bluuebunny/crossref_metadata_2025 huggingface dataset:
Microstructural development from 9-14 years: evidence from the ABCD Study
Authors: Palmer Clare E , Pecheva Diliana , Iversen John R , Hagler Donald J , Sugrue Leo , Nedelec Pierre , Fan Chun Chieh , Thompson Wesley K , Jernigan Terry L , Dale Anders M
Published: June 2021

During late childhood behavioral changes, such as increased risk-taking and emotional reactivity, have been associated with the maturation of cortico-cortico and cortico-subcortical circuits. Understanding microstructural changes in both white matter and subcortical regions may aid our understanding of how individual differences in these behaviors emerge. Restriction spectrum imaging (RSI) is a framework for modelling diffusion-weighted imaging that decomposes the diffusion signal from a voxel into hindered, restricted, and free compartments. This yields greater specificity than conventional methods of characterizing diffusion. Using RSI, we quantified voxelwise restricted diffusion across the brain and measured age associations in a large sample (n=8,086) from the Adolescent Brain and Cognitive Development (ABCD) study aged 9-14 years. Older participants showed a higher restricted signal fraction across the brain, with the largest associations in subcortical regions, particularly the basal ganglia and ventral diencephalon. Importantly, age associations varied with respect to the cytoarchitecture within white matter fiber tracts and subcortical structures, for example age associations differed across thalamic nuclei. This suggests that age-related changes may map onto specific cell populations or circuits and highlights the utility of voxelwise compared to ROI-wise analyses. Future analyses will aim to understand the relevance of this microstructural developmental for behavioral outcomes.
Confusions regarding stochastic fluctuations and accumulators in spontaneous movements
Authors: Bogler Carsten , Grujičić Bojana , Haynes John-Dylan
Published: June 2021

Experiments on choice-predictive brain signals have played an important role in the debate on free will. In a seminal study, Benjamin Libet and colleagues found that a negative-going EEG signal, the readiness potential (RP), can be observed over motor-related brain regions hundreds of ms before the retrospectively reported time of the conscious decision to move. If the onset of the readiness potential is taken as an indicator of the “brain’s decision to move” this could mean that this decision to move is made early, by unconscious brain activity, rather than later, at the time when the subject believes to have decided. However, an alternative kind of interpretation, involving ongoing stochastic fluctuations, has recently been brought to light. One such model, the stochastic decision model (SDM), takes its inspiration from accumulator models of perceptual decision making. It suggests that the RP originates from an accumulation of ongoing stochastic fluctuations. In this view the decision happens only at a much later stage when an accumulated noisy signal (plus imperative) reaches a threshold. Here we clarify a number of confusions regarding both the evidence for the stochastic decision model as well as the interpretation that it offers. We will explore several points that we feel are in need of clarification:(a)that the empirical evidence for the role of stochastic fluctuations is so far only indirect;(b)that the relevance of evidence from animal studies is unclear;(c)that a model that is deterministic during the accumulation stage can explain the data in a similar way;(d)that the primary focus in the literature has been on the role of random fluctuations whereas the deterministic aspects of the model have been largely ignored;(e)that contrary to the original interpretation the deterministic component of the model is the dominant input into the accumulator;(f)that there is confusion regarding the role of “imperative” and “evidence” in the SDM and its link to perceptual decision making; and finally(g)as with other stochastic accumulator processes the question of whether the decision happens early or late depends on the nature of the noise fluctuations, specifically, whether they reflect “absolute” or “epistemic” randomness. Our aim is not to rehabilitate the role of the RP in the free will debate. Rather we aim to address some confusions regarding the evidence for accumulators playing a role in these preparatory brain processes.
The biaxial mechanics of thermally denaturing skin - Part II: Modeling
Authors: Rausch Manuel , Meador William D. , Tubon John Toaquiza , Moreno-Flores Omar , Tepole Adrian Buganza
Published: June 2021

Understanding the response of skin to superphysiological temperatures is critical to the diagnosis and prognosis of thermal injuries, and to the development of temperature-based medical therapeutics. Unfortunately, this understanding has been hindered by our incomplete knowledge about the nonlinear coupling between skin temperature and its mechanics. In Part I of this study we experimentally demonstrated a complex interdependence of time, temperature, direction, and load in skin’s response to superphysiological temperatures. In Part II of our study, we test two different models of skin’s thermo-mechanics to explain our observations. In both models we assume that skin’s response to superphysiological temperatures is governed by the denaturation of its highly collageneous microstructure. Thus, we capture skin’s native mechanics via a microstructurally-motivated strain energy function which includes probability distributions for collagen fiber orientation and waviness. In the first model, we capture skin’s response to superphysiological temperatures as a transition between two states that link the kinetics of collagen fiber denaturation to fiber coiling and to the transformation of each fiber’s constitutive behavior from purely elastic to viscoelastic. In the second model, we capture skin’s response to super-physiological temperatures instead via three states in which a sequence of two reactions link the kinetics of collagen fiber denaturation to fiber coiling, followed by a state of fiber damage. Given the success of both models in qualitatively capturing our observations, we expect that our work will provide guidance for future experiments that could probe each model’s assumptions toward a better understanding of skin’s coupled thermo-mechanics and that our work will be used to guide the engineering design of heat treatment therapies.
Human magnetic field registration capability using low-field magnetic sensors
Authors: Bricina Natalija , Dehtjars Jurijs , Jašina Ksenija , Sorokins Hermanis
Published: June 2021

The aim of the study was to find out whether it is possible to detect the human magnetic field without shielding using sensors. For this, an experiment “the possibility of detecting the human magnetic field using sensors” was conducted. During the experiment it was found that with the help of a low-field magnetic detector it is possible to register a person’s magnetic field, which is changing if there is a change in a heart rate.

During the study, a device for recording the magnetic field of a human was assembled, a methodology for obtaining data was developed, a description of the materials and equipment used was provided. In accordance with the described methods of data collection, measurements of human magnetic field with and without load were made. The data obtained during the study were processed and the results were displayed. Based on the obtained results, an analysis was carried out, conclusions were drawn and recommendations for subsequent studies were indicated. As a result, the possibility of detecting a human’s magnetic field using sensors was first studied.
A mathematical model for phenotypic heterogeneity in breast cancer with implications for therapeutic strategies
Authors: Li Xin , Thirumalai D.
Published: June 2021

Inevitably, almost all cancer patients develop resistance to targeted therapy. Intratumor heterogeneity is a major cause of drug resistance. Mathematical models that explain experiments quantitatively are useful in understanding the origin of intratumor heterogeneity, which then could be used to explore scenarios for efficacious therapy. Here, we develop a mathematical model to investigate intratumor heterogeneity in breast cancer by exploiting the observation that HER2+ and HER2− cells could divide symmetrically or asymmetrically. Our predictions for the evolution of cell fractions are in quantitative agreement with single-cell experiments. Remarkably, the colony size of HER2+ cells emerging from a single HER2− cell (or vice versa), which occurs in about four cell doublings, also agrees with experimental results, without tweaking any parameter in the model. The theory quantitatively explains experimental data on the responses of breast tumors under different treatment protocols. We then used the model to predict that, not only the order of two drugs, but also the treatment period for each drug and the tumor cell plasticity could be manipulated to improve the treatment efficacy. Mathematical models, when integrated with data on patients, make possible exploration of a broad range of parameters readily, which might provide insights in devising effective therapies.
Gut Bacterial Microbiome Profiles Associated with Colorectal Cancer Risk: A Systematic Review and Meta-Analysis
Authors: Russ Christian A , Zertalis Nicholas A , Nanton Veronica
Published: June 2021

Objective
Recent studies have shown a potential link between gut microbiome and colorectal cancer (CRC). Initially, a wide array of research into this topic was discovered from the past decade, illustrating a keen interest in the potential causal relationship between the gut microbiome and CRC. However, the cancer research community is lacking a summarised systematic review of this kind which aims to explore the evidence linking the human gut microbiome to risk of CRC.
Design
This systematic review was carried out with two independent reviewers assessing the database outcomes from Medline and EMBASE during May 2020. A meta-analysis was undertaken studying the link between Helicobacter pylori and CRC; processed through Stata.
Results
31 papers were included in the systematic review, followed by 12 for the meta-analysis. From these papers, Fusobacterium and Bacteroides were reported most frequently as enriched in CRC versus control. The meta-analysis showed an Odds Ratio of 1.49 (95% CI 1.19 - 1.86), including a total of 20,001 events. This meta-analysis concluded that H. pylori infection significantly increases the risk of CRC, albeit with evidence of publication bias.
Conclusions
Bacteria have been discovered to increase the risk of CRC, however a definitive causal relationship cannot be concluded or excluded using case-control studies. To fully understand the potential link of the bacteria listed, alterations in research design and execution are required. The assessment found a need for a large-scale cohort study conducted over a significant period of time to thoroughly evaluate the potential relationship between gut microbiome and CRC risk.
Exogenous extracellular matrix proteins decrease cardiac fibroblast activation in stiffening microenvironment through CAPG
Authors: Wang Xinming , Pierre Valinteshley , Liu Chao , Senapati Subhadip , Park Paul S.-H. , Senyo Samuel E.
Published: June 2021

Controlling fibrosis is an essential part of regenerating the post-ischemic heart. In the post-ischemic heart, fibroblasts differentiate to myofibroblasts that produce collagen-rich matrix to physically stabilize the infarct area. Infarct models in adult mice result in permanent scarring unlike newborn animals which fully regenerate. Decellularized extracellular matrix (dECM) hydrogels derived from early-aged hearts have been shown to be a transplantable therapy that preserves heart function and stimulates cardiomyocyte proliferation and vascularization. In this study, we investigate the anti-fibrotic effects of injectable dECM hydrogels in a cardiac explant model in the context of age-associated tissue compliance. Treatments with adult and fetal dECM hydrogels were tested for molecular effects on cardiac fibroblast activation and fibrosis. Altered sensitivity of fibroblasts to the mechanosignaling of the remodeling microenvironment was evaluated by manipulating the native extracellular matrix in explants and also with elastomeric substrates in the presence of dECM hydrogels. The injectable fetal dECM hydrogel treatment decreases fibroblast activation and contractility and lowers the stiffness-mediated increases in fibroblast activation observed in stiffened explants. The anti-fibrotic effect of dECM hydrogel is most observable at highest stiffness. Experiments with primary cells on elastomeric substrates with dECM treatment support this phenomenon. Transcriptome analysis indicated that dECM hydrogels affect cytoskeleton related signaling including Macrophage capping protein (CAPG) and Leupaxin (LPXN). CAPG was down-regulated by the fetal dECM hydrogel. LPXN expression was decreased by stiffening the explants; however, this effect was reversed by dECM hydrogel treatment. Pharmacological disruption of cytoskeleton polymerization lowered fibroblast activation and CAPG levels. Knocking down CAPG expression with siRNA inhibited fibroblast activation and collagen deposition. Collectively, fibroblast activation is dependent on cooperative action of extracellular molecular signals and mechanosignaling by cytoskeletal integrity.
Neutralization against B.1.351 and B.1.617.2 with sera of COVID-19 recovered cases and vaccinees of BBV152
Authors: Yadav Pragya D. , Sapkal Gajanan N. , Ella Raches , Sahay Rima R. , Nyayanit Dimpal A , Patil Deepak Y. , Deshpande Gururaj , Shete Anita M. , Gupta Nivedita , Mohan V. Krishna , Abraham Priya , Panda Samiran , Bhargava Balram
Published: June 2021

Recently, multiple SARS-CoV-2 variants have been detected across the globe. The recent emergence of B.1.617 lineage has created serious public health problem in India. The high transmissibility was observed with this lineage which has led to daily increase in the number of SARS-CoV-2 infections. Apparently, the sub-lineage B.1.617.2 has slowly dominated the other variants including B1617.1, B.617.3 and B.1.1.7. With this, World Health Organization has described B.1.617.2 as variant of concern. Besides this, variant of concern B.1.351 has been also reported from India, known to showreducedefficacyfor many approved vaccines. With the increasing threat of the SARS-CoV-2 variants, it is imperative to assess the efficacy of the currently available vaccines against these variants. Here, we have evaluated the neutralization potential of sera collected from COVID-19 recovered cases (n=20) and vaccinees with two doses of BBV152 (n=17) against B.1.351 and B.1.617.2 compared to the prototype B.1 (D614G) variant.The finding of the study demonstrated a reduction in neutralization titers with sera of COVID-19 recovered cases(3.3-fold and 4.6-fold) and BBV152 vaccinees (3. 0 and 2.7 fold) against B.1.351 and B.1.617.2 respectively.Although, there is reduction in neutralization titer, the whole-virion inactivated SARS-CoV-2 vaccine (BBV152) demonstrates protective response against VOC B.1351 and B.1.617.2.
Dice-XMBD: Deep learning-based cell segmentation for imaging mass cytometry
Authors: Xiao Xu , Qiao Ying , Jiao Yudi , Fu Na , Yang Wenxian , Wang Liansheng , Yu Rongshan , Han Jiahuai
Published: June 2021

Highly multiplexed imaging technology is a powerful tool to facilitate understanding cells composition and interaction in tumor microenvironment at subcellular resolution, which is crucial for both basic research and clinical applications. Imaging mass cytometry (IMC), a multiplex imaging method recently introduced, can measure up to 40 markers simultaneously in one tissue section by using a high-resolution laser with a mass cytometer. However, due to its high resolution and large number of channels, how to process and interpret the image data from IMC remains a key challenge for its further applications. Accurate and reliable single cell segmentation is the first and a critical step to process IMC image data. Unfortunately, existing segmentation pipelines either produce inaccurate cell segmentation results, or require manual annotation which is very time-consuming. Here, we developed Dice-XMBD, a Deep learnIng-based Cell sEgmentation algorithm for tissue multiplexed imaging data. In comparison with other state-of-the-art cell segmentation methods currently used in IMC, Dice-XMBD generates more accurate single cell masks efficiently on IMC images produced with different nuclear, membrane and cytoplasm markers. All codes and datasets are available at https://github.com/xmuyulab/Dice-XMBD.
Genome-wide reconstruction of rediploidization following autopolyploidization across one hundred million years of salmonid evolution
Authors: Gundappa Manu Kumar , To Thu-Hien , Grønvold Lars , Martin Samuel A.M. , Lien Sigbjørn , Geist Juergen , Hazlerigg David , Sandve Simen R. , Macqueen Daniel J.
Published: June 2021

The long-term evolutionary impacts of whole genome duplication (WGD) are strongly influenced by the ensuing rediploidization process. Following autopolyploidization, rediploidization involves a transition from tetraploid to diploid meiotic pairing, allowing duplicated genes (ohnologues) to diverge genetically and functionally. Our understanding of autopolyploid rediploidization has been informed by a WGD event ancestral to salmonid fishes, where large genomic regions are characterized by temporally delayed rediploidization, allowing lineage-specific ohnologue sequence divergence in the major salmonid clades. Here, we investigate the long-term outcomes of autopolyploid rediploidization at genome-wide resolution, exploiting a recent ‘explosion’ of salmonid genome assemblies, including a new genome sequence for the huchen (Hucho hucho). We developed a genome alignment approach to capture duplicated regions across multiple species, allowing us to create 121,864 phylogenetic trees describing ohnologue divergence across salmonid evolution. Using molecular clock analysis, we show that 61% of the ancestral salmonid genome experienced an initial ‘wave’ of rediploidization in the late Cretaceous (85-106 Mya). This was followed by a period of relative genomic stasis lasting 17-39 My, where much of the genome remained in a tetraploid state. A second rediploidization wave began in the early Eocene and proceeded alongside species diversification, generating predictable patterns of lineage-specific ohnologue divergence, scaling in complexity with the number of speciation events. Finally, using gene set enrichment, gene expression, and codon-based selection analyses, we provide insights into potential functional outcomes of delayed rediploidization. Overall, this study enhances our understanding of delayed autopolyploid rediploidization and has broad implications for future studies of WGD events.
Reporting amyloid beta levelsviabioluminescence imaging with amyloid reservoirs in Alzheimer’s disease models
Authors: Yang Jing , Ding Weihua , Zhu Biyue , Zhen Sherri , Kuang Shi , Zhang Can , Wang Peng , Yang Fan , Yang Liuyue , Yin Wei , Tanzi Rudolph E. , Shen Shiqian , Ran Chongzhao
Published: June 2021

Bioluminescence imaging has changed daily practice in preclinical research of cancers and other diseases in the last decades; however, it has been rarely applied in preclinical research of Alzheimer’s disease (AD). In this report, we demonstrated that bioluminescence imaging could be used to report the levels of amyloid beta (Aβ) species in vivo. We hypothesized that AkaLumine, a newly discovered substrate for luciferase, could bind to Aβ aggregates and plaques. We further speculated that the Aβ species have the reservoir capacity to sequester and release AkaLumine to control the bioluminescence intensity, which could be used to report the levels of Aβs. Our hypotheses have been validatedvia in vitrosolution tests, mimic studies with brain tissues and mice, two-photon imaging with AD mice, andin vivobioluminescence imaging using transgenic AD mice that were virally transduced with aka Luciferase (AkaLuc), a new luciferase that generates bioluminescence in the near infrared window. As expected, compared to the control group, we observed that the Aβ group showed lower bioluminescence intensity due to AkaLumine sequestering at early time points, while higher intensity due to AkaLumine releasing at later time points. Lastly, we demonstrated that this method could be used to monitor AD progression and therapeutic effectiveness of avagacestat, a well-studied gamma-secretase inhibitor. Importantly, a good correlation (R2= 0.81) was established between in vivo bioluminescence signals and Aβ burdens of the tested AD mice. We believe that our approach can be easily implemented into daily imaging experiments and has tremendous potential to change daily practice of preclinical AD research.
Inverse Lansing effect: maternal age and provisioning affecting daughters’ longevity and male offspring production
Authors: Anderson Cora E. , Homa Camille , Jonas-Closs Rachael A , Peshkin Leonid , Kirschner Marc W. , Yampolsky Lev Y.
Published: June 2021

Maternal age effects on life history of offspring has been demonstrated in a variety of organisms, more often than not offspring of older mothers having lower life expectancy (Lansing effect). However, there is no consensus on how general this phenomenon is and what are the genetic and epigenetic mechanisms behind it. We tested the predictions of Lansing effect in several Daphnia magna clones in and observed a significant genotype-by-maternal age interaction, indicating clone-specific magnitude and direction of the effect of maternal age on daughters’ longevity. We then repeated this experiment with more detailed life-history and offspring provisioning data focusing on 2 clones with contrasting life-histories. One of these clones demonstrating the inverse Lansing effect, with daughters of older mothers living longer than those of young mothers. Individuals from a single-generation maternal age reversal treatment showed intermediate lifespan. We also report genotype-specific, ambidirectional, and largely fecundity-independent effects of maternal age on daughters’ propensity to produce male offspring, with daughters of older mothers showing higher male production than daughters of younger mothers in the least male-producing clone and vise versa. We tested whether both effects can be explained by either lipid provisioning of embryos by mothers of different age, or by properties of mitochondria transmitted by mothers of different age to their offspring, using rhodamine-123 assay of mitochondrial membrane potential as a measure of mitochondria quality. We show that once lipid provisioning is accounted for, the effects of maternal age on lifespan and male production disappear and that the effect of lipid provisioning itself is clone-dependent, confirming that maternal provisioning sets daughters life history parameters. In the clone showing the inverse Lansing effect we demonstrated that, contrary to the predictions, neonates produced by older mothers were characterized by higher mitochondrial membrane potential in neural tissues than their counterparts born to younger mothers. We conclude that, in at least some genotypes, a reverse Lansing effect is possible, and hypothesize that it may be a result of lower lipid provisioning creating calorically restricted environment during embryonic development.
FXR inhibition reduces ACE2 expression, SARS-CoV-2 infection and may improve COVID-19 outcome
Authors: Brevini Teresa , Maes Mailis , Webb Gwilym J. , Gelson William T. H. , Forrest Sally , Mlcochova Petra , Dillon Scott , Varankar Sagar , Darvish-Damavandi Mahnaz , Mulcahy Victoria L. , Kuc Rhoda E. , Williams Thomas L. , Galanakis Vasileios , Vila-Gonzalez Marta , Tysoe Olivia C. , Muraro Daniele , Crozier Thomas W. M. , Bargehr Johannes , Sinha Sanjay , Upponi Sara S. , Swift Lisa , Saeb-Parsy Kourosh , Davies Susan E. , Marjot Thomas , Barnes Eleanor , Lohse Ansgar W. , Moon Andrew M. , Sidney Barritt A. , Gupta Ravindra K. , Baker Stephen , Davenport Anthony P. , Corbett Gareth , Buczacki Simon J. A. , Lee Joo-Hyeon , Gibbs Paul , Butler Andrew J. , Watson Christopher J. E. , Mells George F. , Dougan Gordon , Vallier Ludovic , Sampaziotis Fotios
Published: June 2021

Prevention of SARS-CoV-2 entry in cells through the modulation of viral host receptors, such as ACE2, could represent a new therapeutic approach complementing vaccination. However, the mechanisms controlling ACE2 expression remain elusive. Here, we identify the farnesoid X receptor (FXR) as a direct regulator of ACE2 transcription in multiple COVID19-affected tissues, including the gastrointestinal and respiratory systems. We demonstrate that FXR antagonists, including the over-the-counter compound z-guggulsterone (ZGG) and the off-patent drug ursodeoxycholic acid (UDCA), downregulate ACE2 levels, and reduce susceptibility to SARS-CoV-2 infection in lung, cholangiocyte and gut organoids. We then show that therapeutic levels of UDCA downregulate ACE2 in human organs perfused ex situ and reduce SARS-CoV-2 infection ex vivo. Finally, we perform a retrospective study using registry data and identify a correlation between UDCA treatment and positive clinical outcomes following SARS-CoV-2 infection, including hospitalisation, ICU admission and death. In conclusion, we identify a novel function of FXR in controlling ACE2 expression and provide evidence that this approach could be beneficial for reducing SARS-CoV-2 infection, thereby paving the road for future clinical trials.
ProCanBio: a database of manually curated biomarkers for Prostate Cancer
Authors: Sapra Dikscha , Kaur Harpreet , Dhall Anjali , Raghava Gajendra P. S.
Published: June 2021

Background

Prostate Cancer is the second lethal malignancy in men worldwide. In the past, numerous research groups investigated the omics profiles of patients and scrutinized biomarkers for the diagnosis and prognosis of prostate cancer. However, information related to the biomarkers is widely scattered across numerous resources in complex textual format, which poses hindrance to understand the tumorigenesis of this malignancy and scrutinization of robust signature. To the best of authors’ knowledge, there is no resource that can consolidate the information contained in all the published literature.

Results

Here, we present ProCanBio, a manually curated database that maintains detailed data on 2053 entries of potential prostate cancer biomarkers obtained from 412 publications in user friendly tabular format. Among them, 766 protein-based, 488 RNA-based, 157 genomic mutations, 261 miRNA-based, and 122 are metabolites-based biomarkers. To explore the information in the resource, a web-based interactive platform was developed with searching, and browsing facilities. ProCanBio is freely available and is compatible with most web browsers and devices. Eventually, we anticipated this resource will be highly useful for the research community involved in the area of prostate malignancy.

Availability

ProCanBio is available at: https://webs.iiitd.edu.in/raghava/procanbio/
Enrichment analysis of GWAS data in autoimmunity delineates the multiple sclerosis-Epstein Barr virus association
Authors: Mechelli Rosella , Umeton Renato , Rinaldi Virginia , Bellucci Gianmarco , Bigi Rachele , Angelini Daniela F. , Guerrera Gisella , Srinivasan Sundararajan , Romano Silvia , Buscarinu Maria Chiara , Pizzolato Umeton Raffaella , Anastasiadou Eleni , Trivedi Pankaj , Fornasiero Arianna , Ferraldeschi Michela ,   IMSGC and WTCCC2, Centonze Diego , Uccelli Antonio , Di Silvestre Dario , Mauri Pier Luigi , de Candia Paola , Matarese Giuseppe , D’Alfonso Sandra , Battistini Luca , Farina Cinthia , Magliozzi Roberta , Reynolds Richard , Salvetti Marco , Ristori Giovanni
Published: June 2021

We exploited genetic information to assess non-genetic influences in autoimmunity. We isolated gene modules whose products physically interact with environmental exposures related to autoimmunity, and analyzed their nominal statistical evidence of association with autoimmune and non-autoimmune diseases in genome-wide association studies (GWAS) data. Epstein Barr virus (EBV) and other Herpesviruses interactomes emerged as specifically associated with multiple sclerosis (MS), possibly under common regulatory mechanisms. Analyses of MS blood and brain transcriptomes, cytofluorimetric studies of endogenous EBV-infected lymphoblastoid lines, and lesion immunohistochemistry, confirmed a dysregulation of MS-associated EBV interactors, suggesting their contribution to CD40 signaling alterations in MS. These interactors resulted enriched in modules from inherited axonopathies-causing genes, supporting a link between EBV and neurodegeneration in MS, in accord with the observed transcriptomic dysregulations in MS brains. They were also enriched with top-ranked pharmaceutical targets prioritized on a genetic basis. This study delineates a disease-specific influence of herpesviruses on MS biology.
Genome editing in animals with minimal PAM CRISPR-Cas9 enzymes
Authors: Vicencio Jeremy , Sánchez-Bolaños Carlos , Moreno-Sánchez Ismael , Brena David , Kukhtar Dmytro , Ruiz-López Miguel , Cots-Ponjoan Mariona , Vejnar Charles E. , Rubio Alejandro , Melero Natalia Rodrigo , Carolis Carlo , Pérez-Pulido Antonio J. , Giráldez Antonio J. , Kleinstiver Benjamin P. , Cerón Julián , Moreno-Mateos Miguel A.
Published: June 2021

The requirement for Cas nucleases to recognize a specific PAM is a major restriction for genome editing. SpCas9 variants SpG and SpRY, recognizing NGN and NRN PAM, respectively, have contributed to increase the number of editable genomic sites in cell cultures and plants. However, their use has not been demonstrated in animals.

We have characterized and optimized the activity of SpG and SpRY in zebrafish and C. elegans. Delivered as mRNA-gRNA or ribonucleoprotein (RNP) complexes, SpG and SpRY were able to induce mutations in vivo, albeit at a lower rate than SpCas9 in equivalent formulations. This lower activity was overcome by optimizing mRNA-gRNA or RNP concentration, leading to efficient mutagenesis at regions inaccessible to SpCas9. We also found that the CRISPRscan algorithm can predict SpG and SpRY activity in vivo. Finally, we applied SpG and SpRY to generate knock-ins by homology-directed repair. Altogether, our results expand the CRISPR-Cas targeting genomic landscape in animals.
Comparative Analysis of Sorghum EMS Mutants and Natural Populations
Authors: Wang Liya , Lipzen Anna , Lu Zhenyuan , Chen Junping , Wang Xiaofei , Tello-Ruiz Marcela K. , Barry Kerrie , Mortimer Jenny , Ware Doreen , Xin Zhanguo
Published: June 2021

To build a large-scale genomic resource for functional validation of sorghum genes through EMS-mutagenized BTx623 seeds, we deep sequenced (30-60X) an additional 445 phenotyped EMS mutant lines. 4.2 million EMS mutations are called with nearly 36,800 mutations that could have a disruptive effect on functions of over 15,500 genes. Combining variants carried by both the natural population and previous EMS efforts, over 69% of sorghum coding genes (23644) are now presented with one or more mutations that are, or are predicted to be, disruptive to their functions. Our results show that the EMS population carries more significant mutations but less in each sample than the natural population, which makes it more powerful in elucidating sorghum gene functions on a large scale and requiring less work in validation of candidate causal genes. We have made the data available through two ways, one is the integration with the BSAseq workflow that supports retrieving independent EMS samples carrying the same genes with significant mutation for complementary testing, and the other is a web application for directly querying genes with significant mutations onSciApps.org.
Glyoxal as alternative fixative for single cell RNA sequencing
Authors: Bageritz Josephine , Krausse Niklas , Yousefian Schayan , Leible Svenja , Valentini Erica , Boutros Michael
Published: June 2021

Single cell RNA sequencing (scRNA-seq) has become an important method to identify cell types, delineate the trajectories of cell differentiation in whole organisms and understand the heterogeneity in cellular responses. Nevertheless, sample collection and processing remain a severe bottleneck for scRNA-seq experiments. Cell isolation protocols often lead to significant changes in the transcriptomes of cells, requiring novel methods to preserve cell states. Here, we developed and benchmarked protocols using glyoxal as a fixative for scRNA-seq application. Using Drop-seq methodology, we detected high numbers of transcripts and genes from glyoxal-fixed Drosophila cells after scRNA-seq. The effective glyoxal fixation of transcriptomes in Drosophila and human cells was further supported by a high correlation of gene expression data between glyoxal-fixed and unfixed samples. Accordingly, we also found highly expressed genes overlapping to a large extent between experimental conditions. These results indicated that our fixation protocol did not induce considerable changes in gene expression and conserved the transcriptome for subsequent single cell isolation procedures. In conclusion, we present glyoxal as a suitable fixative for Drosophila cells and potentially cells of other species that allows high-quality scRNA-seq applications.
Cross-reactive TCR with alloreactivity for immunodominant HIV-1 epitope Gag TL9 with enhanced control of viral infection
Authors: Liu Yang , San Dan , Yin Lei
Published: June 2021

Although both HLA B*81:01 and HLA B*42:01 are members of the B7 supertype and can present many of the same HIV-1 epitopes, the identification of a dual-reactive T-cell phenotype was unexpected, since structural data suggested that TL9 peptide binds to each allele in a distinct conformation. How the dual-reactive TCR recognizes these radically distinct p-MHC surfaces is revealed by our structural study, that the introduction of TCR T18A induces a molecular switch of the TL9 peptide in B4201 to approach its conformation in B8101. Most importantly, unique docking of CDR3β towards MHC but not peptide ligand strengthens the peptide tolerance of T18A, extends the ability of TCR to adapt mutations. Moreover, the high affinity of dual-reactive TCR for WT and escape mutant TL9 highlights the functional advantage of the alloreactive phenotype.
Magnetic Bead-Based Separation (MBS) of Pneumococcal Serotypes
Authors: York Anna , Huynh Emily T. , Mbodj Sidiya , Yolda-Carr Devyn , Hislop Maikel S. , Echlin Haley , Rosch Jason W. , Weinberger Daniel M. , Wyllie Anne L.
Published: June 2021

The separation of pneumococcal serotypes from a complex polymicrobial mixture may be required for different applications. For instance, a minority strain could be present at a low frequency in a clinical sample, making it difficult to identify and isolate by traditional culture-based methods. We therefore developed an assay to separate mixed pneumococcal samples using serotype-specific antiserum and a magnetic bead-based separation method. Using qPCR and colony counting methods, we first show that serotypes (12F, 23F, 3, 14, 19A and 15A) present at ∼0.1% of a dual serotype mixture can be enriched to between 10% and 90% of the final sample. We demonstrate two applications for this method: extraction of a known pneumococcal serotype from saliva samples and efficient purification of capsule switch variants from experimental transformation experiments. Moreover, this method may have further laboratory or clinical applications when the selection of specific serotypes is required.
Plasmodium falciparum Calcium Dependent Protein Kinase 4 is critical for male gametogenesis and transmission to the mosquito vector
Authors: Kumar Sudhir , Haile Meseret T. , Hoopmann Michael R. , Tran Linh T. , Michaels Samantha A. , Morrone Seamus R. , Ojo Kayode K. , Reynolds Laura M. , Kusebauch Ulrike , Vaughan Ashley M. , Moritz Robert L. , Kappe Stefan H.I. , Swearingen Kristian E.
Published: June 2021

Gametocytes of the malaria parasite Plasmodium are taken up by the mosquito vector with an infectious blood meal, representing a critical stage for parasite transmission. Calcium dependent protein kinases (CDPKs) play key roles in calcium-mediated signaling across the complex life cycle of the parasite. We sought to understand their role in human parasite transmission from the host to the mosquito vector and thus investigated the role of the human-infective parasite Plasmodium falciparum CDPK4 in the parasite life cycle. P. falciparum cdpk4− parasites created by targeted gene deletion showed no effect in blood stage development or gametocyte development. However, cdpk4− parasites showed a severe defect in male gametogenesis and the emergence of flagellated male gametes. To understand the molecular underpinnings of this defect, we performed mass spectrometry-based phosphoproteomic analyses of wild type and Plasmodium falciparum cdpk4− late gametocyte stages, to identify key CDPK4-mediated phosphorylation events that may be important for the regulation of male gametogenesis. We further employed in vitro assays to identify these putative substrates of Plasmodium falciparum CDPK4. This indicated that CDPK4 regulates male gametogenesis by directly or indirectly controlling key essential events such as DNA replication, mRNA translation and cell motility. Taken together, our work demonstrates that PfCDPK4 is a central kinase that regulates exflagellation, and thereby is critical for parasite transmission to the mosquito vector.

IMPORTANCE

Transmission of the malaria parasite to the mosquito vector is critical for the completion of the sexual stage of the parasite life cycle and is dependent on the release of male gametes from the gametocyte body inside the mosquito midgut. In the present study, we demonstrate that PfCDPK4 is critical for male gametogenesis and is involved in phosphorylation of proteins essential for male gamete emergence. Targeting PfCDPK4 and its substrates may provide insights into achieving effective malaria transmission-blocking strategies.
Combining Multi-Dimensional Molecular Fingerprints to Predict hERG Cardiotoxicity of Compounds
Authors: Ding Weizhe , Zhang Li , Nan Yang , Wu Juanshu , Xin Xiangxin , Han Chenyang , Li Siyuan , Liu Hongsheng
Published: June 2021

At present, drug toxicity has become a critical problem with heavy medical and economic burdens. acLQTS (acquired Long QT Syndrome) is acquired cardiac ion channel disease caused by drugs blocking the hERG channel. Therefore, it is necessary to avoid cardiotoxicity in the drug design and computer models have been widely used to fix this plight. In this study, we present a molecular fingerprint based on the molecular dynamic simulation and uses it combined with other molecular fingerprints (multi-dimensional molecular fingerprints) to predict hERG cardiotoxicity of compounds. 203 compounds with hERG inhibitory activity (pIC50) were retrieved from a previous study and predicting models were established using four machine learning algorithms based on the single and multi-dimensional molecular fingerprints. Results showed that MDFP has the potential to be an alternative to traditional molecular fingerprints and the combination of MDFP and traditional molecular fingerprints can achieve higher prediction accuracy. Meanwhile, the accuracy of the best model, which was generated by consensus of four algorithms with multi-dimensional molecular fingerprints, was 0.694 (RMSE) in the test dataset. Besides, the number of hydrogen bonds from MDFP has been determined as a critical factor in the predicting models, followed by rgyr and sasa. Our findings provide a new sight of MDFP and multi-dimensional molecular fingerprints in building models of hERG cardiotoxicity prediction.
SE(3)-Equivariant Energy-based Models for End-to-End Protein Folding
Authors: Wu Jiaxiang , Shen Tao , Lan Haidong , Bian Yatao , Huang Junzhou
Published: June 2021

Accurate prediction of protein structures is critical for understanding the biological function of proteins. Nevertheless, most structure optimization methods are built upon pre-defined statistical energy functions, which may be sub-optimal in formulating the conformation space. In this paper, we propose an end-to-end approach for protein structure optimization, powered by SE(3)-equivariant energy-based models. The conformation space is characterized by a SE(3)-equivariant graph neural network, with substantial modifications to embed the protein-specific domain knowledge. Furthermore, we introduce continuously-annealed Langevin dynamics as a novel sampling algorithm, and demonstrate that such process converges to native protein structures with theoretical guarantees. Extensive experiments indicate that SE(3)-Fold achieves comparable structure optimization accuracy, compared against state-of-the-art baselines, with over 1-2 orders of magnitude speed-up.
Insulin is expressed by enteroendocrine cells during human fetal development
Authors: Egozi Adi , Llivichuzhca-Loja Dhana , McCourt Blake , Farack Lydia , An Xiaojing , Wang Fujing , Chen Kong , Konnikova Liza , Itzkovitz Shalev
Published: June 2021

Generation of beta cells via transdifferentiation of other cell types is a promising avenue for the treatment of diabetes. Here, we reconstruct a single cell atlas of enteroendocrine cells in the human fetal and neonatal small intestine. We identify a subset of fetal enteroendocrine K/L cells that express high levels of insulin and other beta cell genes. Our findings highlight a potential extra-pancreatic source of beta cells and exposes its molecular blueprint.
Chromosome specific telomere lengths and the minimal functional telomere revealed by nanopore sequencing
Authors: Sholes Samantha L. , Karimian Kayarash , Gershman Ariel , Kelly Thomas J. , Timp Winston , Greider Carol W.
Published: June 2021

We developed a method to tag telomeres and measure telomere length by nanopore sequencing in the yeast S. cerevisiae. Nanopore allows long read sequencing through the telomere, subtelomere and into unique chromosomal sequence, enabling assignment of telomere length to a specific chromosome end. We observed chromosome end specific telomere lengths that were stable over 120 cell divisions. These stable chromosome specific telomere lengths may be explained by stochastic clonal variation or may represent a new biological mechanism that maintains equilibrium unique to each chromosomes end. We examined the role of RIF1 and TEL1 in telomere length regulation and found that TEL1 is epistatic to RIF1 at most telomeres, consistent with the literature. However, at telomeres that lack subtelomeric Y’ sequences, tel1Δ rif1Δ double mutants had a very small, but significant, increase in telomere length compared to the tel1Δ single mutant, suggesting an influence of Y’ elements on telomere length regulation. We sequenced telomeres in a telomerase-null mutant (est2Δ) and found the minimal telomere length to be around 75bp. In these est2Δ mutants there were many apparent telomere recombination events at individual telomeres before the generation of survivors, and these events were significantly reduced in est2Δ rad52Δ double mutants. The rate of telomere shortening in the absence of telomerase was similar across all chromosome ends at about 5 bp per generation. This new method gives quantitative, high resolution telomere length measurement at each individual chromosome end, suggests possible new biological mechanisms regulating telomere length, and provides capability to test new hypotheses.
Structure and mechanism of the RNA dependent RNase Cas13a from Rhodobacter capsulatus
Authors: Kick L.M. , von Wrisberg M.-K. , Runtsch L. S. , Schneider S.
Published: June 2021

Cas13a are single-molecule effectors of the Class II, Type VI family of CRISPR-Cas systems that are part of the bacterial and archaeal defense systems. These RNA-guided and RNA-activated RNA endonucleases are characterized by their ability to cleave target RNAs complementary to the crRNA-spacer sequence, as well as bystander RNAs in a sequence-unspecific manner. Due to cleavage of cellular transcripts they induce dormancy in the host cell and thus protect the bacterial population by aborting the infectious cycle of RNA-phages. Here we report the structural and functional characterization of a Cas13a enzyme from the photo-auxotrophic purple bacteria Rhodobacter capsulatus. The X-ray crystal structure of the RcCas13a-crRNA complex reveals its distinct crRNA recognition mode as well as the enzyme in its contracted, pre-activation conformation. Using site-directed mutagenesis in combination with mass spectrometry, we identified key-residues responsible for pre-crRNA processing by RcCas13a in its distinct catalytic site, and elucidated the acid-base mediated cleavage reaction mechanism. In addition, RcCas13a cleaves target-RNA as well as bystander-RNAs in Escherichia coli which requires its catalytic active HEPN (higher eukaryotes and prokaryotes nucleotide binding) domain nuclease activity. Our data provide further insights into the molecular mechanisms and function of this intriguing family of RNA-dependent RNA endonucleases that are already employed as efficient tools for RNA detection and regulation of gene expression.
spicyR: Spatial analysis of in situ cytometry data in R
Authors: Canete Nicolas P. , Iyengar Sourish S. , Wilmott James S. , Ormerod John T. , Harman Andrew N. , Patrick Ellis
Published: June 2021

Motivation

High parameter histological techniques have allowed for the identification of a variety of distinct cell types within an image, providing a comprehensive overview of the tissue environment. This allows the complex cellular architecture and environment of diseased tissue to be explored. While spatial analysis techniques have revealed how cell-cell interactions are important within the disease pathology, there remains a gap in exploring changes in these interactions within the disease process. Specifically, there are currently no established methods for performing inference on cell localisation changes across images, hindering an understanding of how cellular environments change with a disease pathology.

Results

We have developed the spicyR R package to perform inference on changes in the spatial localisation of cell types across groups of images. Application to simulated data demonstrates a high sensitivity and specificity. We demonstrate the utility of spicyR by applying it to a type 1 diabetes imaging mass cytometry dataset, revealing changes in cellular associations that were relevant to the disease progression. Ultimately, spicyR allows changes in cellular environments to be explored under different pathologies or disease states.

Availability and Implementation

R package freely available at http://bioconductor.org/packages/release/bioc/html/spicyR.html and shiny app implementation at http://shiny.maths.usyd.edu.au/spicyR/

Contact

ellis.patrick@sydney.edu.au

Supplementary information

Code for reproducing key figures available at https://github.com/nickcee/spicyRPaper.
Natural selection promotes the evolution of recombination 1: between the products of natural selection*
Authors: Gerrish Philip J , Galeota-Sprung Benjamin , Sniegowski Paul , Colato Alexandre , Chevallier Julien , Ycart Bernard
Published: June 2021

Shuffling one’s genetic material with another individual seems a risky endeavor more likely to decrease than to increase offspring fitness. This intuitive argument is commonly employed to explain why the ubiquity of sex and recombination in nature is enigmatic. It is predicated on the notion that natural selection assembles selectively well-matched combinations of genes that recombination would break up resulting in low-fitness offspring – a notion often stated in the literature as a self-evident premise. We show however that, upon closer examination, this premise is flawed: we find to the contrary that natural selection in fact has an encompassing tendency to assemble selectively mismatched gene combinations; recombination breaks up these selectively mismatched combinations (on average), assembles selectively matched combinations, and should thus be favored. The new perspective our findings offer suggests that sex and recombination are not so enigmatic but are instead unavoidable byproducts of natural selection.