bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genomic and transcriptomic evidence for descent from Plasmodium and loss of blood schizogony in Hepatocystis parasites from naturally infected red colobus monkeys
Authors: Aunin Eerik , Böhme Ulrike , Sanderson Theo , Simons Noah D , Goldberg Tony L , Ting Nelson , Chapman Colin A , Newbold Chris I , Berriman Matthew , Reid Adam J 
Published: December 2019

ABSTRACTHepatocystis is a genus of single-celled parasites infecting monkeys, bats and squirrels. Although thought to descend from malaria parasites (Plasmodium spp.), Hepatocystis spp. are thought not to undergo replication in the blood – the part of the Plasmodium life cycle which causes the symptoms of malaria. Furthermore, Hepatocystis is transmitted by midges, not mosquitoes. Comparative genomics of Hepatocystis and Plasmodium species therefore presents an opportunity to better understand some of the most important aspects of malaria parasite biology. We were able to generate a draft genome for Hepatocystis using DNA sequencing reads from the blood of a naturally infected red colobus monkey. We provide robust phylogenetic support for Hepatocystis as a sister group to Plasmodium parasites infecting rodents. We show transcriptomic support for a lack of replication in the blood and genomic support for a complete loss of a family of genes involved in red blood cell invasion. Our analyses highlight the rapid evolution of genes involved in parasite vector stages, revealing genes that may be critical for interactions between malaria parasites and mosquitoes.
Overexpression of Mig-6 in Limb Mesenchyme Leads to Accelerated Osteoarthritis in Mice
Authors: Bellini Melina Rodrigues , Pest Michael Andrew , Jeong Jae-Wook , Beier Frank 
Published: December 2019

ABSTRACTBackgroundMitogen-inducible gene 6 (Mig-6) is a tumour suppressor gene that is also associated with the development of osteoarthritis (OA)-like disorder. Recent evidence from our lab and others showed that cartilage-specific Mig-6 knockout (KO) mice develop chondro-osseous nodules, along with increased articular cartilage thickness and enhanced EGFR signaling in the articular cartilage. Here, we evaluate the phenotype of mice with skeletal-specific overexpression of Mig-6.MethodsSynovial joint tissues of the knee were assessed in 12 and 36 weeks-old skeleton-specificMig-6overexpressing (Mig-6over/over) and control animals using histological stains, immunohistochemistry, semi-quantitative OARSI scoring, and microCT for skeletal morphometry. Measurement of articular cartilage and subchondral bone thickness were also performed using histomorphometry.ResultsOur results show only subtle developmental effects of Mig-6 overexpression. However, maleMig-6over/overmice show accelerated cartilage degeneration at 36 weeks of age, in both medial and lateral compartments of the knee. Immunohistochemistry for SOX9 and PRG4 showed decreased staining inMig-6over/overmice relative to controls, providing potential molecular mechanisms for the observed effects.ConclusionOverexpression ofMig-6in articular cartilage causes no major developmental phenotype but results in accelerated development of OA during aging. These data demonstrate that precise regulation of the Mig-6/EGFR pathway is critical for joint homeostasis.
Optimizing an eDNA protocol for monitoring endangered Chinook Salmon in the San Francisco Estuary: balancing sensitivity, cost and time
Authors: Sanches Thiago M. , Schreier Andrea M. 
Published: December 2019

AbstractEnvironmental DNA (eDNA) analysis has gained traction as a precise and cost effective method for species and waterways management. To date, publications on eDNA protocol optimization have focused primarily on DNA yield. Therefore, it has not been possible to evaluate the cost and speed of specific components of the eDNA protocol, such as water filtration and DNA extraction method when designing or choosing an eDNA pipeline. At the same time, these two parameters are essential for the experimental design of a project. Here we evaluate and rank different eDNA protocols in the context of Chinook salmon (Oncorhynchus tshawytscha) eDNA detection in an aquatic environment, the San Francisco Estuary. We present a comprehensive evaluation of multiple eDNA protocol parameters, balancing time, cost and DNA yield. For estuarine waters, which are challenging for eDNA studies due to high turbidity, variable salinity, and the presence of PCR inhibitors, we find that a protocol combining glass filters and magnetic beads, along with an extra step for PCR inhibitor removal, is the method that best balances time, cost, and yield. In addition, we provide a generalized decision tree for determining the optimal eDNA protocol for other studies on aquatic systems. Our findings should be applicable to most aquatic environments and provide a clear guide for determining which eDNA pipeline should be used for a given environmental condition.Author SummaryThe use of environmental DNA (eDNA) analysis for monitoring wildlife has steadily grown in recent years. Though, due to differences in the ecology of the environment studied and the novelty of the technique, eDNA currently shows a lack of standards compared to other fields. Here we take a deep look into each step of an eDNA assay, looking at common protocols and comparing their efficiencies in terms of time to process the samples, cost and how much DNA is recovered. We then analyze the data to provide a concise interpretation of best practices given different project constraints. For the conditions of the San Francisco Estuary we suggest the use of glass fiber filtration, the use of paramagnetic beads for DNA extraction and the use of a secondary inhibitor removal. We expect our findings to provide better support for managers to decide their standards ahead of project submission not only for estuarine conditions but for other waterine conditions alike.
Laboratory testing of very low-copper-treated water to prolong pupation and emerging time of mosquito larvae: an alternative method to delay mosquito breeding capability
Authors: Reza Mohamad , Ilmiawati Cimi 
Published: December 2019

ABSTRACTIntroductionLarvicide application in ovitrap is one of the currently available methods used in mosquito eradication campaign because they eliminate the larval stage. We previously reported that copper in liquid form is a promising candidate due to its potent larvicide properties in a laboratory setting and even in the field. In the field study, several larvae survived in the ovitrap due to the dilution of copper concentration by the rain. The surviving larvae were smaller and less motile. This led our interest to study the effect of a sub-lethal dose of copper in ovitrap on larvae development, pupation time and lifespan in the adult stage.MethodsFirst instar larvae of three species of mosquito (Aedes albopictus, Culex pipiens and Anopheles stephensi) were bred in copper-treated water at a concentration of 0.60 ppm, 0.30 ppm, and 0.15 ppm and compared with the control group. The surviving larvae were recorded every day in terms of pupa emerging time and adult emerging time. The number of adult mortality was recorded and compared with the control.ResultsCopper showed potent larvicide effect in the 0.60 ppm concentration and prolonged pupation time and caused a significantly lower number of emerging mosquitoes down to the lowest concentration of 0.15 ppm. The adult lifespan was not different compared to the control.ConclusionThis study demonstrates the capability of copper below 1 ppm to prolong the pupation time and the emerging time of mosquito larvae. Our findings open the possibility of copper application to cut mosquito breeding capacity that eventually will reduce disease transmission.
Developing political-ecological theory: The need for Many-Task Computing
Authors: Haas Timothy C. 
Published: December 2019

AbstractModels of political-ecological systems can inform policies for managing ecosystems that contain endangered species. One way to increase the credibility of these models is to subject them to a rigorous suite of data-based statistical assessments. Doing so involves statistically estimating the model’s parameters, computing confidence intervals for these parameters, determining the model’s prediction error rate, and assessing its sensitivity to parameter misspecification.Here, these statistical algorithms along with a method for constructing politically feasible policies from a statistically fitted model, are coded as JavaSpaces™ programs that run as compute jobs on either supercomputers or a collection of in-house workstations. Several new algorithms for implementing such jobs in distributed computing environments are described.This downloadable code is used to compute each job’s output for the management challenge of conserving the East African cheetah (Acinonyx jubatus). This case study shows that the proposed suite of statistical tools can be run on a supercomputer to establish the credibility of a managerially-relevant model of a political-ecological system that contains one or more endangered species. This demonstration means that the new standard of credibility that any political-ecological model needs to meet before being used to inform ecosystem management decisions, is the one given herein.
Comparative proximity biotinylation implicates RAB18 in sterol mobilization and biosynthesis
Authors: Kiss Robert S. , Chicoine Jarred , Khalil Youssef , Sladek Robert , Chen He , Pisaturo Alessandro , Martin Cyril , Dale Jessica D. , Brudenell Tegan A. , Kamath Archith , Paci Emanuele , Kerksiek Anja , Lütjohann Dieter , Clayton Peter , Wills Jimi C. , von Kriegsheim Alex , Nilsson Tommy , Sheridan Eamonn , Handley Mark T. 
Published: December 2019

ABSTRACTLoss of functional RAB18 causes the autosomal recessive condition Warburg Micro syndrome. To better understand this disease, we used proximity biotinylation to generate an inventory of potential RAB18 effectors. A restricted set of 28 RAB18-interactions were dependent on the binary RAB3GAP1-RAB3GAP2 RAB18-guanine nucleotide exchange factor (GEF) complex. 12 of these 28 interactions are supported by prior reports and we have directly validated novel interactions with SEC22A, TMCO4 and INPP5B. Consistent with a role for RAB18 in regulating membrane contact sites (MCSs), interactors included groups of microtubule/membrane-remodelling proteins, membrane-tethering and docking proteins, and lipid-modifying/transporting proteins. Two of the putative interactors, EBP and OSBPL2/ORP2, have sterol substrates. EBP (emopamil binding protein) is a Δ8-Δ7 sterol isomerase and OSBPL2/ORP2 is a lipid transport protein. This prompted us to investigate a role for RAB18 in cholesterol biosynthesis. We find that the cholesterol precursor and EBP-product lathosterol accumulates in both RAB18-null HeLa cells and RAB3GAP1-null fibroblasts derived from an affected individual. Further,de novocholesterol biosynthesis is impaired in cells in which RAB18 is absent or dysregulated. Our data demonstrate that GEF-dependent Rab-interactions are highly amenable to interrogation by proximity biotinylation and may suggest that Micro syndrome is a cholesterol biosynthesis disorder.
Effective buprenorphine use and tapering strategies: Endorsements and insights by people in recovery from opioid use disorder on a Reddit forum
Authors: Graves Rachel L , Sarker Abeed , Al-Garadi Mohammed Ali , Yang Yuan-chi , Love Jennifer S , O’Connor Karen , Gonzalez-Hernandez Graciela , Perrone Jeanmarie 
Published: December 2019

AbstractOpioid use disorder (OUD) is a public health emergency in the United States. Over 47,000 overdose-related deaths in 2017 involved opioids. Medication-assisted treatment (MAT), in particular, buprenorphine and buprenorphine combination products such as Suboxone®, is the most effective, evidence-based treatment for OUD. However, there are a limited number of conclusive scientific studies that provide guidance to medical professionals about strategies for using buprenorphine to achieve stable recovery. In this study, we used data-driven natural language processing methods to mine a total of 16,146 posts about buprenorphine from 1933 unique users on the anonymous social network Reddit. Analysis of a sample of these posts showed that 74% of the posts described users’ personal experiences and that the top three topics included advice on using Suboxone® (55.0%), Suboxone® dosage information (35.5%) and information about Suboxone® tapering (32.0%). Based on two models, one that incorporated ‘upvoting’ by other members and one that did not, we found that Reddit users reported more successful recovery with longer tapering schedules, particularly from 2.0 mg to 0.0 mg (median: 93 days; mean: 95 days), as compared to shorter tapering schedules investigated in past clinical trials. Diarrhea, insomnia, restlessness, and fatigue were commonly reported adverse events. Physical exercise, clonidine, and Imodium® were frequently reported to help during the recovery process. Due to the difficulties of conducting longer-term clinical trials involving patients with OUD, clinicians should consider other information sources including peer discussions from the abundant, real-time information available on Reddit.Significance StatementOpioid use disorder (OUD) is a national crisis in the United States and buprenorphine is one of the most effective evidence-based treatments. However, few studies have explored successful strategies for using and tapering buprenorphine to achieve stable recovery, particularly due to the difficulties of conducting long-term studies involving patients with OUD. In this study, we show that discussions on the anonymous social network Reddit may be leveraged, via automatic text mining methods, to discover successful buprenorphine use and tapering strategies. We discovered that longer tapering schedules, compared to those investigated in past clinical trials, may lead to (self-reported) sustained recovery. Furthermore, Reddit posts also provide key information regarding buprenorphine withdrawal, cravings, adjunct medications for withdrawal symptoms and relapse prevention strategies.
eVIP2: Expression-based variant impact phenotyping to predict the function of gene variants
Authors: Thornton Alexis M. , Fang Lishan , O’Brien Casey , Berger Alice H. , Giannakis Marios , Brooks Angela N. 
Published: December 2019

AbstractWhile advancements in genome sequencing have identified millions of somatic mutations in cancer, their functional impact is poorly understood. We previously developed the expression-based variant impact phenotyping (eVIP) method to use gene expression data to characterize the function of gene variants. The eVIP method uses a decision tree-based algorithm to predict the functional impact of somatic variants by comparing gene expression signatures induced by introduction of wild-type versus mutant cDNAs in cell lines. The method distinguishes between variants that are gain-of-function, loss-of-function, change-of-function, or neutral. We present eVIP2, software that allows for pathway analysis (eVIP Pathways) and usage with RNA-seq data. To demonstrate the eVIP2 software and approach, we characterized two recurrent frameshift variants in RNF43, a negative regulator of Wnt signaling, frequently mutated in colorectal, gastric and endometrial cancer. RNF43 WT, RNF43 R117fs, RNF43 G659fs, or GFP control cDNA were overexpressed in HEK293T cells. Analysis with eVIP2 predicted that the frameshift at position 117 was a loss-of-function mutation, as expected. The second frameshift at position 659, was, surprisingly, predicted to be a gain-of-function mutation. Additional eVIP Pathways analysis of RNF43 G659fs predicted 10 pathways to be significantly altered, including TNF alpha via NFKB signaling, KRAS signaling, and hypoxia. To validate these predictions, we performed reporter assays and found that all eVIP2 impactful pathways tested in the assay were activated by expression of RNF43 G659fs, but not by expression of RNF43 WT, supporting that RNF43 G659fs is a gain-of-function mutation and its effect on the identified pathways. The eVIP2 method is an important step towards overcoming the current challenge of variant interpretation in the implementation of precision medicine. eVIP2 is available at https://github.com/BrooksLabUCSC/eVIP2.
A Higher Proportion of Craniosynostosis Genes Are Cancer Driver Genes
Authors: Misra Suchir , Shih Andrew , Yan Xiao-Jie , Li Wentian 
Published: December 2019

ABSTRACTCraniosynostosis (CRS) is a congenital abnormality deformity with a heterogenous genetic contribution. Previously, there are two attempts to collect genes that are genetically associated with craniosynostosis and some related syndromes with 57 (Twigg and Wilkie, 2015) and 39 (Goos and Mathijssen, 2019) genes identified, respectively. We expanded this list of craniosynostosis genes by adding another 17 genes with an updated literature search. These genes are shown to be more likely to be intolerant to functional mutations. Of these 113 craniosynostosis genes, 21 (19% vs. 1.5% baseline frequency) are cancer driver genes, a 14-fold enrichment. The cancer-craniosynostosis connection is further validated by an over-representation analysis of craniosynostosis genes in KEGG cancer pathway and several cancer related gene-sets. Many cancer-craniosynostosis overlapping genes participate in intracellular signaling pathways, which play a role in both development and cancer. This connection can be viewed from the oncogenesis recapitulates ontogenesis framework. Nineteen craniosynostosis genes are transcription factor genes (16.8% vs. 8.2% baseline), and craniosynostosis genes are also enriched in targets of certain transcription factors or micro RNAs.
Complex deletion and proximal reinsertion of a 150bp regulatory sequence in the mouse Csf1r promoter mediated by CRISPR-Cas9
Authors: Summers Kim M. , Pridans Clare , Wollscheid-Lengeling Evi , Grabert Kathleen , Adamson Antony , Humphreys Neil E. , Irvine Katharine M. , Hume David A. 
Published: December 2019

AbstractThis paper describes a deletion/reinsertion event encountered in a genome-editing project using CRISPR-Cas9. The objective was to delete a 150bp enhancer region in the mouse Csf1r locus using a pair of guides and a homology-dependent repair (HDR) template. The editing was successful in generating a founder pup with the anticipated precise deletion. However, the deleted fragment and a duplicated copy of part of the HDR template was reinserted around 50bp downstream. The reinsertion event was recognised because the PCR primer site used in genotyping was duplicated, so that there were three PCR products in a heterozygous animal and two in a homozygote. The event we describe is more subtle and more difficult to detect than large-scale rearrangements reported by others. We suggest that any genomic deletion mediated by CRISPR-Cas9 needs to be confirmed by assessing the copy number in the genome.
The C-terminal domain of Clostridioides difficile TcdC is exposed on the bacterial cell surface
Authors: Oliveira Paiva Ana M. , de Jong Leen , Friggen Annemieke H. , Smits Wiep Klaas , Corver Jeroen 
Published: December 2019

AbstractClostridioides difficile is an anaerobic gram-positive bacterium that can can produce the large clostridial toxins, Toxin A and Toxin B, encoded within the pathogenicity locus (PaLoc). The PaLoc also encodes the sigma factor TcdR, that positively regulates toxin gene expression, and TcdC, a putative negative regulator of toxin expression. TcdC is proposed to be an anti-sigma factor, however, several studies failed to show an association between tcdC genotype and toxin production. Consequently, TcdC function is not yet fully understood. Previous studies have characterized TcdC as a membrane-associated protein with the ability to bind G-quadruplex structures. The binding to the DNA secondary structures is mediated through the OB-fold domain present at the C-terminus of the protein. This domain was previously also proposed to be responsible for the inhibitory effect on toxin gene expression, implicating a cytoplasmic localization of the C-terminal OB-fold.In this study we aimed to obtain topological information on the C-terminus of TcdC. Using Scanning Cysteine Accessibility Mutagenesis and a HiBiT-based system, we demonstrate that the C-terminus of TcdC is located extracellularly. The extracellular location of TcdC is not compatible with direct binding of the OB-fold domain to intracellular nucleic acid or protein targets, and suggests a mechanism of action that is different from characterized anti-sigma factors.ImportanceTranscription of the C. difficile large clostrididial toxins (TcdA and TcdB) is directed by the sigma factor TcdR. TcdC has been implicated as a negative regulator, possible acting as an anti-sigma factor.Activity of TcdC has been mapped to its C-terminal OB fold domain. TcdC is anchored in the bacterial membrane, through its hydrophobic N-terminus and acting as an anti-sigma factor would require cytoplasmic localization of the C-terminal domain.Remarkably, topology predictions for TcdC suggest the N-terminus to be membrane localized and the C-terminal domain to be located extracellularly. Using independent assays, we show that the C-terminus of TcdC indeed is located in the extracellular environment, which is incompatible with its proposed role as anti-sigma factor in toxin regulation.
The Min system disassembles FtsZ foci and inhibits polar peptidoglycan remodeling inBacillus subtilis
Authors: Yu Yuanchen , Zhou Jinsheng , Dempwollf Felix , Baker Joshua D. , Kearns Daniel B. , Jacobson Stephen C. 
Published: December 2019

ABSTRACTA microfluidic system coupled with fluorescence microscopy is a powerful approach for quantitative analysis of bacterial growth. Here, we measure parameters of growth and dynamic localization of the cell division initiation protein FtsZ inBacillus subtilis. Consistent with previous reports, we find that after division FtsZ rings remain at the cell pole, and FtsZ ring disassembly coincides with rapid Z-ring accumulation at the midcell. In cells mutated forminD, however, the polar FtsZ rings persist indefinitely, suggesting that the primary function of the Min system is in Z-ring disassembly. The inability to recycle FtsZ monomers in theminDmutant results in maintenance of multiple Z-rings simultaneously, that are restricted by competition for newly synthesized FtsZ. Whereas the parameters of FtsZ dynamics change in theminDmutant, the overall cell cycle remains the same, albeit with elongated cells necessary to accumulate a threshold concentration of FtsZ for promoting medial division. Finally, theminDmutant characteristically produces minicells composed of polar peptidoglycan shown to be inert for remodeling in the wild type. Polar peptidoglycan, however, loses its inert character in theminDmutant suggesting that not only is the Min system important for recycling FtsZ but also may have a secondary role in the regulation of peptidoglycan remodeling.IMPORTANCEMany bacteria grow and divide by binary fission in which a mothercell divides into two identical daughter cells. To produce two equally sized daughters, the division machinery, guided by FtsZ, must dynamically localize to the midcell each cell cycle. Here, we quantitatively analyze FtsZ dynamics during growth and find that the Min system ofBacillus subtilisis essential to disassemble FtsZ rings after division. Moreover, a failure to efficiently recycle FtsZ results in an increase in cell size. Finally, we show that the Min system has an additional role in inhibiting cell wall turnover and contributes to the “inert” property of cell walls at the poles.