bluuebunny/crossref_metadata_2025 huggingface dataset:
Automated Lifespan Determination Across Caenorhabditis Strains and Species Reveals Assay-Specific Effects of Chemical Interventions
Authors: Banse Stephen A. , Lucanic Mark , Sedore Christine A. , Coleman-Hulbert Anna L. , Plummer W. Todd , Chen Esteban , Kish Jason L. , Hall David , Onken Brian , Presley Michael P. , Jones E. Grace , Blue Benjamin W. , Garrett Theo , Abbott Mark , Xue Jian , Guo Suzhen , Johnson Erik , Foulger Anna C. , Chamoli Manish , Falkowski Ron , Melentijevic Ilija , Harinath Girish , Huynh Phu , Patel Shobhna , Edgar Daniel , Jarrett Cody M. , Guo Max , Kapahi Pankaj , Lithgow Gordon J. , Driscoll Monica , Phillips Patrick C.
Published: September 2019

The goal of the Caenorhabditis Intervention Testing Program is to identify robust and reproducible pro-longevity interventions that are efficacious across genetically diverse cohorts in the Caenorhabditis genus. The project design features multiple experimental replicates collected by three different laboratories. Our initial effort employed fully manual survival assays. With an interest in increasing throughput, we explored automation with flatbed scanner-based Automated Lifespan Machines (ALMs). We used ALMs to measure survivorship of 22 Caenorhabditis strains spanning three species. Additionally, we tested five chemicals that we previously found extended lifespan in manual assays. Overall, we found similar sources of variation among trials for the ALM and our previous manual assays, verifying reproducibility of outcome. Survival assessment was generally consistent between the manual and the ALM assays, although we did observe radically contrasting results for certain compound interventions. We found that particular lifespan outcome differences could be attributed to protocol elements such as enhanced light exposure of specific compounds in the ALM, underscoring that differences in technical details can influence outcomes and therefore interpretation. Overall, we demonstrate that the ALMs effectively reproduce a large, conventionally scored dataset from a diverse test set, independently validating ALMs as a robust and reproducible approach towards aging-intervention screening.
Quantifying the Limits of Immunotherapies in Mice and Men
Authors: Brown Liam V , Gaffney Eamonn A , Ager Ann , Wagg Jonathan , Coles Mark C
Published: September 2019

Background

CART-cells have demonstrated clinical success for the treatment of multiple different lymphomas and leukaemias. However, comparable clinical efficacy has not been observed for various solid tumours in human clinical trials, despite promising data from murine cancer models. Lower effective CART-cell delivery rates to human solid tumours compared to haematological malignancies in humans and solid tumours in mice might partially explain these divergent clinical outcomes, requiring the development of quantitative methods to calculate effective dosing in the clinic and models.

Methods

We used anatomical and physiological data for human and rodent circulatory systems to calculate the typical value and expected variation of the perfusion of healthy and tumour tissues, and used these to estimate the upper limits of immune cell delivery rates (maximum possible under optimal conditions) across different organs, tumours types and species.

Results

Estimated maximum delivery rates were up to order 10,000-fold greater in mice than humans yet reported CART-cell doses are typically only 10-100-fold lower in mice, suggesting that the effective delivery rates of CART-cells into tumours in clinical trials are far lower than in corresponding mouse models. Estimated delivery rates were compared to published PET data and found to be consistent.

Conclusions

The results suggest that higher effective human doses may be needed to drive efficacy comparable to mouse solid tumour models. These increased doses raise safety and manufacturing concerns. We posit that quantitation of species and organ-specific delivery and homing of engineered T-cells will be key to unlocking their potential for solid tumours.
Most cancers carry a substantial deleterious load due to Hill-Robertson interference
Authors: Tilk Susanne , Curtis Christina , Petrov Dmitri A , McFarland Christopher D
Published: September 2019

Cancer genomes exhibit surprisingly weak signatures of negative selection1,2. This may be because selective pressures are relaxed or because genome-wide linkage prevents deleterious mutations from being removed (Hill-Robertson interference)3. By stratifying tumors by their genome-wide mutational burden, we observe negative selection (dN/dS ~ 0.47) in low mutational burden tumors, while remaining cancers exhibit dN/dS ratios ~1. This suggests that most tumors do not remove deleterious passengers. To buffer against deleterious passengers, tumors upregulate heat shock pathways as their mutational burden increases. Finally, evolutionary modeling finds that Hill-Robertson interference alone can reproduce patterns of attenuated selection and estimates the total fitness cost of passengers to be 40% per cell on average. Collectively, our findings suggest that the lack of observed negative selection in most tumors is not due to relaxed selective pressures, but rather the inability of selection to remove deleterious mutations in the presence of genome-wide linkage.
Tumor cell-derived lymphotoxin alpha triggers metastatic extravasation through TNFRs/cIAP1
Authors: Vasilikos Lazaros , Hänggi Kay , Spilgies Lisanne M. , Wong W. Wei-Lynn
Published: September 2019

Metastasis involves the interaction of the tumor, immune and endothelial cells. Cell death proteins, such as inhibitors of apoptosis proteins (IAPs), are critical players in survival, inflammation and permeability. Whether the use of Smac mimetics, which target cIAP1/2 for degradation would affect metastasis is unknown. We show Smac mimetics reduced metastasis due to the loss of cIAP1 but not cIAP2 in experimental metastasis models. The endothelial compartment rather than the immune cells was responsible for reduction of extravasation upon loss of cIAP1. Loss of cIAP1 in primary endothelial cells did not lead to cell death but resulted in an unresponsive endothelium barrier to permeability factors causing a reduction in tumor cell extravasation. Unexpectedly, the co-loss of TNFR1 and cIAP1 restored the tumor load. We were surprised to find lymphotoxin alpha (LTA), and not TNF, secreted by the tumor cells was critical for the extravasation. Using TCGA data, we found high levels of LTA mRNA expression correlated with decreased survival in kidney carcinoma and associated with advance disease stage. Our data suggest that Smac mimetics, targeting cIAP1/2, may reduce metastasis to the lung through a LTA/TNFR mechanism by altering the endothelial barrier and inhibiting the ability of tumor cells to extravasate.
Inosine is an alternative carbon supply that supports effector T cell proliferation and antitumor function under glucose restriction
Authors: Wang Tingting , Gnanaprakasam JN Rashida , Chen Xuyong , Kang Siwen , Xu Xuequn , Sun Hua , Liu Lingling , Miller Ethan , Cassel Teresa A. , Sun Qiushi , Vicente-Muñoz Sara , Warmoes Marc O. , Lane Andrew N. , Song Xiaotong , Fan Teresa W.-M. , Wang Ruoning
Published: September 2019

T cells undergo a characteristic metabolic rewiring that fulfills the dramatically increased bioenergetic, biosynthetic, and redox demands following antigen stimulation. A robust adaptive immune system requires effector T cells to respond and adapt to fluctuations in environmental nutrient levels imposed by infectious and inflammatory sites in different tissues. Inevitably, such responsiveness and adaptation reflect metabolic plasticity, allowing T cells to elicit immune functions by using a wide range of nutrient substrates. Here, we show that effector T cells utilize inosine, as an alternative substrate, to support cell growth and function in the absence of glucose. T cells metabolize inosine into hypoxanthine and phosphorylated ribose by purine nucleoside phosphorylase (PNP). Using Stable Isotope-Resolved Metabolomics (SIRM), we demonstrated that ribose moiety of inosine can enter into central metabolic pathways to provide ATP and biosynthetic precursors. Accordingly, the dependence of T cells on extracellular glucose for growth and effector functions can be relieved by inosine. On the other hand, cancer cells display diverse capacity to utilize inosine as a carbon resource. Moreover, the supplement of inosine enhances the anti-tumor efficacy of immune-checkpoint blockade or adoptive T cell transfer, reflecting the capability of inosine in relieving tumor-imposed metabolic restrictions on T cellsin vivo.
A Bayesian implementation of the multispecies coalescent model with introgression for comparative genomic analysis
Authors: Flouris Thomas , Jiao Xiyun , Rannala Bruce , Yang Ziheng
Published: September 2019

Recent analyses suggest that cross-species gene flow or introgression is common in nature, especially during species divergences. Genomic sequence data can be used to infer introgression events and to estimate the timing and intensity of introgression, providing an important means to advance our understanding of the role of gene flow in speciation. Here we implement the multispecies-coalescent-with-introgression (MSci) model, an extension of the multispecies-coalescent (MSC) model to incorporate introgression, in our Bayesian Markov chain Monte Carlo (MCMC) program BPP. The MSci model accommodates deep coalescence (or incomplete lineage sorting) and introgression and provides a natural framework for inference using genomic sequence data. Computer simulation confirms the good statistical properties of the method, although hundreds or thousands of loci are typically needed to estimate introgression probabilities reliably. Re-analysis of datasets from the purple cone spruce confirms the hypothesis of homoploid hybrid speciation. We estimated the introgression probability using the genomic sequence data from six mosquito species in theAnopheles gambiaespecies complex, which varies considerably across the genome, likely driven by differential selection against introgressed alleles.
The nuclear to cytoplasmic ratio directly regulates zygotic transcription inDrosophilathrough multiple modalities
Authors: Syed Sahla , Wilky Henry , Raimundo João , Lim Bomyi , Amodeo Amanda A.
Published: September 2019

Early embryos must rapidly generate large numbers of cells to form an organism. Many species accomplish this through a series of rapid, reductive, and transcriptionally silent cleavage divisions. Previous work has demonstrated that the number of divisions before both cell cycle elongation and zygotic genome activation (ZGA) is regulated by the ratio of nuclear content to cytoplasm (N/C). To understand how the N/C ratio affects the timing of ZGA, we directly assayed the behavior of several previously identified N/C-ratio-dependent genes using the MS2-MCP reporter system in livingDrosophilaembryos with altered ploidy and cell cycle durations. For every gene that we examined, we found that nascent RNA output per cycle is delayed in haploid embryos. Moreover, we found that the N/C ratio influences transcription through three separate modes of action. For some genes (knirpsandsnail) the effect of ploidy can be entirely accounted for by changes in cell cycle duration. However, for other genes (giant, bottleneck and fruhstart) the N/C ratio directly affects ZGA. Forgiantandbottleneck,the N/C ratio regulates the kinetics of transcription activation, while forfruhstartit controls the probability of transcription initiation. Our data demonstrate that the regulatory elements of N/C-ratio-dependent genes respond directly to the N/C ratio, through multiple modes of regulation, independent of interphase length.
Real-time dynamics of Plasmodium NDC80 reveals unusual modes of chromosome segregation during parasite proliferation
Authors: Zeeshan Mohammad , Pandey Rajan , Ferguson David J.P. , Tromer Eelco C. , Markus Robert , Abel Steven , Brady Declan , Daniel Emilie , Limenitakis Rebecca , Bottrill Andrew R. , Le Roch Karine G. , Holder Anthony A. , Waller Ross F. , Guttery David S. , Tewari Rita
Published: September 2019

Eukaryotic cell proliferation requires chromosome replication and precise segregation to ensure daughter cells have identical genomic copies. The genus Plasmodium, the causative agent of malaria, displays remarkable aspects of nuclear division throughout its lifecycle to meet some peculiar and unique challenges of DNA replication and chromosome segregation. The parasite undergoes atypical endomitosis and endoreduplication with an intact nuclear membrane and intranuclear mitotic spindle. To understand these diverse modes of Plasmodium cell division, we have studied the behaviour and composition of the outer kinetochore NDC80 complex, a key part of the mitotic apparatus that attaches the centromere of chromosomes to microtubules of the mitotic spindle. Using NDC80-GFP live-cell imaging in Plasmodium berghei we observe dynamic spatiotemporal changes during proliferation, including highly unusual kinetochore arrangements during sexual stages. We identify a very divergent candidate for the SPC24 subunit of the NDC80 complex, previously thought to be missing in Plasmodium, which completes a canonical, albeit unusual, NDC80 complex structure. Altogether, our studies reveal the kinetochore as an ideal tool to investigate the non-canonical modes of chromosome segregation and cell division in Plasmodium.

Summary Statement

The dynamic localization of kinetochore marker NDC80 protein complex during proliferative stages of the malaria parasite life cycle reveals unique modes of chromosome segregation.
Integrative single-cell and bulk RNA-seq analysis in human retina identified cell type-specific composition and gene expression changes for age-related macular degeneration
Authors: Lyu Yafei , Zauhar Randy , Dana Nico , Strang Christianne E. , Wang Kui , Liu Shanrun , Miao Zhen , Pan Naifei , Gamlin Paul , Kimble James A. , Messinger Jeffrey D. , Curcio Christine A. , Stambolian Dwight , Li Mingyao
Published: September 2019

Age-related macular degeneration (AMD) preferentially affects distinct cell types and topographic regions in retina. To characterize the impact of AMD on gene expression changes across retinal cell types and regions, we generated both single-cell RNA-seq (scRNA-seq) and bulk RNA-seq data from macular and peripheral retina in postmortem human donors with and without AMD. The scRNA-seq data revealed 11 major cell types with many previously reported AMD risk genes showing substantial cell type and region specificity. Cell type proportional changes with advancing AMD stage were significant for Müller glia, rods, astrocytes, microglia and endothelium.
The Wnt pathway scaffold protein Axin promotes signaling specificity by suppressing competing kinase reactions
Authors: Gavagan Maire , Fagnan Erin , Speltz Elizabeth B. , Zalatan Jesse G.
Published: September 2019

GSK3β is a multifunctional kinase that phosphorylates β-catenin in the Wnt signaling network and also acts on other protein targets in response to distinct cellular signals. To test the long-standing hypothesis that the scaffold protein Axin specifically accelerates β-catenin phosphorylation, we measured GSK3β reaction rates with multiple substrates in a minimal, biochemically-reconstituted system. We observed an unexpectedly small, ~2-fold Axin-mediated rate increase for the β-catenin reaction. The much larger effects reported previously may have arisen because Axin can rescue GSK3β from an inactive state that occurs only under highly specific conditions. Surprisingly, Axin significantly slows the reaction of GSK3β with CREB, a non-Wnt pathway substrate. When both β-catenin and CREB are present, Axin accelerates the β-catenin reaction by preventing competition with CREB. Thus, while Axin alone does not markedly accelerate the β-catenin reaction, in physiological settings where multiple GSK3β substrates are present, Axin can promote signaling specificity by suppressing interactions with competing, non-Wnt pathway targets.
Claudin-12 deficiency causes nerve barrier breakdown, mechanical hypersensitivity and painfulness in polyneuropathy
Authors: Chen Jeremy Tsung-Chieh , Hu Xiawei , Doppler Kathrin , Breitkreuz-Korff Olga , Otto Isabel U. C. , Schwabe Joachim , Reinhold Ann-Kristin , Günzel Dorothee , Dithmer Sophie , Hankir Mohammed K. , Fallier-Becker Petra , Winkler Lars , Blasig Rosel , Sommer Claudia , Brack Alexander , Blasig Ingolf E. , Rittner Heike L.
Published: September 2019

Peripheral nerves and their axons are shielded by the blood-nerve and the myelin barrier, but understanding of how these barriers impact nociception is limited. Here, we identified a regulatory axis of the tight junction protein claudin-12, sex-dependently controlling perineurial and myelin barrier integrity. In nerve biopsies, claudin-12 in Schwann cells was lost in male and postmenopausal female patients with painful but not painless polyneuropathy. Global Cldn12 gene-knockout selectively increased perineurial/myelin barrier leakage, damaged tight junction protein expression and morphology, increased proinflammatory cytokines and induced mechanical hypersensitivity in naïve and neuropathic male mice, respectively. Other barriers and neurological function remained intact. In vitro transfection studies documented claudin-12 plasma membrane localisation without interaction with other tight junction proteins or intrinsic sealing properties. Rather, claudin-12 had a regulatory tight junction protein function on the myelin barrier via the morphogen SHH in vivo in Cldn12-KO and after local siRNA knockdown. Fertile female mice were completely protected. Collectively, these studies reveal the critical role of claudin-12 maintaining the myelin barrier and highlight restoration of the claudin-12/SHH pathway as a potential target for painful neuropathy.
Hyaluronic acid particle hydrogels decrease cerebral atrophy and promote pro-reparative astrocyte/axonal infiltration in the core after ischemic stroke
Authors: Sideris Elias , Yu Aaron , Chen Jun , Carmichael S Thomas , Segura Tatiana
Published: September 2019

The death rate due to stroke is decreasing, resulting in more individuals living with stroke related disabilities. Following stroke, dying cells contribute to the large influx of highly reactive astrocytes and pro-inflammatory microglia that release cytokines and lead to a cytotoxic environment that causes further brain damage and prevents endogenous repair. Paradoxically, these same cells also activate pro-repair mechanisms that contribute to endogenous repair and brain plasticity. Here, we show that the direct injection of a hyaluronic acid based microporous annealed particle (HA-MAP) hydrogel into the stroke core reduces the percent of highly reactive astrocytes and increases the percent of alternatively activated microglia in and around the lesion. Further, we show that HA-MAP hydrogel promotes reparative astrocyte infiltration into the lesion, which directly coincides with axonal penetration into the lesion. Additionally, HA-MAP injection decreases cerebral atrophy and preserves nigrostriatal bundles after stroke. This work shows that the injection of a porous scaffold into the stroke core can lead to clinically relevant decrease in cerebral atrophy and modulates the phenotype of astrocytes and microglia towards a pro-repair phenotype.
Deviations from Hardy Weinberg Equilibrium at CCR5-Δ32 in Large Sequencing Data Sets
Authors: Wei Xinzhu , Nielsen Rasmus
Published: September 2019

Previous analyses of the UK Biobank (UKB) genotyping array data in the CCR5-Δ32 locus show evidence for deviations from Hardy-Weinberg Equilibrium (HWE) and an increased mortality rate of homozygous individuals, consistent with a recessive deleterious effect of the deletion mutation. We here examine if similar deviations from HWE can be observed in the newly released UKB Whole Exome Sequencing (WES) data and in the sequencing data of the Genome Aggregation Database (gnomAD). We also examine the reliability of the genotype calls in the UKB array data. The UKB genotyping array probe targeting CCR5-Δ32 (rs62625034) and the WES of Δ32 are strongly correlated (r2 = 0.97). This contrasts to tag SNPs of CCR5-Δ32 in the UKB which have high missing data rates and imputation errors rates. We also show that, while different data sets are subject to different biases, both the UKB-WES and the gnomAD data have a deficiency of homozygous CCR5-Δ32 individuals compared to the HWE expectation (combined P-value < 0.01), consistent with an increased mortality rate in homozygotes. Finally, we perform a survival analysis on data from parents of UKB volunteers, that, while underpowered, is also consistent with the original report of a deleterious effect of CCR5-Δ32 in the homozygous state.
Complex eukaryotic-like actin regulation systems from Asgard archaea
Authors: Akıl Caner , Tran Linh T. , Orhant-Prioux Magali , Baskaran Yohendran , Manser Edward , Blanchoin Laurent , Robinson Robert C.
Published: September 2019

Asgard archaea genomes contain potential eukaryotic-like genes that provide intriguing insight for the evolution of eukaryotes. The actin polymerization/depolymerization cycle is critical for providing force and structure for a variety of processes in eukaryotes, including membrane remodelling. Here, we identify actin filament severing, capping, annealing and bundling, and monomer sequestration activities by gelsolin proteins from Thorarchaeota (Thor), which complete a eukaryote-like actin depolymerization cycle. Thor gelsolins are comprised of one or two copies of the prototypical gelsolin domain and appear to be a record of an initial pre-eukaryotic gene duplication event, since eukaryotic gelsolins are generally comprised of three to six domains. X-ray crystal structure determination of these proteins in complex with mammalian actin revealed similar interactions to the first domain of human gelsolin. Asgard two-domain, but not one-domain, gelsolins contain calcium-binding sites, which is manifested in calcium-controlled activities. Expression of two-domain gelsolins in mammalian cells led to enhanced actin filament disassembly on ionomycin-triggered calcium release. This functional demonstration, at the cellular level, provides evidence for calcium-regulated actin cytoskeleton in Asgard archaea, and indicates that the calcium-regulated actin cytoskeleton predates eukaryotes. In eukaryotes, dynamic bundled filaments are responsible for shaping filopodia and microvilli. By correlation, the formation of the protrusions observed from Lokiarchaeota cell bodies may involve gelsolin-regulated actin structures.
Automated quality control of next generation sequencing data using machine learning
Authors: Albrecht Steffen , Andrade-Navarro Miguel A. , Fontaine Jean-Fred
Published: September 2019

Controlling quality of next generation sequencing (NGS) data files is a necessary but complex task. To address this problem, we statistically characterized common NGS quality features and developed a novel quality control procedure involving tree-based and deep learning classification algorithms. Predictive models, validated on internal data and external disease diagnostic datasets, are to some extent generalizable to data from unseen species. The derived statistical guidelines and predictive models represent a valuable resource for users of NGS data to better understand quality issues and perform automatic quality control. Our guidelines and software are available at the following URL:https://github.com/salbrec/seqQscorer.
RAD51 promotes non-homologous genetic rearrangements that are prevented by 53BP1
Authors: Guirouilh-Barbat Josée , Yu Wei , Babin Loelia , Galende Elisa Yaniz , Popova Tatiana , So Ayeong , Lescale Chloé , Stern Marc-Henri , Brunet Erika , Deriano Ludovic , Lopez Bernard S.
Published: September 2019

Homologous recombination (HR), which requires long sequence homologies, is considered a high fidelity mechanism, preserving genome stability. In contrast, we show here that the central HR players RAD51 or BRCA2, promote genetic instability, fostering translocations and capture of ectopic chromosomal sequences when joining distant DNA breaks. Surprisingly, these events do not involve sequence homologies. Moreover, our data reveal that 53BP1 protects against RAD51-mediated non-homologous genetic rearrangements. Finally, analysis of a large panel of breast tumors revealed that BRCA2 proficiency is associated with increased frequency of capture of non-homologous sequences at junctions of structural variants (translocations, duplications, inversions, deletions). These data reveal that HR proteins (RAD51, BRCA2) possess the intrinsic capacity to generate genetic instability through sequence homology-independent processes, and that 53BP1 protects against it. We propose that BRCA2/RAD51-mediated genome instability occurs in the course of sequence homology search for HR.
On the effect of asymmetrical trait inheritance on models of trait evolution
Authors: Duchen Pablo , Alfaro Michael L. , Rolland Jonathan , Salamin Nicolas , Silvestro Daniele
Published: September 2019

Current phylogenetic comparative methods modeling quantitative trait evolution generally assume that, during speciation, phenotypes are inherited identically between the two daughter species. This, however, neglects the fact that species consist of a set of individuals, each bearing its own trait value. Indeed, because descendent populations after speciation are samples of a parent population, we can expect their mean phenotypes to randomly differ from one another potentially generating a “jump” of mean phenotypes due to asymmetrical trait inheritance at cladogenesis. Here, we aim to clarify the effect of asymmetrical trait inheritance at speciation on macroevolutionary analyses, focusing on model testing and parameter estimation using some of the most common models of quantitative trait evolution. We developed an individual-based simulation framework in which the evolution of species phenotypes is determined by trait changes at the individual level accumulating across generations and cladogenesis occurs then by separation of subsets of the individuals into new lineages. Through simulations, we assess the magnitude of phenotypic jumps at cladogenesis under different modes of trait inheritance at speciation. We show that even small jumps can strongly alter both the results of model selection and parameter estimations, potentially affecting the biological interpretation of the estimated mode of evolution of a trait. Our results call for caution when interpreting analyses of trait evolution, while highlighting the importance of testing a wide range of alternative models. In the light of our findings, we propose that future methodological advances in comparative methods should more explicitly model the intra-specific variability around species mean phenotypes and how it is inherited at speciation.
Finding differentially expressed sRNA-Seq regions with srnadiff
Authors: Zytnicki Matthias , González Ignacio
Published: September 2019

Small RNAs (sRNAs) encompass a great variety of different molecules of different kinds, such as micro RNAs, small interfering RNAs, Piwi-associated RNA, among other. These sRNA have a wide range of activities, which include gene regulation, protection against virus, transposable element silencing, and have been identified as a key actor to study and understand the development of the cell. Small RNA sequencing is thus routinely used to assess the expression of the diversity of sRNAs, usually in the context of differentially expression, where two conditions are compared. Many tools have been presented to detect differentially expressed micro RNAs, because they are well documented, and the associated genes are well defined. However, tools are lacking to detect other types of sRNAs, which are less studied, and have an imprecise “gene” structure. We present here a new method, called srnadiff, to find all kinds of differentially expressed sRNAs. To the extent of our knowledge, srnadiff is the first tool that detects differentially expressed sRNAs without the use of external information, such as genomic annotation or reference sequence of sRNAs.

Author summary

We present here a new method for the ab initio discovery of differentially expressed small RNAs. The standard method, sometimes named annotate-then-identify, first finds possible genes, and tests for differential expression. In contrast, our method skips the first step and scans the genome for potential differentially expressed regions (the identify-then-annotate strategy). Since our method is the first one to use the identify-then-annotate strategy on sRNAs, we compared our method against a similar method, developed for long RNAs (derfinder), and to the annotate-then-identify strategy, where the sRNAs have been identified beforehand using a segmentation tool, on three published datasets, and a simulated one. Results show that srnadiff gives much better results than derfinder, and is also better than the annotate-then-identify strategy on many aspects. srnadiff is available as a Bioconductor package, together with a detailed manual: https://bioconductor.org/packages/release/bioc/html/srnadiff.html
Feasibility of Remotely Supervised Transcranial Direct Current Stimulation and Cognitive Remediation: A Systematic Review
Authors: Gough Nicole , Brkan Lea , Subramaniam Ponnusamy , Chiuccariello Lina , De Petrillo Alessandra , Mulsant Benoit H. , Bowie Christopher R. , Rajji Tarek K.
Published: September 2019

With technological advancements and an aging population, there is growing interest in delivering interventions at home. Transcranial Direct Current Stimulation (tDCS) and Cognitive Remediation (CR) have been widely studied, but mainly in laboratories or hospitals. Thus, the objectives of this review are to examine feasibility and the interventions components to support the domiciliary administration of tDCS and CR. We performed a systematic search of electronic databases, websites and reference lists of included articles from the first date available until October 31, 2018. Articles included had to meet the following criteria: original work published in English using human subjects, majority of tDCS or CR intervention administered remotely. A total of 39 studies were identified (16 tDCS, 23 CR/cognitive training, 5 using both tDCS & cognitive training). Four studies were single case studies and two were multiple case studies. The remaining 33 studies had a range of 9 – 135 participants. Five tDCS and nine CR/cognitive training studies were double blind randomized controlled trials. Most studies focused on schizophrenia (8/39) and multiple sclerosis (8/39). Literature examined suggests the feasibility of delivering tDCS or CR remotely with the support of information and communication technologies.
ChIP-Hub: an Integrative Platform for Exploring Plant Regulome
Authors: Chen Dijun , Fu Liang-Yu , Zhang Peijing , Chen Ming , Kaufmann Kerstin
Published: September 2019

Plant genomes encode a complex and evolutionary diverse regulatory grammar that forms the basis for most life on earth. A wealth of regulome and epigenome data have been generated in various plant species, but no common, standardized resource is available so far for biologists. Here we present ChIP-Hub, an integrative web-based platform in the ENCODE standards that bundles publicly available datasets reanalyzed from >40 plant species, allowing visualization and meta-analysis.
The Trend of Suicide Reporting in the Media: an Effectiveness Study of Daily Surveillance over Nine Years
Authors: Wu Chia-Yi , Lee Ming-Been , Liao Shih-Cheng , Chan Chia-Ta , Chen Chun-Ying
Published: September 2019

Inadequate suicide reports can cause copycat suicide attempts, but legal regulations for the media are rarely seen worldwide. In Taiwan, daily media surveillance with immediate feedback to correct inappropriate reports has been an interactive policy in the national suicide prevention strategy for a decade. We aimed to evaluate the effectiveness of current surveillance program via assessing the adherence rates with 12-item WHO responsible reporting guideline in print newspapers (2010-2018) and online media (2017-2018). The results showed that media reporting of suicide significantly improved in most guideline items under surveillance. But the development of psychiatric-media liaisons should further improve reporting quality.
Whole genome sequence analysis reveals broad distribution of the RtxA type 1 secretion system and four novel type 1 secretion systems throughout theLegionellagenus
Authors: Brown Connor L. , Garner Emily , Jospin Guillaume , Coil David A. , Schwake David O. , Eisen Jonathan A. , Mukhopadhyay Biswarup , Pruden Amy J.
Published: September 2019

Type 1 secretion systems (T1SSs) are broadly distributed among bacteria and translocate effectors with diverse function across the bacterial cell membrane.Legionella pneumophila, the species most commonly associated with Legionellosis, encodes a T1SS at thelssXYZABDlocus which is responsible for the secretion of the virulence factor RtxA. Many investigations have failed to detectlssD, the gene encoding the membrane fusion protein of the RtxA T1SS, in non-pneumophila Legionella, suggesting that this system is a conserved virulence factor inL. pneumophila.Here we discovered RtxA and its associated T1SS in a novelLegionella taurinensisstrain, leading us to question whether this system may be more widespread than previously thought. Through a bioinformatic analysis of publicly available data, we classified and determined the distribution of four T1SSs including the RtxA T1SS and four novel T1SSs among diverseLegionellaspp. The ABC transporter of the novelLegionellaT1SSLegonellarepeat protein secretion system (LRPSS) shares structural similarity to those of diverse T1SS families, including the alkaline protease T1SS inPseudomonas aeruginosa.TheLegionellabacteriocin (1–3) secretion systems (LB1SS-LB3SS) T1SSs are novel putative bacteriocin transporting T1SSs as their ABC transporters include C-39 peptidase domains in their N-terminal regions, with LB2SS and LB3SS likely constituting a nitrile hydratase leader peptide transport T1SSs. The LB1SS is more closely related to the colicin V T1SS inEscherichia coli.Of 45Legionellaspp. whole genomes examined, 19 (42%) were determined to possesslssBandlssDhomologs. Of these 19, only 7 (37%) are known pathogens. There was no difference in the proportions of disease associated and non-disease associated species that possessed the RtxA T1SS (p = 0.4), contrary to the current consensus regarding the RtxA T1SS. These results draw into question the nature of RtxA and its T1SS as a genetic virulence determinant.
Minimally invasive, pressure probe based sampling allows for in-situ gene expression analyses in plant cells
Authors: Wada Hiroshi , Castellarin Simone D. , Matthews Mark A. , Shackel Kenneth A. , Gambetta Gregory A.
Published: September 2019

Background

Gene expression analyses are conducted using multiple approaches and increasingly research has been focused on assessing gene expression at the level of a tissue or even single-cells. To date, methods to assess gene expression at the single-cell in plant tissues have been semi-quantitative, require tissue disruption, and/or involve laborious, possibly artifact-inducing manipulation. In this work, we used grape berries (Vitis vinifera L. Zinfandel) as a model in order to examine the validity and reproducibility of an in-situ gene expression analysis method combining a cell pressure probe (CPP) with quantitative PCR (qPCR).

Results

We developed a method to directly assess gene expression levels via qPCR from cellular fluids sampled in-situ with a CPP. Cellular fluids, with volumes in the picoliter range, were collected from intact berries with a CPP at various depths across skin and mesocarp tissues. The expression of a key anthocyanin biosynthetic gene, UDP-glucose: flavonoid 3-O-glucosyltransferase (VviUFGT), was analyzed as a test case since its expression is restricted to cells producing anthocyanins in grape berry skins during ripening. The method identifies samples contaminated with significant levels of genomic DNA by amplifying a region of VviUFGT that spans an intron. Therefore false positives were discarded which occurred in 28% of the samples tested. Shallow probing of skin cells showed high VviUFGT expression as expected while deeper probing of mesocarp cells resulted in no VviUFGT expression.

Conclusions

The clear correspondence of VviUFGT expression to the targeted cell samples suggests that the in-situ gene expression analysis using a CPP is reliable and does not result in contamination as the probe moves through tissues. This method can be paired to single-cell transcriptomic analyses in the future. We conclude that this technique represents a minimally invasive method of sampling plant cells in-situ which creates an opportunity for the analysis of cellular level, spatiotemporal responses in heterogeneous plant tissues.
LncRNA MIR4435-2HG mediates cisplatin resistance in HCT116 cells by regulating Nrf2 and HO-1
Authors: Luo Ping , Wu ShuGui , Zhou ChaoMing , Yuan Xia , Li HongMi , Chen JinPing , Tian YunFei , Qiu Yang , Zhong XiaoMing
Published: September 2019

PURPOSE

Cisplatin resistance is still a serious problem in clinic. However, the underlying mechanism remains unclear. In this study investigated the drug resistance of cisplatin by the cisplatin resistance cell line HCT116R.

RESULTS

In this study, we found that LncRNA MIR4435-2HG level dramatically increased in the cisplatin resistance cell line HCT116R. Knockdown of MIR4435-2HG in HCR116R significantly restored the sensitivity to cisplatin, inhibited cell proliferation and promoted cell apoptosis. Furthermore, Nrf2 and HO-1 mRNA level, as the critical molecular of the oxidative stress pathway, was inhibited by the siRNA targeting to MIR4435-2HG, displaying MIR4435-2HG-mediated cisplatin resistance through the Nrf2/HO-1 pathway.

CONCLUSION

Our findings demonstrated that LncRNA MIR4435-2HG as a main factor could drive the cisplatin resistance of HCT116.
Prevalence of UGT1A1 Genetic Variants in Argentinean Population, Potential Implications for Pharmacogenomic Testing
Authors: Cruz Cintia V. , Scibona Paula , Belloso Waldo H.
Published: September 2019

The four groups of uridine diphosphate glucuronosyltransferase (UGT) enzymes form a superfamily responsible for the glucuronidation of target substrates. These include hormones, flavonoids, environmental mutagens and pharmaceutical drugs. Thus, UGT enzymes are relevant for pharmacogenetic research.

Most of the members of the UGT family are expressed in the liver, but are also present in intestinal, stomach or breast tissue.

The incidences and types of polymorphisms for different enzymes vary with geographical regions and ethnic groups. This is the first study that examined the frequency of polymorphisms for UGT1 isozymes for a population of 100 healthy argentinians.

The distribution of UGT1A1 in our population was: 70.5% (70.5) for the *1 allele, 21.5% for the *28 allele and 1% for the *36 allele. 48% (48) presented the *1/*1 genotype, while 43 % (43) had *1/*28, 2% (2) had *1/*36 and 7% (7) showed *28/*28. There was no preferential sex distribution.

Since most Argentinians are of Caucasian descent, a European genotype frequency profile is to be expected. That is evident in the wild type prevalence in our population. However, the contribution of Native American ancestry to gene pool components may in part explain the higher prevalence of the *28 genotype in UGT1A1 *1 in our population, in comparison with European cohorts.
Creating Artificial Human Genomes Using Generative Models
Authors: Yelmen Burak , Decelle Aurélien , Ongaro Linda , Marnetto Davide , Tallec Corentin , Montinaro Francesco , Furtlehner Cyril , Pagani Luca , Jay Flora
Published: September 2019

Generative models have shown breakthroughs in a wide spectrum of domains due to recent advancements in machine learning algorithms and increased computational power. Despite these impressive achievements, the ability of generative models to create realistic synthetic data is still under-exploited in genetics and absent from population genetics.

Yet a known limitation of this field is the reduced access to many genetic databases due to concerns about violations of individual privacy, although they would provide a rich resource for data mining and integration towards advancing genetic studies. In this study, we demonstrated that deep generative adversarial networks (GANs) and restricted Boltzmann machines (RBMs) can be trained to learn the high dimensional distributions of real genomic datasets and create high quality artificial genomes (AGs) with none to little privacy loss. To illustrate the promising outcomes of our method, we showed that (i) imputation quality for low frequency alleles can be improved by augmenting reference panels with AGs, (ii) scores obtained from selection tests on AGs and real genomes are highly correlated and (iii) AGs can inherit genotype-phenotype associations. AGs have the potential to become valuable assets in genetic studies by providing high quality anonymous substitutes for private databases.
Arabidopsis PAD4 lipase-like domain is a minimal functional unit in resistance to green peach aphid
Authors: Dongus Joram A. , Bhandari Deepak D. , Patel Monika , Archer Lani , Dijkgraaf Lucas , Deslandes Laurent , Shah Jyoti , Parker Jane E.
Published: September 2019

Plants have evolved mechanisms to attract beneficial microbes and insects while protecting themselves against pathogenic microbes and pests. In Arabidopsis, the immune regulator PAD4 functions with its cognate partner EDS1 to limit pathogen growth. PAD4, independently of EDS1, reduces infestation by Green Peach Aphid (GPA). How PAD4 regulates these defense outputs is unclear. By expressing the N-terminal PAD4-lipase-like domain (LLD) without its C-terminal ‘EDS1-PAD4’ (EP) domain, we interrogated PAD4 functions in plant defense. Here we show that transgenic expression of PAD4LLDin Arabidopsis is sufficient for limiting GPA infestation, but not for conferring basal and effector-triggered pathogen immunity. This suggests that the C-terminal PAD4-EP domain is necessary for EDS1-dependent immune functions. Moreover, PAD4LLDis not sufficient to interact with EDS1, indicating the PAD4-EP domain is required for heterodimerisation. These data provide molecular evidence that PAD4 has domain specific functions.
RNA-dependent RNA polymerase speed and fidelity are not the only determinants of the mechanism or efficiency of recombination
Authors: Kim Hyejeong , Ellis Victor D. , Woodman Andrew , Zhao Yan , Arnold Jamie J. , Cameron Craig E.
Published: September 2019

Using the RNA-dependent RNA polymerase (RdRp) from poliovirus (PV) as our model system, we have shown that Lys-359 in motif-D functions as a general acid in the mechanism of nucleotidyl transfer. A K359H (KH) RdRp derivative is slow and faithful relative to wild-type enzyme. In the context of the virus, RdRp-coding sequence evolves, selecting for the following substitutions: I331F (IF, motif-C) and P356S (PS, motif-D). We have evaluated IF-KH, PS-KH, and IF-PS-KH viruses and enzymes. The speed and fidelity of each double mutant are equivalent. Each exhibits a unique recombination phenotype, with IF-KH being competent for copy-choice recombination and PS-KH being competent for forced-copy-choice recombination. Although the IF-PS-KH RdRp exhibits biochemical properties within twofold of wild type, the virus is impaired substantially for recombination in cells. We conclude that there are biochemical properties of the RdRp in addition to speed and fidelity that determine the mechanism and efficiency of recombination. The interwoven nature of speed, fidelity, the undefined property suggested here, and recombination makes it impossible to attribute a single property of the RdRp to fitness. However, the derivatives described here may permit elucidation of the importance of recombination on the fitness of the viral population in a background of constant polymerase speed and fidelity.

Significance

The availability of a “universal” method to create attenuated viruses for use as vaccine strains would permit a rapid response to outbreaks of newly emerging viruses. Targeting RdRp fidelity has emerged as such a universal approach. However, because polymerase fidelity and speed are inextricably linked, the effort to attribute the attenuated phenotype to a single biochemical property of the RdRp may be futile. Here, we show that this circumstance is even more complex. We provide evidence for the existence of a biochemical parameter that combines with fidelity and speed to govern the mechanism and/or efficiency of recombination. We conclude that the field will be served best by continued emphasis on discovery of manipulatable functions of the RdRp instead of debating the importance of individual properties.
A cross-scale assessment of productivity-diversity relationships
Authors: Craven Dylan , van der Sande Masha T. , Meyer Carsten , Gerstner Katharina , Bennett Joanne M. , Giling Darren P. , Hines Jes , Phillips Helen R. P. , May Felix , Bannar-Martin Katherine H. , Chase Jonathan M. , Keil Petr
Published: September 2019

Aim

Biodiversity and ecosystem productivity vary across the globe and considerable effort has been made to describe their relationships. Biodiversity-ecosystem functioning research has traditionally focused on how experimentally controlled species richness affects net primary productivity (S→NPP) at small spatial grains. In contrast, the influence of productivity on richness (NPP→S) has been explored at many grains in naturally assembled communities. Mismatches in spatial scale between approaches have fostered debate about the strength and direction of biodiversity-productivity relationships. Here we examine the direction and strength of productivity’s influence on diversity (NPP→S) and of diversity’s influence on productivity (S→NPP), and how this varies across spatial grains.

Location

contiguous USA

Time period

1999 - 2015

Major taxa studied

woody species (angiosperms and gymnosperms)

Methods

Using data from North American forests at grains from local (672 m2) to coarse spatial units (median area = 35,677 km2), we assess relationships between diversity and productivity using structural equation and random forest models, while accounting for variation in climate, environmental heterogeneity, management, and forest age.

Results

We show that relationships between S and NPP strengthen with spatial grain. Within each grain, S→NPP and NPP→S have similar magnitudes, meaning that processes underlying S→NPP and NPP→S either operate simultaneously, or that one of them is real and the other is an artifact. At all spatial grains, S was one of the weakest predictors of forest productivity, which was largely driven by biomass, temperature, and forest management and age.

Main conclusions

We conclude that spatial grain mediates relationships between biodiversity and productivity in real-world ecosystems and that results supporting predictions from each approach (NPP→S and S→NPP) serve as an impetus for future studies testing underlying mechanisms. Productivity-diversity relationships emerge at multiple spatial grains, which should widen the focus of national and global policy and research to larger spatial grains.