bluuebunny/crossref_metadata_2025 huggingface dataset:
RFcaller: a machine learning approach combined with read-level features to detect somatic mutations
Authors: Díaz-Navarro Ander , Bousquets-Muñoz Pablo , Nadeu Ferran , López-Tamargo Sara , Beà Silvia , Campo Elias , Puente Xose S.
Published: May 2022

Motivation

The cost reduction in sequencing and the extensive genomic characterization of a wide variety of cancers is expanding the use of tumor sequencing approaches to a wide number of research groups and to the clinical practice. Although specific pipelines have been generated for the identification of somatic mutations, their results usually differ considerably, and a common approach in many projects is to use several callers to achieve a more reliable set of mutations. This procedure is computationally very expensive and time-consuming, and it suffers from the same limitations in sensitivity and specificity as other approaches. Expert revision of mutant calls is therefore required to verify calls that might be used for clinical diagnosis. Machine learning techniques provide a useful approach to incorporate expert-reviewed information for the identification of somatic mutations.

Results

We have developed RFcaller, a pipeline based on machine learning algorithms, for the detection of somatic mutations in tumor-normal paired samples. RFcaller shows high accuracy for the detection of substitutions and indels from whole genome or exome data. It allows the detection of mutations in driver genes missed by other approaches, and has been validated by comparison to deep sequencing and Sanger sequencing. The pipeline is able to analyze a whole genome in a small period of time, and with a small computational footprint.

Availability and implementation

RFcaller is available at GitHub repository (https://github.com/xa-lab/RFcaller) and DockerHub (https://hub.docker.com/repository/docker/labxa/rfcaller).

Contact

xspuente@uniovi.es

Supplementary information

Supplementary data is available online.
Integrated Single-Cell Genotyping and Chromatin Accessibility ChartsJAK2V617FHuman Hematopoietic Differentiation
Authors: Myers Robert M. , Izzo Franco , Kottapalli Sanjay , Prieto Tamara , Dunbar Andrew , Bowman Robert L. , Mimitou Eleni P. , Stahl Maximilian , El Ghaity-Beckley Sebastian , Arandela JoAnn , Raviram Ramya , Ganesan Saravanan , Mekerishvili Levan , Hoffman Ronald , Chaligné Ronan , Abdel-Wahab Omar , Smibert Peter , Marcellino Bridget , Levine Ross L. , Landau Dan A.
Published: May 2022

In normal somatic tissue differentiation, changes in chromatin accessibility govern priming and commitment of precursors towards cellular fates. In turn, somatic mutations can disrupt differentiation topologies leading to abnormal clonal outgrowth. However, defining the impact of somatic mutations on the epigenome in human samples is challenging due to admixed mutated and wildtype cells. To chart how somatic mutations disrupt epigenetic landscapes in human clonal outgrowths, we developed Genotyping of Targeted loci with single-cell Chromatin Accessibility (GoT-ChA). This high-throughput, broadly accessible platform links genotypes to chromatin accessibility at single-cell resolution, across thousands of cells within a single assay. We applied GoT-ChA to CD34+cells from myeloproliferative neoplasm (MPN) patients withJAK2V617F-mutated hematopoiesis, where theJAK2mutation is known to perturb hematopoietic differentiation. Differential accessibility analysis between wildtype andJAK2V617Fmutant progenitors revealed both cell-intrinsic and cell state-specific shifts within mutant hematopoietic precursors. An early subset of mutant hematopoietic stem and progenitor cells (HSPCs) exhibited a cell-intrinsic pro-inflammatory signature characterized by increased NF-κB and JUN/FOS transcription factor motif accessibility. In addition, mutant HSPCs showed increased myeloid/erythroid epigenetic priming, preceding increased erythroid and megakaryocytic cellular output. Erythroid progenitors displayed aberrant regulation of the γ-globin locus, providing an intrinsic epigenetic basis for the dysregulated fetal hemoglobin expression observed in MPNs. In contrast, megakaryocytic progenitors exhibited a more specialized inflammatory chromatin landscape relative to early HSPCs, with increased accessibility of pro-fibrotic JUN/FOS transcription factors. Notably, analysis of myelofibrosis patients treated with JAK inhibitors revealed an overall loss of mutant-specific phenotypes without modifying clonal burden, consistent with clinical responses. Finally, expansion of the multi-modality capability of GoT-ChA to integrate mitochondrial genome profiling and cell surface protein expression measurement enabled genotyping imputation and discovery of aberrant cellular phenotypes. Collectively, we show that theJAK2V617Fmutation leads to epigenetic rewiring in a cell-intrinsic and cell type-specific manner. We envision that GoT-ChA will thus serve as a foundation for broad future explorations to uncover the critical link between mutated somatic genotypes and epigenetic alterations across clonal populations in malignant and non-malignant contexts.
Life history and deleterious mutation rate coevolution
Authors: Avila Piret , Lehmann Laurent
Published: May 2022

The cost of germline maintenance gives rise to a trade-off between lowering the deleterious mutation rate and investing in life history functions. Therefore, life history and the mutation rate coevolve, but this coevolution is not well understood. We develop a mathematical model to analyse the evolution of resource allocation traits, which simultaneously affect life history and the deleterious mutation rate. First, we show that the invasion fitness of such resource allocation traits can be approximated by the basic reproductive number of the least-loaded class; the expected lifetime production of offspring without deleterious mutations born to individuals without deleterious mutations. Second, we apply the model to investigate (i) the coevolution of reproductive effort and germline maintenance and (ii) the coevolution of age-at-maturity and germline maintenance. This analysis provides two resource allocation predictions when exposure to environmental mutagens is higher. First, selection favours higher allocation to germline maintenance, even if it comes at the expense of life history functions, and leads to a shift in allocation towards reproduction rather than survival. Second, life histories tend to be faster, characterized by individuals with shorter lifespans and smaller body sizes at maturity. Our results suggest that mutation accumulation via the cost of germline maintenance can be a major force shaping life-history traits.
Deaza-modification of MR1 ligands modulates recognition by MR1-restricted T cells
Authors: Jin Haihong , Ladd Nicole A. , Peev Andrew M. , Swarbrick Gwendolyn M. , Cansler Meghan , Null Megan , Boughter Christopher T. , McMurtrey Curtis , Nilsen Aaron , Dobos Karen M. , Hildebrand William H. , Lewinsohn Deborah A. , Adams Erin J. , Lewinsohn David M. , Harriff Melanie J.
Published: May 2022

MR1-restricted T (MR1T) cells recognize microbial small molecule metabolites presented on the MHC Class I-like molecule MR1 and have been implicated in early effector responses to microbial infection. As a result, there is considerable interest in identifying chemical properties of metabolite ligands that permit recognition by MR1T cells, for consideration in therapeutic or vaccine applications. Here, we made chemical modifications to known MR1 ligands to evaluate the effect on MR1T cell activation. Specifically, we modified 6,7-dimethyl-8-D-ribityllumazine (DMRL) to generate 6,7-dimethyl-8-D-ribityldeazalumazine (DZ), and then further derivatized DZ to determine the requirements for retaining MR1 surface stabilization and agonistic properties. Interestingly, the IFN-γ response toward DZ varied widely across a panel of T cell receptor (TCR)-diverse MR1T cell clones; while one clone was agnostic toward the modification, most displayed either an enhancement or depletion of IFN-γ production when compared with its response to DMRL. To gain insight into a putative mechanism behind this phenomenon, we used in silico molecular docking techniques for DMRL and its derivatives and performed molecular dynamics simulations of the complexes. In assessing the dynamics of each ligand in the MR1 pocket, we found that DMRL and DZ exhibit differential dynamics of both the ribityl moiety and the aromatic backbone, which may contribute to ligand recognition. Together, our results support an emerging hypothesis for flexibility in MR1:ligand-MR1T TCR interactions and enable further exploration of the relationship between MR1:ligand structures and MR1T cell recognition for downstream applications targeting MR1T cells.
Enteric bacterial infection inDrosophilainduces whole-body alterations in metabolic gene expression independently of the Immune Deficiency (Imd) signalling pathway
Authors: Deshpande Rujuta , Lee Byoungchun , Grewal Savraj S
Published: May 2022

When infected by intestinal pathogenic bacteria, animals initiate both local and systemic defence responses. These responses are required to reduce pathogen burden and also to alter host physiology and behaviour to promote infection tolerance, and they are often mediated through alterations in host gene expression. Here, we have used transcriptome profiling to examine gene expression changes induced by enteric infection with the gram-negative bacteriaPseudomonas entomophila (P.e)in adult femaleDrosophila. We find that infection induces a strong upregulation of metabolic gene expression, including gut and fat body-enriched genes involved in lipid transport, lipolysis, and beta-oxidation, as well as glucose and amino acid metabolism genes. Furthermore, we find that the classic innate immune deficiency (Imd)/Relish/NF-KappaB pathway is not required for, and in some cases limits, these infection-mediated increases in metabolic gene expression. We also see that enteric infection withP.e. down regulates the expression of many transcription factors and cell-cell signaling molecules, particularly those previously shown to be involved in gut-to-brain and neuronal signaling. Moreover, as with the metabolic genes, these changes occurred largely independent of the Imd pathway. Together, our study identifies many metabolic, signaling and transcription factor gene expression changes that may contribute to organismal physiological and behavioural responses to enteric pathogen infection.
Response of the plant core microbiome toFusarium oxysporuminfection and identification of the pathobiome
Authors: Qiu Zhiguang , Verma Jay Prakash , Liu Hongwei , Wang Juntao , Batista Bruna D , Kaur Simranjit , de Araujo Pereira Arthur Prudêncio , Macdonald Catriona A. , Trivedi Pankaj , Weaver Tim , Conaty Warren C. , Tissue David T. , Singh Brajesh K.
Published: May 2022

Plant core microbiomes consist of persistent key members that provide critical host functions, but their assemblages can be interrupted by biotic and abiotic stresses. The pathobiome is comprised of dynamic microbial interactions in response to disease status of the host. Hence, identifying variation in the core microbiome and pathobiome can significantly advance our understanding of microbial-microbial interactions and consequences for disease progression and host functions. In this study, we combined glasshouse and field studies to analyse the soil and plant rhizosphere microbiome of cotton plants (Gossypium hirsutum) in the presence of a cotton-specific fungal pathogen,Fusarium oxysporumf. sp.vasinfectum(FOV). We found that FOV directly and consistently altered the rhizosphere microbiome, but the biocontrol agents enabled microbial assemblages to resist pathogenic stress. Using co-occurrence network analysis of the core microbiome, we identified the pathobiome comprised of the pathogen and key associate phylotypes in the cotton microbiome. Isolation and application of some negatively correlated pathobiome members provided protection against plant infection. Importantly, our field survey from multiple cotton fields validated the pattern and responses of core microbiomes under FOV infection. This study advances key understanding of core microbiome responses and existence of plant pathobiomes, which provides a novel framework to better manage plant diseases in agriculture and natural settings.
Delivery of Circular mRNA via Degradable Lipid Nanoparticles against SARS-CoV-2 Delta Variant
Authors: Huang Ke , Li Na , Li Yingwen , Zhu Jiafeng , Fan Qianyi , Yang Jiali , Gao Yinjia , Liu Yupin , Hou Qiangbo , Gao Shufeng , Wei Ke , Deng Chao , Zuo Chijian , Sun Zhenhua
Published: May 2022

mRNA vaccines have emerged as a most promising and potent platform in the fight against various diseases including the COVID-19 pandemic. However, the intrinsic instability, varying side effects associated with the delivery systems, and continuous emergence of virus variants highlight the urgent need for the development of stable, safe and efficacious mRNA vaccines. In this study, by screening a panel of proprietary biodegradable ionizable lipidoids, we reported on a novel mRNA vaccine (cmRNA-1130) formed from a biodegradable lipidoid with eight ester bonds in the branched tail (AX4) and synthetic circular mRNA (cmRNA) encoding the trimeric Delta receptor binding domain (RBD) of SARS-CoV-2 spike protein for the induction of robust immune activation. The AX4-based lipid nanoparticles (AX4-LNP) revealed much faster elimination rate from liver and spleen in comparison with commercialized MC3-based LNP (MC3-LNP) and afforded normal level of alanine transferase (ALT), aspartate aminotransferase (AST), and creatinine (CRE) in BALB/c mice. Following intramuscular (IM) administration in BALB/c mice, cmRNA-1130 elicited potent and sustained neutralizing antibodies, RBD-specific CD4+ and CD8+ T effector memory cells (Tem), and Th1-biased T cell activations. cmRNA-1130 vaccine showed excellent stability against 6-month storage at 4 □ and freezing-thawing cycles. In brief, our study highlights mRNA vaccines based on cmRNA and biodegradable AX4 lipids hold great potential as superb therapeutic platforms for the treatment of varying diseases.
VPS9D1-AS1 overexpression amplifies intratumoral TGF-β signaling and promotes tumor cell escape from CD8+ T cell killing in colorectal cancer
Authors: Yang Lei , Dong Xichen , Liu Zheng , Tan Jinjing , Huang Xiaoxi , Wen Tao , Qu Hao , Wang Zhenjun
Published: May 2022

Efficacy of immunotherapy is limited in patients with colorectal cancer (CRC) because high expression of tumor-derived transforming growth factor (TGF)-β pathway molecules and interferon (IFN)-stimulated genes (ISGs) promotes tumor immune evasion. Here, we identified a long noncoding RNA (lncRNA), VPS9D1-AS1, which was located in ribosomes and amplified TGF-β signaling and ISG expression. We show that high expression of VPS9D1-AS1 was negatively associated with T lymphocyte infiltration in two independent cohorts of CRC. VPS9D1-AS1 served as a scaffolding lncRNA by binding with ribosome protein S3 (RPS3) and a competing endogenous RNA (ceRNA) to sponge miR-22-5p/514a-3p to increase the translation of TGF-β, TGFBR1, and SMAD1/5/9. VPS9D1-AS1 knockout downregulated OAS1, an ISG gene, which further reduced IFNAR1 levels in tumor cells. Conversely, tumor cells overexpressing VPS9D1-AS1 were resistant to CD8+ T cell killing and lowered IFNAR1 expression in CD8+ T cells. In a conditional overexpression mouse model, VPS9D1-AS1 enhanced tumorigenesis and suppressed the infiltration of CD8+ T cells. Treating tumor-bearing mice with antisense oligonucleotide drugs targeting VPS9D1-AS1 significantly suppressed tumor growth. Our findings indicate that the tumor-derived VPS9D1-AS1/TGF-β/ISG signaling cascade promotes tumor growth and enhances immune evasion and may thus serve as a potential therapeutic target for CRC.
Delineating the transcriptional landscape and clonal diversity of virus-specific CD4+T cells during chronic viral infection
Authors: Zander Ryan , Khatun Achia , Kasmani Moujtaba Y. , Chen Yao , Cui Weiguo
Published: May 2022

CD4+T cells responding to chronic viral infection often acquire a dysfunctional phenotype that is characterized by a progressive loss in Th1 differentiation and function, as well as an upregulation of multiple co-inhibitory receptors. Conversely, CD4+T cells, and particularly Tfh cells, gradually increase their production of IL-21 during chronic viral infection, which is critical to sustain humoral immunity and also effector CD8+T cell responses. Recent evidence further indicates that a memory-like CD4+T cell population also develops in the face of persistent infection, although how the transcriptional landscape of this subset, along with the Th1 and Tfh cell subsets from chronic infection, differ from their acute infection counterparts remains unclear. Additionally, whether cell-intrinsic factors such as TCR usage influence CD4+T cell fate commitment during chronic infection has not previously been studied. Herein, we perform single-cell RNA sequencing (scRNA-seq) combined with single-cell T cell receptor sequencing (scTCR-seq) on virus-specific CD4+T cells during chronic lymphocytic choriomeningitis virus (LCMV) infection. We identify several transcriptionally distinct states among the Th1, Tfh, and memory-like T cell subsets that form at the peak of chronic infection, including the presence of a previously unrecognized Slamf7+subset with cytolytic features, and show that the relative distribution of these populations differs substantially between acute and persistent LCMV infection. Moreover, while the progeny of most T cell clones displays membership within each of these transcriptionally unique populations, overall supporting a one cell-multiple fate model, a small fraction of clones display a biased cell fate decision, suggesting that TCR usage may impact CD4+T cell development during chronic viral infection. Importantly, a comparative analysis further reveals both subset-specific and core gene expression programs that are differentially regulated between CD4+T cells responding to acute and chronic viral infection. Together, these data may serve as a useful framework and allow for a detailed interrogation into the clonal distribution and transcriptional circuits underlying CD4+T cell differentiation during chronic viral infection.
Stromal Hippo-YAP signaling in stem cell niche controls intestinal homeostasis
Authors: Dang Kyvan , Singh Alka , Cotton Jennifer L. , Tao Zhipeng , Liu Haibo , Zhu Lihua J. , Wu Xu , Mao Junhao
Published: May 2022

Intestinal homeostasis is tightly regulated by the reciprocal interaction between gut epithelium and adjacent mesenchyme. The mammalian Hippo-YAP pathway is intimately associated with intestinal epithelial homeostasis and re-generation; however, its role in postnatal gut mesenchyme remains poorly defined. We find that, although removal of the core Hippo kinases Lats1/2 or activation of YAP in adult intestinal smooth muscle has largely no effect; Hippo-YAP signaling in Gli1/PDGFR-expressing intestinal stromal cells is critical to maintain the stem cell niche. We show that YAP/TAZ activation drives over-proliferation and suppresses smooth muscle actin expression in the niche-forming Gli1+ mesenchymal progenitors. In addition, mesenchymal YAP/TAZ activation disrupts the epithelial-mesenchymal crosstalk by promoting Wnt ligand production, leading to epithelial Wnt pathway activation. Our data also reveal that YAP/TAZ are upregulated in the stroma during DSS-induced injury and stromal YAP activation promotes intestinal epithelial regeneration. Altogether, our data identify an essential requirement for stromal Hippo-YAP signaling in the stem cell niche during intestinal homeostasis.

HIGHTLIGHTS

Lats1/2 control proliferation and differentiation of adult gut mesenchymal progenitors.

Mesenchymal YAP/TAZ promotes Wnt ligand production in intestinal stem cell niche.

YAP/TAZ is up-regulated in the mesenchyme during intestinal injury.

Stromal YAP activation promotes intestinal epithelial regeneration.
Cerebellar motor memory expression requires learned alterations to the activity of inhibitory molecular layer interneurons
Authors: Bonnan Audrey , Zhang Ke , Christie Jason M.
Published: May 2022

Procedural memories formed in the cerebellum in response to motor errors depend on changes to Purkinje cell (PC) spiking patterns that correct movement when the erroneous context is repeated. Because molecular layer interneurons (MLIs) inhibit PCs, learning-induced changes to MLI output may participate in reshaping PC spiking patterns. Yet, it remains unclear whether error-driven learning alters MLI activity and whether such changes are necessary for the memory engram. We addressed this knowledge gap by measuring and manipulating MLI activity in the flocculus of both sexes of mice before and after vestibulo-ocular reflex (VOR) adaptation. We found that MLIs are activated during vestibular stimuli and that their population response exhibits a phase shift after the instantiation of gain-increase VOR adaptation, a type of error-driven learning requiring climbing-fiber-mediated instructive signaling. Although acute optogenetic suppression of MLI activity did not affect baseline VOR performance, it negated the expression of gain-increase learning, demonstrating a specific causal role of MLI activity changes in motor memory expression. This effect was transitory; after a multi-day consolidation period, the expression of VOR gain-increase learning was no longer sensitive to MLI activity suppression. Together, our results indicate that error-driven alteration of MLI activity is necessary for labile, climbing-fiber-induced motor memory expression.

Significance Statement

In the cerebellum, motor learning induces an associative memory of the sensorimotor context of an erroneous movement that, when recalled, results in a new pattern of output that improves subsequent trials of performance. Our study shows that error-driven motor learning induces changes to the activity pattern of cerebellar molecular layer interneurons and that this new pattern of activity is required to express the corrective motor memory.
Evaluating Stored Platelet Shape Change Using Imaging Flow Cytometry
Authors: Yakovenko Olga , Özpolat Tahsin , Stratiievska Anastasiia , Bailey S. Lawrence , Miles Jeffrey , Usaneerungrueng Chomkan , Wu Xiaoping , Stolla Moritz
Published: May 2022

Platelets are routinely stored at room temperature for 5-7 days before transfusion. Stored platelet quality is traditionally assessed by Kunicki’s morphology score. This method requires extensive training, experience, and is highly subjective. Moreover, the number of laboratories familiar with this technique is decreasing. Cold storage of platelets has recently regained interest because of potential advantages such as reduced bacterial growth and preserved function. However, platelets exposed to cold temperatures change uniformly from a discoid to a spherical shape, reducing the morphology score outcomes to a binary “spheres versus discs” during cooling. We developed a simpler, unbiased screening tool to measure temperature-induced platelet shape change using imaging flow cytometry. When reduced to two dimensions, spheres appear circular, while discs are detected on a spectrum from fusiform to circular. We defined circular events as having a transverse axis of > 0.8 of the longitudinal axis and fusiform events ≤ 0.8 of the longitudinal axis. We show that most EGTA-treated platelets and spherical beads are detected in the gate for circular events, while fresh platelets are found mainly in the gate for fusiform events. Using this assay, mouse and human platelets show a temperature and time-dependent, two-dimensional shape change from fusiform to circular, consistent with their three-dimensional change from discs to spheres. The method we describe here is a valuable tool for detecting shape change differences in response to agonists or temperature and will help screen for therapeutic measures to mitigate the cold-induced storage lesion.

Plain language summary

What is the context?

Platelets for transfusion are currently stored for 5-7 days at room temperature, increasing the risk for bacterial growth

Cold storage reduces the risk for bacterial growth but reduces circulation time

Stored platelet quality can be assessed by the light microscopy-based Morphology Score, first described in the 1970s

Downsides of the Morphology Score include subjectivity, extensive training, and reduced availability in platelet laboratories.

What is new?

In this study, we provide data showing that the Morphology score is reduced to a binary spheres versus discs response in cold-exposed platelets

We developed an imaging flow cytometry-based approach to quantify platelets’ response to cold based on the two-dimensional projection of the three-dimensional shapes, i.e., fusiform (discoid) versus circular (discoid and spherical)

We provide validation of this approach in mouse and human platelets

We provide evidence for increased temperature sensitivity in mouse platelets

What is the impact?

This study provides an easy and unbiased tool for laboratories working on circumventing the cold-induced storage lesion or documenting spherical shape change in general
Differential modification of the C-terminal tails of different α-tubulins and their importance for microtubule functionin vivo
Authors: Bao Mengjing , Dörig Ruth , Vazquez-Pianzola Paula , Beuchle Dirk , Suter Beat
Published: May 2022

Microtubules (MTs) are built from α-/β-tubulin dimers and used as tracks by kinesin and dynein motors to transport a variety of cargos, such as mRNAs, proteins, and organelles, within the cell. Tubulins are subjected to several post-translational modifications (PTMs). Glutamylation is one of them, and it is responsible for adding one or more glutamic acid residues as branched peptide chains to the C-terminal tails of both α- and β-tubulin. However, very little is known about the specific modifications found on the different tubulin isotypesin vivoand the role of these PTMs in MT transport and other cellular processesin vivo. In this study, we found that inDrosophilaovaries, glutamylation of α-tubulin isotypes occurred clearly on the C-terminal ends of αTub84B and αTub84D (αTub84B/D). In contrast, the ovarian α-tubulin, αTub67C, is not glutamylated. The C-terminal ends of αTub84B/D are glutamylated at several glutamyl side chains in various combinations.Drosophila TTLL5is required for the mono- and poly-glutamylation of ovarian αTub84B/D and with this for the proper localization of glutamylated microtubules. Similarly, proper Kinesin-1 distribution in the germline also depends onTTLL5as well as the refining of Staufen localization and the normal fast ooplasmic streaming with its directional movement, two processes known to depend on Kinesin-1 activities. In the nervous system, the pausing of anterograde axonal transport of mitochondria is affected by an enzymatically dead mutant ofTTLL5. Our results demonstratein vivoroles ofTTLL5in differential glutamylation of α-tubulins and point to thein vivoimportance of α-tubulin glutamylation for Kinesin-1-dependent processes.

α-tubulin glutamylation was established in the C-terminal domain ofDrosophilaαTub84B and αTub84D (αTub84B/D). Multiple glutamyl residues were pinpointed in this domain. The female germline α-tubulin, αTub67C, is, however, not glutamylated.

TTLL5is required for mono- and poly-glutamylation of αTub84B/D.

TTLL5is required for the proper Kinesin heavy chain (Khc) distribution in the germline, and the kinesin-based refinement of Staufen localization and ooplasmic streaming during late oogenesis.

TTLL5is needed for the pausing of anterograde trafficking of mitochondria in axons.
Structural insights for neutralization of BA.1 and BA.2 Omicron variants by a broadly neutralizing SARS-CoV-2 antibody
Authors: Kumar Sanjeev , Patel Anamika , Lai Lilin , Chakravarthy Chennareddy , Valanparambil Rajesh , Davis-Gardner Meredith E. , Edara Venkata Viswanadh , Linderman Susanne , Reddy Elluri Seetharami , Gottimukkala Kamalvishnu , Nayak Kaustuv , Bajpai Prashant , Singh Vanshika , Frank Filipp , Cheedarla Narayanaiah , Verkerke Hans P. , Neish Andrew S. , Roback John D. , Mantus Grace , Goel Pawan Kumar , Rahi Manju , Davis Carl W. , Wrammert Jens , Suthar Mehul S. , Ahmed Rafi , Ortlund Eric , Sharma Amit , Murali-Krishna Kaja , Chandele Anmol
Published: May 2022

The SARS-CoV-2 BA.1 and BA.2 (Omicron) variants contain more than 30 mutations within the spike protein and evade therapeutic monoclonal antibodies (mAbs). Here, we report a receptor-binding domain (RBD) targeting human antibody (002-S21F2) that effectively neutralizes live viral isolates of SARS-CoV-2 variants of concern (VOCs) including Alpha, Beta, Gamma, Delta, and Omicron (BA.1 and BA.2) with IC50 ranging from 0.02 – 0.05 μg/ml. This near germline antibody 002-S21F2 has unique genetic features that are distinct from any reported SARS-CoV-2 mAbs. Structural studies of the full-length IgG in complex with spike trimers (Omicron and WA.1) reveal that 002-S21F2 recognizes an epitope on the outer face of RBD (class-3 surface), outside the ACE2 binding motif and its unique molecular features enable it to overcome mutations found in the Omicron variants. The discovery and comprehensive structural analysis of 002-S21F2 provide valuable insight for broad and potent neutralization of SARS-CoV-2 Omicron variants BA.1 and BA.2.
Medial temporal lobe structure, mnemonic and perceptual discrimination in healthy older adults and those at risk for mild cognitive impairment
Authors: Gellersen Helena M. , Trelle Alexandra N. , Farrar Benjamin G. , Coughlan Gillian , Korkki Saana M. , Henson Richard N. , Simons Jon S.
Published: May 2022

Cognitive tests sensitive to the integrity of the medial temporal lobe (MTL), such as mnemonic discrimination of perceptually similar stimuli, may be useful early markers of risk for cognitive decline in older populations. Perceptual discrimination of stimuli with overlapping features also relies on MTL, but remains relatively unexplored in this context. We assessed mnemonic discrimination in two test formats (Forced Choice, Yes/No) and perceptual discrimination of objects and scenes in 111 community-dwelling older adults at different risk status for cognitive impairment based on neuropsychological screening. We also investigated associations between performance and MTL subregion volume and thickness. The at-risk group exhibited reduced entorhinal thickness and impaired perceptual and mnemonic discrimination. Perceptual discrimination impairment partially explained group differences in mnemonic discrimination and correlated with entorhinal thickness. Executive dysfunction accounted for Yes/No deficits in at-risk adults, demonstrating the importance of test format for the interpretation of memory decline. These results suggest that perceptual discrimination tasks may be useful tools for detecting incipient cognitive impairment related to reduced MTL integrity in non-clinical populations.
More accurate estimation of cell composition in bulk expression through robust integration of single-cell information
Authors: Karimnezhad Ali
Published: May 2022

The rapid single-cell transcriptomic technology developments has led to an increasing interest in cellular heterogeneity within cell populations. Although cell-type proportions can be obtained directly from single-cell RNA sequencing (scRNA-seq), it is costly and not feasible in every study. Alternatively, with fewer experimental complications, cell-type compositions are characterized from bulk RNA-seq data. Many computational tools have been developed and reported in the literature. However, they fail to appropriately incorporate the covariance structures in both scRNA-seq and bulk RNA-seq datasets in use.

We present a covariance-based single-cell decomposition (CSCD) method that estimates cell-type proportions in bulk data through building a reference expression profile based on a single-cell data, and learning gene-specific bulk expression transformations using a constrained linear inverse model. The approach is similar to Bisque, a cell-type decomposition method that was recently developed. Bisque is limited to a univariate model, thus unable to incorporate gene-gene correlations into the analysis. We introduce a more advanced model that successfully incorporates the covariance structures in both scRNA-seq and bulk RNA-seq datasets into the analysis, and fixes the collinearity issue by utilizing a linear shrinkage estimation of the corresponding covariance matrices. We applied CSCD to several publicly available datasets and measured the performance of CSCD, Bisque and six other common methods in the literature. Our results indicate that CSCD is more accurate and comprehensive than most of the existing methods.
Generating parallel representations of position and identity in the olfactory system
Authors: Taisz István , Donà Erika , Münch Daniel , Bailey Shanice N. , Morris Billy J. , Meechan Kimberly I. , Stevens Katie M. , Varela Irene , Gkantia Marina , Schlegel Philipp , Ribeiro Carlos , Jefferis Gregory S.X.E. , Galili Dana S.
Published: May 2022

Sex pheromones are key social signals in most animals. In Drosophila a dedicated olfactory channel senses a male pheromone, cis-vaccenyl acetate (cVA) that promotes female courtship while repelling males. Here we show that flies use separate cVA processing streams to extract qualitative and positional information. cVA olfactory neurons are sensitive to concentration differences in a 5 mm range around a male. Second-order projection neurons detect inter-antennal differences in cVA concentration, encoding the angular position of a male. We identify a circuit mechanism increasing left-right contrast through an interneuron which provides contralateral inhibition. At the third layer of the circuit we identify neurons with distinct response properties and sensory integration motifs. One population is selectively tuned to an approaching male with speed-dependent responses. A second population responds tonically to a male’s presence and controls female mating decisions. A third population integrates a male taste cue with cVA; only a simultaneous presentation of both signals promotes female mating via this pathway. Thus the olfactory system generates a range of complex percepts in discrete populations of central neurons that allow the expression of appropriate behaviors depending on context. Such separation of olfactory features resembles the mammalian what and where visual streams.

Highlights

cVA male pheromone has a 5 mm signaling range, activating two parallel central pathways

Pheromone-sensing neurons have spatial receptive fields sharpened by contralateral inhibition

Position (where) and identity (what) are separated at the 3rd layer of cVA processing

Integrating taste and cVA in sexually dimorphic aSP-g controls female receptivity
Topological analysis of brain dynamics in autism based on graph and persistent homology
Authors: Jafadideh Alireza Talesh , Asl Babak Mohammadzadeh
Published: May 2022

Autism spectrum disorder (ASD) is a heterogeneous disorder with a rapidly growing prevalence. In recent years, the dynamic functional connectivity (DFC) technique has been used to reveal the transient connectivity behavior of ASDs’ brains by clustering connectivity matrices in different states. However, the states of DFC have not been yet studied from a topological point of view. In this paper, this study was performed using global metrics of the graph and persistent homology (PH) and resting-state functional magnetic resonance imaging (fMRI) data. The PH has been recently developed in topological data analysis and deals with persistent structures of data. The structural connectivity (SC) and static FC (SFC) were also studied to better show the advantages of DFC analysis. Significant discriminative features between ASDs and typical controls (TC) were only found in states of DFC. Moreover, the best classification performance was offered by persistent homology-based metrics in two out of four states. In these two states, some networks of ASDs compared to TCs were more segregated and isolated (showing the disruption of network integration in ASDs). The results of this study demonstrated that topological analysis of DFC states could offer discriminative features which were not discriminative in SFC and SC. Also, PH metrics compared to graph global metrics can open a brighter avenue for studying ASD and finding candidate biomarkers.

Highlights

States of dynamic functional connectivity (DFC) were more informative than static FC and structural connectivity when comparing ASDs with controls.

Global metrics of persistent homology (PH) in comparison to graph ones could better distinguish between ASDs and controls.

The PH metrics could offer the best classification performance in dynamic states where the networks of ASDs compared to controls were more segregated and isolated.
Negative emotional behavior during fentanyl abstinence is mediated by adaptations in nucleus accumbens neuron subtypes
Authors: Fox Megan E. , Wulff Andreas B. , Franco Daniela , Choi Eric , Calarco Cali A. , Engeln Michel , Turner Makeda D. , Chandra Ramesh , Rhodes Victoria M. , Thompson Scott M. , Ament Seth A. , Lobo Mary Kay
Published: May 2022

Opioid discontinuation generates a withdrawal syndrome marked by a negative emotional state. Increased anxiety and dysphoria during opioid discontinuation are a significant barrier to achieving long-term abstinence in opioid-dependent individuals. Adaptations in brain-reward circuitry are implicated in the opioid abstinence syndrome, but current knowledge is limited to changes following natural and semi-synthetic opioids. Here we report abstinence from the synthetic opioid fentanyl engenders structural, functional, and molecular plasticity in nucleus accumbens neuron subtypes (MSNs) that mediate negative emotional behaviors. We show fentanyl abstinence causes dendritic atrophy and increased excitatory drive exclusive to D1-receptor containing MSNs. Using subtype specific RNAseq and Weighted Gene Co-Expression Network Analysis, we identified molecular signatures of fentanyl abstinence in MSN subtypes. We found a network of co-expressed genes downregulated selectively in D1-MSNs, and transcriptionally co-regulated by E2F1. We show targeting abstinence-induced molecular changes protects D1-MSNs from maladaptive plasticity and alleviates negative emotional behaviors after fentanyl abstinence.
Remote sensing tools for plant invasions assessment in native tropical forests of a volcanic island
Authors: Guillaume Roussel , Olivier Flores
Published: May 2022

Surveying and monitoring biological invasions by plants can greatly benefit from the application of remote sensing techniques. In tropical insular enviroments however, multiple challenges makes the task difficult. Invasive species can be diverse and many, so that evaluating an overall invasion level may help to distinguish uninvaded native forests from forests invaded at various levels. Also, accessibility can limit the availability of field-based data documenting the ground truth of plant invasions. Here we present a methodological study with the doublefold objective of first estimating an overall index of invasion and level of native forest canopies and second detect two particular exotic (Cinamomum camphora, Lauraceae and Cryptomeria japonica, Taxodiaceae) planted in monospecific stands. The index of overall invasion level comprises four classes derived elsewhere from field observations and expert knowledge. A thematic map provided polygons representing monospecif plantations. Textural features of sub-regional regions of interest and polygons were derived using Haralick coefficients on co-occurrence matrices, and morphological profiles. Classification algorithms were applied to produce invasion classes (k-means) or detect target species (Support Vector Machine, SVM) based on pixels features.
Late Fetal and Newborn Granulopoiesis but not Active Renin is Increased by Maternal Captopril Treatment During Perinatal Kidney Development
Authors: Buckley C , L’Huillier N , Mullins L , Semprini S , Christian H , Mullins JJ
Published: May 2022

Renin expression follows vascular development through the mouse kidney, regressing to glomerular poles by about P10, where renin is stored in dense core granules in juxtaglomerular cells. Homeostatic challenge to blood pressure causes release of active renin from the granules and recruitment of the renin lineage cells. We investigated the response to homeostatic challenge during late fetal development and following birth in a transgenic line expressing GFP under the renin promotor. Pregnant females were treated with water or captopril (30mg/kg/day), which inhibits angiotensin converting enzyme, from E15.5. We found an increase in renin transcription and expression by P1 following captopril treatment, with granulation increased at the glomerular poles and major arteries from E18.5. At P1, the granules showed a wide variation in electron density. Notably, rough endoplasmic reticulum was expanded in vascular smooth muscle cells (VSMCs) of captopril-treated pups at both time-points suggesting increased transcriptional activity. Paracrystalline material was observed in granules of captopril treated fetuses at E18.5 and in both treated and untreated pups at P1. Renin expression and some granules were confirmed in the kidney VSMCs by immuno-gold staining against GFP at E18.5. Importantly, we found no difference in active renin content between kidneys from treated and untreated pups at either age group. We therefore demonstrate a disconnect between granulation and active renin production in newborns when exposed to homeostatic challenge in utero.
Leishmaniainfection-derived extracellular vesicles drive transcription of genes involved in M2 polarization
Authors: Emerson Lisa , Gioseffi Anna , Barker Hailey , Sheppe Austin , Morrill Julianne K. , Edelmann Mariola , Kima Peter
Published: May 2022

Although it is known that the composition of EVs is determined by the characteristics of the cell and its environment, the effects of intracellular infection on EV composition and functions are not well understood. We had previously shown that cultured macrophages infected withLeishmaniaparasites release EVs that contain parasite derived molecules (LiEVs). In this study we show that LdVash, a molecule previously identified in LiEVs fromL. donovaniinfected RAW264.7 macrophages is widely distributed in the liver ofL. donovaniinfected mice. This result shows for the first time that parasite molecules are released in EVs and distributed in infected tissues where they can be endocytosed by cells in the liver, including macrophages that undergo a significant increase in numbers as the infection progresses. To commence evaluating the potential impact of LiEVs on macrophage functions, we show that primary peritoneal exudate macrophages (PECs) express transcripts of signature molecules of M2 macrophages such as arginase 1, IL-10 and IL-4R when incubated with LiEVs. In comparative studies that illustrate how intracellular pathogens control the composition and functions of EVs released from macrophages, we show that EVs from RAW264.7 macrophages infected with Salmonella enterica serovar Typhimurium activate PECs to express transcripts of signature molecules of M1 macrophages such as iNOS, TNF alpha and IFN gamma and not M2 signature molecules. Finally, we show that in contrast to the polarized responses observed in in vitro studies of macrophages, both M1 and M2 signature molecules are detected inL. donovaniinfected livers although they exhibit differences in their spatial distribution in infected tissues.
Post-transcriptional control of SRSF9 promotes the epithelial-to-mesenchymal transition (EMT) in colorectal cancer cells
Authors: Rao Chaitra , Svoboda Robert A. , Southekal Siddesh , Vieira Heidi M. , Huisman Dianna H. , Chatterjee Deepan , Guda Chittibabu , Fisher Kurt W. , Anczuków Olga A , Lewis Robert E.
Published: May 2022

In human colorectal cancer (CRC) cells the Raf/MEK/ERK scaffold Kinase Suppressor of Ras 1 (KSR1)-dependent signaling is required for the epithelial-to-mesenchymal transition (EMT)-like phenotype. Here we show that KSR1 promotes the association of differentially spliced mRNA bearing recognition sites for the Serine/Arginine-Rich (SR) splicing factor SRSF9. CRISPR/Cas9 disruption of KSR1 destabilizes SRSF9 protein, which interacts preferentially with mRNA encoding Epithelial Stromal Interaction 1 (EPSTI1). EPSTI1 protein mediates Ras and KSR1-dependent induction of EMT. Analysis ofEPSTI1splice variants reveals that inclusion of exon 8 is critical to the ability of EPSTI1 to promote the E-to N-cadherin switch and CRC cell motile and invasive behavior. These data reveal a mechanism in CRC cells in which Ras-induced and KSR1-dependent signaling affects pre-mRNA splicing to control behaviors critical to cancer cell dissemination and metastasis.
Anaerobic degradation of acid red 73 by obligately aerobic Aspergillus tabacinus LZ-M though a self-redox mechanism
Authors: Yu Xuan , Zong Simin , Mao Chunlan , Khan Aman , Wang Wenxue , Yun Hui , Zhang Peng , Li Xiangkai
Published: May 2022

Fungi are potential biological resources for refractory organics degradation, but their anaerobic degradation of azo dyes are rarely reported. In this study, a fungus Aspergillus tabacinus LZ-M was isolated grown aerobically and degraded acid red 73 (AR73) with a decolorization rate of 90.28% in 5 days at 400 mg/L of concentration anaerobically. Metabolic pathway showed that AR73 was reduced into 2-hydroxynaphthalene and aniline then mineralized into CO2. The anaerobic self-redox process revealed electrons generated in carbon oxidation and transferred to -C-N= and -N=N, resulting in complete mineralization of AR73 in strain LZ-M. Data of transcriptome analysis showed that the benzene compounds produced from AR73 by declorizing reductase entered the catechol pathway and glycolysis process to mineralize. Enzymes involved in aromatics degradation, glycolysis processes, cytochrome C and quinone oxidoreductases were up-regulate, but the key reductase responsible to cleave AR73 to phenylhydrazine was not found. A novel enzyme Ord95 containing a glutamate S-transferase domain was identified in the unknown genes as a reductase which cleaving -C-N= in AR73 using NADH as electron donor, and three arginines key active sites. These observations reveal a new degradation mechanism of AR73 in strain LZ-M which would be potential candidate for treatment of azo dyes wastewater.

Graphical abstract
Long-duration and non-invasive photoacoustic imaging of multiple anatomical structures in a live mouse using a single contrast agent
Authors: Khadria Anjul , Paavola Chad D. , Zhang Yang , Davis Samuel P. X. , Grealish Patrick , Maslov Konstantin , Shi Junhui , Beals John M. , Oladipupo Sunday S , Wang Lihong V.
Published: May 2022

Long-durationin vivosimultaneous imaging of multiple anatomical structures is useful for understanding physiological aspects of diseases, informative for molecular optimization in preclinical models, and has potential applications in surgical settings to improve clinical outcomes. Previous studies involving simultaneous imaging of multiple anatomical structures, e.g., blood and lymphatic vessels as well as peripheral nerves and sebaceous glands, have used genetically engineered mice, which require expensive and time-consuming methods. Here, an IgG4 isotype control antibody is labeled with a near-infrared dye and injected into a mouse ear to enable simultaneous visualization of blood and lymphatic vessels, peripheral nerves, and sebaceous glands for up to 3 hours using photoacoustic microscopy. For multiple anatomical structure imaging, peripheral nerves and sebaceous glands are imaged inside the injected dye-labeled antibody mass while the lymphatic vessels are visualized outside the mass. The efficacy of the contrast agent to label and localize deep medial lymphatic vessels and lymph nodes using photoacoustic computed tomography is demonstrated. The capability of a single injectable contrast agent to image multiple structures for several hours will potentially improve preclinical therapeutic optimization, shorten discovery timelines, and enable clinical treatments.