bluuebunny/crossref_metadata_2025 huggingface dataset:
The Drosophila MOZ homolog Enok controls Notch-dependent induction of the RUNX genelozengeindependently of its histone-acetyl transferase activity
Authors: Genais Thomas , Gigan Delhia , Augé Benoit , Moussalem Douaa , Waltzer Lucas , Haenlin Marc , Gobert Vanessa
Published: July 2020

The human KAT6 lysine acetyltransferase MOZ has been shown to be an essential player in the field of normal and malignant hematopoiesis. It belongs to a highly conserved family of epigenetic factors and remodels chromatin by acetylating histone tails in association with its partners of the ING5 complex. Here, we report that its Drosophila counterpart Enok is required during larval hematopoiesis to control the Notch-dependent induction of circulating crystal cells. In particularenokis essential to allow expression of the RUNX factor Lozenge (Lz) that controls the crystal cell specific transcriptional program. We demonstrate that this function involves neither the Eaf6 and Ing5 subunits of the Drosophila ING5 complex, nor Enok own acetyltransferase activity. We identify inlzthird intron a hematopoietic enhancer, which is both required to promote expression in Notch-activated crystal cell precursors in anenok-dependent manner and bound by Enok. The non-catalytic mode of action of Enok is likely conserved in MOZ/KAT6 proteins and might be of high relevance in mammalian hematopoiesis, whether normal or malignant.
Modelling white matter in gyral blades as a continuous vector field
Authors: Cottaar Michiel , Bastiani Matteo , Boddu Nikhil , Glasser Matthew , Haber Suzanne , van Essen David C. , Sotiropoulos Stamatios N. , Jbabdi Saad
Published: July 2020

1

Many brain imaging studies aim to measure structural connectivity with diffusion tractography. However, biases in tractography data, particularly near the boundary between white matter and cortical grey matter can limit the accuracy of such studies. When seeding from the white matter, streamlines tend to travel parallel to the convoluted cortical surface, largely avoiding sulcal fundi and terminating preferentially on gyral crowns. When seeding from the cortical grey matter, streamlines generally run near the cortical surface until reaching deep white matter. These so-called “gyral biases” limit the accuracy and effective resolution of cortical structural connectivity profiles estimated by tractography algorithms, and they do not reflect the expected distributions of axonal densities seen in invasive tracer studies or stains of myelinated fibres. We propose an algorithm that concurrently models fibre density and orientation using a divergence-free vector field within gyral blades to encourage an anatomically-justified streamline density distribution along the cortical white/grey-matter boundary while maintaining alignment with the diffusion MRI estimated fibre orientations. Usingin vivodata from the Human Connectome Project, we show that this algorithm reduces tractography biases. We compare the structural connectomes to functional connectomes from resting-state fMRI, showing that our model improves cross-modal agreement. Finally, we find that after parcellation the changes in the structural connectome are very minor with slightly improved interhemispheric connections (i.e, more homotopic connectivity) and slightly worse intrahemispheric connections when compared to tracers.
Targeting the endolysosomal host-SARS-CoV-2 interface by clinically licensed functional inhibitors of acid sphingomyelinase (FIASMA) including the antidepressant fluoxetine
Authors: Schloer Sebastian , Brunotte Linda , Goretzko Jonas , Mecate-Zambrano Angeles , Korthals Nadia , Gerke Volker , Ludwig Stephan , Rescher Ursula
Published: July 2020

The Corona Virus Disease 2019 (COVID-19) pandemic caused by the Severe Acute Respiratory Syndrome Related Coronavirus 2 (SARS-CoV-2) is a global health emergency. As only very limited therapeutic options are clinically available, there is an urgent need for the rapid development of safe, effective, and globally available pharmaceuticals that inhibit SARS-CoV-2 entry and ameliorate COVID-19. In this study, we explored the use of small compounds acting on the homeostasis of the endolysosomal host-pathogen interface, to fight SARS-CoV-2 infection. We find that fluoxetine, a widely used antidepressant and a functional inhibitor of acid sphingomyelinase (FIASMA), efficiently inhibited the entry and propagation of SARS-CoV-2 in the cell culture model without cytotoxic effects and also exerted potent antiviral activity against two currently circulating influenza A virus subtypes, an effect which was also observed upon treatment with the FIASMAs amiodarone and imipramine. Mechanistically, fluoxetine induced both impaired endolysosomal acidification and the accumulation of cholesterol within the endosomes. As the FIASMA group consists of a large number of small compounds that are well-tolerated and widely used for a broad range of clinical applications, exploring these licensed pharmaceuticals may offer a variety of promising antivirals for host-directed therapy to counteract enveloped viruses, including SARS-CoV-2 and COVID 19.
Charged Pore-lining Residues are Required for Normal Channel Kinetics in the Eukaryotic Mechanosensitive Ion Channel MSL1
Authors: Schlegel Angela M. , Haswell Elizabeth S.
Published: July 2020

Mechanosensitive (MS) ion channels are widespread mechanisms for cellular mechanosensation that can be directly activated by membrane tension. The well-studied MscS family of MS ion channels is found in bacteria, archaea, and plants. MscS-Like (MSL)1 is localized to the inner mitochondrial membrane ofArabidopsis thaliana, where it is required for normal mitochondrial responses to oxidative stress. LikeEscherichia coliMscS, MSL1 has a pore-lining helix that is kinked. However, in MSL1 this kink is comprised of two charged pore-lining residues, R326 and D327. Using single channel patch-clamp electrophysiology inE. coli, we show that altering the size and charge of R326 and D327 leads to dramatic changes in open state dwell time. Modest changes in gating pressure and open state stability were also observed while no effects on channel rectification or conductance were detected. MSL1 channel variants had differing physiological function inE. colihypoosmotic shock assays, without clear correlation between function and particular channel characteristics. Taken together, these results demonstrate that altering pore-lining residue charge and size disrupts normal channel state stability and gating transitions, and led us to propose the “sweet spot” model. In this model, the transition to the closed state is facilitated by attraction between R326 and D327 and repulsion between R326 residues of neighboring monomers. In the open state, expansion of the channel reduces inter-monomeric repulsion, rendering open state stability influenced mainly by attractive forces. This work provides insight into how unique charge-charge interactions can be combined with an otherwise conserved structural feature to help modulate MS channel function.
Computational and experimental characterization of the novel ECM glycoprotein SNED1 and prediction of its interactome
Authors: Vallet Sylvain D. , Davis Martin N. , Barqué Anna , Ricard-Blum Sylvie , Naba Alexandra
Published: July 2020

The extracellular matrix (ECM) protein SNED1 has been shown to promote breast cancer metastasis and control neural crest cell-specific craniofacial development, but the cellular and molecular mechanisms by which it does so remain unknown. ECM proteins exert their functions by binding to cell surface receptors, sequestering growth factors, and interacting with other ECM proteins, actions that can be predicted using knowledge of protein’s sequence, structure and post-translational modifications. Here, we combined in-silico and in-vitro approaches to characterize the physico-chemical properties of SNED1 and infer its putative functions. To do so, we established a mammalian cell system to produce and purify SNED1 and its N-terminal fragment, which contains a NIDO domain. We have determined experimentally SNED1’s potential to be glycosylated, phosphorylated, and incorporated into insoluble ECM produced by cells. In addition, we used biophysical and computational methods to determine the secondary and tertiary structures of SNED1 and its N-terminal fragment. The tentative ab-initio model we built of SNED1 suggests that it is an elongated protein presumably able to bind multiple partners. Using computational predictions, we identified 114 proteins as putative SNED1 interactors. Pathway analysis of the newly-predicted SNED1 interactome further revealed that binding partners of SNED1 contribute to signaling through cell surface receptors, such as integrins, and participate in the regulation of ECM organization and developmental processes. Altogether, we provide a wealth of information on an understudied yet important ECM protein with the potential to decipher its functions in physiology and diseases.
Poly(ADP-ribose)-binding and macroH2A mediate recruitment and functions of KDM5A at DNA lesions
Authors: Kumbhar Ramhari , Perren Jullian , Gong Fade , Corujo David , Medina Frank , Matouschek Andreas , Buschbeck Marcus , Miller Kyle M.
Published: July 2020

The histone demethylase KDM5A removes histone H3 lysine 4 methylation, which is involved in transcription and DNA damage responses (DDR). While DDR functions of KDM5A have been identified, how KDM5A recognizes DNA lesion sites within chromatin is unknown. Here, we identify two factors that act upstream of KDM5A to promote its association with DNA damage sites. We have identified a non-canonical poly(ADP-ribose), (PAR), binding region unique to KDM5A. Loss of the PAR-binding region or treatment with PAR polymerase (PARP) inhibitors (PARPi) blocks KDM5A-PAR interactions and DNA repair functions of KDM5A. The histone variant macroH2A1.2 is also specifically required for KDM5A recruitment and functions at DNA damage sites, including homology-directed repair of DNA double-strand breaks and repression of transcription at DNA breaks. Overall, this work reveals the importance of PAR-binding and macroH2A1.2 in KDM5A recognition of damage sites that drive transcriptional and repair activities at DNA breaks within chromatin that are essential for maintaining genome integrity.

The histone demethylase KDM5A demethylates H3K4 to promote repair and transcriptional responses at DNA breaks. We identified poly(ADP-ribose)-binding and macroH2A1.2 as modulators of KDM5A association with DNA damage sites, revealing how KDM5A engages DNA breaks within chromatin.
RNA-binding protein RBM3 negatively regulates innate lymphoid cells (ILCs) and lung inflammation
Authors: Badrani Jana H. , Amadeo Michael , Cavagnero Kellen , Naji Luay H. , Lund Sean J. , Leng Anthea , Lacasa Lee , Strohm Allyssa , Kim Hyojoung , Baum Rachel E. , Khorram Naseem , Mondal Monalisa , Seumois Grégory , Pilotte Julie , Vanderklish Peter W. , Doherty Taylor A.
Published: July 2020

Innate lymphoid cells (ILCs) promote lung inflammation through cytokine production in diseases such as asthma. RNA-binding proteins (RBPs) are critical post-transcriptional regulators of cellular function, including inflammatory responses, though the role of RBPs in innate lymphoid cells is unknown. Here, we demonstrate that RNA-binding motif 3 (RBM3) is one of the most highly expressed RBPs in Thy1.2+ lung ILCs after fungal allergen challenge and is further induced by epithelial cytokines TSLP and IL-33 in both human and mouse ILCs. Single (rbm3−/−) and double (rbm3−/−rag2−/−) knockout mice exposed via the airway to the asthma-associated fungal allergen Alternaria alternata displayed increases in eosinophilic lung inflammation and ILC activation compared to control mice. In addition to increased Th2 cytokine production, rbm3−/− ILCs produced elevated IL-17A. The negative regulation by RBM3 in ILC responses was direct as purified rbm3−/− ILCs were hyperinflammatory in vitro and in vivo after stimulation with IL-33. Transcriptomic analysis by RNA-sequencing of rbm3−/− lung ILCs showed increased type 2 and 17 cytokines as well as global expression differences in critical cytokines, receptors, transcription factors, and survival transcripts compared with WT ILCs. Intriguingly, these transcript changes did not correlate with the presence of AU-rich elements (AREs), which RBM3 is known to bind. Thus, regulation of ILC responses by RNA-binding proteins offers novel mechanistic insight into lung ILC biology and ILC-driven inflammatory diseases.
Modulation of the mTOR pathway plays a central role in dendritic cell functions after Echinococcus granulosus antigen recognition
Authors: Rodrigues Christian Rodriguez , Nicolao María Celeste , Chop Maia , Plá Natalia , Massaro Mora , Loos Julia , Cumino Andrea C.
Published: July 2020

1.

Immune evasion is a hallmark of persistent echinococcal infection, comprising modulation of innate immune cells and antigen-specific T cell responses. However, recognition ofEchinococcus granulosusby dendritic cells (DCs) is a key determinant of the host’s response to this parasite. Given that mTOR signaling pathway has been described as a regulator linking metabolism and immune function in DCs, we reported for the first time in these cells, global translation levels, antigen uptake, phenotype, cytokine transcriptional levels, and splenocyte priming activity upon recognition of the hydatid fluid (HF) and the highly glycosylated laminar layer (LL). We found that LL induced a slight up-regulation of CD86 and MHC II in DCs and also stimulated the production of IL-6 and TNF-α. By contrast, HF did not increase the expression of any co-stimulatory molecules, but also down-modulated CD40 and stimulated the expression of the anti-inflammatory cytokine IL-10. Both parasitic antigens promoted protein synthesis through mTOR activation. The use of rapamycin decreased the expression of the cytokines tested, empowered the down-modulation of CD40 and also reduced splenocyte proliferation. Finally, we showed thatE. granulosusantigens increase the amounts of LC3-positive structures in DCs which play critical roles in the presentation of these antigens to T cells.
Multiomic Immunophenotyping of COVID-19 Patients Reveals Early Infection Trajectories
Authors: Su Yapeng , Chen Daniel , Lausted Christopher , Yuan Dan , Choi Jongchan , Dai Cheng , Voillet Valentin , Scherler Kelsey , Troisch Pamela , Duvvuri Venkata R. , Baloni Priyanka , Qin Guangrong , Smith Brett , Kornilov Sergey , Rostomily Clifford , Xu Alex , Li Jing , Dong Shen , Rothchild Alissa , Zhou Jing , Murray Kim , Edmark Rick , Hong Sunga , Jones Lesley , Zhou Yong , Roper Ryan , Mackay Sean , O’Mahony D. Shane , Dale Christopher R , Wallick Julie A , Algren Heather A , Michael Zager A , Magis Andrew , Wei Wei , Price Nathan D. , Huang Sui , Subramanian Naeha , Wang Kai , Hadlock Jennifer , Hood Leroy , Aderem Alan , Bluestone Jeffrey A. , Lanier Lewis L. , Greenberg Phil , Gottardo Raphael , Davis Mark M. , Goldman Jason D. , Heath James R. ,   the ISB-Swedish COVID19 Biobanking Unit
Published: July 2020

Host immune responses play central roles in controlling SARS-CoV2 infection, yet remain incompletely characterized and understood. Here, we present a comprehensive immune response map spanning 454 proteins and 847 metabolites in plasma integrated with single-cell multi-omic assays of PBMCs in which whole transcriptome, 192 surface proteins, and T and B cell receptor sequence were co-analyzed within the context of clinical measures from 50 COVID19 patient samples. Our study reveals novel cellular subpopulations, such as proliferative exhausted CD8+and CD4+T cells, and cytotoxic CD4+T cells, that may be features of severe COVID-19 infection. We condensed over 1 million immune features into a single immune response axis that independently aligns with many clinical features and is also strongly associated with disease severity. Our study represents an important resource towards understanding the heterogeneous immune responses of COVID-19 patients and may provide key information for informing therapeutic development.
Tryptophan residues in TDP-43 and SOD1 mediate the cross-seeding and toxicity of SOD1
Authors: Pokrishevsky Edward , DuVal Michèle G. , McAlary Luke , Louadi Sarah , Pozzi Silvia , Roman Andrei , Plotkin Steven S , Dijkstra Anke , Julien Jean-Pierre , Allison W. Ted , Cashman Neil R.
Published: July 2020

Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disease of motor neurons. Neuronal superoxide dismutase-1 (SOD1) inclusion bodies are characteristic of familial ALS with SOD1 mutations, while a hallmark of sporadic ALS is inclusions containing aggregated wild-type TAR DNA-binding protein 43 (TDP-43). Co-expression of mutant or wild-type TDP-43 with SOD1 leads to misfolding of endogenous SOD1 and aggregation of SOD1 reporter protein G85R-GFP in HEK293FT cells, and promotes synergistic axonopathy in zebrafish. This pathological interaction is dependent upon natively solvent-exposed tryptophans in SOD1 (tryptophan-32) and TDP-43 RRM1 (tryptophan-172), in concert with natively sequestered TDP-43 N-terminal domain tryptophan-68. TDP-43 RRM1 intrabodies reduce wild-type SOD1 misfolding in HEK293FT cells, via blocking tryptophan-172. Tryptophan-68 becomes antibody-accessible in aggregated TDP-43 in sporadic ALS motor neurons and cell culture. 5-fluorouridine inhibits TDP-43-induced G85R-GFP SOD1 aggregation in HEK293FT cells, and ameliorates axonopathy in zebrafish, via its interaction with SOD1 tryptophan-32. Collectively, our results establish a novel and potentially druggable tryptophan-mediated mechanism whereby two principal ALS disease effector proteins might directly interact in disease.
Laser induced isolation and cultivation of single microbial cells
Authors: Liang Peng , Wang Huan , Wang Yun , Zhao Yinping , Huang Wei E. , Li Bei
Published: July 2020

Single cell isolation and cultivation play an important role in studying physiology, gene expression and functions of microorganisms. Laser Induced Forward Transfer Technique (LIFT) has been applied to isolate single cells but the cell viability after sorting is unclear. We demonstrate that a three-layer LIFT system could be applied to isolate single cells of Gram-negative (E. coli), Gram-positive (Lactobacillus rhamnosusGG, LGG), and eukaryotic microorganisms (Saccharomyces cerevisiae) and the sorted single cells were able to be cultured. The experiment results showed that the average cultivation recovery rate of the ejected single cells were 58% forSaccharomyces cerevisiae, 22% forE. coli, and 74% forLactobacillus rhamnosusGG (LGG). The identities of the cultured cells from single cell sorting were confirmed by using colony PCR with 16S-rRNA for bacteria and large unit rRNA for yeast and subsequent sequencing. This precise sorting and cultivation technique of live single microbial cells can be coupled with other microscopic approaches (e.g. fluorescent and Raman microscopy) to culture single microorganisms with specific functions, revealing their roles in the natural community.

Importance

Single cell isolation and cultivation are crucial to recover microorganisms for the study of physiology, gene expression and functions. We developed a laser induced cell sorting technology to precisely isolate single microbial cells from a microscopic slide. More importantly, the isolated single microbial cells are still viable for cultivation. We demonstrate to apply the live sorting method to isolate and cultivate single cells of Gram-negative (E. coli), Gram-positive (Lactobacillus rhamnosusGG, LGG), and eukaryotic microorganisms (Saccharomyces cerevisiae). This precise sorting and cultivation technique can be coupled with other microscopic approaches (e.g. fluorescent and Raman microscopy) to culture specifically targeted single microorganisms from microbial community.

Abstract Graphic
Eleven Routine Clinical Features Predict COVID-19 Severity
Authors: Zhou Kai , Sun Yaoting , Li Lu , Zang Zelin , Wang Jing , Li Jun , Liang Junbo , Zhang Fangfei , Zhang Qiushi , Ge Weigang , Chen Hao , Sun Xindong , Yue Liang , Wu Xiaomai , Shen Bo , Xu Jiaqin , Zhu Hongguo , Chen Shiyong , Yang Hai , Huang Shigao , Peng Minfei , Lv Dongqing , Zhang Chao , Zhao Haihong , Hong Luxiao , Zhou Zhehan , Chen Haixiao , Dong Xuejun , Tu Chunyu , Li Minghui , Zhu Yi , Chen Baofu , Li Stan Z. , Guo Tiannan
Published: July 2020

Severity prediction of COVID-19 remains one of the major clinical challenges for the ongoing pandemic. Here, we have recruited a 144 COVID-19 patient cohort consisting of training, validation, and internal test sets, longitudinally recorded 124 routine clinical and laboratory parameters, and built a machine learning model to predict the disease progression based on measurements from the first 12 days since the disease onset when no patient became severe. A panel of 11 routine clinical factors, including oxygenation index, basophil counts, aspartate aminotransferase, gender, magnesium, gamma glutamyl transpeptidase, platelet counts, activated partial thromboplastin time, oxygen saturation, body temperature and days after symptom onset, constructed a classifier for COVID-19 severity prediction, achieving accuracy of over 94%. Validation of the model in an independent cohort containing 25 patients achieved accuracy of 80%. The overall sensitivity, specificity, PPV and NPV were 0.70, 0.99, 0.93 and 0.93, respectively. Our model captured predictive dynamics of LDH and CK while their levels were in the normal range. This study presents a practical model for timely severity prediction and surveillance for COVID-19, which is freely available at webserverhttps://guomics.shinyapps.io/covidAI/.
The Impact of COVID-19 on Mental Health outcomes among hospital fever clinic attendants across Nepal: A community-based cross-sectional study
Authors: Devkota Hridaya Raj , Sijali Tula Ram , Bogati Ramji , Ahmad Meraj , Shakya Karuna Laxmi , Adhikary Pratik
Published: July 2020

Background

The COVID-19 pandemic has been creating a panic and distressing situations among the entire population globally including Nepal. No study has been conducted assessing the psychological impact of this pandemic on the general public in Nepal. The objective of this study is to assess the mental health status during COVID-19 outbreak and explore the potential influencing factors among the population attending the hospital fever clinics with COVID–19 symptoms.

Methods

A cross-sectional survey was conducted between May - June, 2020 with a sample of 645 participants aged 18 and above in 26 hospitals across Nepal. Telephone interviews were conducted using a semi-structured questionnaire along with a validated psychometric tool, the Depression, Anxiety and Stress (DASS-21) scale. The metrics and scores of symptoms and their severity were created and analyzed. Multivariate logistic regression was used to determine the association of potential covariates with outcome variables.

Results

The prevalence of anxiety, depression and stress were 14%, 7% and 5% respectively. Participants from Bagmati province reported higher level of anxiety (OR 3.87, 95% CI 1.42 – 10.59), while stress (OR 4.78, 95% CI 1.09 – 21.29) and depressive symptoms (OR 3.37, 95% CI 1.10 – 10.35) observed higher among the participants in Province 1. Women were more at risk of anxiety (OR 4.26, 95% CI 2.21 – 8.20) and depression (2.75, 95% CI 1.16 – 6.51) than men. Similarly, people with primary level education found more prone to all factors, stress (OR 20.35, 95% CI 2.06 – 201.19), anxiety (OR 3.10, 95% CI 1.24 – 7.91), and depression (OR 4.41, 95% CI 1.29 – 15.07). More farmers than labors showed higher odds (OR 2.25, 95% CI 1.01 – 5.01) for anxiety, while individuals surveyed who reported their health status as poor-had higher odds (OR 5.95, 95% CI 1.08 – 32.68) for depression. Also, people currently living in rented houses reported more stress (OR 3.11, 95% CI 1.07 – 9.05) and those living far from family reported higher rates of depressive symptoms (OR 3.57, 95% CI 1.01 – 12.58).

Conclusion

The study identified increased prevalence of stress, anxiety and depressive symptoms during the initial stage of COVID-19 pandemic in Nepal. Considering the findings, there is urgent need to develop and implement appropriate community-based mental health programs targeting individuals who have had COVID-19 symptoms and who are prone to develop adverse mental health outcomes.
The effective reproductive number (Rt) of COVID-19 and its relationship with social distancing
Authors: Felizola Diniz-Filho José Alexandre , Jardim Lucas , Toscano Cristiana M. , Rangel Thiago Fernando
Published: July 2020

The expansion of the new coronavirus disease (COVID-19) triggered a renewed interest in epidemiological models and on how parameters can be estimated from observed data. Here we investigated the relationship between average number of transmissions though time, the reproductive number Rt, and social distancing index as reported by mobile phone data service inloco, for Goiás State, Brazil, between March and June 2020. We calculated Rt values using EpiEstim package in R-plataform for confirmed cases incidence curve. We found a correlation equal to −0.72 between Rt values and isolation index at a time lag of 8 days. As the Rt values were paired with center of the moving window of 7 days, the delay matches the mean incubation period of the virus. Our findings reinforce that isolation index can be an effective surrogate for modeling and epidemiological analyses and, more importantly, helpful for anticipating the need for early interventions, a critical issue in public health.
Integrating large-scale neuroimaging research datasets: harmonisation of white matter hyperintensity measurements across Whitehall and UK Biobank datasets
Authors: Bordin Valentina , Bertani Ilaria , Mattioli Irene , Sundaresan Vaanathi , McCarthy Paul , Suri Sana , Zsoldos Enikő , Filippini Nicola , Mahmood Abda , Melazzini Luca , Laganà Maria Marcella , Zamboni Giovanna , Singh-Manoux Archana , Kivimäki Mika , Ebmeier Klaus P , Baselli Giuseppe , Jenkinson Mark , Mackay Clare E , Duff Eugene P , Griffanti Ludovica
Published: July 2020

Large scale neuroimaging datasets present the possibility of providing normative distributions for a wide variety of neuroimaging markers, which would vastly improve the clinical utility of these measures. However, a major challenge is our current poor ability to integrate measures across different large-scale datasets, due to inconsistencies in imaging and non-imaging measures across the different protocols and populations. Here we explore the harmonisation of white matter hyperintensity (WMH) measures across two major studies of healthy elderly populations, the Whitehall II imaging sub-study and the UK Biobank. We identify pre-processing strategies that maximise the consistency across datasets and utilise multivariate regression to characterise sample differences contributing to study-level differences in WMH variations. We also present a parser to harmonise WMH-relevant non-imaging variables across the two datasets. We show that we can provide highly calibrated WMH measures from these datasets with: (1) the inclusion of a number of specific standardised processing steps; and (2) appropriate modelling of sample differences through the alignment of demographic, cognitive and physiological variables. These results open up a wide range of applications for the study of WMHs and other neuroimaging markers across extensive databases of clinical data.

HIGHLIGHTS

We harmonised measures of WMHs across two studies on healthy ageing

Specific pre-processing strategies can increase comparability across studies

Modelling of biological differences is crucial to provide calibrated measures
Lamin C regulates genome organization after mitosis
Authors: Wong X , Hoskins VE , Harr JC , Gordon M , Reddy KL
Published: July 2020

The dynamic 3D organization of the genome is central to the regulation of gene expression and developmental progression, with its disruption being implicated in various diseases. The nuclear lamina, a proteinaceous meshwork underlying the nuclear envelope (NE), provides both structural and regulatory influences on genome organization through the tethering of large inactive genomic regions, called Lamina Associated Domains (LADs), to the nuclear periphery. Evidence suggests that the A type lamins, lamins A and C, are the predominant lamins involved in the peripheral association of LADs, with these two isotypes forming distinct networks and potentially involved in different cellular processes. Here we tested whether lamins A and C have distinct roles in genome organization by examining chromosome architecture in cells in which lamin C or lamin A are specifically down-regulated. We find that lamin C (not lamin A) is required for the 3D organization of LADs and overall chromosome organization in the cell nucleus. Striking differences in the localization of lamin A and lamin C are present as cells exit mitosis that persist through early G1. Whereas lamin A associates with the nascent NE during telophase, lamin C remains in the interior surrounding nucleoplasmic LAD clusters. Lamin C association with the NE is delayed until several hours into G1 and correlates temporally and spatially with the post-mitotic NE association of LADs. Post-mitotic LAD association with the NE, and consequently global 3D genome organization, is perturbed only in cells depleted of lamin C, and not in cells depleted of lamin A. We conclude that lamin C regulates LAD dynamics after mitosis and is a key regulator of genome organization in mammalian cells. These findings reveal an unexpectedly central role for lamin C in genome organization, including both inter-chromosomal LAD-LAD segregation and LAD scaffolding at the NE.
Distinctiveness of genes contributing to growth ofPseudomonas syringaein diverse host plant species
Authors: Helmann Tyler C. , Deutschbauer Adam M. , Lindow Steven E.
Published: July 2020

A variety of traits are necessary for bacterial colonization of the interior of plant hosts, including well-studied virulence effectors as well as other phenotypes contributing to bacterial growth and survival within the apoplast. High-throughput methods such as transposon sequencing (TnSeq) are powerful tools to identify such genes in bacterial pathogens. However, there is little information as to the distinctiveness of traits required for bacterial colonization of different hosts. Here, we utilize randomly barcoded TnSeq (RB-TnSeq) to identify the genes that contribute to the ability ofPseudomonas syringaestrain B728a to grow within common bean (Phaseolus vulgaris), lima bean (Phaseolus lunatus), and pepper (Capsicum annuum); species representing two different plant families. The magnitude of contribution of most genes to apoplastic fitness in each of the plant hosts was similar. However, 50 genes significantly differed in their fitness contributions to growth within these species. These genes encoded proteins in various functional categories including polysaccharide synthesis and transport, amino acid metabolism and transport, cofactor metabolism, and phytotoxin synthesis and transport. Six genes that encoded unannotated, hypothetical proteins also contributed differentially to growth in these hosts. The genetic repertoire of a relatively promiscuous pathogen such asP. syringaemay thus be shaped, at least in part, by the conditional contribution of some fitness determinants.
IlvY is an important regulator ofShigellainfectionin vitroandin vivo
Authors: Holly Mayumi K. , Anderson Mark C. , Rabago Lesley M. , Saffarian Azadeh , Marteyn Benoit S. , Arnold Samuel L.M.
Published: July 2020

Shigellosis results from oral ingestion of the Gram-negative bacteriaShigella, and symptoms include severe diarrhea and dysentery. In the absence of vaccines, small molecule antibacterial drugs have provided treatment options for shigellosis. However,Shigelladrug resistance is rapidly emerging, andShigellastrains with resistance to both third-generation cephalosporins and azithromycin have been identified in Asia. A re-conceptualization is needed regarding the development of therapeutics that target bacterial pathogens in order to reduce resistance development and alteration of gut microbiota, which is depleted upon treatment with wide spectrum antibiotics, thereby increasing susceptibility to subsequent enteric infections. A more organism-specific approach is to develop agents targeting virulence factors such as toxins, adhesins, invasins, quorum sensing, and protein secretion systems. ForShigella, there is interest in targeting transcription factors essential forShigellainfectionin vivorather than specific effectors. Here we describe the importance of theShigellatranscription factor IlvY inShigellavirulencein vitroandin vivo. This work included the development of a novel, oral mouse model ofShigellainfection with wild-type adult mice. Unlike previous models, mice do not require antibiotic pretreatment or diet modifications. This mouse model was used to demonstrate the importance of IlvY forShigella in vivosurvival and that deletion ofilvYimpacts host responses to infection. These results illustrate that IlvY is a potential therapeutic target for the treatment of shigellosis. In addition, the novel mouse model provides an exciting new opportunity to investigate therapeutic efficacy againstShigellainfection and host responses to infection.
Integrating structure-based machine learning and co-evolution to investigate specificity in plant sesquiterpene synthases
Authors: Durairaj Janani , Melillo Elena , Bouwmeester Harro J , Beekwilder Jules , de Ridder Dick , van Dijk Aalt DJ
Published: July 2020

Sesquiterpene synthases (STSs) catalyze the formation of a large class of plant volatiles called sesquiterpenes. While thousands of putative STS sequences from diverse plant species are available, only a small number of them have been functionally characterized. Sequence identity-based screening for desired enzymes, often used in biotechnological applications, is difficult to apply here as STS sequence similarity is strongly affected by species. This calls for more sophisticated computational methods for functionality prediction. We investigate the specificity of precursor cation formation in these elusive enzymes. By inspecting multi-product STSs, we demonstrate that STSs have a strong selectivity towards one precursor cation. We use a machine learning approach combining sequence and structure information to accurately predict precursor cation specificity for STSs across all plant species. We combine this with a co-evolutionary analysis on the wealth of uncharacterized putative STS sequences, to pinpoint residues and distant functional contacts influencing cation formation and reaction pathway selection. These structural factors can be used to predict and engineer enzymes with specific functions, as we demonstrate by predicting and characterizing two novel STSs fromCitrus bergamia.

Author summary

Predicting enzyme function is a popular problem in the bioinformatics field that grows more pressing with the increase in protein sequences, and more attainable with the increase in experimentally characterized enzymes. Terpenes and terpenoids form the largest classes of natural products and find use in many drugs, flavouring agents, and perfumes. Terpene synthases catalyze the biosynthesis of terpenes via multiple cyclizations and carbocation rearrangements, generating a vast array of product skeletons. In this work, we present a three-pronged computational approach to predict carbocation specificity in sesquiterpene synthases, a subset of terpene synthases with one of the highest diversities of products. Using homology modelling, machine learning and co-evolutionary analysis, our approach combines sparse structural data, large amounts of uncharacterized sequence data, and the current set of experimentally characterized enzymes to provide insight into residues and structural regions that likely play a role in determining product specifcity. Similar techniques can be repurposed for function prediction and enzyme engineering in many other classes of enzymes.
Diminazene resistance inTrypanosoma congolenseis linked to reduced mitochondrial membrane potential and not to reduced transport capacity
Authors: Carruthers Lauren V. , Munday Jane C. , Ebiloma Godwin U. , Steketee Pieter , Jayaraman Siddharth , Campagnaro Gustavo D. , Ungogo Marzuq A. , Donachie Anne-Marie , Rowan Tim G. , Peter Rose , Morrison Liam J. , Barrett Michael P. , De Koning Harry P.
Published: July 2020

Trypanosoma congolenseis one of the principal agents causing livestock trypanosomiasis in sub-Saharan Africa. This wasting disease is costing these developing economies billions of dollars and undermining food security. Only two old drugs, the diamidine diminazene and the phenanthridine isometamidium are regularly used, and resistance is widespread but poorly understood. We induce diminazene resistance inT. congolenselaboratory strain IL3000 in vitro. Resistance was stable and not deleterious to in vitro growth. There was no cross-resistance with the phenanthridine drugs, with melaminophenyl arsenicals, with two promising new oxaborole trypanocides, nor with other diamidine trypanocides such as pentamidine, except the close structural analogues DB829 and DB75. Fluorescence microscopy showed that accumulation of DB75 was inhibited by folate. Uptake of [3H]-diminazene was also partly inhibited by folate, as well as by competing diamidine drugs, albeit at quite high concentrations, and uptake of tritiated diminazene and pentamidine was slow and low affinity. Uptake of [3H]-folate was in turn partly inhibited by diminazene, and inhibition of diminazene uptake by folate and pentamidine appeared to be additive, indicating multiple low affinity transport mechanisms for the drug. Expression of theT. congolensefolate transporters TcoFT1-3 in diminazene-resistantT. b. bruceisignificantly sensitized the cells to diminazene and DB829, but not to oxaborole AN7973. However, [3H]-diminazene uptake was not different inT. congolenseIL3000 and its diminazene resistant clones and RNAseq and whole-genome sequencing of multiple resistant clones did not reveal major changes in folate transporter sequence or expression. Instead, flow cytometry revealed a strong and stable reduction in the mitochondrial membrane potential Ψm in all resistant clones. We conclude that diminazene uptake inT. congolenseproceed via multiple low affinity mechanisms including folate transporters and that resistance is the result of a reduction in Ψm that limits mitochondrial accumulation of the drug.
coronaSPAdes: from biosynthetic gene clusters to RNA viral assemblies
Authors: Meleshko Dmitry , Hajirasouliha Iman , Korobeynikov Anton
Published: July 2020

Motivation

The COVID-19 pandemic has ignited a broad scientific interest in viral research in general and coronavirus research in particular. The identification and characterization of viral species in natural reservoirs typically involvesde novoassembly. However, existing genome, metagenome and transcriptome assemblers often are not able to assemble many viruses (including coronaviruses) into a single contig. Coverage variation between datasets and within dataset, presence of close strains, splice variants and contamination set a high bar for assemblers to process viral datasets with diverse properties.

Results

We developed coronaSPAdes, a novel assembler for RNA viral species recovery in general and coronaviruses in particular. coronaSPAdes leverages the knowledge about viral genome structures to improve assembly extending ideas initially implemented in biosyntheticSPAdes. We have shown that coronaSPAdes outperforms existing SPAdes modes and other popular short-read metagenome and viral assemblers in the recovery of full-length RNA viral genomes.

Availability

coronaSPAdes version used in this article is a part of SPAdes 3.15 release and is freely available athttp://cab.spbu.ru/software/spades.

Contact

a.korobeynikov@spbu.ru

Supplementary information

Supplementary data are available atBioinformatics
The presynaptic glycine transporter GlyT2 is regulated by the Hedgehog pathway in vitro and in vivo
Authors: de la Rocha-Muñoz A. , Núñez E. , Gómez-López S. , López-Corcuera B. , de Juan-Sanz J. , Aragón C.
Published: July 2020

The identity of a glycinergic synapse is maintained presynaptically by the activity of a surface glycine transporter, GlyT2, which recaptures glycine back to presynaptic terminals to preserve vesicular glycine content. GlyT2 loss-of-function mutations cause Hyperekplexia, a rare neurological disease in which loss of glycinergic neurotransmission causes generalized stiffness and strong motor alterations. However, the molecular underpinnings controlling GlyT2 activity remain poorly understood. In this work, we identify the Hedgehog pathway as a robust controller of GlyT2 expression and transport activity. Modulating the activation state of the Hedgehog pathwayin vitroin rodent primary spinal cord neurons orin vivoin zebrafish embryos induced a selective control in GlyT2 expression, regulating GlyT2 transport activity. Our results indicate that activation of Hedgehog reduces GlyT2 expression by decreasing its mRNA levels and increasing its ubiquitination and degradation. This work describes a new molecular link between the Hedgehog signaling pathway and presynaptic glycine availability.
A genetic screen to identify factors affected by undecaprenyl phosphate recycling uncovers novel connections to morphogenesis inEscherichia coli
Authors: Jorgenson Matthew A. , Bryant Joseph C.
Published: July 2020

Undecaprenyl phosphate (Und-P) is an essential lipid carrier that ferries cell wall intermediates across the cytoplasmic membrane in bacteria. Und-P is generated by dephosphorylating undecaprenyl diphosphate (Und-PP). InEscherichia coli, BacA, PgpB, YbjG, and LpxT dephosphorylate Und-PP and are conditionally essential. To identify vulnerabilities that arise when Und-P metabolism is defective, we developed a genetic screen for synthetic mutations in combination with ΔybjGΔlpxTΔbacA. The screen uncovered system-wide connections, including novel connections to cell division, DNA replication and repair, signal transduction, and glutathione metabolism. Further analysis revealed several new morphogenes; loss of one of these,qseC, caused cells to enlarge and lyse. QseC is the sensor kinase component of the QseBC two-component system. In the absence of QseC, the QseB response regulator is overactivated by PmrB cross-phosphorylation. Here, we show that deletingqseBcompletely reverses the shape defect of ΔqseCcells, as does overexpressingrprA(a small RNA). Surprisingly, deletingpmrBonly partially suppressedqseC-related shape defects. Thus, QseB is activated by multiple factors in the absence of QseC and functions ascribed to QseBC may be related to cell wall defects. Altogether, our findings provide a framework for identifying new determinants of cell integrity that could be targeted in future therapies.
Understanding the Human Brain using Brain Organoids and a Structure-Function Theory
Authors: Silva Gabriel A. , Muotri Alysson R. , White Christopher
Published: July 2020

A basic neurobiology-clinical trial paradigm motivates our use of constrained mathematical models and analysis of personalized human-derived brain organoids toward predicting clinical outcomes and safely developing new therapeutics. Physical constraints imposed on the brain can guide the analyses an interpretation of experimental data and the construction of mathematical models that attempt to make sense of how the brain works and how cognitive functions emerge. Development of these mathematical models for human-derived brain organoids offer an opportunity for testing new hypotheses about the human brain. When it comes to testing ideas about the brain that require a careful balance between experimental accessibility, manipulation, and complexity, in order to connect neurobiological details with higher level cognitive properties and clinical considerations, we argue that fundamental structure-function constraints applied to models of brain organoids offer a path forward. Moreover, we show these constraints appear in canonical and novel math models of neural activity and learning, and we make the case that constraint-based modeling and use of representations can bridge to machine learning for powerful mutual benefit.
Nonlinear effects of intrinsic dynamics on temporal encoding in a model of avian auditory cortex
Authors: Fehrman Christof , Robbins Tyler D , Meliza C Daniel
Published: July 2020

Neurons exhibit diverse intrinsic dynamics, which govern how they integrate synaptic inputs to produce spikes. Intrinsic dynamics are often plastic during development and learning, but the effects of these changes on stimulus encoding properties are not well known. To examine this relationship, we simulated auditory responses to zebra finch song using a linear-dynamical cascade model, which combines a linear spectrotemporal receptive field with a dynamical, conductance-based neuron model, then used generalized linear models to estimate encoding properties from the resulting spike trains. We focused on the effects of a low-threshold potassium current (KLT) that is present in a subset of cells in the zebra finch caudal mesopallium and is affected by early auditory experience. We found that KLTaffects both spike adaptation and the temporal filtering properties of the receptive field. The direction of the effects depended on the temporal modulation tuning of the linear (input) stage of the cascade model, indicating a strongly nonlinear relationship. These results suggest that small changes in intrinsic dynamics in tandem with differences in synaptic connectivity can have dramatic effects on the tuning of auditory neurons.

Author summary

Experience-dependent developmental plasticity involves changes not only to synaptic connections, but to voltage-gated currents as well. Using biophysical models, it is straightforward to predict the effects of this intrinsic plasticity on the firing patterns of individual neurons, but it remains difficult to understand the consequences for sensory coding. We investigated this in the context of the zebra finch auditory cortex, where early exposure to a complex acoustic environment causes increased expression of a low-threshold potassium current. We simulated responses to song using a detailed biophysical model and then characterized encoding properties using generalized linear models. This analysis revealed that this potassium current has strong, nonlinear effects on how the model encodes the song’s temporal structure, and that the sign of these effects depend on the temporal tuning of the synaptic inputs. This nonlinearity gives intrinsic plasticity broad scope as a mechanism for developmental learning in the auditory system.