bluuebunny/crossref_metadata_2025 huggingface dataset:
Natural and Pathogenic Protein Sequence Variation Affecting Prion-Like Domains Within and Across Human Proteomes
Authors: Cascarina Sean M. , Ross Eric D.
Published: May 2019

Protein aggregation is involved in a variety of muscular and neurodegenerative disorders. For many of these disorders, current models suggest a prion-like molecular mechanism of disease, whereby proteins aggregate and spread to neighboring cells in an infectious manner. A variety of proteins with prion-like domains (PrLDs) have recently been linked to these disorders. The development of prion prediction algorithms has facilitated the large-scale identification of PrLDs among “reference” proteomes for various organisms. However, the degree to which intraspecies protein sequence diversity influences predicted aggregation propensity for PrLDs has not been systematically examined. Here, we explore protein sequence variation introduced at genetic, post-transcriptional, and post-translational levels, and its influence on predicted aggregation propensity for human PrLDs. We find that sequence variation is relatively common among PrLDs and in some cases can result in relatively large differences in predicted aggregation propensity. Analysis of a database of sequence variants associated with human disease reveals a number of mutations within PrLDs that are predicted to increase aggregation propensity. Our analyses expand the list of candidate human PrLDs, estimate the effects of sequence variation on the aggregation propensity of PrLDs, and suggest the involvement of prion-like mechanisms in additional human diseases.
Genetic Risk Factors for Colorectal Cancer in Multiethnic Indonesians
Authors: Yusuf Irawan , Miskad Upik A. , Lusikooy Ronald E. , Arsyad Arham , Irwan Akram , Mathew George , Suriapranata Ivet , Kusuma Rinaldy , Pardamean Bens , Fitra Kacamarga Muhamad , Budiarto Arif , Wawan Cenggoro Tjeng , Pardamean Carissa I. , McMahan Christopher , Joyner Chase , Baurley James W.
Published: May 2019

Purpose

Colorectal cancer is a common cancer in Indonesia, yet it has been understudied. We conduct a genome-wide association study focused on evaluation and discovery of colorectal cancer risk factors in Indonesians.

Methods

We administered detailed questionnaires and collecting blood samples from 162 colorectal cancer cases throughout Makassar, Indonesia. We also established a control set of 193 healthy individuals frequency matched by age, sex, and ethnicity. A genome-wide association analysis was performed on 84 cases and 89 controls passing quality control. We evaluated known colorectal cancer genetic variants using logistic regression and established a genome-wide polygenic risk model using a Bayesian variable selection technique.

Results

We replicate associations for rs9497673, rs6936461 and rs7758229 on chromosome 6; rs11255841 on chromosome 10; and rs4779584, rs11632715, and rs73376930 on chromosome 15. Polygenic modeling identified 10 SNP associated with colorectal cancer risk.

Conclusions

This work helps characterize the relationship between variants in theSCL22A3,SCG5,GREM1, andSTXBP5-AS1genes and colorectal cancer in a diverse Indonesian population. With further biobanking and international research collaborations, variants specific to colorectal cancer risk in Indonesians will be identified.
Timing of arrival in the breeding area is repeatable and affects reproductive success in a non-migratory population of blue tits
Authors: Gilsenan Carol , Valcu Mihai , Kempenaers Bart
Published: May 2019

Events in one part of the annual cycle often affect the performance (and subsequently fitness) of individuals later in the season (carry-over effects). An important aspect of this relates to the timing of activities. For example, many studies on migratory birds have shown that relatively late spring arrival in the breeding area reduces both the likelihood of getting a mate or territory and reproductive success.

In contrast, relatively little is known about movements of individuals in non-migratory populations during the non-breeding season. Few studies have investigated the timing of arrival at the breeding area in such species, possibly due to the assumption that most individuals remain in the area during the non-breeding season.

In this study, we used four years of data from a transponder-based automated recording system set up in a non-migratory population of blue tits (Cyanistes caeruleus) to describe individual variation in arrival at the breeding site. We investigated whether this variation can be explained by individual characteristics (sex, body size, or status), and we assessed its effect on aspects of reproductive success in the subsequent breeding season.

We found substantial variation in arrival date and demonstrate that this trait is individual-specific (repeatable). Females arrived later than males, but the arrival dates of social pair members were more similar than expected by chance. Arrival predicted both whether an individual would end up breeding that season, and several aspects of its breeding success.

Our study suggests that non-migratory species show a form of incipient migration behaviour in that they leave the breeding area during the non-breeding season. We conclude that the timing of pre-breeding events, in particular arrival date, may be an overlooked, but important, fitness-relevant trait in non-migratory species.
Mitochondrial mass governs the extent of T cell senescence
Authors: Callender Lauren A. , Carroll Elizabeth C. , Bober Emilia A , Akbar Arne N. , Solito Egle , Henson Sian M.
Published: May 2019

The susceptibility of human CD4+ and CD8+ T cells to senesce differs, with CD8+ T cells acquiring an immunosenescent phenotype faster than their CD4+ T cell compartment. We show here that it is the inherent difference in mitochondrial content that drives this phenotype, with senescent human CD4+ T cells displaying a higher mitochondrial mass. The loss of mitochondria in the senescent human CD8+ T cells has knock-on consequences for nutrient usage, metabolism and function. Mitochondrial dysfunction has been linked to both cellular senescence and ageing, however it is still unclear whether mitochondria play a causal role in senescence. Our data shows that reducing mitochondrial function in human CD4+ T cells, through the addition of low dose rotenone, causes the generation of a CD4+ T cell with a CD8+ -like phenotype. Therefore we wish to propose that it is the inherent metabolic stability that governs the susceptibility to an immunosenescent phenotype.
Chromatin interaction analysis with updated ChIA-PET Tool (V3)
Authors: Li Guoliang , Sun Tongkai , Chang Huidan , Cai Liuyang , Hong Ping , Zhou Qiangwei
Published: May 2019

Understanding chromatin interactions is important since they create chromosome conformation and link the cis- and trans-regulatory elements to their target genes for transcriptional regulation. Chromatin Interaction Analysis with Paired-End Tag (ChIA-PET) sequencing is a genome-wide high-throughput technology that detects chromatin interactions associated with a specific protein of interest. Previously we developed ChIA-PET Tool in 2010 for ChIA-PET data analysis. Here we present the updated version of ChIA-PET Tool (V3), is a computational package to process the next-generation sequence data generated from ChIA-PET experiments. It processes the short-read data and long-read ChIA-PET data with multithreading and generates the statistics of results in a HTML file. In this paper, we provide a detailed demonstration of the design of ChIA-PET Tool V3 and how to install it and analyze a specific ChIA-PET data set with it. At present, other ChIA-PET data analysis tools have developed including ChiaSig, MICC, Mango and ChIA-PET2 and so on. We compared our tool with other tools using the same public data set in the same machine. Most of peaks detected by ChIA-PET Tool V3 overlap with those from other tools. There is higher enrichment for significant chromatin interactions of ChIA-PET Tool V3 in APA plot. ChIA-PET Tool V3 is open source and is available at GitHub (https://github.com/GuoliangLi-HZAU/ChIA-PET_Tool_V3/).
Dietary methionine restriction targets one carbon metabolism in humans and produces broad therapeutic responses in cancer
Authors: Gao Xia , Sanderson Sydney M. , Dai Ziwei , Reid Michael A. , Cooper Daniel E. , Lu Min , Richie John P. , Ciccarella Amy , Calcagnotto Ana , Mikhael Peter G. , Mentch Samantha J. , Liu Juan , Ables Gene , Kirsch David G. , Hsu David S. , Nichenametla Sailendra N. , Locasale Jason W.
Published: May 2019

Nutrition exerts profound effects on health and dietary interventions are commonly used to treat diseases of metabolic etiology. Although cancer has a substantial metabolic component, the principles that define whether nutrition may be used to influence tumour outcome are unclear. Nevertheless, it is established that targeting metabolic pathways with pharmacological agents or radiation can sometimes lead to controlled therapeutic outcomes. In contrast, whether specific dietary interventions could influence the metabolic pathways that are targeted in standard cancer therapies is not known. We now show that dietary restriction of methionine (MR), an essential amino acid, and the reduction of which has aging and obesogenic properties, influences cancer outcome through controlled and reproducible changes to one carbon metabolism. This pathway metabolizes methionine and further is the target of a host of cancer interventions involving chemotherapy and radiation. MR produced therapeutic responses in chemoresistant RAS-driven colorectal cancer patient derived xenografts and autochthonous KRASG12D+/−;TP53−/− -driven soft tissue sarcomas resistant to radiation. Metabolomics revealed the therapeutic mechanisms to occur through tumor cell autonomous effects on the flux through one carbon metabolism that impacted redox and nucleotide metabolism, thus interacting with the antimetabolite or radiation intervention. Finally, in a controlled and tolerated feeding study in humans, MR resulted in similar effects on systemic metabolism as obtained in responsive mice. These findings provide evidence that a targeted dietary manipulation can affect specific tumor cell metabolism to mediate broad aspects of cancer outcome.
Combinatorial perturbation analysis reveals divergent regulations of mesenchymal genes during epithelial-to-mesenchymal transition
Authors: Watanabe Kazuhide , Panchy Nicholas , Noguchi Shuhei , Suzuki Harukazu , Hong Tian
Published: May 2019

Epithelial-to-mesenchymal transition (EMT), a fundamental transdifferentiation process in development, produces diverse phenotypes in different physiological or pathological conditions. Many genes involved in EMT have been identified to date, but mechanisms contributing to the phenotypic diversity and those governing the coupling between the dynamics of epithelial (E) genes and that of the mesenchymal (M) genes are unclear. In this study, we employed combinatorial perturbations to mammary epithelial cells to induce a series of EMT phenotypes by manipulating two essential EMT-inducing elements, namely TGF-β and ZEB1. By measuring transcriptional changes in more than 700 E- and M-genes, we discovered that the M-genes exhibit a significant diversity in their dependency to these regulatory elements and identified three groups of M-genes that are controlled by different regulatory circuits. Notably, functional differences were detected among the M-gene clusters in motility regulation and in survival of breast cancer patients. We computationally predicted and experimentally confirmed that the reciprocity and reversibility of EMT are jointly regulated by ZEB1. Our integrative analysis reveals the key roles of ZEB1 in coordinating the dynamics of a large number of genes during EMT, and it provides new insights into the mechanisms for the diversity of EMT phenotypes.
Shavenbaby protein isoforms orchestrate the self-renewalversusdifferentiation ofDrosophilaintestinal stem cells
Authors: Al Hayek Sandy , Alsawadi Ahmad , Kambris Zakaria , Boquete Jean-Philippe , Bohère Jérôme , Ronsin Brice , Plaza Serge , Lemaitre Bruno , Payre François , Osman Dani
Published: May 2019

Signaling pathways are key regulators of adult stem cell homeostasis and underlying mechanisms are often deregulated in cancers. Recent studies of epithelial tumors have involved OvoL/Svb transcription factors, which produce isoforms with antagonistic activities. Here we show that Svb, the unique OvoL factor inDrosophila, directly integrates multiple signaling inputs to coordinate the behavior of adult intestinal stem cell lineage. Under steady state, Svb mediates Wnt and EGFR signaling to ensure stem cell renewal and progenitor survival. This requires the post-translational processing of Svb into a transcriptional activator by Polished rice (Pri) regulatory peptides, under the regulation of ecdysone signaling. In response to PDM1, Svb expression is specifically maintained in enterocytes where it acts as a transcriptional repressor sufficient to override mitogenic signals and impose differentiation. Altogether, these results demonstrate that the OvoL/Svb transcriptional switch controls the balance between stem cell survival, self-renewal and differentiation.
The neutrophil enzyme myeloperoxidase directly modulates neuronal response after subarachnoid hemorrhage, a sterile injury model
Authors: Coulibaly Aminata P. , Pezuk Pinar , Varghese Paul , Gartman William , Triebwasser Danielle , Kulas Joshua A. , Liu Lei , Syed Mariam , Tvrdik Petr , Ferris Heather , Provencio J. Javier
Published: May 2019

Neutrophil infiltration into the central nervous system (CNS) after injury is associated with cognitive deficits. Using a murine model of aneurysmal subarachnoid hemorrhage (SAH), we elucidate the location and mode of action of neutrophils in the CNS. Following SAH, neutrophils infiltrate the meninges, and not the brain parenchyma. Mice lacking functional myeloperoxidase (MPO KO), a neutrophil enzyme, lack both the meningeal neutrophil infiltration and the cognitive deficits associated with delayed cerebral injury from SAH. The re-introduction of biologically active MPO, and its substrate hydrogen peroxide, to the cerebrospinal fluid of MPO KO mice at the time of hemorrhage restores the spatial memory deficit observed after SAH. This implicates MPO as a mediator of neuronal dysfunction in SAH. Using primary neuronal and astrocyte cultures, we demonstrate that MPO directly affects the function of both cell types. Neurons exposed to MPO and its substrate show decreased calcium activity at baseline and after stimulation with potassium chloride. In addition, MPO and its substrate lead to significant astrocyte loss in culture, a result observed in the brain after SAH as well. These results show that, in SAH, the activity of innate immune cells in the meninges modulates the activity and function of the underlying brain tissue.
Role of aggregate size, multistability and communication in determining cell fate and patterning inM. xanthus
Authors: Del Angel Juan A. Arias , Rivera-Yoshida Natsuko , Escalante Ana E. , Martínez-Castilla León Patricio , Benítez Mariana
Published: May 2019

1.

The emergence of multicellular organisms that exhibit cell differentiation and stereotypic spatial arrangements has been recognized as one of the major transitions in evolution. Myxobacteria have emerged as a useful study model to investigate multicellular evolution and development. Here, we propose a multiscale model that considers cellular adhesion and movement, molecular regulatory networks (MRNs), and cell-to-cell communication to study the emergence of cell fate determination and spatial patterning ofMyxococcus xanthusfruiting bodies. The model provides a dynamic accounting of the roles of MRN multistability, intercellular communication and conglomerate size in determining cell fate and patterning duringM. xanthusdevelopment. It also suggests that for cell fate determination and patterning to occur, the cell aggregate must surpass a minimum size. The model also allows us to contrast alternative scenarios for the C-signal mechanism and provides stronger support for an indirect effect (as a diffusible molecule) than a direct one (as a membrane protein).
Honey bee queens are vulnerable to heat-induced loss of fertility
Authors: McAfee Alison , Chapman Abigail , Higo Heather , Underwood Robyn , Milone Joseph , Foster Leonard J , Guarna M Marta , Tarpy David R , Pettis Jeffery S
Published: May 2019

All species need to reproduce to maintain viable populations, but heat stress kills sperm cells across the animal kingdom and rising frequencies of heatwaves are a threat to biodiversity. Honey bees (Apis mellifera) are globally distributed micro-livestock; therefore, they could serve as environmental biomonitors for fertility losses. Here, we found that queens have two potential routes of temperaturestress exposure: within colonies and during routine shipping. Our data suggest that temperatures of 15 to 38°C are safe for queens at a tolerance threshold of 11.5% loss of sperm viability, which is the viability difference associated with queen failure in the field. Heat shock activates expression of specific stressresponse proteins in the spermatheca, which could serve as molecular biomarkers (indicators) for heat stress. This protein fingerprint may eventually enable surveys for the prevalence of heat-induced loss of sperm viability in diverse landscapes as part of a biomonitoring program.
Long metabarcoding of the eukaryotic rDNA operon to phylogenetically and taxonomically resolve environmental diversity
Authors: Jamy Mahwash , Foster Rachel , Barbera Pierre , Czech Lucas , Kozlov Alexey , Stamatakis Alexandros , Bass David , Burki Fabien
Published: May 2019

High-throughput environmental DNA metabarcoding has revolutionized the analysis of microbial diversity, but this approach is generally restricted to amplicon sizes below 500 base pairs. These short regions contain limited phylogenetic signal, which makes it impractical to use environmental DNA in full phylogenetic inferences. However, new long-read sequencing technologies such as the Pacific Biosciences platform may provide sufficiently large sequence lengths to overcome the poor phylogenetic resolution of short amplicons. To test this idea, we amplified soil DNA and used PacBio Circular Consensus Sequencing (CCS) to obtain a ~4500 bp region of the eukaryotic rDNA operon spanning most of the small (18S) and large subunit (28S) ribosomal RNA genes. The CCS reads were first treated with a novel curation workflow that generated 650 high-quality OTUs containing the physically linked 18S and 28S regions of the long amplicons. In order to assign taxonomy to these OTUs, we developed a phylogeny-aware approach based on the 18S region that showed greater accuracy and sensitivity than similarity-based and phylogenetic placement-based methods using shorter reads. The taxonomically-annotated OTUs were then combined with available 18S and 28S reference sequences to infer a well-resolved phylogeny spanning all major groups of eukaryotes, allowing to accurately derive the evolutionary origin of environmental diversity. A total of 1019 sequences were included, of which a majority (58%) corresponded to the new long environmental CCS reads. Comparisons to the 18S-only region of our amplicons revealed that the combined 18S-28S genes globally increased the phylogenetic resolution, recovering specific groupings otherwise missing. The long-reads also allowed to directly investigate the relationships among environmental sequences themselves, which represents a key advantage over the placement of short reads on a reference phylogeny. Altogether, our results show that long amplicons can be treated in a full phylogenetic framework to provide greater taxonomic resolution and a robust evolutionary perspective to environmental DNA.
Rotavirus Calcium Dysregulation Manifests as Dynamic Calcium Signaling in the Cytoplasm and Endoplasmic Reticulum
Authors: Chang-Graham Alexandra L. , Perry Jacob L. , Strtak Alicia C. , Ramachandran Nina K. , Criglar Jeanette M. , Philip Asha A. , Patton John T. , Estes Mary K. , Hyser Joseph M.
Published: May 2019

Like many viruses, rotavirus (RV) dysregulates calcium homeostasis by elevating cytosolic calcium ([Ca2+]cyt) and decreasing endoplasmic reticulum (ER) stores. While an overall, monophasic increase in [Ca2+]cyt during RV infection has been shown, the nature of the RV-induced aberrant calcium signals and how they manifest over time at the single-cell level have not been characterized. Thus, we generated cell lines and human intestinal enteroids (HIEs) stably expressing cytosolic and/or ER-targeted genetically-encoded calcium indicators to characterize calcium signaling throughout RV infection by time-lapse imaging. We found that RV induces highly dynamic [Ca2+]cyt signaling that manifest as hundreds of discrete [Ca2+]cyt spikes, which increase during peak infection. Knockdown of nonstructural protein 4 (NSP4) attenuates the [Ca2+]cyt spikes, consistent with its role in dysregulating calcium homeostasis. RV-induced [Ca2+]cyt spikes were primarily from ER calcium release and were attenuated by inhibiting the store-operated calcium entry (SOCE) channel Orai1. RV-infected HIEs also exhibited prominent [Ca2+]cyt spikes that were attenuated by inhibiting SOCE, underlining the relevance of these [Ca2+]cyt spikes to gastrointestinal physiology and role of SOCE in RV pathophysiology. Thus, our discovery that RV increases [Ca2+]cyt by dynamic Ca2+signaling, establishes a new, paradigm-shifting understanding of the spatial and temporal complexity of virus-induced Ca2+signaling.
Corticomuscular control of walking in older people and people with Parkinson’s disease
Authors: Roeder Luisa , Boonstra Tjeerd W , Kerr Graham K
Published: May 2019

Changes in human gait that result from ageing or neurodegenerative diseases are multifactorial. Here we assess the effects of age and Parkinson’s disease (PD) on corticospinal control in electrophysiological activity recorded during treadmill and overground walking. Electroencephalography (EEG) from 10 electrodes and electromyography (EMG) from two leg muscles were acquired from 22 healthy young, 24 healthy older and 20 adults with PD. Event-related power, corticomuscular coherence (CMC) and inter-trial coherence were assessed for EEG from bilateral sensorimotor cortices and EMG from tibialis anterior muscles during the double support phase of the gait cycle. CMC and EMG power in the low beta band (13-21 Hz) was significantly decreased in older and PD participants compared to young people, but there was no difference between older and PD groups. Older and PD participants spent shorter time in the swing phase than young individuals. These findings indicate age-related changes in the temporal coordination of gait. The decrease in beta CMC suggests reduced cortical input to spinal motor neurons in older people during the double support phase. We also observed multiple changes in electrophysiological measures at high beta and low gamma frequencies during treadmill compared to overground walking, indicating task-dependent differences in corticospinal locomotor control.
Bridging the TB data gap: in silico extraction of rifampicin-resistant tuberculosis diagnostic test results from whole genome sequence data
Authors: Ng Kamela Charmaine S. , Ngabonziza Jean Claude S. , Lempens Pauline , de Jong Bouke Catherine , van Leth Frank , Meehan Conor Joseph
Published: May 2019

Background

Mycobacterium tuberculosis rapid diagnostic tests (RDTs) are widely employed in routine laboratories and national surveys for detection of rifampicin-resistant (RR)-TB. However, as next generation sequencing technologies have become more commonplace in research and surveillance programs, RDTs are being increasingly complemented by whole genome sequencing (WGS). While comparison between RDTs is difficult, all RDT results can be derived from WGS data. This can facilitate continuous analysis of RR-TB burden regardless of the data generation technology employed. By converting WGS to RDT results, we enable comparison of data with different formats and sources particularly for low and middle income high TB burden countries that employ different diagnostic algorithms for drug resistance surveys. This allows national TB control programs (NTPs) and epidemiologists to utilize all available data in the setting for improved RR-TB surveillance.

Methods

We developed the Python-based MTB Genome to Test (MTBGT) tool that transforms WGS-derived data into laboratory-validated results of the primary RDTs – Xpert MTB/RIF, XpertMTB/RIF Ultra, GenoType MDRTBplus v2.0, and GenoscholarNTM+MDRTB II. The tool was validated through RDT results of RR-TB strains with diverse resistance patterns and geographic origins and applied on routine-derived WGS data.

Results

The MTBGT tool correctly transformed the SNP data into the RDT results and generated tabulated frequencies of the RDT probes as well as rifampicin susceptible cases. The tool supplemented the RDT probe reactions output with the RR-conferring mutation based on identified SNPs. The MTBGT tool facilitated continuous analysis of RR-TB and Xpert probe reactions from different platforms and collection periods in Rwanda.

Conclusion

Overall, the MTBGT tool allows low and middle income countries to make sense of the increasingly generated WGS in light of the readily available RDT results, and assess whether currently implemented RDTs adequately detect RR-TB in their setting. With its feature to transform WGS to RDT results and facilitate continuous RR-TB data analysis, the MTBGT tool may bridge the gap between and among data from periodic surveys, continuous surveillance, research, and routine tests, and may be integrated within the existing national connectivity platform for use by the NTP and epidemiologists to improve setting-specific RR-TB control. The MTBGT source code and accompanying documentation is available at https://github.com/KamelaNg/MTBGT.
Corticostriatal stimulation compensates for medial frontal inactivation during interval timing
Authors: Emmons Eric B. , Kennedy Morgan , Kim Youngcho , Narayanan Nandakumar S.
Published: May 2019

Prefrontal dysfunction is a common feature of brain diseases such as schizophrenia and contributes to deficits in executive functions, including working memory, attention, flexibility, inhibitory control, and timing of behaviors. Currently, few interventions can compensate for impaired prefrontal function. Here, we tested whether stimulating the axons of prefrontal neurons in the striatum could compensate for deficits in temporal processing related to prefrontal dysfunction. We used an interval-timing task that requires working memory for temporal rules and attention to the passage of time. Our previous work showed that inactivation of the medial frontal cortex (MFC) impairs interval timing and attenuates ramping activity, a key form of temporal processing in the dorsomedial striatum (DMS). We found that 20-Hz optogenetic stimulation of MFC axon terminals in the DMS shifted response times and improved interval-timing behavior. Furthermore, optogenetic stimulation of terminals modulated time-related ramping of medium spiny neurons in the striatum. These data suggest that corticostriatal stimulation can compensate for deficits caused by MFC inactivation and they imply that frontostriatal projections are sufficient for controlling responses in time.
K. pneumoniaeST258 genomic variability and bacteriophage susceptibility
Authors: Venturini Carola , Zakour Nouri Ben , Bowring Bethany , Morales Sandra , Cole Robert , Kovach Zsuzsanna , Branston Steven , Kettle Emma , Thomson Nicholas , Iredell Jonathan
Published: May 2019

Multidrug resistant carbapenemase-producingKlebsiella pneumoniaecapable of causing severe disease in humans is classified as an urgent threat by health agencies worldwide. Bacteriophages are being actively explored as potential therapeutics against these multidrug resistant pathogens. We are currently developing bacteriophage therapy against carbepenem-resistantK. pneumoniaebelonging to the genetically diverse, globally disseminated clonal group CG258. In an effort to define a robust experimental approach for effective selection of lytic viruses for therapy, we have fully characterized the bacterial genomes of 18 target strains, tested them against novel lytic bacteriophages, and generated phage-susceptibility profiles. The genomes ofK. pneumoniaeisolates carryingblaNDMandblaKPCwere sequenced and isolates belonging to CG258 were selected for susceptibility testing using a panel of lytic bacteriophages (n=65). The localK. pneumoniaeCG258 population was dominated by isolates belonging to sequence type ST258 clade 1 (86%). The primary differences between ST258 genomes were variations in the capsular locus (cps) and in prophage content. We showed that CG258-specific lytic phages primarily target the capsule, and that successful infection is blocked in many, post-adsorption, by immunity conferred by existing prophages. Five bacteriophages specifically active againstK. pneumoniaeST258 clade 1 (n=5) belonging to the Caudovirales order were selected for further characterization. Our findings show that effective control ofK. pneumoniaeCG258 with phage will require mixes of diverse lytic viruses targeting all relevantcpsvariants and allowing for variable prophage content. These insights will facilitate identification and selection of therapeutic phage candidates against this serious pathogen.

Importance

Bacteriophages are natural agents that exclusively and selectively kill bacteria and have the potential to be useful in the treatment of multidrug resistant infections.K. pneumoniaeCG258 is a main agent of life-threatening sepsis that is often resistant to last-line antibiotics. Our work highlights some key requirements for developing bacteriophage preparations targeting this pathogen. By defining the genomic profile of our clinicalK. pneumoniaeCG258 population and matching it with bacteriophage susceptibility patterns, we found that bacteriophage ability to lyse each strain correlates well withK. pneumoniaeCG258 structural subtypes (capsule variants). This indicates that preparation of bacteriophage therapeutics targeting this pathogen should aim at including phages against each bacterial capsular subtype. This necessitates a detailed understanding of the diversity of circulating isolates in different geographical areas in order to make rational therapeutic choices.
Performance analysis of novel toxin-antidote CRISPR gene drive systems
Authors: Champer Jackson , Kim Isabel , Champer Samuel E. , Clark Andrew G. , Messer Philipp W.
Published: May 2019

Gene drives can potentially fixate in a population by biasing inheritance in their favor, opening up a variety of potential applications in areas such as disease-vector control and conservation. CRISPR homing gene drives have shown much promise for providing an effective drive mechanism, but they typically suffer from the rapid formation of resistance alleles. Even if the problem of resistance can be overcome, the utility of such drives would still be limited by their tendency to spread into all areas of a population. To provide additional options for gene drive applications that are substantially less prone to the formation of resistance alleles and could potentially remain confined to a target area, we developed several designs for CRISPR-based gene drives utilizing toxin-antidote (TA) principles. These drives target and disrupt an essential gene with the drive providing rescue. Here, we assess the performance of several types of TA gene drive systems using modeling and individual-based simulations. We show that Toxin-Antidote Recessive Embryo (TARE) drive should allow for the design of robust, regionally confined, population modification strategies with high flexibility in choosing drive promoters and recessive lethal targets. Toxin-Antidote Dominant Embryo (TADE) drive requires a haplolethal target gene and a germline-restricted promoter but should enable the design of both faster regional population modification drives and even regionally-confined population suppression drives. Toxin-antidote dominant sperm (TADS) drive can be used for population modification or suppression. It spreads nearly as quickly as a homing drive and can flexibly use a variety of promoters, but unlike the other TA systems, it is not regionally confined and requires highly specific target genes. Overall, our results suggest that CRISPR-based TA gene drives provide promising candidates for further development in a variety of organisms and may allow for flexible ecological engineering strategies.
Density-Weighted Concentric Ring Trajectory using simultaneous multi-band acceleration: 3D Metabolite-cycled Magnetic Resonance Spectroscopy Imaging at 3 T
Authors: Xia Pingyu , Chiew Mark , Zhou Xiaopeng , Thomas Albert , Dydak Ulrike , Emir Uzay E
Published: May 2019

Simultaneous multi-slice or multi-band parallel imaging is frequently used in fMRI to accelerate acquisition. In this study, we propose a new a non-water-suppressed multi-band MRSI using a density weighted concentric ring trajectory (DW-CRT) acquisition. The properties of multi-band acquisition scheme were compared against single-band acquisition in phantoms and in-vivo experiments. High-quality spectra were acquired for all simultaneously acquired three slices from a limited volume of interest with an in-plane resolution of 5 × 5 mm2 in 19.2 min. The achieved in vivo spectral quality of the multi-band method allowed the reliable metabolic mapping of four major metabolites with Cramér-Rao lower bounds below 50%, using a LCModel analysis. Metabolite maps and LCModel quality metrics were compared between multi-band and single-band acquisition schemes for both phantom and in-vivo measurements. Structural similarity (SSIM) index and conventional coefficient of variance analysis of both phantom and in-vivo measurements revealed a SSIM index higher than 0.83, corresponding to a coefficient of variance of less than 30%. These findings demonstrate that our multi-band DW-CRT MRSI demonstrate a multi-band acceleration, simultaneously acquired 3 slices, with no apparently loss in spectral quality, reducing scan time by a factor of 3 without any significant penalty.
A new role for Notch in the control of polarity and asymmetric cell division of developing T cells
Authors: Charnley Mirren , Ludford-Menting Mandy , Pham Kim , Russell Sarah M.
Published: May 2019

A fundamental question in biology is how single cells can reliably produce progeny of different cell types. Notch signalling frequently facilitates fate determination. Asymmetric cell division (ACD) often controls segregation of Notch signalling by imposing unequal inheritance of regulators of Notch. Here, we assessed the functional relationship between Notch and ACD in mouse T cell development. To attain immunological specificity, developing T cells must pass through a pivotal stage termed β-selection, which involves Notch signalling and ACD. We assessed functional interactions between Notch and ACD during β-selection using direct presentation of Notch ligands, DL1 and DL4, and pharmacological inhibition of Notch signalling. Contrary to prevailing models, we find Notch controls distribution of Notch1 itself and cell fate determinants, α-Adaptin and Numb. Notch and CXCR4 signalling cooperated to drive polarity during division. Thus, Notch signalling directly orchestrates ACD, and Notch1 is differentially inherited by sibling cells.
Breast Tumor Cellularity Assessment using Deep Neural Networks
Authors: Rakhlin Alexander , Tiulpin Aleksei , Shvets Alexey A. , Kalinin Alexandr A. , Iglovikov Vladimir I. , Nikolenko Sergey
Published: May 2019

Breast cancer is one of the main causes of death world-wide. Histopathological cellularity assessment of residual tumors in post-surgical tissues is used to analyze a tumor’s response to a therapy. Correct cellularity assessment increases the chances of getting an appropriate treatment and facilitates the patient’s survival. In current clinical practice, tumor cellularity is manually estimated by pathologists; this process is tedious and prone to errors or low agreement rates between assessors. In this work, we evaluated three strong novel Deep Learning-based approaches for automatic assessment of tumor cellularity from post-treated breast surgical specimens stained with hematoxylin and eosin. We validated the proposed methods on the BreastPathQ SPIE challenge dataset that consisted of 2395 image patches selected from whole slide images acquired from 64 patients. Compared to expert pathologist scoring, our best performing method yielded the Cohen’s kappa coefficient of 0.69 (vs. 0.42 previously known in literature) and the intra-class correlation coefficient of 0.89 (vs. 0.83). Our results suggest that Deep Learning-based methods have a significant potential to alleviate the burden on pathologists, enhance the diagnostic workflow, and, thereby, facilitate better clinical outcomes in breast cancer treatment.
C. elegans RHY-1 and CYSL-1 act independently of HIF-1 to promote survival in hydrogen sulfide
Authors: Horsman Joseph W. , Heinis Frazer I. , Miller Dana L.
Published: May 2019

Hydrogen sulfide (H2S) is an endogenously produced signaling molecule that can be cytoprotective, especially in conditions of ischemia/reperfusion injury. However, exposure to exogenous H2S can be toxic, perhaps due to unregulated activation of endogenous H2S signaling pathways. We use the nematode C. elegans to define mechanisms that mediate the physiological effects of H2S in animals. We have previously shown that in C. elegans the hypoxia inducible factor (hif-1) coordinates the initial transcriptional response to H2S and is essential to survive exposure to low concentrations of H2S. In this study, we performed a forward genetic screen to identify mutations that suppress the lethality of hif-1 mutant animals in H2S. The mutations we recovered do not suppress embryonic lethality or reproductive arrest of hif-1 mutant animals in hypoxia, nor can they improve viability of hif-1 mutant animals exposed to hydrogen cyanide, indicating that these are specific for H2S. We found that the hif-1 suppressor mutations activate the skn-1/Nrf2 transcription factor. Activation of SKN-1 by hif-1 suppressor mutations increased the expression of a subset of H2S-responsive genes, consistent with our previous finding that skn-1 plays a role in the transcriptional response to H2S. Using transgenic rescue, we show a single gene, rhy-1, alone is sufficient to protect hif-1 mutant animals in H2S. Our data indicate that RHY-1 acts in concert with CYSL-1, an orthologue of human cystathionine β-synthase, to promote survival in H2S. The rhy-1 gene encodes a predicated O-acyltransferase enzyme that has previously been shown to negatively regulate HIF-1 activity. Our studies reveal a novel function of RHY-1, which is independent of hif-1, that protects against toxic effects of H2S.
Flow restoration and the impacts of multiple stressors on fish communities in regulated rivers
Authors: Göthe Emma , Degerman Erik , Sandin Leonard , Segersten Joel , Tamario Carl , Mckie Brendan G.
Published: May 2019

River regulation for hydropower is undertaken worldwide, causing profound alterations to hydrological regimes and running water habitats. Regulated catchments are often subjected to additional stressors, arising inter alia from agriculture, forestry and industry, which are likely to interact with impacts of river regulation on fish and other biota. Such interactions are poorly understood, hindering planning of effective mitigation and restoration.

We investigated fish responses to increased discharge (as a restoration measure) in regulated rivers in Sweden. We compiled electrofishing data from river channels downstream of hydropower dams, each of which either has or lacks a mandated minimum discharge corresponding to c. 5% of pre‐regulation discharge. We further analysed interactions between flow restoration and co‐occurring local and regional stressors.

River channels without a mandated minimum discharge were characterized by a low diversity of fish species with traits favouring persistence under unpredictable environmental conditions, including omnivory, short life cycles and small size. Additional stressors further reduced diversity and increased dominance by broad‐niched, opportunistic species.

Both the presence and magnitude of a mandated minimum discharge were positively related to fish diversity and density, and the relative density of three economically and recreationally valuable species. However, the size of these relationships frequently varied with the presence of additional stressors.

Increasing levels of hydrological degradation and reduced connectivity at the catchment scale reduced positive flow–ecology relationships and hindered the restoration of fish communities towards reference conditions. However, application of a mandated minimum discharge also assisted in mitigating impacts of some co‐occurring stressors, especially reduced riparian integrity.

Synthesis and applications. Additional stressors can strongly influence the outcomes of flow restoration for fish community diversity and composition. Our approach combining fish species and trait data from multiple flow restoration projects with information on additional stressors yielded valuable insights into factors affecting flow restoration success, useful for (a) identifying the systems most likely to benefit from mandated minimum flows, (b) modelling influences of multiple stressors on flow–ecology relationships, (c) prioritizing additional measures to manage co‐occurring stressors and enhance outcomes from flow restoration.
An empirical pipeline for choosing the optimal clustering threshold in RADseq studies
Authors: McCartney‐Melstad Evan , Gidiş Müge , Shaffer H. Bradley
Published: May 2019

Genomic data are increasingly used for high resolution population genetic studies including those at the forefront of biological conservation. A key methodological challenge is determining sequence similarity clustering thresholds for RADseq data when no reference genome is available. These thresholds define the maximum permitted divergence among allelic variants and the minimum divergence among putative paralogues and are central to downstream population genomic analyses. Here we develop a novel set of metrics to determine sequence similarity thresholds that maximize the correct separation of paralogous regions and minimize oversplitting naturally occurring allelic variation within loci. These metrics empirically identify the threshold value at which true alleles at opposite ends of several major axes of genetic variation begin to incorrectly separate into distinct clusters, allowing researchers to choose thresholds just below this value. We test our approach on a recently published data set for the protected foothill yellow‐legged frog (Rana boylii). The metrics recover a consistent pattern of roughly 96% similarity as a threshold above which genetic divergence and data missingness become increasingly correlated. We provide scripts for assessing different clustering thresholds and discuss how this approach can be applied across a wide range of empirical data sets.
AeRobiology: The computational tool for biological data in the air
Authors: Rojo Jesús , Picornell Antonio , Oteros Jose
Published: May 2019

Aerobiological databases are constantly increasing. Many of them contain long and extensive time series of data which are very difficult and tedious to manage.

The development of new real‐time automatic sampling devices also requires new tools to reduce time of calculations and data management. In this sense, the AeRobiology r package has been implemented to accelerate and facilitate these tasks.

This package was structured in three sections based on (a) the checking of the database, (b) calculation of the main aerobiological indexes and (c) visualization of the results.

The AeRobiology package contains numerous functions which, in conjunction, solve the main general tasks that scientists must assume for the analysis of the biological data.

The package is freely distributed under GNU General Public License and can directly be installed from CRAN (http://cran.r-project.org/). The reference manual is available at https://cran.r-project.org/web/packages/AeRobiology. Contact: aerobiology.package@gmail.com.
Depletion of B cells rejuvenates the peripheral B‐cell compartment but is insufficient to restore immune competence in aging
Authors: Avivi Irit , Zisman‐Rozen Simona , Naor Shulamit , Dai Isabelle , Benhamou David , Shahaf Gitit , Tabibian‐Keissar Hilla , Rosenthal Noemie , Rakovsky Aviya , Hanna Ammuri , Shechter Arik , Peled Eli , Benyamini Noam , Dmitrukha Ekaterina , Barshack Iris , Mehr Ramit , Melamed Doron
Published: May 2019

Aging is associated with increasing prevalence and severity of infections caused by a decline in bone marrow (BM) lymphopoiesis and reduced B‐cell repertoire diversity. The current study proposes a strategy to enhance immune responsiveness in aged mice and humans, through rejuvenation of the B lineage upon B‐cell depletion. We used hCD20Tg mice to deplete peripheral B cells in old and young mice, analyzing B‐cell subsets, repertoire and cellular functions in vitro, and immune responsiveness in vivo. Additionally, elderly patients, previously treated with rituximab healthy elderly and young individuals, were vaccinated against hepatitis B (HBV) after undergoing a detailed analysis for B‐cell compartments. B‐cell depletion in old mice resulted in rejuvenated B‐cell population that was derived from de novo synthesis in the bone marrow. The rejuvenated B cells exhibited a "young"‐like repertoire and cellular responsiveness to immune stimuli in vitro. Yet, mice treated with B‐cell depletion did not mount enhanced antibody responses to immunization in vivo, nor did they survive longer than control mice in "dirty" environment. Consistent with these results, peripheral B cells from elderly depleted patients showed a "young"‐like repertoire, population dynamics, and cellular responsiveness to stimulus. Nevertheless, the response rate to HBV vaccination was similar between elderly depleted and nondepleted subjects, although antibody titers were higher in depleted patients. This study proposes a proof of principle to rejuvenate the peripheral B‐cell compartment in aging, through B‐cell depletion. Further studies are warranted in order to apply this approach for enhancing humoral immune responsiveness among the elderly population.
Neuronal HMGB1 in nucleus accumbens regulates cocaine reward memory
Authors: Gao Shuang‐Qi , Zhang Hai , He Jin‐Gang , Zheng Hui‐Ling , Zhang Pei‐Wei , Xu Jun‐Feng , Shen Zu‐Cheng , Zhao Huan‐Huan , Wang Fang , Hu Zhuang‐Li , Chen Jian‐Guo
Published: May 2019

Cocaine is a common abused drug that can induce abnormal synaptic and immune responses in the central nervous system (CNS). High mobility group box 1 (HMGB1) is one kind of inflammatory molecules that is expressed both on neurons and immune cells. Previous studies of HMGB1 in the CNS have largely focused on immune function, and the role of HMGB1 in neurons and cocaine addiction remains unknown. Here, we show that cocaine exposure induced the translocation and release of HMGB1 in the nucleus accumbens (NAc) neurons. Gain and loss of HMGB1 in the NAc bidirectionally regulate cocaine‐induced conditioned place preference. From the nucleus to the cytosol, HMGB1 binds to glutamate receptor subunits (GluA2/GluN2B) on the membrane, which regulates cocaine‐induced synaptic adaptation and the formation of cocaine‐related memory. These data unveil the role of HMGB1 in neurons and provide the evidence for the HMGB1 involvement in drug addiction.