bluuebunny/crossref_metadata_2025 huggingface dataset:
Sequence of aCoxiellaendosymbiont of the tickAmblyomma nuttallisuggests a pattern of convergent genome reduction in theCoxiellagenus
Authors: Nardi Tiago , Olivieri Emanuela , Kariuki Edward , Sassera Davide , Castelli Michele
Published: July 2020

Ticks require bacterial symbionts for the provision of necessary compounds that are absent in their hematophagous diet. Such symbionts are frequently vertically transmitted and, most commonly, belong to theCoxiellagenus, which also includes the human pathogenCoxiella burnetii. This genus can be divided in four main clades, presenting partial but incomplete co-cladogenesis with the tick hosts. Here we report the genome sequence of a novelCoxiella, endosymbiont of the African tickAmblyomma nuttalli, and the ensuing comparative analyses. Its size (∼1 Mb) is intermediate between symbionts ofRhipicephalusspecies and otherAmblyommaspecies. Phylogenetic analyses show that the novel sequence is the first genome of the B clade, the only one for which no genomes were previously available. Accordingly, it allows to draw an enhanced scenario of the evolution of the genus, one of parallel genome reduction of different endosymbiont lineages, which are now at different stages of reduction from a more versatile ancestor. Gene content comparison allows to infer that the ancestor could be reminiscent ofCoxiella burnetii. Interestingly, the convergent loss of mismatch repair could have been a major driver of such reductive evolution. Predicted metabolic profiles are rather homogenous amongCoxiellaendosymbionts, in particular vitamin biosynthesis, consistently with a host-supportive role. Concurrently, similarities amongCoxiellaendosymbionts according to host genus and despite phylogenetic unrelatedness hint at possible host-dependent effects.

Significance statement

The genusCoxiellaincludes the pathogenCoxiella burnetiiand widespread nutritional mutualists in ticks. Current knowledge on their evolution is hampered by the limited genomic resources available.

Here we provide the first genome sequence of aCoxiellaendosymbiont of clade B, the only clade for which none was available.

These data allow to infer an evolutionary scenario of parallel genome reduction amongCoxiellaendosymbionts, with similar constraints, leading to selective retention of biosynthetic pathways beneficial for the host. The combined predicted functional capabilities of the symbionts appear to be a subset of those ofC. burnetii. Accordingly, this pathogen could be closer to an ancestral state of the endosymbionts, rather than being derived from an endosymbiotic ancestor, as previously hypothesized.
Echis carinatussnake venom metalloprotease-induced toxicities in mice: therapeutic intervention by a repurposed drug, tetraethylthiuram disulfide (disulfiram)
Authors: Rudresha Gotravalli V. , Urs Amog P. , Manjuprasanna Vaddarahally N. , Milan Gowda Mallanayakanakatte D. , Jayachandra Krishnegowda , Rajaiah Rajesh , Vishwanath Bannikuppe S.
Published: July 2020

Echis carinatus(EC) is known as saw-scaled viper and it is endemic to the Indian subcontinent. Envenoming by EC represents a major cause of snakebite mortality and morbidity in the Indian subcontinent. Zinc (Zn++)-dependent snake venom metalloproteases (SVMPs) present inEchis carinatusvenom is well known to cause systemic hemorrhage and coagulopathy in experimental animals. An earlier report has shown that ECV activates neutrophils and releases neutrophil extracellular traps (NETs) that blocks blood vessels leading to severe tissue necrosis. However, the direct involvement of SVMPs in the release of NETs is not clear. Here, we investigated the direct involvement of EC SVMPs in observed pathological symptoms in a preclinical setup using zinc (Zn++) metal chelator, Tetraethylthiuram disulfide (TTD)/disulfiram. TTD potently antagonizes the activity of SVMPs-mediated ECM protein degradation in vitro and skin hemorrhage in mice. In addition, TTD protected mice from ECV-induced footpad tissue necrosis by reduced expression of citrullinated H3 (citH3) and myeloperoxidase (MPO) in footpad tissue. TTD also neutralized ECV-induced systemic hemorrhage and conferred protection against lethality in mice. Moreover, TTD inhibited ECV-induced NETosis in human neutrophils and decreased the expression of peptidylarginine deiminase (PAD) 4, citH3, MPO and pERK. Further, we demonstrated that ECV-induced NETosis and tissue necrosis is mediated via PAR-1-ERK axis. Overall, our results provide an insight into SVMPs-induced toxicities and the promising protective efficacy of TTD can be extrapolated to treat severe tissue necrosis complementing ASV.
Leptospiraspp. seroprevalence in humans involved in a cross-sectional study in Garissa and Tana River Counties, Kenya
Authors: Mutembei Arithi , Mutai Festus K. , Mwololo Damaris , Muriuki John , Obonyo Mark , Kairu-Wanyoike S.W. , Wainaina M. , Lindahl J. , Ontiri E. , Bukachi S. , Njeru I. , Karanja J. , sang R. , Grace D. , Bett B.
Published: July 2020

Introduction

Leptospirosis is a neglected bacterial zoonotic infection caused by spirochetes ofLeptospira genus.Humans get infected through direct or indirect contact with urine of infected animals or environment. It accounts for more than 300,000 severe cases annually worldwide with case fatality rates of over 30%. Costs of diagnosis and treatment for human and animals, disruption of international trade of animals and products, reduced productivity and reproductivity in animals constitute economic importance. In Kenya, leptospirosis burden is significant but under-diagnosis and under-reporting affects the awareness of the disease. This study aimed to determine and compare the sero-prevalence and factors associated withLeptospiraspp. in the two counties.

Methods

We conducted a cross-sectional study that involved apparently healthy people of at least 5 years of age in randomly selected households in Garissa and Tana River Counties. Blood samples were collected and tested forLeptospiraspp antibodies using IgM ELISA. Standardized structured questionnaires were administered to collect socio-demographic and exposure information. We calculated frequencies and proportions for categorical variables and odds ratios (OR) and 95% confidence interval (CI) to evaluate association between sero-positivity and exposure factors. We used Wilcoxon test to evaluate statistical difference in sero-positivity for continuous variables and calculated test statistic (H) and p-value.

Results

A total of 952 subjects were recruited into the study – these included 482 persons from Garissa and 470 from Tana River. The overall sero-prevalence was 26% [(244/952); (CI: 23% to 29%)]. Garissa County had significantly higherLeptospiraspp. seroprevalence (31%, n = 147; CI: 27% to 35%) compared to Tana River County (21 %, n = 97; CI: 17% to 25%). Being a female (OR=1.6, CI: 1.2-2.2) and engaging in pastoralism (OR=2.7, CI: 1.8-3.9) were significantly associated with higher odds ofLeptospiraspp. seropositivity compared to being a male or working in irrigated areas. The mean altitude of residence of sero-positive patients was 73m ± 21 SD (standard deviation) above sea level and that for sero-negative was 80m ± 22 SD (H=35, p-value = 0.00).

Conclusion

This study determined the seroprevalence and risk factors forLeptospiraspp. exposure in Garissa and Tana River Counties, Kenya. Females in pastoral communities experience high burden of the disease. Enhanced surveillance in humans and animals and further research is required to understand the complex and multifactorial drivers of leptospirosis transmission in the two Counties.
Modeling the Impact of Lock-down on COVID-19 Spread in Malaysia
Authors: Altahir Altahir A. , Mathur Nirbhay , Thiruchelvam Loshini , Mustafa Abro Ghulam E. , Radzi Syaimaa’ S. M. , Dass Sarat C. , Gill Balvinder Singh , Sebastian P. , Zulkifli Saiful A.M. , Asirvadam Vijanth S.
Published: July 2020

After a breakdown notified in Wuhan, China in December 2019, COVID-19 is declared as pandemic diseases. To the date more than 13 million confirmed cases and more than half a million are dead around the world. This virus also attached Malaysia in its immature stage where 8718 cases were confirmed and 122 were declared as death. Malaysia responsibly controlled the spread by enforcing MCO. Hence, it is required to visualize the pattern of Covid-19 spread. Also, it is necessary to estimate the impact of the enforced prevention measures. In this paper, an infectious disease dynamic modeling (SEIR) is used to estimate the epidemic spread in Malaysia. The main assumption is to update the reproduction number Rt with respect to the implemented prevention measures. For a time-frame of five month, the Rt was assumed to vary between 2.9 and 0.3. Moreover, the manuscript includes two possible scenarios: the first will be the extension of the stricter measures all over the country, and the second will be the gradual lift of the lock-down. After implementing several stages of lock-down we have found that the estimated values of theRtwith respect to the strictness degree varies between 0.2 to 1.1. A continuous strict lock-down may reduce theRtto 0.2 and accordingly the estimated active cases will be reduced to 20 by the beginning of September 2020. In contrast, the second scenario considers a gradual lift of the enforced prevention measures by the end of June 2020, here we have considered three possible outcomes according to the MCO relaxation. Thus, the estimated values ofRt= 0.7, 0.9, 1.1, which shows a rapid increase in the number of active cases. The implemented SEIR model shows a close resemblance with the actual data recorded from 10, March till 7, July 2020.

Author summary

Conceptualization, A.A.A; methodology, A.A.A, N.M; validation, A.A.A, N.M; formal analysis, A.A.A; investigation, N.M, A.A.A; resources, G.E.M.A, L.T; data collection, L.T, N.M; writing—original draft preparation, A.A.A, L.T, G.E.M.A, N.M; writing—review and editing, V.S.A, S.C.D, B.S.G, P.S, S.A.B.M.Z, N.M; visualization, N.M; supervision, V.S.A; project administration, V.S.A. All authors have read and agreed to the published version of the manuscript
Integrated aqueous humor ceRNA and miRNA-TF-mRNA network analysis reveals potential molecular mechanisms governing primary open-angle glaucoma pathogenesis
Authors: Wang Xiaoqin , Chen Ming , Zeng Liuzhi , Liu Longqian
Published: July 2020

Primary open-angle glaucoma (POAG) is the leading cause of blindness globally, which develops through complex and poorly understood biological mechanisms. Herein, we conducted an integrated bioinformatics analysis of extant aqueous humor (AH) gene expression datasets in order to identify key genes and regulatory mechanisms governing POAG progression. We downloaded AH gene expression datasets (GSE101727 and GSE105269) corresponding to healthy controls and POAG patients from the Gene Expression Omnibus. We then identified mRNAs, microRNAs (miRNAs), and long non-coding RNAs (lncRNAs) that were differentially expressed (DE) between control and POAG patients. DEmRNAs and DElncRNAs were then subjected to pathway enrichment analyses, after which a protein-protein interaction (PPI) network was generated. This network was then expanded to establish lncRNA-miRNA-mRNA and miRNA-transcription factor(TF)-mRNA networks. In total, the GSE101727 dataset was used to identify 2746 DElncRNAs and 2208 DEmRNAs, while the GSE105269 dataset was used to identify 45 DEmiRNAs. We ultimately constructed a competing endogenous RNA (ceRNA) network incorporating 37, 5, and 14 of these lncRNAs, miRNAs and mRNAs, respectively. The proteins encoded by these 14 hub mRNAs were found to be significantly enriched for activities that may be linked to POAG pathogenesis. In addition, we generated a miRNA-TF-mRNA regulatory network containing 2 miRNAs (miR-135a-5p and miR-139-5p), 5 TFs (TGIF2, TBX5, HNF1A, TCF3, and FOS) and 5 mRNAs (SHISA7, ST6GAC2, TXNIP, FOS, and DCBLD2). The SHISA7, ST6GAC2, TXNIP, FOS, and DCBLD2 genes that may be viable therapeutic targets for the prevention or treatment of POAG, and regulated by the TFs (TGIF2, HNF1A, TCF3, and FOS).
Diversified agroforestry systems improve carbon foot printand farmer’s livelihood under limited irrigation conditions
Authors: Rathore Sanjay Singh , Shekhawat Kapila , Singh VK , Babu Subhash , Singh RK , Upadhyay PK , Bhattacharyya Ranjan
Published: July 2020

Increasing weather aberrations cause frequent crop failure in monoculture cropping system. Specialized crop production systems, where few seasonal crops occupy vast arable lands, resulting in more biotic and abiotic stresses in agri-ecosystem. Therefore a diversified agroforestry systemwas evaluated to ensure resilience underlimited water conditions, with an aim to augment carbon footprint with enhanced productivity and profitability. The study hypothesised that integration of perennial fruits trees with seasonal crops will have benign effect for sequestering more carbon and improving livelihood of the farmers. This is one of the first timesthat arid fruits tress along with leguminous,and other low water requiring crops were studied for improved carbon sequestration, livelihood of the farmers andfor better resilience in production system. The experimental findings showed that arid fruit trees along with leguminous, oilseeds and cash crops resulted in higher profitability and thus improved livelihood of the farmersin arid and semi-arid areas of South Asia. Diversified phalsa-mung bean-potato and moringa-mung bean-potato were the most productive agroforestry system (36.7t/ha and 36.2 t/ha respectively. Under limited irrigation conditions, Karonda (Carisa spp.)-mung bean potato system was found best in improving livelihood with maximum net return of $ 3529.1/ha with higher profitability/day ($ 19.9/day). Phalsa -MB-potato system was also recorded maximum water use efficiency (33.0 kg/ha-mm), whereas density of SOC was in Phalsa-cowpea-mustard (9.10 Mg/ha) andmoringa-mung bean -potato AFS (9.16 Mg/ha). Carbon footprint analysis revealed that maximum net C gain was in Phalsa-mung bean -potato system (7030 Carbon equivalent kg CE/ha/year).
Coffee consumption and risk of breast cancer: a Mendelian Randomization study
Authors: Ellingjord-Dale Merete , Papadimitriou Nikos , Katsoulis Michalis , Yee Chew , Dimou Niki , Gill Dipender , Aune Dagfinn , Ong Jue-Sheng , MacGregor Stuart , Elsworth Benjamin , Lewis Sarah J , Martin Richard M , Riboli Elio , Tsilidis Konstantinos K
Published: July 2020

Background

Observational studies have reported either null or weak protective associations for coffee consumption and risk of breast cancer.

Methods

We conducted a two-sample Mendelian randomization randomization (MR) analysis to evaluate the relationship between coffee consumption and breast cancer risk using 33 single-nucleotide polymorphisms (SNPs) associated with coffee consumption from a genome-wide association (GWA) study on 212,119 female UK Biobank participants of White British ancestry. Risk estimates for breast cancer were retrieved from publicly available GWA summary statistics from the Breast Cancer Association Consortium (BCAC) on 122,977 cases (of which 69,501 were estrogen receptor (ER)-positive, 21,468 ER-negative) and 105,974 controls of European ancestry. Random-effects inverse variance weighted (IVW) MR analyses were performed along with several sensitivity analyses to assess the impact of potential MR assumption violations.

Results

One cup per day increase in genetically predicted coffee consumption in women was not associated with risk of total (IVW random-effects; odds ratio (OR): 0.91, 95% confidence intervals (CI): 0.80-1.02, P: 0.12, P for instrument heterogeneity: 7.17e-13), ER-positive (OR=0.90, 95% CI: 0.79-1.02, P: 0.09) and ER-negative breast cancer (OR: 0.88, 95% CI: 0.75-1.03, P: 0.12). Null associations were also found in the sensitivity analyses using MR-Egger (total breast cancer; OR: 1.00, 95% CI: 0.80-1.25), weighted median (OR: 0.97, 95% CI: 0.89-1.05) and weighted mode (OR: 1.00, CI: 0.93-1.07).

Conclusions

The results of this large MR study do not support an association of genetically predicted coffee consumption on breast cancer risk, but we cannot rule out existence of a weak inverse association.
SARS-CoV-2 RNA shedding in recovered COVID-19 cases and the presence of antibodies against SARS-CoV-2 in recovered COVID-19 cases and close contacts
Authors: Chirathaworn Chintana , Sripramote Manit , Chalongviriyalert Piti , Jirajariyavej Supunee , Kiatpanabhikul Phatharaporn , Saiyarin Jatuporn , Soudon Chulikorn , Thienfaidee Orawan , Na Ayuthaya Thitisan Palakawong , Brukesawan Chantapat , Chaiwanichsiri Dootchai , Intharasongkroh Duangnapa , Wanlapakorn Nasamon , Chansaenroj Jira , Puenpa Jiratchaya , Yorsaeng Ritthideach , Thitithanyanont Arunee , Kitphati Rungrueng , Mungaomklang Anek , Nagavajara Pijaya , Poovorawan Yong
Published: July 2020

Coronavirus disease 2019 (COVID-19) is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). COVID-19 emerged in December 2019 and has spread globally. Although Thailand has been effective at controlling the spread of COVID-19, disease surveillance and information on antibody responses in infected cases and close contacts are needed because there is still no specific treatment or vaccine available. We investigated 217 recovered COVID-19 cases to monitor their viral RNA shedding and production of antibodies against SARS-CoV-2. The presence of antibodies in blood samples from 308 close contacts of COVID-19 cases was also determined. Viral RNA was still detectable in 6.6 % of recovered COVID-19 cases. The most prolonged duration of viral RNA shedding detected in this study was 105 days. IgM, IgG, and IgA antibodies against SARS-CoV-2 were detected in 13.82, 88.48, and 83.41 % of the recovered cases 4–12 weeks after disease onset, respectively. Although the patients had recovered from their illness, the levels of antibodies detected showed association with their symptoms during their stay in hospital. Fifteen of the 308 contacts (4.87 %) of COVID-19 cases tested positive for IgG antibodies. The presence of antibodies against SARS-CoV-2 suggested that there was viral exposure among close contacts. Viral clearance and the pattern of antibody responses in infected individuals are both crucial for effectively combatting SARS-CoV-2. Our study provides additional information on the natural history of this newly emerging disease related to both natural host defenses and a strategy for vaccine development.
CXCR5gene expression in human lymph node CD8+T cells is regulated by DNA methylation and nucleosomal occupancy
Authors: Ogunshola Funsho J. , Smidt Werner , Naidoo Anneta F. , Nkosi Thandeka , Ngubane Thandekile , Khaba Trevor , Baiyegunhi Omolara O. , Rasehlo Sam , Jajbhay Ismail , Dong Krista L. , Ramsuran Veron , Pansegrouw Johan , Ndung’u Thumbi , Walker Bruce D. , de Oliveria Tulio , Ndhlovu Zaza M.
Published: July 2020

CD8+T cells play an important role in viral and tumour control. However, in human lymph nodes (LNs), only a small subset of CD8+T cells called follicular CD8+T cells (fCD8s) expresses CXCR5, the chemokine receptor required for cell migration into B cell follicles, thought to promote immune evasion. Here we obtained LNs from HIV infected persons to investigate regulation of CXCR5 expression in lymphoid CD8+T cells, and compared this to the more abundant CXCR5 expressing T follicular CD4+helper cells (GCTfh). Our results show that DNA hypermethylation and closed chromatin at the transcriptional start site (TSS) prevent CXCR5 expression in non-fCD8s. We also found that greater nucleosomal density at the CXCR5 TSS could be responsible for reduced CXCR5 expression in fCD8s relative to GCTfh. Together, these data provide critical insights into both the underlying molecular mechanisms that repress CXCR5 expression in non-fCD8s and the plausible mechanism responsible for the low CXCR5 expression in fCD8s, with implications for HIV cure strategies.

Author Summary

A paucity of CD8+T cells that express CXCR5, the chemokine receptor critical for entering the B cell follicles of secondary lymphoid tissues have recently been described. Animal studies have revealed transcriptional networks that govern the expression of CXCR5 in CD8+T cells. However, it is not known if similar or additional networks regulate the expression of CXCR5 in human CD8+T cells. In this study, we demonstrated that DNA methylation coupled with chromatin compaction at the transcriptional start site (TSS) ofCXCR5gene prevent the expression CXCR5 in human CD8+T cells. In addition, we observed greater nucleosomal occupancy at the TSS ofCXCR5gene which could impact expression levels of CXCR5 in human CXCR5+CD8+T cells. This study revealed multitiered epigenetic mechanisms that repress CXCR5 expression in human CD8+T cells, with implications for HIV cure strategy or eradication of B cell-derived tumours.
Phosphatidylinositol-3 kinase activity controls survival and stemness of zebrafish hematopoietic stem/progenitor cells
Authors: Blokzijl-Franke Sasja , Ponsioen Bas , Schulte-Merker Stefan , Herbomel Philippe , Kissa Karima , Choorapoikayil Suma , den Hertog Jeroen
Published: July 2020

Hematopoietic Stem and Progenitor Cells (HSPCs) are multipotent cells giving rise to all blood lineages during life. HSPCs emerge from the ventral wall of the dorsal aorta (VDA) during a specific timespan in embryonic development through endothelial hematopoietic transition (EHT). We investigated the ontogeny of HSPCs in mutant zebrafish embryos lacking functional pten, an important tumor suppressor with a central role in cell signaling. Through in vivo live imaging, we discovered that inptenmutant embryos a proportion of the HSPCs died upon emergence from the VDA, an effect rescued by inhibition of phosphatidylinositol-3 kinase (PI3K). Surprisingly, inhibition of PI3K in wild type embryos also induced HSPC death. Surviving HSPCs colonized the caudal hematopoietic tissue (CHT) normally and committed to all blood lineages. Single cell RNA sequencing indicated that inhibition of PI3K enhanced survival of multi-potent progenitors, whereas the number of HSPCs with more stem-like properties was reduced. At the end of the definitive wave, loss of Pten caused a shift to more restricted progenitors at the expense of HSPCs. We conclude that PI3K signaling tightly controls HSPCs survival and both up- and downregulation of PI3K signaling reduces stemness of HSPCs.

2

Key points

Loss of Pten and inhibition of PI3K induced apoptosis of hematopoietic stem/progenitor cells upon endothelial to hematopoietic transition

Surviving hematopoietic stem/progenitor cells committed to all blood lineages but displayed reduced stemness
The mechanism of selective kinesin inhibition by kinesin binding protein
Authors: Atherton Joseph , Hummel Jessica J. A. , Olieric Natacha , Locke Julia , Peña Alejandro , Rosenfeld Steven S. , Steinmetz Michel O. , Hoogenraad Casper C. , Moores Carolyn A.
Published: July 2020

Subcellular compartmentalisation is necessary for eukaryotic cell function. Spatial and temporal regulation of kinesin activity is essential for building these local environments via control of intracellular cargo distribution. Kinesin binding protein (KBP) interacts with a subset of kinesins via their motor domains, inhibits their microtubule (MT) attachment and blocks their cellular function. However, its mechanisms of inhibition and selectivity have been unclear. Here we use cryo-electron microscopy to reveal the structure of KBP and of a KBP-kinesin motor domain complex. KBP is a TPR-containing, crescent-shaped right-handed α-solenoid that sequesters the tubulin-binding surface of the kinesin motor domain, structurally distorting the motor domain and sterically blocking MT attachment. KBP uses its α-solenoid concave face and edge loops to bind the kinesin motor domain and selective mutation of this extended binding surface disrupts KBP inhibition of kinesin transport in cells. The KBP-interacting surface of the motor domain contains motifs exclusively conserved in KBP-interacting kinesins, providing a basis for kinesin selectivity.
DEXOM: Diversity-based enumeration of optimal context-specific metabolic networks
Authors: Rodríguez-Mier Pablo , Poupin Nathalie , de Blasio Carlo , Le Cam Laurent , Jourdan Fabien
Published: July 2020

The correct identification of metabolic activity in tissues or cells under different environmental or genetic conditions can be extremely elusive due to mechanisms such as post-transcriptional modification of enzymes or different rates in protein degradation, making difficult to perform predictions on the basis of gene expression alone. Context-specific metabolic network reconstruction can overcome these limitations by leveraging the integration of multi-omics data into genome-scale metabolic networks (GSMN). Using the experimental information, context-specific models are reconstructed by extracting from the GSMN the sub-network most consistent with the data, subject to biochemical constraints. One advantage is that these context-specific models have more predictive power since they are tailored to the specific organism and condition, containing only the reactions predicted to be active in such context. A major limitation of this approach is that the available information does not generally allow for an unambiguous characterization of the corresponding optimal metabolic sub-network, i.e., there are usually many different sub-network that optimally fit the experimental data. This set of optimal networks represent alternative explanations of the possible metabolic state. Ignoring the set of possible solutions reduces the ability to obtain relevant information about the metabolism and may bias the interpretation of the true metabolic state. In this work, we formalize the problem of enumeration of optimal metabolic networks, we implement a set of techniques that can be used to enumerate optimal networks, and we introduceDEXOM, a novel strategy for diversity-based extraction of optimal metabolic networks. Instead of enumerating the whole space of optimal metabolic networks, which can be computationally intractable,DEXOMsamples solutions from the set of optimal metabolic sub-networks maximizing diversity in order to obtain a good representation of the possible metabolic state. We evaluate the solution diversity of the different techniques using simulated and real datasets, and we show how this method can be used to improve in-silico gene essentiality predictions inSaccharomyces Cerevisiaeusing diversity-based metabolic network ensembles. Both the code and the data used for this research are publicly available on GitHub1.
H3.1K27me1 maintains transcriptional silencing and genome stability by preventing GCN5-mediated histone acetylation
Authors: Dong Jie , LeBlanc Chantal , Poulet Axel , Mermaz Benoit , Villarino Gonzalo , Webb Kimberly M. , Joly Valentin , Mendez Josefina , Voigt Philipp , Jacob Yannick
Published: July 2020

In plants, genome stability is maintained during DNA replication by the H3.1K27 methyltransferases ATXR5 and ATXR6, which catalyze the deposition of K27me1 on replicationdependent H3.1 variants. Loss of H3.1K27me1 inatxr5 atxr6double mutants leads to heterochromatin defects, including transcriptional de-repression and genomic instability, but the molecular mechanisms involved remain largely unknown. In this study, we identified the conserved histone acetyltransferase GCN5 as a mediator of transcriptional de-repression and genomic instability in the absence of H3.1K27me1. GCN5 is part of a SAGA-like complex in plants that requires ADA2b and CHR6 to mediate the heterochromatic defects ofatxr5 atxr6mutants. Our results show that Arabidopsis GCN5 acetylates multiple lysine residues on H3.1 variantsin vitro,but that H3.1K27 and H3.1K36 play key roles in inducing genomic instability in the absence of H3.1K27me1. Overall, this work reveals a key molecular role for H3.1K27me1 in maintaining genome stability by restricting histone acetylation in plants.
Characterization of a membrane enzymatic complex for heterologous production of poly-γ-glutamate inE. coli
Authors: Nascimento Bruno Motta , Nair Nikhil U.
Published: July 2020

Poly-γ-glutamic acid (PGA) produced by manyBacillusspecies is a polymer with many distinct and desirable characteristics. However, the multi-subunit enzymatic complex responsible for its synthesis, PGA Synthetase (PGS), has not been well characterized yet, in native nor in recombinant contexts. Elucidating structural and functional properties are crucial for future engineering efforts aimed at altering the catalytic properties of this enzyme. This study focuses on expressing the enzyme heterologously in theEscherichia colimembrane and characterizing localization, orientation, and activity of this heterooligomeric enzyme complex. InE. coli, we were able to produce high molecular weight PGA polymers with minimal degradation at titers of approximately 13 mg/L in deep-well microtiter batch cultures. Using fusion proteins, we observed, for the first time, the association and orientation of the different subunits with the inner cell membrane. These results elucidate provide fundamental structural information on this poorly studied enzyme complex and will aid future fundamental studies and engineering efforts.

HIGHLIGHTS

Successfully expressed active poly-γ-glutamate synthetase (PGS) inE. coli.

Confirmed PGS localization at inner membrane ofE. coli.

Elucidated topology of PGS components inE. colimembrane.

Culture and expression in microplates might allow future screening of a high number of samples.

Faster production of poly-γ-glutamate inE. colisupernatant compared toB. subtilis.
Biological and molecular characterization of six Shiga toxin-producingEscherichia coli(STEC) strains encoding the stx2gene in Colombia
Authors: Arango-Gil Brayan Stiven , Peña-Buitrago Sebastián , Castaño-Osorio Jhon Carlos , Granobles-Velandia Claudia Viviana
Published: July 2020

Shiga toxin-producingEscherichia coli(STEC) is a bacterial pathogen that cause diarrhea and severe human diseases. Its principal virulence factor are the Shiga toxins Stx1 and Stx2 which have been identified diverse subtypes considered to be responsible for severe complications of STEC infection. These toxins are encoded in temperate bacteriophages and their expression is linked to phage lithic cycle, which is regulated by late genes and the Q anti-terminator protein. The aim of this study was to characterize biologically and molecularly STEC strains encoding stx2gene isolated from cattle feces in Colombia. We selected six STEC strains, which were evaluated its Stx production, the Stx2subtypes, induction of the lithic cycle of bacteriophages and its late region. The results evidenced two highlighted strains with high levels of Stx production and induction of the lithic cycle, compared with the others. Likewise, the strains evaluated showed three Stx2subtypes: Stx2a, Stx2c, and Stx2d. Regarding the late region, most of the strains carried theqO111allele and only one strain showed differences in theninGgene. Although the sample was limited, variability was observed in the Stx production assay, induction of the lithic cycle, Stx2subtypes and late region of the phages, which could indicate the diversity of the phages carrying STEC strains in Colombia.
Resveratrol shortens the chronological lifespan ofSaccharomyces cerevisiaeby a pro-oxidant mechanism
Authors: Canedo-Santos Juan Carlos , Mora-Martinez Iridian , Gutierrez-Garcia Ingrid Karina , Ramirez-Romero Maria Guadalupe , Madrigal-Perez Luis Alberto
Published: July 2020

Resveratrol consumption has linked with normalization of the risk factors of some diseases such as colon cancer and type 2 diabetes. The antioxidant phenotype caused by resveratrol has recognized as a key piece in the health benefits exerted by this phytochemical. Although the antioxidant activity showed by resveratrol has attributed at the moleculeper se, recent evidence indicates that the antioxidant effect occasioned by resveratrol could be associated with a pro-oxidant mechanism. The hypothesis that resveratrol inhibits complex III of the electron transport chain as its main target suggests that resveratrol increases reactive oxygen species (ROS) generation produces via reverse electron transport. This idea also explains that cells respond to the oxidative damage caused by resveratrol, inducing their antioxidant systems. The free radical theory of aging postulates that organisms age due to the accumulation of the harmful effects of ROS in cells. For these reasons, we hypothesize that resveratrol shortens the chronological life span (CLS) ofSaccharomyces cerevisiaedue to a pro-oxidant activity. Herein, we provide evidence that 100 μM resveratrol supplementation at 5% glucose: 1) shorted the CLS ofCTT1andYAP1genes deleted strains; 2) decreased the H2O2release in the WT strain, and maintain unaltered the H2O2release in thectt1Δ strain; 3) lessened exponential growth ofctt1Δ strain, which was reverted with the adding of GSH; 4) increased catalase activity in the WT strain, a phenotype that was not observed in thectt1Δ strain. Altogether, these results indicate that resveratrol decreases CLS by a pro-oxidant mechanism.
Rapid tolerance to morphine in the myenteric neurons of the small intestine is independent of β-arrestin-2 and mediated by PKC
Authors: Muchhala Karan H. , Jacob Joanna C. , Alam Imran , Hasan Shahzeb , Khan Aliyeen , Kang Minho , Dewey William L. , Akbarali Hamid I.
Published: July 2020

Background and Purpose

G-protein biased μ-opioid agonists against β-arrestin-2 activation are being investigated to reduce adverse effects. While opioid tolerance is strongly linked to the development of dependence, there is a dissociation between the two phenomena in the gut as tolerance does not develop to opioid-induced constipation, but diarrhea still manifests upon withdrawal. Here, we investigated the mechanism by which morphine tolerance in the small intestine develops.

Experimental Approach

Mechanism of morphine tolerance in the small intestine was evaluatedin vivoand at the neuronal level. Whole-cell patch clamp electrophysiology was used to investigate tolerance in individual ileum myenteric neurons. Rate of morphine tolerance development in the small intestine was assessed against peripheral antinociception and whole gut transit.

Key Results

Tolerance develops to inhibition of small intestinal motility after one day of morphine exposure, and is more rapid compared to peripheral antinociception and constipation in chronic morphine-treated mice. Morphine tolerance was reversed by the PKC inhibitor, Tamoxifen, but not by β-arrestin-2 deletion. Similarly, β-arrestin-2 deletion did not prevent morphine tolerance to inhibition of neuronal excitability in ileum myenteric neurons. However, neuronal tolerance was attenuated by inhibiting PKC.

Conclusions and Implications

Unlike antinociceptive tolerance, rapid morphine tolerance in the small intestine is independent of β-arrestin-2 but is PKC-mediated. These findings reveal a potential mechanism for differences in the rates of tolerances to opioids, implicate myenteric neurons of the ileum as the primary cause for opioid-induced withdrawal effects and suggest that undesired gastrointestinal effects will persist with biased opioid agonist use.

What is already known:

Tolerance does not develop to chronic-opioid-induced constipation but diarrhea is produced upon withdrawal

Novel G-protein biased agonists that preclude β-arrestin-2 activation at the μ-opioid receptor are in development

What this study adds:

Morphine tolerance in the ileum develops systemically and in individual myenteric neurons independent of β-arrestin-2

Morphine tolerance in the small intestine develops before antinociception and is reversed by PKC inhibition

Clinical significance:

Clinical use of G-protein biased opioid agonists will not prevent tolerance development in the ileum

Tolerance in ileum myenteric neurons might be the basis of opioid-induced withdrawal in the gut
A preliminary model to describe the transmission dynamics of Covid-19 between two neighboring cities or countries
Authors: Isea Raúl
Published: July 2020

We present a mathematical model that would allow one to describe the transmission dynamics of Covid-19 between two neighboring cities or countries. This model is analyzed both analytical and numerically. It is a preliminary model because it assumes that the migration rate and the mortality rate are constant over time. Despite these simplifications, only two of the four equilibrium conditions were deduced from the system of equations proposed in this paper. Finally, we show an example the transmission dynamics between Portugal and Spain according to the cases registered before June 3, 2020.
Genetic risk score for ovarian cancer based on chromosomal-scale length variation
Authors: Toh Chris , Brody James P.
Published: July 2020

Introduction

Twin studies indicate that a substantial fraction of ovarian cancers should be predictable from genetic testing. Genetic risk scores can stratify women into different classes of risk. Higher risk women can be treated or screened for ovarian cancer, which should reduce overall death rates due to ovarian cancer. However, current ovarian cancer genetic risk scores, based on SNPs, do not work that well. We developed a genetic risk score based on structural variation, quantified by variations in the length of chromosomes.

Methods

We evaluated this genetic risk score using data collected by The Cancer Genome Atlas. From this dataset, we synthesized a dataset of 414 women who had ovarian serous carcinoma and 4225 women who had no form of ovarian cancer. We characterized each woman by 22 numbers, representing the length of each chromosome in their germ line DNA. We used a gradient boosting machine, a machine learning algorithm, to build a classifier that can predict whether a woman had been diagnosed with ovarian cancer in this dataset.

Results

The genetic risk score based on chromosomal-scale length variation could stratify women such that the highest 20% had a 160x risk (95% confidence interval 50x-450x) compared to the lowest 20%. The genetic risk score we developed had an area under the curve of the receiver operating characteristic curve of 0.88 (estimated 95% confidence interval 0.86-0.91).

Conclusion

A genetic risk score based on chromosomal-scale length variation of germ line DNA provides an effective means of predicting whether or not a woman will develop ovarian cancer.
SARS-CoV-2 Transmission in Alberta, British Columbia, and Ontario, Canada, January 1-July 6, 2020
Authors: Fung Isaac Chun-Hai , Hung Yuen Wai , Ofori Sylvia K. , Muniz-Rodriguez Kamalich , Lai Po-Ying , Chowell Gerardo
Published: July 2020

Objective

To investigate COVID-19 epidemiology in Alberta, British Columbia and Ontario, Canada.

Methods

We calculated the incidence rate ratio (January 1—July 6, 2020) between the 3 provinces, and estimated time-varying reproduction number, Rt, starting from March 1, using EpiEstim package in R.

Results

Using British Columbia as a reference, the incidence rate ratios in Alberta and Ontario are 3.1 and 4.3 among females, and 3.4 and 4.0 among males. In Ontario, Rt fluctuated ~1 in March, reached values >1 in early and mid-April, then dropped <1 in late April and early May. Rt rose to ~1 in mid-May and then remained <1 from late May through early July. In British Columbia, Rt dropped <1 in early April, but it increased towards the end of April. Rt <1 in May while it fluctuated around 1.0 in June and early July. In Alberta, Rt > 1 in March; Rt dropped in early April and rose again in late April. In much of May, Rt <1, but Rt increases in early June and fluctuates ~1 since mid-June.

Conclusions

Rt wavering around 1.0 indicated that three provinces of Canada have managed to achieve limited onward transmission of SARS-CoV-2 as of early July 2020.
Restoration of β-globin expression with optimally designed lentiviral vector for β-thalassemia treatment in Chinese patients
Authors: Ouyang Wenjie , Dong Guoyi , Zhao Weihua , Li Jing , Zhou Ziheng , Yang Gaohui , Liu Rongrong , Li Yue , Zhang Qiaoxia , Du Xin , Sun Haixi , Gu Ying , Lai Yongrong , Liu Sixi , Liu Chao
Published: July 2020

β-thalassemia is one of the most prevalent genetic diseases worldwide. The current treatment for β–thalassemia is allogeneic hematopoietic stem cell transplantation (HSCT), which is limited due to lack of matched donors. Gene therapy has been developed as an alternative therapeutic option for transfusion-ependent β-thalassemia (TDT). However, successful gene therapy for β-thalassemia patients in China has not been reported. Here we present the results of preclinical studies of an optimally designed LV named LentiHBBT87Q in hematopoietic stem cells (HSCs) derived from Chinese TDT patients. LentiHBBT87Q was selected from a series of LVs with optimized backbone and de novo cloning strategy. It contains an exogenous T87Q β-globin gene (HBBT87Q) driven by a specific reconstituted locus control region (rLCR) and efficiently express HBB mRNA and HBB protein in erythroblasts derived from cord blood (CB) HSCs. To facilitate clinical transformation, we manufactured clinical grade LentiHBBT87Q (cLentiHBBT87Q) and optimized its transduction procedure. Importantly, transduction of cLentiHBBT87Qrestored expression of HBB monomer and adult hemoglobin (HbA) tetramer to relatively normal level in erythroblasts from bone marrow (BM) HSCs of Chinese TDT patients, that carry the most common mutation types and cover various genotypes, including β0/β0. Furthermore, viral integration sites (VIS) of cLentiHBBT87Q were similar to other LVs safely used in previous clinical trials and the associated risk of tumorigenesis was not observed in cLentiHBBT87Q transduced HSCs through comprehensive analysis. Taken together, we have engineered the cLentiHBBT87Q that can restore β-globin expression in the HSCs-derived erythroblasts of Chinese TDT patients with minimal risk on tumorigenesis, providing a favorable starting point for future clinical application.
Clinical Characteristics and Outcomes for 7,995 Patients with SARS-CoV-2 Infection
Authors: McPadden Jacob , Warner Frederick , Young H. Patrick , Hurley Nathan C. , Pulk Rebecca A. , Singh Avinainder , Durant Thomas JS , Gong Guannan , Desai Nihar , Haimovich Adrian , Taylor Richard Andrew , Gunel Murat , Cruz Charles S. Dela , Farhadian Shelli F. , Siner Jonathan , Villanueva Merceditas , Churchwell Keith , Hsiao Allen , Torre Charles J. , Velazquez Eric J. , Herbst Roy S. , Iwasaki Akiko , Ko Albert I. , Mortazavi Bobak J. , Krumholz Harlan M. , Schulz Wade L.
Published: July 2020

Objective

Severe acute respiratory syndrome virus (SARS-CoV-2) has infected millions of people worldwide. Our goal was to identify risk factors associated with admission and disease severity in patients with SARS-CoV-2.

Design

This was an observational, retrospective study based on real-world data for 7,995 patients with SARS-CoV-2 from a clinical data repository.

Setting

Yale New Haven Health (YNHH) is a five-hospital academic health system serving a diverse patient population with community and teaching facilities in both urban and suburban areas.

Populations

The study included adult patients who had SARS-CoV-2 testing at YNHH between March 1 and April 30, 2020.

Main outcome and performance measures

Primary outcomes were admission and in-hospital mortality for patients with SARS-CoV-2 infection as determined by RT-PCR testing. We also assessed features associated with the need for respiratory support.

Results

Of the 28605 patients tested for SARS-CoV-2, 7995 patients (27.9%) had an infection (median age 52.3 years) and 2154 (26.9%) of these had an associated admission (median age 66.2 years). Of admitted patients, 1633 (75.8%) had a discharge disposition at the end of the study period. Of these, 192 (11.8%) required invasive mechanical ventilation and 227 (13.5%) expired. Increased age and male sex were positively associated with admission and in-hospital mortality (median age 81.9 years), while comorbidities had a much weaker association with the risk of admission or mortality. Black race (OR 1.43, 95%CI 1.14-1.78) and Hispanic ethnicity (OR 1.81, 95%CI 1.50-2.18) were identified as risk factors for admission, but, among discharged patients, age-adjusted in-hospital mortality was not significantly different among racial and ethnic groups.

Conclusions

This observational study identified, among people testing positive for SARS-CoV-2 infection, older age and male sex as the most strongly associated risks for admission and in-hospital mortality in patients with SARS-CoV-2 infection. While minority racial and ethnic groups had increased burden of disease and risk of admission, age-adjusted in-hospital mortality for discharged patients was not significantly different among racial and ethnic groups. Ongoing studies will be needed to continue to evaluate these risks, particularly in the setting of evolving treatment guidelines.
Simulating drug effects on blood glucose laboratory test time series with a conditional WGAN
Authors: Yahi Alexandre , Tatonetti Nicholas P.
Published: July 2020

The unexpected effects of medications has led to more than 14 million drug adverse events reported to the Food and Drug Administration (FDA) over the past 10 years in the United States alone, with a little over 1.3 million of them linked to death, and represents a medical and financial burden on our healthcare. Laboratory tests have the potential to capture inter-individual variability in drug responses, but a significant portion of the patient population has unique treatment pathways that impedes forecasting and optimal decision making.

Generative Adversarial Networks (GANs) are flexible implicit generative models that have demonstrated their ability to capture complex correlations in field like computer vision and natural language. Their latent representation capacity is an opportunity for drug effect simulation on laboratory test trajectories. In this paper, we developed and evaluated conditional GANs on glucose laboratory tests in patients exposed to drug combinations and showed a proof of concept for these models in the simulation of unseen drug combinations. By using conditional Wasserstein GANs (WGANs) to simulate drug effects in laboratory tests, we hope to pave the way for novel clinical decision support (CDM) systems and enable the development of better predictive models for rare cohorts of patients.
Plexin-B1 mutation drives prostate cancer metastasis
Authors: Shorning Boris , Trent Neil , Griffiths David , Worzfeld Thomas , Offermanns Stefan , Masters John , Clarke Alan R. , Smalley Matthew J. , Williamson Magali
Published: July 2020

Prostate cancer mortality is associated with the metastatic spread of tumour cells. A better understanding of the mechanisms which allow a locally advanced tumour to disseminate around the body will identify new therapeutic targets to block this process. One of set of genes implicated in metastasis are plexins, which can promote or suppress tumour progression depending on cancer type and cellular context. We have taken a mouse genetics approach to gain insight into the role of Plexin-B1 in prostate cancer progressionin vivo.

We show here that genetic deletion of Plexin-B1 inPbCre+Ptenfl/flKrasG12VandPbCre+Ptenfl/flp53fl/flmouse prostate cancer models significantly decreased metastasis. High levels of prostate epithelial cell-specific expression of wild-type Plexin-B1 in knock-in mice with aPbCre+Ptenfl/flKrasG12Vbackground also significantly decreased metastasis. In contrast, expression of a Plexin-B1 mutant (P1597L; identified from metastatic deposits in prostate cancer patients) in prostate epithelial cells inPbCre+Ptenfl/flKrasG12VandPbCre+Ptenfl/flp53fl/flmice significantly increased metastasis, in particular metastasis to distant sites. In line with these findings, both deletion and overexpression of wild-type Plexin-B1 reduced invasion of tumour cells into the prostate stroma, while overexpression of mutant Plexin-B1 significantly increased invasion, suggesting that Plexin-B1 has a role in the initial stages of metastasis. Invasion and metastasis also correlated with phosphorylation of myosin light chain, suggesting that Plexin-B1 signals via the Rho/ROCK pathway to promote metastasis.

Our results demonstrate that mutant Plexin-B1 promotes metastasis in prostate cancer and represents a new therapeutic target to suppress tumour spread.