bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cellular orientational fluctuations, rotational diffusion and nematic order under periodic driving
Authors: Moriel Avraham , Livne Ariel , Bouchbinder Eran 
Published: May 2022

AbstractThe ability of living cells to sense the physical properties of their microenvironment and to respond to dynamic forces acting on them plays a central role in regulating their structure, function and fate. Of particular importance is the cellular sensitivity and response to periodic driving forces in noisy environments, encountered in vital physiological conditions such as heart beating, blood vessels pulsation and breathing. Here, we first test and validate two predictions of a mean-field theory of cellular reorientation under periodic driving, which combines the minimization of cellular anisotropic elastic energy with active remodeling forces. We then extend the mean-field theory to include uncorrelated, additive nonequilibrium fluctuations, and show that the theory quantitatively agrees with the experimentally observed stationary probability distributions of the cell body orientation, under a range of biaxial periodic driving forces. The fluctuations theory allows to extract the dimensionless active noise amplitude of various cell types, and consequently their rotational diffusion coefficient. We then focus on intra-cellular nematic order, i.e. on orientational fluctuations of actin stress fibers around the cell body orientation, and show experimentally that intra-cellular nematic order increases with both the magnitude of the driving forces and the biaxiality strain ratio. These results are semi-quantitatively explained by applying the same cell body fluctuations theory to orientationally correlated actin stress fiber domains. The implications of these findings, which make the quantitative analysis of cell mechanosensitivity more accessible, are discussed.
An in situ quantitative map of initial human colorectal HIV transmission
Authors: Baharlou Heeva , Canete Nicolas , Vine Erica E , Hu Kevin , Yuan Di , Sandgren Kerrie J , Bertram Kirstie M , Nasr Najla , Rhodes Jake W , Gosselink Martijn P , Di Re Angelina , Reza Faizur , Ctercteko Grahame , Pathma-Nathan Nimalan , Collins Geoff , Toh James , Patrick Ellis , Haniffa Muzlifah A , Estes Jacob D. , Byrne Scott N , Cunningham Anthony L , Harman Andrew N 
Published: May 2022

AbstractThe initial immune response to HIV is critical in determining transmission. However, due to technical limitations we still do not have a comparative map of early mucosal transmission events. We combined RNAscope, cyclic-immunofluorescence and novel image analysis tools to quantify HIV transmission dynamics in intact human colorectal tissue. We mapped HIV enrichment to mucosal dendritic cells (DC) and submucosal macrophages, but not CD4+ T-cells, the primary targets of downstream infection. DCs appeared to funnel virus to lymphoid aggregates which acted as early sanctuaries of high viral titres whilst facilitating HIV passage to the submucosa. Finally, HIV entry induced rapid recruitment and clustering of target cells, facilitating DC and macrophage mediated HIV transfer and enhanced infection of CD4+ T-cells. These data demonstrate a rapid response to HIV structured to maximise the likelihood of mucosal infection, and provide a framework for in situ studies of host pathogen interactions and immune mediated pathologies.Highlights-in situ quantification of host cellular microenvironment response to pathogen invasion in human colorectal tissue.-HIV first localises to mucosal DCs and submucosal macrophages, but not CD4+ T cells.-Viral enrichment first occurs in lymphoid aggregates which is associated with passage into the submucosa.-Early localisation of HIV to CD4+ T cells is associated with interactions with DCs and macrophages.Graphical Abstract
Relationship between common polymorphisms of NRAMP1 gene and pulmonary tuberculosis in Lorestan LUR population
Authors: Amiri Ali , Sabooteh Toomaj , Shahsavar Farhad 
Published: May 2022

AbstractIntroductionTuberculosis (TB) is caused by Mycobacterium tuberculosis. In humans, a number of genes have been identified as susceptible to pulmonary tuberculosis. The relationship between NRAMP1 polymorphisms and pulmonary tuberculosis has been studied in different populations and has reported contradictory results. The aim of this study was to investigate the relationship between the common polymorphisms of NRAMP1 gene and the susceptibility to pulmonary tuberculosis in the LUR Population of Lorestan province of Iran.Materials and MethodsIn this case control study, three common polymorphisms of NRAMP1 gene (3’UTR, INT4 and D543N) were genotyped using PCR-RFLP technique in the LUR population of Lorestan province. In this study, 100 patients with pulmonary tuberculosis (PTB) were studied as case group and 100 healthy controls that matched for age and sex with the patient group, studied as control group. Statistical analysis was performed using SPSS 18 software.ResultsIn the present study we observed that the GG genotype of D543N polymorphism was statistically significantly associated with increased susceptibility to TB (84% in the case group vs. 72% in the control group, %95CI=1.024-4.071, OR=2.042, P=0.0405). Also, G allele of D543N polymorphism was statistically significantly associated with increased susceptibility to pulmonary tuberculosis (90% in the case group vs. 81.5% in the control group, %95CI=1.140-3.663, OR=2.043, P=0.015). On the other hand, the frequency of allele A of D543N polymorphism was significantly lower in patients than in the control group (10% in the case group vs. 18.5% in the control group, %95CI=0.273-0.878, OR=0.489, P=0.015). Although genotypic and allelic frequency of 3’UTR and INT4 polymorphisms between patients and controls showed no significant differences in the study population.Discussion and conclusionOur observations showed that GG genotype and G allele of D543N polymorphism have a significant role in increasing the susceptibility to pulmonary tuberculosis in the LUR Population of Lorestan province. Also, allele A of D543N polymorphism has a significant effect on resistance to pulmonary tuberculosis in this population. Although there was no significant correlation between genotypes and alleles of 3’UTR and INT4 polymorphisms with susceptibility to or resistance to pulmonary TB in this population. It is suggested that a larger sample size be used in future studies. It is also recommended to conduct this type of study on other ethnicities.
SENSITIVITY ANALYSIS OF A TUBERCULOSIS (TB) MATHEMATICAL MODEL
Authors: Vaachia Vegha , Terna Mande Timothy 
Published: May 2022

AbstractIn this work, we have constructed a Mathematical model for the transmission dynamics of tuberculosis TB. Feasibility and positivity of solutions of the model are determined and it is established that the model is well posed and that the solutions are all positive. The disease-free equilibrium (DFE) is also determined and the basic reproduction number R0 is computed. Sensitivity analysis of the basic reproduction number is conducted to find parameters of the model that are most sensitive and should be targeted by intervention strategies. It was therefore, observed through sensitivity analysis that TB induced death (d) has a high impact on R0 and varies inversely with R0. Graphical simulation of the model parameters was performed. It was observed that model parameters such as infection rate (β), recruitment rate (π) and rate of movement from latent to active TB (α) are directly proportional to the basic reproduction numberR0. Finally, it is observed that the basic reproduction number R0 is a decreasing function of the recovery rate (γ) and natural death rate (μ).
Magnetic Enrichment of Immuno-Specific Extracellular Vesicles for Mass Spectrometry Using Biofilm-Derived Iron Oxide Nanowires
Authors: Pham Quang Nghia , Winter Marnie , Milanova Valentina , Young Clifford , Condina Mark R. , Hoffmann Peter , Pham Nguyen T. H. , Tung Tran Thanh , Losic Dusan , Thierry Benjamin 
Published: May 2022

AbstractImmuno-specific enrichment of extracellular vesicles (EVs) originating from specific cells/tissues is a promising source of information towards improving insights into cellular pathways underpinning various pathologies and developing novel non-invasive diagnostic methods. Enrichment is an important aspect in mass spectrometry-based analyses of EVs. Herein, we report a protocol for immuno-magnetic enrichment of subtype specific EVs and their subsequent processing for mass spectrometry. Specifically, we conjugated placental alkaline phosphatase (PLAP) antibodies to magnetic iron oxide nanowires (NWs) derived from bacterial biofilms and demonstrated the utility of this approach by enriching placental specific EVs (containing PLAP) from cell culture media. We demonstrate efficient PLAP+ve EV enrichment for both NW-PLAP and Dynabeads™-PLAP, with PLAP protein recovery (83.7±8.9% and 83.2±5.9%, respectively), high particle-to-protein ratio (7.5±0.7×109 and 7.1 ± 1.2×109, respectively), and low non-specific binding of non-target EVs (7±3.2% and 5.4±2.2%, respectively). Furthermore, our optimized EV enrichment and processing approach identified 2518 and 2545 protein groups with mass spectrometry for NW-PLAP and Dynabead™-PLAP, respectively, with excellent reproducibility (Pearson correlation 0.986 and 0.988). The proposed immuno-specific EVs enrichment and liquid chromatography-tandem mass spectrometry method using naturally occurring iron oxide magnetic NWs or gold-standard Dynabeads™ enables high-quality EV proteomic studies.
The Breast Cancer Epigenomics Track Hub
Authors: Ambrosini Giovanna , Agnoletto Andrea , Brisken Cathrin , Bucher Philipp 
Published: May 2022

AbstractBackgroundPioneering research has shown that high-throughput epigenomics assays such as ChlP-seq and ATAC-seq are applicable to patient-derived breast tumor samples. A host of public data has been accumulated since then, which are potentially of high value for basic research as well as personalized medicine. Such data sets constitute encyclopedias of biological knowledge. However, their impact has so far been limited by access obstacles, especially with regard to extraction and visualization of small portions of data that could potentially answer specific questions arising in a research context.ResultsWe developed the breast cancer epigenomics track hub (BC hub), a resource intended to make it easy for occasional users to find, access and view data of their interest. The BC hub harbors ChIP-seq, ATAC-seq and copy number data from breast tumors, normal breast cells, patient-derived xenografts and breast cancer cell lines in a genome browsable track format. The tracks can be accessed via hyperlinks that automatically configure customized views for different interest groups. Here, we present a detailed description of the resource and informative use cases illustrating its potential in answering specific biological questions.ConclusionsWe show that track hubs constitute a powerful way of bringing epigenomics data to the user who could benefit from them. The examples presented highlight the added-value of joint visualization of breast cancer data from different sources. The proof-of-concept provided here exemplifies and underscores the importance of efforts to make biological data FAIR (findable, accessible, interoperable and reusable), and may serve as an encouragement of similar bottom-up initiatives in other research fields. The BC hub is freely accessible at https://bchub.epfl.ch.
Deep mutational scanning and machine learning reveal structural and molecular rules governing allosteric hotspots in homologous proteins
Authors: Leander Megan , Liu Zhuang , Cui Qiang , Raman Srivatsan 
Published: May 2022

AbstractA fundamental question in protein science is where allosteric hotspots – residues critical for allosteric signaling – are located, and what properties differentiate them. We carried out deep mutational scanning (DMS) of four homologous bacterial allosteric transcription factors (aTF) to identify hotspots and built a machine learning model with this data to glean the structural and molecular properties of allosteric hotspots. We found hotspots to be distributed protein-wide rather than being restricted to “pathways” linking allosteric and active sites as is commonly assumed. Despite structural homology, the location of hotspots was not superimposable across the aTFs. However, common signatures emerged when comparing hotspots coincident with long-range interactions, suggesting that the allosteric mechanism is conserved among the homologs despite differences in molecular details. Machine learning with our large DMS datasets revealed that global structural and dynamic properties to be a strong predictor of whether a residue is a hotspot than local and physicochemical properties. Furthermore, a model trained on one protein can predict hotspots in a homolog. In summary, the overall allosteric mechanism is embedded in the structural fold of the aTF family, but the finer, molecular details are sequence-specific.
Activation of Transposable Elements Upon Statin Treatment
Authors: Valdebenito-Maturana Franco , Valdebenito-Maturana Braulio 
Published: May 2022

AbstractHigh cholesterol levels have been associated with cardiovascular diseases, and lowering them has been a key focus in the treatment of such diseases. Statins are drugs used with that aim, and can be divided in the lipophilic Simvastatin and the hydrophilic Rosuvastatin. Regardless of the statin type, a high proportion (∼70%) of patients stop using statins due to suffering from side effects on skeletal muscle, such as myalgia, and muscle cramps. Thus, there has been a considerable effort in understanding how statins contribute to these side effects. A catalogue of genes and molecular pathways that change upon statin treatment has been recently published, allowing further understanding how the side effects occur. However, Transposable Elements (TEs) were not studied. TEs can move within a genome, and they are highly repetitive, representing about half of the human genome. Currently, most TEs in the human genome are inactive, but it has been shown that TEs can still transcribe, and that either via their transposition or their transcriptional activity, can influence gene expression. Here, using novel computational tools to accurately estimate TE expression, we studied their activity and predicted their potential impact on gene expression. We developed a catalogue of TEs expressed upon statin treatment, and the putative genes whose expression might be influenced by TEs. Overall, we speculate that based on our findings, TEs might be a key target in order to understand statin-mediated side effects.
Metabarcoding metacommunities: time, space, and land use interact to structure aquatic macroinvertebrate communities in streams
Authors: Gleason Jennifer Erin , Hanner Robert H. , Cottenie Karl 
Published: May 2022

AbstractThere is an increasing need to move beyond evaluating the effect of land use on stream communities by only studying local variables, and instead incorporate a metacommunity perspective which integrates environmental and spatial factors across larger spatial scales. The use of molecular tools (DNA metabarcoding) to identify bioindicator groups, such as aquatic macroinvertebrates, can provide greater taxonomic resolution to explore patterns in stream metacommunities. In this study, we collected aquatic macroinvertebrates from streams in southern Ontario which spanned a gradient of agricultural disturbance and used DNA metabarcoding to identify the species composition from these samples. We address a significant knowledge gap in previous stream aquatic macroinvertebrate metacommunity studies by incorporating molecular identification as well as a temporal component. We observed that a combination of local habitat conditions, regional agricultural land use, and spatial position influenced aquatic macroinvertebrate community composition, suggesting there is an interaction between environmental filtering and dispersal processes that structures these communities. However, aquatic macroinvertebrate communities were also highly dissimilar between streams and composed of many rare species, and a large percentage of unexplained variation suggests that there is a strong stochastic component to community assembly. We also observed that there is a seasonal component to metacommunity dynamics, with different water quality variables being significant to community composition in each sampling month. While we expected that an increased percentage of surrounding agricultural land use would result in more homogenous macroinvertebrate communities, we only detected this relationship in May and found evidence that a larger riparian buffer width can mitigate the effects of agricultural land use. We demonstrate the utility of DNA metabarcoding for revealing patterns in metacommunity dynamics that may not be detectable using coarse taxonomic identifications, and reveal the importance of incorporating a seasonal component when evaluating the influence of land use on community composition.
One-Pot Endonucleolytically Exponentiated Rolling Circle Amplification by CRISPR-Cas12a Affords Sensitive, Expedited Isothermal Detection of MicroRNAs
Authors: Yan He , Wen Yunjie , Han Song , Hughes Steven J. , Zeng Yong 
Published: May 2022

AbstractMicroRNAs (miRNAs) are a class of short non-coding RNAs that play essential roles in gene expression regulation. While miRNAs offer a promising source for developing potent cancer biomarkers, the progress towards clinical utilities remains largely limited, due in part to the long-standing challenge in sensitive, specific, and robust detection of miRNAs in human biofluids. Emerging next-generation molecular technologies, such as the CRISPR-based methods, promise to transform nucleic acid testing. The prevailing strategy used in existing CRISPR-based methods is to hyphenate two separate reactions for pre-amplification,e.g., rolling circle amplification (RCA), and amplicon detection by Cas12a/13atrans-cleavage in tandem. Thus, existing CRISPR-based miRNA assays require multiple manual steps and lack the analytical performance of the gold standard, RT-qPCR. Radically deviating from the existing strategies, we developed a one-step, one-pot isothermal miRNA assay termed “Endonucleolytically eXponenTiated Rolling circle Amplification with the dual-functional CRISPR-Cas12a” (EXTRA-CRISPR) to afford RT-PCR-like performance for miRNA detection. We demonstrated the superior analytical performance of our EXTRA-CRISPR assay to detect miRNAs (miR-21, miR-196a, miR-451a, and miR-1246) in plasma extracellular vesicles, which allowed us to define a potent EV miRNA signature for detection of pancreatic cancer. The analytical and diagnostic performance of our one-pot assay were shown to be comparable with that of the commercial RT-qPCR assays, while greatly simplifying and expediting the analysis workflow. Therefore, we envision that our technology provides a promising tool to advance miRNA analysis and clinical marker development for liquid biopsy-based cancer diagnosis and prognosis.
RNA exosome ribonuclease DIS3 degrades Pou6f1 to promote mouse pre-implantation cell differentiation
Authors: Wu Di , Dean Jurrien 
Published: May 2022

SUMMARYMammalian development is precisely controlled by cell differentiation. Discovery of new regulators and investigating their crosstalk provide insights into genetic networks defining pre-implantation development. To identify novel developmental repressors, we established a knockout mouse model of Dis3, an RNA exosome associated RNase. Homozygous Dis3 null embryos arrest at the morula-to-blastocyst transition. Using single embryo RNA-seq, we discovered persistence of Pou6f1 mRNA in homozygous null Dis3 embryos and determined that the cognate protein represses transcription of Nanog and Cdx2. The resultant defects in cell differentiation disrupted the morula-to-blastocyst transition and was embryonic lethal. To overcome the paucity of embryos, homozygous Dis3 null mouse embryonic stem cells were derived to identify additional gene targets of POU6F1. While microinjection of the Dis3 cRNA into zygotes rescued the morula-to-blastocyst block, point mutations of Dis3 in individual blastomeres transformed the cell and prevented incorporation into embryos. Our findings uncover a not heretofore reported regulatory pathway of DIS3-POU6F1 in pre-implantation mammalian embryogenesis.In BriefMammalian pre-implantation development is regulated by master transcription factors and their crosstalk. Wu and Dean report that an RNA exosome associated RNase, DIS3, degrades Pou6f1 mRNA to de-repress transcription of Nanog and Cdx2 genes. In the absence of DIS3, POU6F1 protein persists and embryos arrest as morulae unable to become blastocysts due to lack of cell differentiation.HighlightsDis3 knockout mice have morula arrest due to lack of cell differentiation.DIS3 binds and degrades Pou6f1 mRNA before the morula stage.POU6F1 globally occupies promoters to regulate gene transcription.DIS3 mutation results in cell transformation in embryonic development.
Staining-Free, In-Flow Enumeration of Tumor Cells in Blood Using Digital Holographic Microscopy and Deep Learning
Authors: Gangadhar Anirudh , Sari-Sarraf Hamed , Vanapalli Siva A. 
Published: May 2022

AbstractCurrently, detection of circulating tumor cells (CTCs) in cancer patient blood samples relies on immunostaining, which does not provide access to live CTCs, limiting the breadth of CTC-based applications. As a first step to address this limitation, here, we demonstrate staining-free enumeration of tumor cells spiked into lysed blood samples using digital holographic microscopy (DHM), microfluidics and machine learning (ML). A 3D-printed module for laser assembly was developed to simplify the optical set up for holographic imaging of cells flowing through a sheath-based microfluidic device. Computational reconstruction of the holograms was performed to localize the cells in 3D and obtain the plane of best focus images to train deep learning models. First, we evaluated the classification performance of two convolutional neural networks (CNNs): ResNet-50 and a custom-designed shallow Network dubbed s-Net. The accuracy, sensitivity and specificity of these networks were found to range from 97.08% and 99.32%. Upon selecting the s-Net due to its simple architecture and low computational burden, we formulated a decision gating strategy to significantly lower the false positive rate (FPR). By applying an optimized decision threshold to mixed samples prepared in silico, the FPR was reduced from 1×10−2 to 2.77×10−4. Finally, the developed DHM-ML framework was successfully applied to enumerate spiked MCF-7 breast cancer cells from lysed blood samples containing a background of white blood cells (WBCs). We conclude by discussing the advances that need to be made to translate the DHM-ML approach to staining-free enumeration of CTCs in cancer patient blood samples.