Enio , Didangelos Athanasios , Barratt Jonathan , Saez-Rodriguez Julio
Published: February 2019

While gene expression profiling is commonly used to gain an overview of cellular processes, the identification of upstream processes that drive expression changes remains a challenge. To address this issue, we introduce CARNIVAL, a causal network building tool which derives network architectures from gene expression footprints.

CARNIVAL (CAusal Reasoning pipeline for Network identification using Integer VALue programming) integrates different sources of prior knowledge, including signed and directed protein-protein interactions, transcription factor targets, and pathway signatures. The use of prior knowledge in CARNIVAL allows the capture of a broad set of upstream cellular processes and regulators, which in turn delivered results with higher accuracy when benchmarked against related tools. Implementation as an integer linear programming (ILP) problem also guarantees efficient computation. As a case study, we applied CARNIVAL to contextualize signaling networks from gene expression data in IgA nephropathy, a chronic kidney disease. CARNIVAL identified specific signaling pathways and associated mediators with important bioactivity in IgAN including WNT and TGF-β, that we subsequently validated experimentally.

In summary, we demonstrated how CARNIVAL generates hypotheses on potential upstream alterations that propagate through signaling networks, providing valuable insights into disease processes. CARNIVAL, freely available as an R-package at https://saezlab.github.io/CARNIVAL, can be applied to any field of biomedical research to contextualize signaling networks and identify the causal relationships between downstream gene expression and upstream regulators.
Trans-generational transcriptomic response to natural variation in host plant toxicity and insecticides in a specialist insect.
Authors: Birnbaum Stephanie S.L. , Abbot Patrick
Published: February 2019

Insects have been challenged by plant secondary metabolites throughout their evolutionary history. An important mechanism thought to promote insecticide resistance is the ability of insects to use preexisting detoxification systems originally evolved for tolerance of plant defenses. However, it remains unclear what level of convergence exists in metabolic mechanisms employed against various natural and xenobiotic chemicals? How do transcriptomic responses to these stressors change in response to novel and long-term exposure? We employ an experimental evolution approach in a milkweed- specialist aphid (Aphis nerii) model to test the effects of a more toxic host plant species and two insecticides commonly used in rotation in agriculture (a neonicotinoid, Imidacloprid, and a general homopteran blocker, Pymetrozine) on aphid gene expression and fitness over multiple generations of selection. Aphids were selected on three stress treatments: a toxic host plant species and two pesticides (Imidacloprid and Pymetrozine) for five generations. Whole transcriptome gene expression changes and changes in development time and fecundity were compared at generations one and five. While there were no consistent fitness costs or benefits to long-term exposure, exposure to stress is associated with increased transcriptional plasticity and changes in genes associated with the metabolism of secondary metabolites as well as genes important in transcription, translation, and post-translation processes.
Accurate and Efficient KIR Gene and Haplotype Inference from Genome Sequencing Reads with Novel K-mer Signatures
Authors: Roe David , Kuang Rui
Published: February 2019

The killer cell immunoglobulin-like receptor (KIR) proteins evolve to fight viruses and mediate the body’s reaction to pregnancy. These roles provide selection pressure for variation at both the structural/haplotype and base/allele levels. At the same time, the genes have evolved relatively recently by tandem duplication and therefore exhibit very high sequence similarity over thousands of bases. These variation-homology patterns make it impossible to interpret KIR haplotypes from abundant short-read genome sequencing data at population scale using existing methods. Here, we developed an efficient computational approach for in silico KIR probe interpretation (KPI) to accurately interpret individual’s KIR genes and haplotype-pairs from KIR sequencing reads. We designed synthetic 25-base sequence probes by analyzing previously reported haplotype sequences, and we developed a bioinformatics pipeline to interpret the probes in the context of 16 KIR genes and 16 haplotype structures. We demonstrated its accuracy on a synthetic data set as well as a real whole genome sequences from 748 individuals from The Genome of the Netherlands (GoNL). The GoNL predictions were compared with predictions from SNP-based predictions. Our results show 100% accuracy rate for the synthetic tests and a 99.6% family-consistency rate in the GoNL tests. Agreement with the SNP-based calls on KIR genes ranges from 72-100% with a mean of 92%; most differences occur in genes KIR2DS2, KIR2DL2, KIR2DS3, and KIR2DL5 where KPI predicts presence and the SNP-based interpretation predicts absence. Overall, the evidence suggests that KPI’s accuracy is 97% or greater for both KIR gene and haplotype-pair predictions, although the presence/absence genotyping leads to ambiguous haplotype-pair predictions with 16 reference KIR haplotype structures. KPI is free, open, and easily executable as a Nextflow workflow supported by a Docker environment at https://github.com/droeatumn/kpi.
Single-cell determination of iron content in magnetotactic bacteria: implications for the iron biogeochemical cycle
Authors: Amor Matthieu , Tharaud Mickaël , Gélabert Alexandre , Komeili Arash
Published: February 2019

Magnetotactic bacteria (MTB) are ubiquitous aquatic microorganisms that biomineralize dissolved iron from the environment into intracellular nanoparticles of magnetite [Fe(II)Fe(III)2O4] or greigite [Fe(II)Fe(III)2S4] in a genetically controlled manner. After cell death, these magnetite and greigite crystals are trapped into sediments which effectively removes iron from the soluble pool. MTB may significantly impact the iron biogeochemical cycle, especially in the ocean where dissolved iron limits nitrogen fixation and primary productivity. Although MTB are ubiquitous in the environment, their impact on the biogeochemical cycling of metallic elements is still poorly constrained. A thorough assessment of the mass of iron incorporated by MTB has been hampered by a lack of methodology to accurately measure the amount of, and variability in, their intracellular iron content. Here, we quantify the mass of iron contained in single MTB cells of the model organism, Magnetospirillum magneticum sp. AMB-1, using a time-resolved mass spectrometry methodology. Bacterial iron content depends on the external iron concentration, and reaches a maximum value of 10-6 ng of iron per cell when bacteria are cultivated with initial iron concentrations of 100 μM or higher. From our experimental results, we calculated the flux of dissolved iron incorporation into natural MTB populations and conclude that MTB may mineralize a significant fraction of environmental dissolved iron into crystals.
The dynamics of the HIV-1 latent reservoir – considering the heterogeneous subpopulations
Authors: Ke Ruian , Deng Kai
Published: February 2019

A major barrier to finding a cure for human immunodeficiency virus type-I (HIV-1) infection is the existence and persistence of the HIV-1 latent reservoir. Although the size of the reservoir is shown to be extremely stable under effective antiretroviral therapy, multiple lines of evidence suggest that the reservoir is composed of dynamic and heterogeneous subpopulations. Quantifying the dynamics of these subpopulations and the processes that maintain the latent reservoir is crucial to the development of effective strategies to eliminate this reservoir. Here, we constructed a mathematical model to consider four latently infected subpopulations, according to their ability to proliferate and the type of virus they are infected. Our model explains a wide range of clinical observations, including variable estimates of the reservoir half-life and dynamical turnover of cytotoxic T lymphocyte (CTL) escape viruses in the reservoir. It suggests that very early treatment leads to a reservoir that is small in size and is composed of less stable latently infected cells (compared to the reservoir in chronically infected individuals). The shorter half-lives estimated from individuals treated during acute infection is likely driven by cells that are less prone to proliferate; in contrast, the remarkably consistent estimate of the long half-lives in individuals who are treated during chronic infection are driven by fast proliferating cells that are likely to be infected by CTL escape mutants. Our model shed light on the dynamics of the reservoir in the absence and presence of antiretroviral therapy. More broadly, it can be used to estimate the turnover rates of subpopulations of the reservoir as well as to design and evaluate the impact of various therapeutic interventions to purge the HIV-1 reservoir.

Author summary

Human immunodeficiency virus (HIV) infects tens of millions of people globally and causes approximately a million death each year. Current treatment for HIV infection suppresses viral load but does not eradicates the virus. A major barrier to cure HIV infection is the existence and persistence of populations of cells that are latently infected by HIV, i.e. the HIV latent reservoir. Understanding and quantifying the kinetics of the reservoir is therefore critical for developing and evaluating effective therapies to purge the reservoir. Recent studies suggested that this reservoir is heterogenous in their population dynamics; yet most previous mathematical models consider this reservoir as a homogenous population. Here we developed a model explicitly tracking the heterogenous subpopulations of the reservoir. We show that this model explains a wide range of clinical observations, and then demonstrate its utility to make quantitative predictions about varies interventions that aim to restrict or reduce the size of the reservoir.
B cells engineered to express pathogen-specific antibodies using CRISPR/Cas9 protect against infection
Authors: Moffett Howell F , Harms Carson K , Fitzpatrick Kristin S , Tooley Marti R , Boonyaratankornkit Jim , Taylor Justin J
Published: February 2019

Effective vaccines inducing lifelong protection against many important infections such as respiratory syncytial virus (RSV), human immunodeficiency virus (HIV), influenza and Epstein-Barr virus (EBV) are not yet available despite decades of research. As an alternative to a protective vaccine we developed a genetic engineering strategy in which CRISPR/Cas9 was utilized to replace endogenously-encoded antibodies with antibodies protective against RSV, HIV, influenza or EBV in primary human or murine B cells. The engineered antibodies were expressed in up to 59% of primary B cells under the control of endogenous regulatory elements, which maintained normal antibody expression and secretion. Importantly, a single transfer of murine B cells engineered to express an antibody protective against RSV resulted in potent and durable protection against RSV infection in immunocompromised hosts. This approach offers the opportunity to achieve sterilizing immunity against pathogens for which traditional vaccination has failed to induce or maintain protective antibody responses.
Fast and scalable genome-wide inference of local tree topologies from large number of haplotypes based on tree consistent PBWT data structure
Authors: Shchur Vladimir , Ziganurova Liliia , Durbin Richard
Published: February 2019

Estimation of the relationship between DNA sequences is one of the most important problems in genomics. Understanding these relationships is central to demographic inference, correction of population structure in GWAS, identifying signals of selection etc. The data structure containing the full information about sample genealogy is called the ancestral recombination graph (ARG). However, ARG inference is a very difficult problem, not least due to a very complex state space. In this work we describe a new approach for fast and scalable generation of local tree topologies relating large numbers of haplotypes. Our method is closely related to the estimation of ARG, and captures both local and global properties of an ARG. It is based on a data structure which we call tree consistent PBWT, a modification of PBWT data structure introduced by R. Durbin (2014). We also explore some methods to estimate the quality of the generated tree topologies and to make inferences based on them. At the end we discuss a probabilistic model which could potentially lead to the estimation of ARG node times.
The structure of a highly conserved picocyanobacterial protein reveals a Tudor domain with a novel tRNA binding function
Authors: Bauer Katherine M , Dicovitsky Rose , Pellegrini Maria , Zhaxybayeva Olga , Ragusa Michael J
Published: February 2019

Cyanobacteria of the Prochlorococcus and marine Synechococcus genera are the most abundant photosynthetic microbes in the ocean. Intriguingly, the genomes of these bacteria are very divergent even within each genus, both in gene content and at amino acid level of the encoded proteins. One striking exception to this is a 62 amino acid protein, termed Prochlorococcus/SynechococcusHyper Conserved Protein (PSHCP). PSHCP is not only found in all sequenced Prochlorococcus and marine Synechococcus genomes but it is also nearly 100% identical in its amino acid sequence across all sampled genomes. Such universal distribution and sequence conservation suggests an essential cellular role of the encoded protein in these bacteria. However, the function of PSHCP is unknown. We used Nuclear Magnetic Resonance (NMR) spectroscopy to determine its structure. We found that 52 of the 62 amino acids in PSHCP form a Tudor domain, while the remainder of the protein is disordered. NMR titration experiments revealed that PSHCP has only a weak affinity for DNA, but an 18.5 fold higher affinity for tRNA, hinting at an involvement of PSHCP in translation. Computational docking and mutagenesis studies identified a positively charged patch surrounding residue K30 that serves as the primary docking site for tRNA on PSHCP. These results provide the first insight into the structure and function of PSHCP and suggest a new function for Tudor domains in recognizing tRNA.
Neutral processes and high inter-annual turnover shape the assembly of soil bacterial communities in a Mediterranean watershed
Authors: Tsiknia Myrto , Fodelianakis Stilianos , Nikolaidis Nikolaos P. , Paranychianakis Nikolaos V.
Published: February 2019

There is a renewed interest in recent years on the ecological processes (stochastic vs selective) driving the assembly of microbial communities. Such information could potentially improve our understanding on ecosystem functioning and resilience to disturbances, ecosystem response to environmental shifts, and adoption of sustainable soil management practices. Herein, employing a suite of existing methodologies, we show that stochastic processes have an important role on the assembly of soil bacterial communities at a Mediterranean watershed. Moreover, we document that the relative contribution of assembly processes varies over the years. The observed intensification of stochastic processes was accompanied by a decrease in the contribution of variable selection in favor of homogeneous selection and dispersal and this trend was only marginally affected by land use (natural vs agricultural lands) or soil depth. Our study also revealed a high inter-annual turnover of soil microbial communities that was likely stimulated by the weak environmental selection and the prevailing environmental conditions (drying-wetting cycles) in Mediterranean landscapes, implying potential impacts on ecosystem functioning and our ability to predict soil response to environmental shifts. Using nitrogen mineralization rate (NMR) as a representative function we document highly variable NMR over the sampling years, land uses and soil depths and lack of significant associations with the monitored environmental variables and individual taxa. In summary, our study provides novel insights on the organization and functioning of microbial communities at Mediterranean ecosystems and sets directions towards a more advanced understanding of the relationships among environmental factors, microbial community structure, and ecosystem functioning that could contribute to sustainable management of these severely degraded ecosystems.
Clonal plasma cells in AL amyloidosis are dependent on pro survival BCL-2 family proteins and sensitive to BH3 mimetics
Authors: Fraser Cameron , Presser Adam , Sanchorawala Vaishali , Sarosiek Shayna , Sarosiek Kristopher
Published: February 2019

Immunoglobulin light chain (AL) amyloidosis is a protein misfolding disorder characterized by the production of amyloidogenic immunoglobulin light chains by clonal populations of plasma cells. These abnormal light chains misfold and accumulate as amyloid fibrils in healthy tissues causing devastating multi-organ dysfunction that is rapidly fatal. Current treatment regimens, which include proteasome inhibitors, alkylating agents, and immunomodulatory agents, were developed for the treatment of the more common plasma cell disease, multiple myeloma, and have limited efficacy in AL amyloidosis as demonstrated by the median survival of 2-3 years. The recent development of novel small-molecule inhibitors of the major pro-survival proteins from the apoptosis-regulating BCL-2 family has created an opportunity to therapeutically target abnormal cell populations, yet identifying the extent of these dependencies and how to target them clinically has thus far been challenging. Using bone marrow-derived plasma cells from 45 patients with AL amyloidosis, we find that clonal plasma cells are highly primed to undergo apoptosis and exhibit strong dependencies on pro-survival BCL-2 family proteins. Specifically, we find that clonal plasma cells in a majority of patients are highly dependent on the pro-survival protein MCL-1 and undergo apoptosis when treated with an MCL-1 inhibitor as a single agent. In addition, BCL-2 inhibition sensitizes clonal plasma cells to several current standard of care therapies. Our results suggest that BH3 mimetics, when deployed rationally, may be highly effective therapies for AL amyloidosis.
Evolutionary rates are correlated between cockroach symbiont and mitochondrial genomes
Authors: Arab Daej A. , Bourguignon Thomas , Wang Zongqing , Ho Simon Y. W. , Lo Nathan
Published: February 2019

Bacterial endosymbionts evolve under strong host-driven selection. Factors influencing host evolution might affect symbionts in similar ways, potentially leading to correlations between the molecular evolutionary rates of hosts and symbionts. Although there is evidence of rate correlations between mitochondrial and nuclear genes, similar investigations of hosts and symbionts are lacking. Here we demonstrate a correlation in molecular rates between the genomes of an endosymbiont (Blattabacterium cuenoti) and the mitochondrial genomes of their hosts (cockroaches). We used partial genome data for multiple strains of B. cuenoti to compare phylogenetic relationships and evolutionary rates for 55 cockroach/symbiont pairs. The phylogenies inferred for B. cuenoti and the mitochondrial genomes of their hosts were largely congruent, as expected from their identical maternal and cytoplasmic mode of inheritance. We found a correlation between evolutionary rates of the two genomes, based on comparisons of root-to-tip distances and on comparisons of the branch lengths of phylogenetically independent species pairs. Our results underscore the profound effects that long-term symbiosis can have on the biology of each symbiotic partner.
Estimating the abundance of benthic macrofauna from across shore transects
Authors: Totterman Stephen
Published: February 2019

Benthic macrofauna of the intertidal zone are commonly sampled at low tide by excavating and sieving quadrats or cores on across shore transects. This paper examines different equations for estimating transect scale abundance, introduces the sampling theorem for calculating the maximum sampling interval and uses simulations to investigate sampling issues. Adaptive transect designs are recommended, where the sampling interval and replication of quadrats are carefully selected according to the width and density of macrofauna bands.
A mixed nitrogen diet and compartmentalized utilization for Mycobacterium tuberculosis replicating in host cells: results of a systems-based analysis
Authors: Borah Khushboo , Beyss Martin , Theorell Axel , Wu Huihai , Basu Piyali , Mendum Tom , Noh Katharina , Beste Dany , McFadden Johnjoe
Published: February 2019

Nitrogen metabolism of Mycobacterium tuberculosis (Mtb) is crucial for the survival and virulence of this pathogen inside host macrophages but little is known about the nitrogen sources acquired from the host or their route of assimilation. Here we performed a systems-based analysis of nitrogen metabolism in intracellullar Mtb and developed 15N-Flux Spectral Ratio Analysis (FSRA) to probe the metabolic cross-talk between the host cell and Mtb. We demonstrate that intracellular Mtb acquires nitrogen from multiple amino acids in the macrophage including glutamate, glutamine, aspartate, alanine, glycine and valine, with glutamine being the predominant nitrogen donor. Each nitrogen source is uniquely assimilated into specific intracellular pools indicating compartmentalised metabolism. This was not observed for in vitro-grown Mtb indicating that there is a switch in nitrogen metabolism when the pathogen enters the intracellular environment. These results provide clues about the potential metabolic targets for development of innovative anti-tuberculosis therapies.