bluuebunny/crossref_metadata_2025_split huggingface dataset:
Ultra-conserved sequences in the genomes of highly diverseAnophelesmosquitoes, with implications for malaria vector control
Authors: O’Loughlin Samantha M. , Forster Annie J. , Fuchs Silke , Dottorini Tania , Nolan Tony , Crisanti Andrea , Burt Austin 
Published: January 2021

ABSTRACTDNA sequences that are exactly conserved over long evolutionary time scales have been observed in a variety of taxa. Such sequences are likely under strong functional constraint and they have been useful in the field of comparative genomics for identifying genome regions with regulatory function. A potential new application for these ultra-conserved elements has emerged in the development of gene drives to control mosquito populations. Many gene drives work by recognising and inserting at a specific target sequence in the genome, often imposing a reproductive load as a consequence. They can therefore select for target sequence variants that provide resistance to the drive. Focusing on highly conserved, highly constrained sequences lowers the probability that variant, gene drive-resistant alleles can be tolerated.Here we search for conserved sequences of 18bp and over in an alignment of 21Anophelesgenomes, spanning an evolutionary timescale of 100 million years, and characterise the resulting sequences according to their location and function. Over 8000 ultra-conserved elements were found across the alignment, with a maximum length of 164 bp. Length-corrected gene ontology analysis revealed that genes containingAnophelesultra-conserved elements were over-represented in categories with structural or nucleotide binding functions. Known insect transcription factor binding sites were found in 48% of intergenicAnophelesultra-conserved elements. When we looked at the genome sequences of 1142 wild-caught mosquitoes we found that 15% of theAnophelesultra-conserved elements contained no polymorphisms. Our list ofAnophelesultra-conserved elements should provide a valuable starting point for the selection and testing of new targets for gene-drive modification in the mosquitoes that transmit malaria.
Targeting conserved viral virulence determinants by single domain antibodies to block SARS-CoV2 infectivity
Authors: Singh Sudhakar , Dahiya Surbhi , Singh Yuviana J. , Beeton Komal , Jain Ayush , Sarkar Roman , Dubey Abhishek , Tehseen Syed Azeez , Sehrawat Sharvan 
Published: January 2021

AbstractWe selected SARS-CoV2 specific single domain antibodies (sdAbs) from a previously constructed phage display library using synthetic immunogenic peptides of the virus spike (S) protein as bait. The sdAbs targeting the cleavage site (CS) and the receptor binding domain (RBD) in S protein efficiently neutralised the infectivity of a pseudovirus expressing SARS-CoV2 S protein. Anti-CS sdAb blocked the virus infectivity by inhibiting proteolytic processing of SARS-CoV2 S protein. Both the sdAbs retained characteristic structure within the pH range of 2 to 12 and remained stable upto 65°C. Furthermore, structural disruptions induced by a high temperature in both the sdAbs were largely reversed upon their gradual cooling and the resulting products neutralised the reporter virus. Our results therefore suggest that targeting CS in addition to the RBD of S protein by sdAbs could serve as a viable option to reduce SARS-CoV2 infectivity and that proteolytic processing of the viral S protein is critical for infection.
Dynlt3, a novel fundamental regulator of melanosome movement, distribution, maturation and transfer
Authors: Aktary Zackie , Conde-Perez Alejandro , Rambow Florian , Marco Mathilde Di , Amblard François , Hurbain Ilse , Raposo Graça , Delevoye Cédric , Coscoy Sylvie , Larue Lionel 
Published: January 2021

ABSTRACTSkin pigmentation is dependent on cellular processes including melanosome biogenesis, transport, maturation and transfer to keratinocytes. However, how the cells finely control these processes in space and time to ensure proper pigmentation remains unclear. Here, we show that a component of the cytoplasmic dynein complex, Dynlt3, is required for efficient melanosome transport, maturation and transfer. In melanocytes with decreased levels of Dynlt3, pigmented melanosomes undergo a more directional (convective) motion leading to their peripheral location in the cell, and are not fully matured. Stage IV melanosomes are more acidic, but still heavily pigmented, resulting in a less efficient melanosome transfer. Finally, the level of Dynlt3 is dependent on β-catenin activity, revealing a novel function of the Wnt/β-catenin signalling pathway during melanocyte and skin pigmentation, by coupling the transport, position and maturation of melanosomes required for their transfer.
Gating current noise produced by Brownian models of a voltage sensor
Authors: Catacuzzeno Luigi , Franciolini Fabio , Bezanilla Francisco , Eisenberg Robert S. 
Published: January 2021

AbstractThe activation of voltage-dependent ion channels is associated with the movement gating charges, that give rise to gating currents. Although gating currents originating from a single channel are too small to be detected, analysis of the fluctuations of macroscopic gating currents originating from a population of channels can make a good guess of their magnitude. The analysis of experimental gating current fluctuations, when interpreted in terms of a Markov model of channel activation, are in accordance with the presence of a main step along the activation pathway carrying 2.3-2.4 e0of charge. To give a physical interpretation to these results and to relate them to the known atomic structure of the voltage sensor domain, we employed a Brownian model of voltage-dependent gating that we recently developed using structural information and applying the laws of electrodynamics. The model was capable to reproduce gating currents and gating current fluctuations essentially similar to those experimentally observed. The detailed study of this model output, also performed by making several simplifications aimed at understanding the basic dependencies of the gating current fluctuations, suggests that in real ion channels the voltage sensor does not move in a fully Markovian regimen due to the relatively low (<5 kT) energy barriers separating successive intermediate states. As a consequence, the simultaneous jump of multiple gating charges through the gating pore becomes frequent, and this occurrence is at the origin of the relatively high single-step charge detected by assuming Markovian behavior.
Chemical synthesis and purification of a non-hydrolyzable CTP analog CTPγS
Authors: Rejzek M , Le Tung B. K. 
Published: January 2021

AbstractSlowly- or non-hydrolyzable analogs of ATP and GTP, for example adenosine 5’-(γ-thio)triphosphate (ATPγS) and guanosine 5’-(γ-thio)triphosphate (GTPγS), have been widely employed to probe the roles of ATP and GTP in biosystems, and these compounds are readily available from commercial sources. In contrast, cytosine 5’-(γ-thio)triphosphate (CTPγS) is not widely available commercially. The recent discovery of ParB as the founding member of a new class of CTPase enzyme (Osorio-Valerianoet al., 2019; Sohet al., 2019) and the possibility of multiple other undiscovered CTPases necessitate the use of the CTPγS to elucidate the roles of CTP hydrolysis in these systems. Here, we adapt a procedure for the synthesis of modified phosphoanhydrides (Hoferet al., 2015) to chemically synthesize and purify a milligram-scale of CTPγS.
The epigenetic eraser LSD1 lies at the apex of a reversible erythroid to myeloid cell fate decision
Authors: Yu Lei , Myers Greggory , Ku Chia-Jui , Schneider Emily , Wang Yu , Singh Sharon A. , Jearawiriyapaisarn Natee , White Andrew , Moriguchi Takashi , Khoriaty Rami , Yamamoto Masayuki , Rosenfeld M. Geoffrey , Pedron Julien , Bushweller John H. , Lim Kim-Chew , Engel James Douglas 
Published: January 2021

AbstractH3K4Me demethylase KDM1a/LSD1 is a therapeutic target for multiple diseases, including the β-globinopathies (sickle cell disease and β-thalassemia) since its inactivation has been shown to lead to robust induction of the fetal globin genes. Here we examined the consequences of conditional inactivation ofLsd1in adult red blood cells using a newGata1creERT2BAC transgene. Loss ofLsd1activity in mice blocked erythroid differentiation and expanded GMP-like cells, converting hematopoietic differentiation potential from an erythroid to a myeloid fate. The analogous phenotype was also observed in human HSPC, coincident with induction of myeloid transcription factors (e.g. PU.1 andCEBPα). Finally, blocking the activity of myeloid transcription factors PU.1 or RUNX1 at the same time as LSD1 reverted myeloid lineage conversion to an erythroid phenotype. The data show that LSD1 promotes erythropoiesis by repressing myeloid cell fate, and that inhibition of myeloid differentiation reverses the lineage switch caused by LSD1 inactivation.
BRN2 is a non-canonical melanoma tumor-suppressor
Authors: Hamm Michael , Sohier Pierre , Petit Valérie , Raymond Jérémy H , Delmas Véronique , Le Coz Madeleine , Gesbert Franck , Kenny Colin , Aktary Zackie , Pouteaux Marie , Rambow Florian , Sarasin Alain , Bellacosa Alfonso , Sanchez-del-Campo Luis , Mosteo Laura , Lauss Martin , Meijer Dies , Steingrimsson Eirikur , Jönsson Göran B , Cornell Robert A , Davidson Irwin , Goding Colin R , Larue Lionel 
Published: January 2021

ABSTRACTWhile the major drivers of melanoma initiation, including activation of NRAS/BRAF and loss ofPTENorCDKN2A, have been identified, the role of key transcription factors that impose altered transcriptional states in response to deregulated signaling is not well understood. The POU domain transcription factor BRN2 is a key regulator of melanoma invasion, yet its role in melanoma initiation remains unknown. Here, we show thatBRN2haplo-insufficiency is sufficient to promote melanoma initiation and metastasis, acting as a non-canonical tumor suppressor. Mechanistically, BRN2 directly modulatesPTENexpression, and PI3K signaling, to drive tumor initiation and progression. Collectively our results reveal that somatic deletion of oneBRN2allele elicits melanoma initiation and progression.SIGNIFICANCEHere, we report frequent mono-allelic loss of the transcription factor BRN2 in human cutaneous melanoma metastases. We developed a mouse model for Brn2-deficient melanoma based on the most common alterations (BrafV600EandPtenloss) in human melanoma and established the role of Brn2 as a functional regulator of tumor initiation, tumor growth, and the formation of metastasesin vivo. Mechanistically, BRN2 loss increases PI3K-signaling through PTEN repression, either via MITF induction or not. Overall, we describe a novel tumor suppressor of high prevalence in human melanoma that regulates several steps ofin vivomelanomagenesis through two previously unknown molecular mechanisms.
The genetic architecture of human cortical folding
Authors: van der Meer Dennis , Kaufmann Tobias , Shadrin Alexey A. , Makowski Carolina , Frei Oleksandr , Roelfs Daniel , Sánchez Jennifer Monereo , Linden David E.J. , Rokicki Jaroslav , de Leeuw Christiaan , Thompson Wesley K. , Loughnan Robert , Fan Chun Chieh , Thompson Paul M. , Westlye Lars T. , Andreassen Ole A. , Dale Anders M. 
Published: January 2021

ABSTRACTThe folding of the human cerebral cortex is a highly genetically regulated process that allows for a much larger surface area to fit into the cranial vault and optimizes functional organization. Sulcal depth is a robust, yet understudied measure of localized folding, previously associated with a range of neurodevelopmental disorders. Here, we report the first genome-wide association study of sulcal depth. Through the Multivariate Omnibus Statistical Test (MOSTest) applied to vertexwise measures from 33,748 participants of the UK Biobank (mean age 64.3 years, 52.0% female) we identified 856 genetic loci associated with sulcal depth at genome-wide significance (α=5×10-8). Comparison with two other measures of cortical morphology, cortical thickness and surface area, indicated that sulcal depth has higher yield in terms of loci discovered, higher heritability and higher effective sample size. There was a large amount of genetic overlap between the three traits, with gene-based analyses indicating strong associations with neurodevelopmental processes. Our findings demonstrate sulcal depth is a promising MRI phenotype that may enhance our understanding of human cortical morphology.
Examining the effect of chronic intranasal oxytocin administration on the neuroanatomy and behavior of three autism-related mouse models
Authors: Lindenmaier Zsuzsa , Ellegood Jacob , Stuive Monique , Easson Kaitlyn , Yee Yohan , Fernandes Darren , Foster Jane , Anagnostou Evdokia , Lerch Jason P. 
Published: January 2021

1AbstractAlthough initially showing great potential, oxytocin treatment has encountered a translational hurdle in its promise of treating the social deficits of autism. Some debate surrounds the ability of oxytocin to successfully enter the brain, and therefore modify neuroanatomy. Moreover, given the heterogeneous nature of autism, treatment will only amerliorate symptoms in a subset of patients. Therefore, to determine whether oxytocin changes brain circuitry, and whether it does so variably, depending on genotype, we implemented a large randomized, blinded, placebo-controlled, preclinical study on chronic intranasal oxytocin treatment in three different mouse models related to autism with a focus on using neuroanatomical phenotypes to assess and subset treatment response. Intranasal oxytocin (0.6IU) was administered daily, for 28 days, starting at 5 weeks of age to the16p11.2deletion,Shank3(exon 4-9) knockout, andFmr1knockout mouse models. Given the sensitivity of structural magnetic resonance imaging (MRI) to the neurological effects of interventions like drugs, along with many other advantages, the mice underwentin vivolongitudinal and high-resolutionex vivoimaging with MRI. The scans included threein vivoT1-weighted, 90um isotropic resolution scans and a T2-weighted, 3D fast spin echo with 40um isotropic resolutionex vivoscan to assess the changes in neuroanatomy using established automated image registration and deformation based morphometry approaches in response to oxytocin treatment. The behavior of the mice was assessed in multiple domains, including social behaviours and repetitive behaviours, among others. Treatment effect on the neuroanatomy did not reach significance, although the pattern of trending effects was promising. No significant effect of treatment was found on social behavior in any of the strains, although a significant effect of treatment was found in theFmr1mouse, with treatment normalizing a grooming deficit. No other treatment effect on behavior was observed that survived multiple comparisons correction. Overall, chronic treatment with oxytocin had limited effects on the three mouse models related to autism, and no promising pattern of response susceptibility emerged.
Using image-based haplotype alignments to map global adaptation of SARS-CoV-2
Authors: Ouellette Tom W. , Shaw Jim , Awadalla Philip 
Published: January 2021

AbstractQuantifying evolutionary change among viral genomes is an important clinical device to track critical adaptations geographically and temporally. We built image-based haplotype-guided evolutionary inference (ImHapE) to quantify adaptations in expanding populations of non-recombining SARS-CoV-2 genomes. By combining classic population genetic summaries with image-based deep learning methods, we show that different rates of positive selection are driving evolutionary fitness and dispersal of SARS-CoV-2 globally. A 1.35-fold increase in evolutionary fitness is observed within the UK, associated with expansion of both the B.1.177 and B.1.1.7 SARS-CoV-2 lineages.
New SHIVs and Improved Design Strategy for Modeling HIV-1 Transmission, Immunopathogenesis, Prevention and Cure
Authors: Li Hui , Wang Shuyi , Lee Fang-Hua , Roark Ryan S. , Murphy Alex I. , Smith Jessica , Zhao Chengyan , Rando Juliette , Chohan Neha , Ding Yu , Kim Eunlim , Lindemuth Emily , Bar Katharine J. , Pandrea Ivona , Apetrei Christian , Keele Brandon F. , Lifson Jeffrey D. , Lewis Mark G. , Denny Thomas N. , Haynes Barton F. , Hahn Beatrice H. , Shaw George M. 
Published: January 2021

AbstractSimian-human immunodeficiency virus (SHIV) chimeras contain the HIV-1 envelope (env) gene embedded within an SIVmac proviral backbone. Previously, we showed that substitution of Env residue 375-Ser by bulky aromatic residues enhances Env binding to rhesus CD4 and enables primary or transmitted/founder (T/F) HIV-1 Envs to support efficient SHIV replication in rhesus macaques (RMs). Here, we test this design strategy more broadly by constructing and analyzing SHIVs containing ten strategically selected primary or T/F HIV-1 Envs corresponding to subtypes A, B, C, AE and AG, each with six allelic variants at position 375. All ten SHIVs bearing wildtype Env375 residues replicated efficiently in human CD4+T cells, but only one of these replicated efficiently in rhesus CD4+T cells. This was a SHIV whose subtype AE Env naturally contained a bulky aromatic His residue at position 375. Replacement of wildtype Env375 residues by Trp, Tyr, Phe or His in the other nine SHIVs uniformly led to efficient replication in rhesus CD4+ Tin vitroand in RMsin vivo. Env375-Trp – the residue found most frequently among SIV strains infecting Old World monkeys – was favored for SHIV replication in RMs, although some SHIVs preferred Env375-Tyr, -His or -Phe. Nine SHIVs containing optimized Env375 alleles were grown large scale in primary activated rhesus CD4+T cells to serve as challenge stocks in preclinical prevention trials. These virus stocks were genetically homogeneous, native-like in Env antigenicity and tier-2 neutralization sensitivity, transmissible by rectal, vaginal, penile, oral or intravenous inoculation routes, and exhibited acute and early replication kinetics that were indistinguishable from HIV-1 infection in humans. Finally, to expedite future SHIV constructions and eliminate short redundant elements intat1andenvgp41 that were spontaneously deleted in chronically infected monkeys, we engineered a simplified second-generation SHIV design scheme and validated it in RMs. Overall, our findings demonstrate that SHIVs bearing primary or T/F Envs with bulky aromatic amino acid substitutions at position Env375 consistently replicate in RMs, recapitulating many features of HIV-1 infection in humans. We further show that SHIV challenge stocks grown in primary rhesus CD4+T cells are efficiently transmitted by mucosal routes common to HIV-1 infection and can be used effectively to test for vaccine efficacy in preclinical monkey trials.
Induced systemic resistance impacts the phyllosphere microbiome through plant-microbe-microbe interactions
Authors: Sommer Anna , Wenig Marion , Knappe Claudia , Kublik Susanne , Fösel Bärbel , Schloter Michael , Vlot A. Corina 
Published: January 2021

AbstractBoth above- and below-ground parts of plants are constantly confronted with microbes, which are main drivers for the development of plant-microbe interactions. Plant growth-promoting rhizobacteria enhance the immunity of above-ground tissues, which is known as induced systemic resistance (ISR). We show here that ISR also influences the leaf microbiome. We compared ISR triggered by the model strainPseudomonas simiaeWCS417r (WCS417) to that triggered byBacillus thuringiensis israelensis(Bti) inArabidopsis thaliana. In contrast to earlier findings, immunity elicited by both strains depended on salicylic acid. Both strains further relied on MYC2 for signal transduction in the plant, while WCS417-elicited ISR additionally depended on SAR-associated metabolites, including pipecolic acid. A metabarcoding approach applied to the leaf microbiome revealed a significant ISR-associated enrichment of amplicon sequence variants with predicted plant growth-promoting properties. WCS417 caused a particularly dramatic shift in the leaf microbiota with more than 50% of amplicon reads representing two bacterial species: WCS417 andFlavobacteriumsp.. Co-inoculation experiments using WCS417 andAt-LSPHEREFlavobacteriumsp. Leaf82, suggest that the proliferation of these bacteria is influenced by both microbial and plant-derived factors. Together, our data connect systemic immunity with leaf microbiome dynamics and highlight the importance of plant- microbe-microbe interactions for plant health.
Standardized quality control workflow to evaluate the reproducibility and differentiation potential of human iPSCs into neurons
Authors: Chen Carol X.-Q. , Abdian Narges , Maussion Gilles , Thomas Rhalena A. , Demirova Iveta , Cai Eddie , Tabatabaei Mahdieh , Beitel Lenore K. , Karamchandani Jason , Fon Edward A. , Durcan Thomas M. 
Published: January 2021

AbstractInduced pluripotent stem cells (iPSCs) derived from human somatic cells have created new opportunities to generate disease-relevant cells. Thus, as the use of patient-derived stem cells has become more widespread, having a workflow to monitor each line is critical. This ensures iPSCs pass a suite of quality control measures, promoting reproducibility across experiments and between labs. With this in mind, we established a multistep workflow to assess our newly generated iPSCs for variations and reproducibility relative to each other and iPSCs obtained from external sources. Our benchmarks for evaluating iPSCs include examining iPSC morphology and proliferation in two different media conditions and evaluating their ability to differentiate into each of the three germ layers, with a particular focus on neurons. Genomic integrity in the human iPSCs was analyzed by G-band karyotyping and a qPCR-based test for the detection of hotspot mutations test. Cell-line identity was authenticated by Short Tandem Repeat (STR) analysis. Using standardized dual SMAD inhibition methods, all iPSC lines gave rise to neural progenitors that could subsequently be differentiated into cortical neurons. Neural differentiation was analyzed qualitatively by immunocytochemistry and quantitatively by qPCR for progenitor, neuronal, cortical, and glial markers. Taken together, we present a multistep quality control workflow to evaluate variability and reproducibility across and between iPSCs.