bluuebunny/crossref_metadata_2025 huggingface dataset:
Deep Learning in Spatial Transcriptomics: Learning From the Next Next-Generation Sequencing
Authors: Heydari A. Ali , Sindi Suzanne S.
Published: March 2022

Spatial transcriptomics (ST) technologies are rapidly becoming the extension of single-cell RNA sequencing (scRNAseq), holding the potential of profiling gene expression at a single-cell resolution while maintaining cellular compositions within a tissue. Having both expression profiles and tissue organization enables researchers to better understand cellular interactions and heterogeneity, providing insight into complex biological processes that would not be possible with traditional sequencing technologies. The data generated by ST technologies are inherently noisy, high-dimensional, sparse, and multi-modal (including histological images, count matrices, etc.), thus requiring specialized computational tools for accurate and robust analysis. However, many ST studies currently utilize traditional scRNAseq tools, which are inadequate for analyzing complex ST datasets. On the other hand, many of the existing ST-specific methods are built upon traditional statistical or machine learning frameworks, which have shown to be sub-optimal in many applications due to the scale, multi-modality, and limitations of spatially-resolved data (such as spatial resolution, sensitivity and gene coverage). Given these intricacies, researchers have developed deep learning (DL)-based models to alleviate ST-specific challenges. These methods include new state-of-the-art models in alignment, spatial reconstruction, and spatial clustering among others. However, deep-learning models for ST analysis are nascent and remain largely underexplored. In this review, we provide an overview of existing state-of-the-art tools for analyzing spatially-resolved transcriptomics, while delving deeper into the DL-based approaches. We discuss the new frontiers and the open questions in this field and highlight the domains in which we anticipate transformational DL applications.
Diversity of sex chromosomes in Sulawesian medaka fishes
Authors: Ansai Satoshi , Montenegro Javier , Masengi Kawilarang W.A. , Nagano Atsushi J. , Yamahira Kazunori , Kitano Jun
Published: March 2022

Recent genetic and genomic studies have revealed tremendous diversity in sex chromosomes across diverse taxa. Although theoretical studies predict that sex chromosome evolution can drive the evolution of sexual dimorphism, empirical studies are still limited. A taxonomic group that shows diversity in both sex chromosomes and sexual dimorphism provides excellent opportunity to investigate the link between the evolution of sex chromosomes and sexual dimorphism. The medaka fishes (family Adrianichthyidae) exhibit both rapid sex chromosome turnovers and diversification of sexually dimorphic traits. In the present study, we investigated the sex chromosomes of 13 Oryzias species from Sulawesi, Indonesia, that have diversified in sexual dichromatism. Using pooled sequencing we found sex chromosomes in 9 species that all had XY systems, with a few species being possibly modified by multiple loci. Seven species (O. woworae, O. asinua, O. wolasi, O. matanensis, O. celebensis, O. hadiatyae, and O. dopingdopingensis) share linkage group (LG) 24 as sex chromosomes; however, they differed in the length and magnitude of sequence divergence between the X and Y chromosomes. The sex chromosome of O. eversi was LG4, which has not been reported as a sex chromosome in any other medaka species. In O. sarasinorum, LG16 and LG22 are associated with sex. Although LG16 was found to be sex-linked in another medaka species previously examined, the sex-determining regions did not overlap. Frequent turnovers and the great diversity of the sex chromosomes make Sulawesian medaka species a model system for investigating the roles of sex chromosome evolution in the diversification of sexual dimorphism.
Psilocybin induces spatially constrained alterations in thalamic functional organizaton and connectivity
Authors: Gaddis Andrew , Lidstone Daniel E. , Nebel Mary Beth , Griffiths Roland , Mostofsky Stewart H. , Mejia Amanda , Barrett Frederick
Published: March 2022

Background

Serotonin 2A receptor (5-HT2AR) agonist psychedelics including psilocybin and LSD (“classic” psychedelics) evoke acute alterations in perception and cognition. Altered thalamocortical connectivity has been proposed to underlie these effects, which is supported by some functional MRI (fMRI) studies. Likely due to sample size limitations, these studies have treated the thalamus as a unitary structure, despite known differential 5-HT2ARexpression and functional specificity of different intrathalamic nuclei. Independent Component Analysis (ICA) has been employed to generate functional subdivisions of the thalamus from resting state fMRI (rsfMRI) data. This report utilizes a novel data-sparing ICA approach in order to examine psilocybin-induced changes in intrathalamic functional organization and thalamocortical connectivity.

Methods

Baseline rsfMRI data (n=38) was utilized to generate a template, which was then applied in a novel ICA-based analysis of the acute effects of psilocybin on intra- and extra-thalamic functional organization and connectivity in a smaller sample (n=18). Correlations with subjective reports of drug effect and comparisons with a previously reported analytic approach (treating the thalamus as a single functional unit) were conducted.

Results

Several intrathalamic components showed significant psilocybin-induced alterations in intrathalamic spatial organization, largely localized to the mediodorsal and pulvinar nuclei, and correlated with reported subjective effects. These same components demonstrated alterations in thalamocortical connectivity, largely with visual and default mode networks. Analysis in which the thalamus is treated as a singular unitary structure showed an overall numerical increase in thalamocortical connectivity, consistent with previous literature using this approach, but this increase did not reach statistical significance.

Conclusions

Utilization of a novel analytic approach demonstrated changes in intra- and extra-thalamic functional organization and connectivity of intrathalamic nuclei and cortical networks known to express the 5-HT2AR. Given that these changes were not observed using whole-thalamus analyses, it seems that psilocybin may cause widespread but modest increases in thalamocortical connectivity that are offset by strong focal decreases in functionally relevant intrathalamic nuclei.
Shaping the Genome via Lengthwise Compaction, Phase Separation, and Lamina Adhesion
Authors: Brahmachari Sumitabha , Contessoto Vinícius , Di Pierro Michele , Onuchic José N.
Published: March 2022

The link between genomic structure and biological function is yet to be consolidated, it is, however, clear that physical manipulation of the genome, driven by the activity of a variety of proteins, is a crucial step. To understand the consequences of the physical forces underlying genome organization, we build a coarse-grained polymer model of the genome, featuring three fundamentally distinct classes of interactions: lengthwise compaction, i.e., compaction of chromosomes along its contour, self-adhesion among epigenetically similar genomic segments, and adhesion of chromosome segments to the nuclear envelope or lamina. We postulate that these three types of interactions sufficiently represent the concerted action of the different proteins organizing the genome architecture and show that an interplay among these interactions can recapitulate the architectural variants observed across the tree of life. The model elucidates how an interplay of forces arising from the three classes of genomic interactions can drive drastic, yet predictable, changes in the global genome architecture, and makes testable predictions. We posit that precise control over these interactions in vivo is key to the regulation of genome architecture.
P4HA2: A link between tumor-intrinsic hypoxia, partial EMT and collective migration
Authors: Aggarwal Vaishali , Sahoo Sarthak , Donnenberg Vera S. , Chakraborty Priyanka , Jolly Mohit Kumar , Sant Shilpa
Published: March 2022

Epithelial-to-mesenchymal transition (EMT), a well-established phenomenon studied across pan-cancer types, has long been known to be a major player in driving tumor invasion and metastasis. Recent studies have highlighted the importance of partial EMT phenotypes in metastasis [1]. Initially thought as a transitional state between epithelial and mesenchymal phenotypic states, partial EMT state is now widely recognized as a key driver of intra-tumoral heterogeneity and phenotypic plasticity, further accelerating tumor metastasis and therapeutic resistance. However, how tumor microenvironments regulate partial EMT phenotypes remains unclear. We have developed unique size-controlled three-dimensional microtumor models that recapitulate tumor-intrinsic hypoxia and the emergence of collectively migrating cells. In this study, we further interrogate these microtumor models to understand how tumor-intrinsic hypoxia regulates partial EMT and collective migration in hypoxic large microtumors fabricated from T47D breast cancer cells. We also compared global gene expression profiles of hypoxic, migratory microtumors to that of non-hypoxic, non-migratory microtumors at early and late time-points. Using our microtumor models, we identified unique gene signatures for tumor-intrinsic hypoxia (early versus late), partial EMT and migration (pre-migratory versus migratory phenotype). Through differential gene expression analysis between the microtumor models with an overlap of hypoxia, partial EMT and migration signatures, we identified prolyl 4-hydroxylase subunit 2 (P4HA2), a hypoxia responsive gene, as a central regulator common to hypoxia, partial EMT and collective migration. Further, the inhibition of P4HA2 significantly blocked collective migration in hypoxic microtumors. Thus, using the integrated computational-experimental analysis, we identify the key role of P4HA2 in tumor-intrinsic hypoxia-driven partial EMT and collective migration.
Case Study of Single-cell Protein Activity Based Drug Prediction for Precision Treatment of Cholangiocarcinoma
Authors: Obradovic Aleksandar , Tomassoni Lorenzo , Yu Daoqi , Guillan Kristina , Souto Katie , Fraser Elise , Bates Susan , Drake Charles G. , Saenger Yvonne , Cruz Filemon Dela , Kung Andrew , Califano Andrea
Published: March 2022

Cholangiocarcinoma is a rare, aggressive malignancy with limited treatment options, due to a paucity of actionable mutations and low response to immune checkpoint inhibitors. Furthermore, its extreme heterogeneity prevents identification of actionable dependencies from bulk-tissue profiles. To address these challenges, we introduce a highly generalizable, single-cell framework for the mechanism-based prioritization of drugs to treat rare, highly heterogeneous tumors. Analysis of transformed cells, accounting for only 10% of a cholangiocarcinoma patient biopsy revealed three molecularly-distinct subpopulations, predicted to be sensitive to four drugs by regulatory network-based analysis. Validation in a low-passage, patient-derived xenograft (PDX) from the same patient confirmed tumor growth rate control by two of these drugs (plicamycin and dacinostat) and further validated predicted subpopulation-specific effects, suggesting they may represent promising candidates for follow-up clinical trials, either alone or in combination with current standard-of-care chemotherapies. The proposed approach can be generalized to elucidate complementary dependencies of rare, heterogeneous tumors, at the single cell level.
A Standardized Framework for Taxonomy Analysis in Bacterial Kingdom based on Protein Domain
Authors: Wang Boqian , Zhou Jianglin , Jin Yuan , Hu Mingda , Zhao Yunxiang , Wang Xin , Liang Long , Yue Junjie , Ren Hongguang
Published: March 2022

The taxonomy research on the bacterial kingdom is important and can be usually conducted by the analysis on conserved genes, 16s rRNA, protein domain, and so on. Comparatively, the protein domains maintain a most direct relationship with phenotypes. In this paper, based on the protein domain, we propose a 3-step framework to standardize the classification process of bacteria. Different model candidates are involved and discussed in each step. By comparing the classification results with existing taxonomy, we select the most appropriate candidate to improve the framework, and furthermore, discuss their biological significance. Finally, we put forward taxonomy suggestions based on the best classification results.

Importance

We standardize a 3-step framework to carry out bacterial taxonomy research based on protein domain. Furthermore, we filter out the best solution in each step that can together generate the most appropriate classification result, and at the same time, we discuss the biological significant it indicates. Finally, we propose suggestions on NCBI bacterial taxonomy based on the classification results.
Development of a vocal biomarker for fatigue monitoring in people with COVID-19
Authors: Elbéji Abir , Zhang Lu , Higa Eduardo , Fischer Aurélie , Despotovic Vladimir , Nazarov Petr V. , Aguayo Gloria A. , Fagherazzi Guy
Published: March 2022

Objective

To develop a vocal biomarker for fatigue monitoring in people with COVID-19.

Design

Prospective cohort study.

Setting

Predi-COVID data between May 2020 and May 2021.

Participants

A total of 1772 voice recordings was used to train an AI-based algorithm to predict fatigue, stratified by gender and smartphone’s operating system (Android/iOS). The recordings were collected from 296 participants tracked for two weeks following SARS-CoV-2 infection.

primary and secondary outcome measures

Four machine learning algorithms (Logistic regression, k-nearest neighbors, support vector machine, and soft voting classifier) were used to train and derive the fatigue vocal biomarker. A t-test was used to evaluate the distribution of the vocal biomarker between the two classes (Fatigue and No fatigue).

Results

The final study population included 56% of women and had a mean (±SD) age of 40 (±13) years. Women were more likely to report fatigue (P<.001). We developed four models for Android female, Android male, iOS female, and iOS male users with a weighted AUC of 79%, 85%, 86%, 82%, and a mean Brier Score of 0.15, 0.12, 0.17, 0.12, respectively. The vocal biomarker derived from the prediction models successfully discriminated COVID-19 participants with and without fatigue (t-test P<.001).

Conclusions

This study demonstrates the feasibility of identifying and remotely monitoring fatigue thanks to voice. Vocal biomarkers, digitally integrated into telemedicine technologies, are expected to improve the monitoring of people with COVID-19 or Long-COVID.
Impact and cost-effectiveness of frequent HIV re-testing among key populations in Viet Nam: a modeling study
Authors: Green Dylan , Coomes David , Barnabas Ruanne V. , Sharma Monisha , Barr-Dichiara Magdalena , Jamil Muhammad S. , Owiredu Morkor Newman , Macdonald Virginia , Nguyen Van , Hai Son Vo , Wi Theodora E. , Johnson Cheryl , Drake Alison L.
Published: March 2022

Background

HIV testing and counseling is a key component of HIV prevention and the entry point into the treatment cascade, which improves for individual clinical outcomes and reduces onward HIV transmission. Current guidelines recommend at least annual testing for key populations. More frequent testing could provide health benefits, but these additional services increase the program the cost-effectiveness is not well-evaluated.

Methods

We used a compartmental mathematical model to simulate the health and economic impact of HIV testing one to four times per year for men who have sex with men, people who inject drugs, and female sex workers in Viet Nam. Model outcomes included costs, HIV infections, HIV-related deaths, and disability-adjusted life years (DALYs) associated with each scenario. We used an opportunity cost-based cost-effectiveness threshold of US $2,255 per DALY averted, discounted costs and health benefits at 3% annually, and used a time horizon from 2021 to 2030 to calculate incremental cost-effectiveness ratios (ICERs).

Results

Compared to the baseline scenario, more frequent HIV testing was estimated to incrementally avert 10.2%, 5.2%, 3.0%, and 1.6% discounted infections for one-, two-, three-, and four-tests per year, respectively. ICERs associated with each scenario ranged from $464, $1,190, $1,762, and $2,727 per DALY averted for one-, two-, three-, and four-tests per year, respectively.

Conclusions

Increased HIV testing frequency for key populations was projected to avert HIV incidence, mortality, and disability in Viet Nam and was cost-effective. Settings with a similar context should consider strategies on how to optimize retesting among key populations.
Treatment Outline and Clinical Outcome of Hospitalized COVID-19 Patients: Experiences from a Combined Military Hospital of Bangladesh
Authors: Mahboob Sabiha , Johora Fatema , Abbasy Asma Akter , Jeenia FatihaTasmin , Ali Mohammad , Kabir Md Humayun , Sojib Ferdaush Ahmed , Ferdoush Jannatul
Published: March 2022

Background

Global knowledge of treatment and outcomes of COVID-19 has been evolving since the onset of the pandemic.

Materials and Methods

The objective of this cross-sectional study was to explore treatment and outcome of COVID-19 patients admitted in a Combined Military Hospital of Bangladesh. Data were collected from treatment records of patients of the CMH Bogura during the period of June 2020 to August 2020. Total 219 RT-PCR positive admitted patients were included as study population.

Result

Among 219 patients, 78.6% were male and 21.5% were female, mean age of patients was 34.3 ± 12.2. About14.6% patients had one or more comorbidities. Most (83.1%) of the admitted patients were diagnosed as mild cases. Antimicrobials were used in 98.8% cases, and frequent use of doxycycline (80.4%) and ivermectine (77.2%) was found. Anticoagulant and steroid therapy were used in 42.0% and 15.5% patients respectively. O2 therapy was required in 6.0% cases and intensive care unit (ICU) support was needed in 2.3% cases.Duration of hospital stay was 12.1± 4.4 days and 100% of patients were discharged from hospital. There was no single mortality during the study period.

Conclusion

High prevalence of antimicrobials use was observed among the hospitalized COVID-19 patients in this single center study.Supportive care was effective with no incidence of mortality.
APOEε4 and exercise interact to influence systemic and cerebral risk factors for dementia
Authors: Foley Kate E. , Diemler Cory A. , Hewes Amanda A. , Garceau Dylan T. , Sasner Michael , Howell Gareth R.
Published: March 2022

INTRODUCTION

APOEε4 is the strongest genetic risk factor for Alzheimer’s disease and related dementias (ADRDs) affecting many different pathways that lead to cognitive decline. Exercise is one of the most widely proposed prevention, and intervention strategies to mitigate risk and symptomology of ADRDs. Importantly, exercise and APOEε4 affect similar processes on the body and brain. While both APOEε4, and exercise have been studied extensively, their interactive effects are not well understood.

METHODS

To address this, male and female APOEε3/ε3, APOEε3/ε4 and APOEε4/ε4 mice ran voluntarily from wean (1mo) to midlife (12mo). Longitudinal and cross-sectional phenotyping was performed on the periphery and the brain, on markers of risk for dementia such as weight, body composition, circulating cholesterol composition, activities of daily living, energy expenditure, and cortical and hippocampal transcriptional profiling.

RESULTS

Data revealed chronic running decreased age-dependent weight gain, lean and fat mass, and serum LDL concentration dependent on APOE genotype. Additionally, murine activities of daily living and energy expenditure were significantly influenced by an interaction between APOE genotype and running in both sexes. Transcriptional profiling of the cortex and hippocampus predicted that APOE genotype and running interact to affect numerous biological processes including vascular integrity, synaptic/neuronal health, cell motility, and mitochondrial metabolism, in a sex-specific manner.

DISCUSSION

These data provide compelling evidence that APOE genotype should be considered for population-based strategies that incorporate exercise to prevent ADRDs.
Speeded Inference Game: Opening a new chapter in the assessment of error awareness
Authors: Niessen Eva , Wickert Jonas , Schober Martin , Fink Gereon R. , Stahl Jutta , Weiss Peter H.
Published: March 2022

Influential theories on error processing assume that when we conduct errors adaptive processes are triggered to improve our behaviour and prevent errors in the future. These processes appear to be more effective after participants have detected an error. Therefore, the assessment of error awareness allowing a differential analysis of detected and undetected errors in the context of cognitive control and behavioural adjustments has gained more and more attention in the past decades. A common methodological challenge posed on all studies investigating error detection is that the number of undetected errors is usually relatively low.

Here, we introduce a gamified experimental task that uses an adaptive algorithm to generate a robust and stable amount of errors with a high rate of undetected errors. Further, we were able to identify error types, which interestingly differed in terms of their detection rate. Moreover, the game-like appearance of the novel experimental task led to highly motivated participants. The results of the first study were replicated and extended by a second behavioural study. Notably, in study 2, a change in task design specifically modulated error detection, while these changes did not affect the total error rate.

Potential applications of the open-source code will be discussed. With this newly developed paradigm, we wish to lay the ground for future research to understand better (neural) processes associated with error awareness.
Deletion of proU suppresses proQ phenotypes in Escherichia coli
Authors: Smith-Frieday Michelle N. , Kerr Craig H. , Wood Janet M.
Published: March 2022

The ProQ protein interacts as an RNA chaperone with diverse RNA molecules in Escherichia coli. ProQ is implicated in the bacterial osmotic stress response. When the osmotic pressure is high, cells maintain their hydration by accumulating organic solutes denoted osmolytes. Transporters ProP and ProU (which is ProVWX) mediate osmolyte accumulation by Escherichia coli. Mutations at proQ impair ProP activity by reducing ProP levels (the ProQ transport phenotype) but do not impair ProU activity or reduce the level of ProX. The proQ- bacteria are longer than proQ+ bacteria during growth in either low or high salinity medium and they grow slowly at high salinity (the ProQ growth phenotype). In addition, spherical cells with crescent-shaped, nucleic acid-rich foci appear and cells lyse (the ProQ morphological phenotypes). In this work, the proQ transport phenotype was suppressed by deletions of proU, or by an insertion of IS5 in proU, when proP was expressed from the chromosome or from the heterologous, plasmid-based PBAD promoter. A point mutation disrupting the Walker B motif of ProV inactivated ProU but did not suppress the transport phenotype. ProP activities and ProP levels varied in parallel, so proQ and proU act at the same level to regulate ProP expression. Deletion of the proU operon also suppressed the growth and morphological phenotypes. The proU locus may overlap the gene encoding a regulatory sRNA that acts with ProQ, contributing to cellular morphogenesis and osmotic stress tolerance, or the relationship between ProQ and proU may be indirect.
Spatiotemporal changes in genetic diversity and structure of a recent fish invasion in eastern North America
Authors: Bernos Thaïs A. , Avlijaš Sunčica , Hill Jaclyn , Morissette Olivier , Ricciardi Anthony , Mandrak Nicholas E. , Jeffries Kenneth M.
Published: March 2022

Introduced and geographically expanding populations experience similar eco-evolutionary challenges, including founder events, genetic bottlenecks, and novel environments. Theory predicts that reduced genetic diversity resulting from such genetic phenomena limits the colonization success of introduced populations. We examined an invasive population of a Eurasian freshwater fish, Tench (Tinca tinca), that has been expanding geographically in eastern North America for three decades. Using genomic data, we evaluated evidence for single versus multiple introductions and the connectivity of the population across the entire range in which it has been spreading. Tench exhibited low levels of genetic diversity, a lack of marked population subdivision across time and space, and evidence of a recent genetic bottleneck. These results suggest that the invasion stemmed from a single introduction, consistent with the reported invasion history. Furthermore, the large genetic neighbourhood size and weak within-population genetic substructure suggest high connectivity across the invaded range, despite the large area occupied, and no evidence of substantial diminution of genetic diversity from the invasion core to the margins. As eradicating the species within a ~112 km radius would be necessary to prevent recolonization, eradicating Tench is likely not feasible at watershed—and possibly local—scales. Management should instead focus on reducing abundance in priority conservation areas to mitigate adverse impacts. Our study supports the argument that introduced populations can thrive despite recent bottlenecks and low levels of genetic diversity, and it suggests that landscape heterogeneity and population demographics can generate variability in spatial patterns of genetic diversity within a single range expansion.
Discovery of compounds that inhibit SARS-CoV-2 Mac1-ADP-ribose binding by high-throughput screening
Authors: Roy Anu , Alhammad Yousef M. , McDonald Peter , Johnson David K. , Zhuo Junlin , Wazir Sarah , Ferraris Dana , Lehtiö Lari , Leung Anthony K.L. , Fehr Anthony R.
Published: March 2022

The emergence of several zoonotic viruses in the last twenty years, especially the pandemic outbreak of SARS-CoV-2, has exposed a dearth of antiviral drug therapies for viruses with pandemic potential. Developing a diverse drug portfolio will be critical for our ability to rapidly respond to novel coronaviruses (CoVs) and other viruses with pandemic potential. Here we focus on the SARS-CoV-2 conserved macrodomain (Mac1), a small domain of non-structural protein 3 (nsp3). Mac1 is an ADP-ribosylhydrolase that cleaves mono-ADP-ribose (MAR) from target proteins, protects the virus from the anti-viral effects of host ADP-ribosyltransferases, and is critical for the replication and pathogenesis of CoVs. In this study, a luminescent-based high-throughput assay was used to screen ∼38,000 small molecules for those that could inhibit Mac1-ADP-ribose binding. We identified 5 compounds amongst 3 chemotypes that inhibit SARS-CoV-2 Mac1-ADP-ribose binding in multiple assays with IC50 values less than 100µM, inhibit ADP-ribosylhydrolase activity, and have evidence of direct Mac1 binding. These chemotypes are strong candidates for further derivatization into highly effective Mac1 inhibitors.
Therapeutic targeting of differentiation state-dependent metabolic vulnerabilities in DIPG
Authors: Mbah Nneka E. , Myers Amy L. , Chung Chan , Thompson Joyce K. , Hong Hanna S. , Sajjakulnukit Peter , Nwosu Zeribe C. , Shan Mengrou , Sweha Stefan R. , Maydan Daniella D. , Chen Brandon , Zhang Li , Magnuson Brian , Zui Zirui , Wahl Daniel R. , Franchi Luigi , Agnihotri Sameer , Koschmann Carl J. , Venneti Sriram , Lyssiotis Costas A.
Published: March 2022

H3K27M diffuse intrinsic pontine gliomas (DIPG) exhibit cellular heterogeneity comprising less-differentiated, stem-like glioma cells that resemble oligodendrocyte precursors (OPC) and more differentiated astrocyte (AC)-like cells. H3K27M DIPG stem-like cells exhibit tumor-seeding capabilities in vivo, a feature lost or greatly diminished in the more differentiated AC-like cells. In this study, we established isogenic in vitro models of DIPG that closely recapitulated the OPC-like and AC-like phenotypes of DIPG cells. Using these tools, we performed transcriptomics, metabolomics, and bioenergetic profiling to identify metabolic programs operative in the different cellular states. From this, we defined new strategies to selectively target metabolic vulnerabilities within the specific tumor populations. Namely, we showed that the AC-like cells exhibited a more mesenchymal phenotype and were thus sensitized to ferroptotic cell death. In contrast, OPC-like cells upregulated cholesterol metabolism and mitochondrial oxidative phosphorylation (OXPHOS) and were accordingly more sensitive to statins and OXPHOS inhibitors. Additionally, statins and OXPHOS inhibitors showed efficacy and extended survival in preclinical orthotopic models established with stem-like H3K27M DIPG cells. Together, this study demonstrates that cellular subtypes within DIPGs harbor distinct metabolic vulnerabilities that can be uniquely and selectively targeted for therapeutic gain.
Double knockout CRISPR screen in cancer resistance to T cell cytotoxicity
Authors: Park Jonathan J. , Codina Adan , Ye Lupeng , Lam Stanley , Guo Jianjian , Clark Paul , Zhou Xiaoyu , Peng Lei , Chen Sidi
Published: March 2022

Immunotherapy has transformed cancer treatments; however, a large fraction of patients encounter resistance. Such resistance is mediated by complex factors, often involving interactions between multiple genes. Thus, it is crucially important to identify genetic interactions between genes that are significantly mutated in cancer patients and those involved in immune responses, ideally the ones that currently have chemical compounds for direct targeting. To systematically interrogate such genetic interactions that mediate cancer cells’ response to T cell killing, we designed an asymmetric CRISPR/Cas9 dual perturbation library targeting the matched combinations between significantly mutated tumor suppressors and immune resistance genes. We performed a combinatorial double knockout screen on 1,159 gene pairs and identified those where joint loss-of-function renders altered cellular response to T cell cytotoxicity. With individual double knockout constructs we validated these genetic interactions including Jak1-Trp53, Jak1-Kmt2d, and Ifngr1-Kmt2d. Interactions between significantly mutated tumor suppressors and potentially druggable immune resistance genes may offer insights on potential new concepts of how to target clinically relevant cancer mutations with currently available agents. This study also provides a technology platform and an asymmetric CRISPR double knockout library for interrogating genetic interactions between cancer mutations and immune resistance pathways under various settings.
Impact of Delta and Vaccination on SARS-CoV-2 transmission risk: Lessons for Emerging Breakthrough infections
Authors: Sriraman Kalpana , Shaikh Ambreen , Vaswani Smriti , Mestry Tejal , Patel Grishma , Sakthivel Shalini , Oswal Vikas , Kadam Pratibha , Nilgiriwala Kayzad , Shah Daksha , Gomare Mangala , Mistry Nerges
Published: March 2022

With the continuous emergence of SARS-CoV-2 variants of concern and implementation of mass-scale interventions like vaccination, understanding factors affecting disease transmission has critical implications for control efforts. Here we used a simple adapted N95 mask sampling method to demonstrate the impact of circulating SARS-CoV-2 variants and vaccination on 92 COVID-19 patients to expel virus into the air translating to a transmission risk. Between July and September 2021, when the Delta was the dominant circulating strain in Mumbai, we noted a two-fold increase in the proportion of people expelling virus (95%), about an eighty-fold increase in median viral load and a three-fold increase in high emitter type (41%; people expelling >1000 viral copy numbers in 30 minutes) compared to initial strains of 2020. Eight percent of these patients continued to be high emitters even after eight days of symptom onset, suggesting a probable increased transmission risk for Delta strain even at this stage. There was no significant difference in expelling pattern between partial, full and un-vaccinated individuals suggesting similar transmission risk. We noted significantly more infections among vaccinated study patients and their household members than unvaccinated, probably due to increased duration from vaccination and/or increased risk behaviour upon vaccination due to lower perceived threat. This study provides biological evidence for possible continued transmission of the Delta strain even with vaccination, emphasizing the need to continue COVID-19 appropriate behaviour. The study also indicates that the mask method may be useful for screening future vaccine candidates, therapeutics or interventions for their ability to block transmission.
Recurrent SARS-CoV-2 Mutations in Immunodeficient Patients
Authors: Wilkinson Sam AJ , Richter Alex , Casey Anna , Osman Husam , Mirza Jeremy D , Stockton Joanne , Quick Josh , Ratcliffe Liz , Sparks Natalie , Cumley Nicola , Poplawski Radoslaw , Nicholls Sam , Kele Beatrix , Harris Kathryn ,   The COVID-19 Genomics UK (COG-UK) consortium, Peacock Thomas P , Loman Nicholas J
Published: March 2022

Long-term SARS-CoV-2 infections in immunodeficient patients are an important source of variation for the virus but are understudied. Many case studies have been published which describe one or a small number of long-term infected individuals but no study has combined these sequences into a cohesive dataset. This work aims to rectify this and study the genomics of this patient group through a combination of literature searches as well as identifying new case series directly from the COG-UK dataset. The spike gene receptor binding domain (RBD) and N-terminal domains (NTD) were identified as mutation hotspots. Numerous mutations associated with variants of concern were observed to emerge recurrently. Additionally a mutation in the envelope gene, - T30I was determined to be the most recurrent frequently occurring mutation arising in persistent infections. A high proportion of recurrent mutations in immunodeficient individuals are associated with ACE2 affinity, immune escape, or viral packaging optimisation.

There is an apparent selective pressure for mutations which aid intra-host transmission or persistence which are often different to mutations which aid inter-host transmission, although the fact that multiple recurrent de novo mutations are considered defining for variants of concern strongly indicates that this potential source of novel variants should not be discounted.
Cell-specific regulation of gene expression using splicing-dependent frameshifting
Authors: Ling Jonathan P. , Bygrave Alexei M. , Santiago Clayton P. , Carmen-Orozco Rogger P. , Trinh Vickie , Yu Minzhong , Li Yini , Han Jeong , Taneja Kamil , Liu Ying , Dongmo Rochinelle , Babola Travis A. , Parker Patrick , Jiang Lizhi , Leavey Patrick J. , Smith Jennifer J. , Vistein Rachel , Gimmen Megan Y. , Dubner Benjamin , Helmenstine Eric , Teodorescu Patric , Karantanos Theodore , Ghiaur Gabriel , Kanold Patrick O. , Bergles Dwight , Langmead Ben , Sun Shuying , Nielsen Kristina J. , Peachey Neal , Singh Mandeep S. , Dalton W. Brian , Rajaii Fatemeh , Huganir Richard L. , Blackshaw Seth
Published: March 2022

Precise and reliable cell-specific gene delivery remains technically challenging. Here we report a splicing-based approach for controlling gene expression whereby separate translational reading frames are coupled to the inclusion or exclusion of cell-specific alternative exons. Candidate exons are identified by analyzing thousands of publicly available RNA sequencing datasets and filtering by cell specificity, sequence conservation, and local intron length. This method, which we denote splicing-linked expression design (SLED), can be combined in a Boolean manner with existing techniques such as minipromoters and viral capsids. SLED vectors can leverage the strong expression of constitutive promoters, without sacrificing precision, by decoupling the tradeoff between promoter strength and selectivity. We generated SLED vectors to selectively target all neurons, photoreceptors, or excitatory neurons, and demonstrated that specificity was retainedin vivowhen delivered using AAVs. We further demonstrated the utility of SLED by creating what would otherwise be unobtainable research tools, specifically a GluA2 flip/flop reporter and a dual excitatory/inhibitory neuronal calcium indicator. Finally, we show the translational potential of SLED by rescuing photoreceptor degeneration inPrph2rds/rdsmice and by developing an oncolytic vector that can selectively induce apoptosis in SF3B1 mutant cancer cells. The flexibility of SLED technology enables new avenues for basic and translational research.
The 3D structure of lipidic fibrils of α-synuclein
Authors: Frieg Benedikt , Antonschmidt Leif , Dienemann Christian , Geraets James A. , Najbauer Eszter E. , Matthes Dirk , de Groot Bert L. , Andreas Loren B. , Becker Stefan , Griesinger Christian , Schröder Gunnar F.
Published: March 2022

α-synuclein (αSyn) is abundant in neurons, but its misfolding and abnormal fibrillization are associated with severe neurodegenerative diseases. Although interactions between αSyn and phospholipid membranes are relevant during αSyn fibril assembly, insights into the interactions of αSyn fibrils with phospholipids have remained elusive. Here, we present six novel polymorphic atomic structures of αSyn fibrils aggregated in the presence of phospholipids. The structures reveal that phospholipids favor a novel protofilament fold, mediate an unusual arrangement of protofilaments, and fill the central cavities between the protofilaments. These findings provide a structural rationale for fibril-induced lipid extraction, a mechanism likely to be involved in the development of α-synucleinopathies.
Characterizing circadian connectome ofO. tenuiflorumusing an integrated network theoretic framework
Authors: Singh Vikram , Singh Vikram
Published: March 2022

Ocimum tenuiflorum(Tulsi) is among the most valuable medicinal plants as almost every part of this herb and the essential oil it produces possess pharmaceutical properties that have been utilized since ancient times to cure a large number of diseases. Like in other plants, circadian clock in Tulsi regulate important physiological processes like growth, development, defenceetc. by anticipating environmental cues. In the present work, identification and characterization of core circadian clock and clock associated proteins in Tulsi genome is reported. We mined 24 core clock (CC) proteins in 56 template plant genomes to build their hidden Markov models (HMMs). These HMMs were used to identify 24 core clock proteins inO. tenuiflorumwhich were further subjected to functional annotation. A hybrid network theoretic methodology comprising of random walk with restart (RWR) and graphlet degree vectors (GDV) was implemented to explore the local topology of the interologous, Tulsi protein interaction network (TulsiPIN) and mine CC associated raw candidate proteins. Statistical and biological significance of the raw candidates was determined using permutation and enrichment tests. A total of 70 putative CC associated proteins were identified which were further subjected to functional annotation.
Peptidoglycan recognition protein S2 is crucial for activation the Toll pathway against Israeli acute paralysis virus infection in honey bee Apis mellifera
Authors: Deng Yanchun , Yang Sa , Zhao Hongxia , Luo Ji , Lu Zhiqiang , Hou Chunsheng
Published: March 2022

Although honey bee responses to pathogens have been systematically described in the past decades, antiviral signalling pathways mechanisms are not thoroughly characterized. To decipher direct antiviral roles of an immune pathway, we firstly used the infectious clone of Israeli acute paralysis virus (IAPV) to screen 42 immune genes involved in mTOR, MAPK, Toll, Endocytosis, Jak-STAT pathway and homeobox protein, heat shock protein, as well as antimicrobial peptides (AMPs), and found that Toll pathway was a potential predominant immune pathway in Apis mellifera. Consistent with this, only dsRNA-PGRP-S2 treated A. mellifera significantly exhibited impaired activation of Toll pathway, promoting susceptibility to the IAPV infection. Finally, immunofluorescence results confirmed that the Toll pathway was initiated by peptidoglycan recognition protein S2 (PGRP-S2) interacting with Toll protein. Co-immunoprecipitation findings also further preliminarily confirmed PGRP-S2 directly interacting with viral capsid protein IAPV-VP3 to induce the activation of the Toll pathway in A. mellifera. These findings highlight that the Toll pathway is demanded efficient inhibitions of IAPV replication as a specific antiviral pathway in A. mellifera, and PGRP-S2, acting as a pattern recognition receptor, could be a new approach for control of the viral disease.

Author summary

Honey bee viruses, particularly IAPV, had been implicated in the colony decline with a global distribution resulting in insufficient pollination services. However, little is known about the antiviral mechanism of honey bee. In this study, we found that the Toll pathway was required for A. mellifera against IAPV infection and initiated by PGRP-S2. We also confirmed that dsRNA-PGRP-S2 treated A. mellifera exhibited impaired Toll pathway activation and promoted susceptibility to the IAPV infection. As a result, we employed co-immunoprecipitation technique to identify the interaction between the PGRP-S2 with Toll. Moreover, it was found the PGRP-S2 directly recognized IAPV-VP3 to activate the immune pathway against IAPV infection. Our work provides novel evidence that honey bees own a specific antiviral immune pathway and suggests that targeting PGRP-S2 could be a new approach for controlling the viral disease.
Effects of Sanhuang plaster on expression of MyD88, TRAF6, MIP-1β and IL-23 in rats infected by MRSA
Authors: Pan Haibang , Chen Qian , Fu Qi , Wang Tianming , Li Xiaoli , Li Richeng , Liu Mei , Guo Tiankang
Published: March 2022

Objective: To investigate the effects of Sanhuang plaster on expression of myeloid differentiation factor 88 (MyD88), tumor necrosis factor receptor-related factor 6 (TRAF6), macrophage inflammatory protein-lβ (MIP-1β) and its mediated cytokine interleukin-23 (IL-23) in soft tissues of rats infected by methicillin-resistant Staphylococcus aureus (MRSA). Methods: Ninety-six healthy rats were randomly divided into normal control group, model control group, Mupirocin group, high, medium and low dose groups of Sanhuang plaster, with 16 rats in each group. MRSA bacterial liquid was used to make skin and soft tissue infection models. The rats in the normal control group and the model control group were not given any treatment measures. The high, medium, and low dose groups of Sanhuang plaster were given to the affected area with Sanhuang plaster, and the Mupirocin group was given to the affected area for treatment for 10 days. The wound pathological changes were observed. The levels of MIP-1β and IL-23 in serum and infected tissues of rats in each group were measured by ELISA. The mRNA expressions of MyD88, TRAF6, MIP-lβ and IL-23 were measured by Quantitative Real-time PCR, and Western blot was used to measure MyD88 and TRAF6 protein expression. Results: Compared with the model control group, the general condition of the Sanhuang plaster groups was significantly improved, and the pathological damage was reduced. The MIP-1β and IL-23 levels in the serum and infected tissues of the high dose group of Sanhuang plaster, the mRNA expressions of MyD88, TRAF6, MIP-1β and IL-23and in large and medium dose groups of Sanhuang plaster, and the protein expressions of Myd88 and TRAF6 in high dose of Sanhuang plaster were significantly decreased (p<0.05 or p<0.01). Conclusion: Sanhuang plaster may play a role in promoting healing of infected wounds by down-regulating the expression levels of MyD88, TRAF6, and MIP-1β, and inhibiting the abnormal secretion of cytokine IL-23.
Phase separation in amino acid mixtures is governed by composition
Authors: De Sancho David
Published: March 2022

Macromolecular phase separation has recently come to immense prominence as it is central to the formation of membraneless organelles, leading to a new paradigm of cellular organization. This type of phase transition, often termed liquid-liquid phase separation (LLPS), is mediated by molecular interactions between biomolecules, including nucleic acids and both ordered and disordered proteins. In the latter case, the separation between protein-dense and dilute phases is often interpreted using models adapted from polymer theory. Specifically, the “stickers and spacers” model proposes that the formation of condensate-spanning networks in protein solutions originates from the interplay between two classes of residues and that the main determinants for phase separation are multivalency and sequence patterning. The duality of roles of stickers (aromatics like Phe and Tyr) and spacers (Gly and polar residues) may apply more broadly in protein-like mixtures, and the presence of these two types of components alone may suffice for LLPS to take place. In order to explore this hypothesis, we use atomistic molecular dynamics simulations of capped amino-acid residues as a minimal model system. We study the behaviour of pure amino acids in water for three types of residues corresponding to the spacer and sticker categories, and their multicomponent mixtures. In agreement with previous observations, we find that the spacer-type amino acids fail to phase-separate on their own, while the sticker is prone to aggregation. However, ternary amino acid mixtures involving both types of amino acids phase-separate into two phases that retain intermediate degrees of compaction and greater fluidity than sticker-only condensates. Our results suggest that LLPS is an emergent property of amino acid mixtures determined by composition.
Decoding COVID-19 mRNA Vaccine Immunometabolism in Central Nervous System: human brain normal glial and glioma cells by Raman imaging
Authors: Abramczyk H. , Brozek-Pluska B. , Beton Karolina
Published: March 2022

The paper presents the effect of COVID-19 mRNA (Pfizer/BioNT) vaccine on in vitro glial cells of the brain studied by means of Raman spectroscopy and imaging.. The results obtained for human brain normal and tumor glial cells of astrocytes, astrocytoma, glioblastoma incubated with the Covid-19 mRNA vaccine Pfizer/BioNT vaccine show alterations in the reduction-oxidation pathways associated with Cytochrome c.

We found that the Pfizer/BioNT vaccine down regulate the concentration of cytochrome c in mitochondria upon incubation with normal and tumorous glial cells. Concentration of oxidized form of cytochrome c in brain cells has been shown to decrease upon incubation the mRNA vaccine. Lower concentration of oxidized cytochrome c results in lower effectiveness of oxidative phosphorylation (respiration), reduced apoptosis and lessened ATP production. Alteration of Amide I concentration, which may reflect the decrease of mRNA adenine nucleotide translocator. Moreover, mRNA vaccine leads to alterations in biochemical composition of lipids that suggest the increasing role of signaling. mRNA vaccine produce statistically significant changes in cell nucleus due to histone alterations. The results obtained for mitochondria, lipid droplets, cytoplasm may suggest that COVID-19 mRNA (Pfizer/BioNT) vaccine reprograms immune responses. The observed alterations in biochemical profiles upon incubation with COVID-19 mRNA in the specific organelles of the glial cells are similar to those we observe for brain cancer vs grade of aggressiveness.