bluuebunny/crossref_metadata_2025 huggingface dataset:
Phylogenomics provides insights into the evolution of cactophily and host plant shifts inDrosophila
Authors: Moreyra Nicolás Nahuel , Almeida Francisca Cunha , Allan Carson , Frankel Nicolás , Matzkin Luciano Matías , Hasson Esteban
Published: May 2022

Cactophilic species of theDrosophila buzzatiicluster (repletagroup) comprise an excellent model group to investigate genomic changes underlying adaptation to extreme climate conditions and host plants. In particular, these species offer a subject to study the transition from chemically simpler breeding sites (like prickly pears of the genusOpuntia) to chemically more complex hosts (columnar cacti). Here, we report four highly contiguous genome assemblies of three species of thebuzzatiicluster. Based on this genomic data and inferred phylogenetic relationships, we identified candidate taxonomically restricted genes (TRGs) likely involved in the evolution of cactophily and cactus host specialization in internal branches of the subgenusDrosophila. Functional enrichment analyses of TRGs within thebuzzatiicluster identified genes involved in detoxification, water preservation, immune system response, anatomical structure development, and morphogenesis. In contrast, processes that regulate responses to stress, as well as the metabolism of nitrogen compounds, transport, and secretion were found in the set of species that are columnar cacti dwellers. These findings are in line with the hypothesis that those genomic innovations brought about instrumental mechanisms underlying adaptation in a group of species that speciated in the arid regions of South America.
Distinct Effects of the Male-Killing BacteriaWolbachiaandSpiroplasmaand a Partiti-Like Virus in the Tea Pest Moth,Homona magnanima
Authors: Arai Hiroshi , Takamatsu Takumi , Lin Shiou-Ruei , Mizutani Tetsuya , Omatsu Tsutomu , Katayama Yukie , Nakai Madoka , Kunimi Yasuhisa , Inoue Maki N.
Published: May 2022

Male killing, the phenomenon of male death during development, is considered to be one of the advantageous strategies exerted by maternally transmitted microbes. Male killing has attracted interest in the fields of evolutionary biology and ecology for decades; however, little is known about its mechanism and origin. Here, we characterized and compared the effects of three distinct male killers,Wolbachia(Alphaproteobacteria),Spiroplasma(Mollicutes), and Osugoroshi virus (OGV) (Partitiviridae) in the tea pest mothHomona magnanima(Lepidoptera, Tortricidae). Regardless of the genetic sex (male: ZZ; female: ZW), female specific splice variants of the doublesex gene (dsx), a downstream regulator of the sex-determining gene cascade, was expressed inH. magnanimaharbored either male-killingWolbachiaorSpiroplasma. However, OGV and non-male-killingWolbachiadid not alterdsxsplicing. RNA sequencing and quantitative PCR assays demonstrated that male-killingWolbachiaimpaired the host’s dosage compensation system by altering the global gene expression of the Z chromosome (corresponding toBombyx morichromosome 1 and 15) in males, whereasSpiroplasmadid not affect dosage compensation. In contrast, the partiti-like virus OGVs did not affect sex-determination cascades or dosage compensation systems. Besides, male killers distinctly altered host gene expression and metabolomes associated with physiology, morphology, and diverse metabolic pathways. Moreover,WolbachiaandSpiroplasmainfections triggered abnormal apoptosis only in male embryos. These findings suggest that distantly related microbes employ distinct machineries to kill identical host males, which have been acquired through independent evolutionary processes.

Importance

Male-killing caused by diverse microbes has attracted substantial attention. However, it remains unclear how such male killers have evolved similar phenotypes, in part because male-killing mechanisms have been studied using different insect models. Here, by comparing three phylogenetically distinct male killers,Wolbachia, Spiroplasma, and a partiti-like virus, in an identical host, we provide evidence that microbes can affect male viability through distinct machinery, demonstrating distinct evolutionary scenarios for microbes to acquire make-killing ability. These findings provide insight into new directions for studying microbe–host interactions.
Evolution is not uniform along protein sequences
Authors: Bricout Raphaël , Weil Dominique , Stroebel David , Genovesio Auguste , Crollius Hugues Roest
Published: May 2022

Amino acids evolve at different speeds within protein sequences, because their functional and structural roles are different. However, the position of an amino-acid within the sequence is not known to influence this evolutionary speed. Here we discovered that amino-acid evolve almost twice faster at protein termini than in their centre, hinting at a strong topological bias along the sequence length. We further show that the distribution of functional domains and of solvent-accessible residues in proteins readily explain how functional constrains are weaker at their termini, leading to the observed excess of amino-acid substitutions. Finally, we show that methods inferring sites under positive selection are strongly biased towards protein termini, suggesting that they may confound positive selection with weak negative selection. These results suggest that accounting for positional information should improve evolutionary models.
Tree diversity and density affect damage caused by the invasive pest Cameraria ohridella in urban areas
Authors: Stemmelen Alex , Jactel Hervé , Castagneyrol Bastien
Published: May 2022

Invasive, non-native invasive pests pose a growing threat to urban trees and the services they provide to urban residents. With the reluctance to use chemical insecticides in cities, environmentally friendly methods of pest management are needed. Tree diversity is known to affect insect herbivory in forest, with higher tree species diversity leading to lower level of damage. However, the validity of those findings for a non-native insect in an urban environment remains to be demonstrated.

We monitored 54 horse chestnut trees attacked by the invasive horse chestnut leafminer Cameraria ohridella in the city of Bordeaux, France. We analyzed the effects of neighboring tree diversity and density on the abundance, damage and parasitism rate of these leafminers.

We showed that the abundance and damage of C. ohridella significantly increased with higher local tree canopy cover. We found that the parasitism rate of C. ohridella increased with the species diversity of neighboring trees. However, this increase in parasitism rate was not associated with a decrease in leaf area damaged.

Our results pave the way for the management of exotic insect pests in cities based on the manipulation of spatial distribution and species diversity of urban trees.
Uncovering Additional Predictors of Urothelial Carcinoma from Voided Urothelial Cell Clusters Through a Deep Learning Based Image Preprocessing Technique
Authors: Levy Joshua J. , Liu Xiaoying , Marotti Jonathan D. , Kerr Darcy A. , Gutmann Edward J. , Glass Ryan E. , Dodge Caroline P. , Suriawinata Arief A. , Vaickus Louis J.
Published: May 2022

Urine cytology is commonly used as a screening test for high grade urothelial carcinoma for patients with risk factors or hematuria and is an essential step in longitudinal monitoring of patients with a prior bladder cancer history. However, the semi-subjective nature of current reporting systems for urine cytology (e.g., The Paris System) can hamper reproducibility. For instance, the incorporation of urothelial cell clusters into the classification schema is still an item of debate and perplexity amongst expert cytopathologists, as several previous works have disputed their diagnostic relevance. Recently, several machine learning and morphometric algorithms have been proposed to provide quantitative descriptors of urine cytology specimens in an effort to reduce subjectivity and include automated assessments of cell clusters. However, it remains unclear how these computer algorithms interpret/analyze cell clusters. In this work, we have developed an automated preprocessing tool for urothelial cell cluster assessment that divides urothelial cell clusters into meaningful components for downstream assessment (i.e., population-based studies, workflow automation). Results indicate that cell cluster atypia (i.e., defined by whether the cell cluster harbored multiple atypical cells, thresholded by a minimum number of cells), cell border overlap and smoothness, and total number of clusters are important markers of specimen atypia when considering assessment of urothelial cell clusters. Markers established through techniques to separate cell clusters may have wider applicability for the design and implementation of machine learning approaches for urine cytology assessment.
An automated approach to quantify chemotaxis index in Caenorhabditis nematodes
Authors: Crombie Timothy A. , Chikuturudzi Chido , Cook Daniel E. , Andersen Erik C.
Published: May 2022

Chemotaxis assays are used extensively to study behavioral responses of Caenorhabditis nematodes to environmental cues. These assays result in a chemotaxis index (CI) that denotes the behavioral response of a population of nematodes to a particular compound and can range from 1 (maximum attraction) to −1 (maximum avoidance). Traditional chemotaxis assays have low throughput because researchers must manually setup experimental populations and score CIs. Here, we describe an automated methodology that increases throughput by using liquid-handling robots to setup experimental populations and a custom image analysis package, ct, to automate the scoring of CIs from plate images.
Cellular orientational fluctuations, rotational diffusion and nematic order under periodic driving
Authors: Moriel Avraham , Livne Ariel , Bouchbinder Eran
Published: May 2022

The 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

The 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

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in situ quantification of host cellular microenvironment response to pathogen invasion in human colorectal tissue.

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HIV first localises to mucosal DCs and submucosal macrophages, but not CD4+ T cells.

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Viral enrichment first occurs in lymphoid aggregates which is associated with passage into the submucosa.

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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

Introduction

Tuberculosis (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 Methods

In 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.

Results

In 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 conclusion

Our 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

In 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

Immuno-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

Background

Pioneering 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.

Results

We 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.

Conclusions

We 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

A 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

High 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

There 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

MicroRNAs (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

Mammalian 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 Brief

Mammalian 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.

Highlights

Dis3 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

Currently, 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.
The impact of post-traumatic stress disorder in pharmacological intervention outcomes for adults with bipolar disorder: a protocol for a systematic review and meta-analysis
Authors: Russell Samantha E. , Wrobel Anna L. , Skvarc David , Kavanagh Bianca E , Ashton Melanie M , Dean Olivia M. , Berk Michael , Turner Alyna
Published: May 2022

Background

Recent data indicates high prevalence of post-traumatic stress disorder (PTSD) in bipolar disorder (BD). PTSD may play a role in poor treatment outcomes and quality of life for people with BD. Despite this, few studies have examined the pharmacological treatment interventions and outcomes for this comorbidity. This systematic review will bring together currently available evidence regarding the impact of comorbid PTSD on pharmacological treatment outcomes in adults with BD.

Methods

A systematic search of Embase, MEDLINE Complete, PsycINFO, and the Cochrane Central Register of Controlled Trials (CENTRAL) will be conducted to identify randomised and non-randomised studies of pharmacological interventions for adults with diagnosed bipolar disorder and PTSD. Data will be screened and extracted by two independent reviewers. Literature will be searched from the creation of the databases until April 1 2021. Risk of bias will be assessed using the Newcastle-Ottawa Scale and the Cochrane Collaborations Risk of Bias tool. A meta-analysis will be conducted if sufficient evidence is identified in the systematic review. The meta-analysis will employ a random-effects model and be evaluated using the I2 statistic.

Discussion

This review and meta-analysis will be the first to systematically explore and integrate the available evidence on the impact of PTSD on pharmacological treatments and outcome in those with BD. The results and outcomes of this systematic review will provide directions for future research and be published in relevant scientific journals and presented at research conferences.

Systematic review registration

The protocol has been registered at the International Prospective Register of Systematic Reviews (PROSPERO; registration number: CRD42020182540).
Bridging Structural MRI with Cognitive Function for Individual Level Classification of Early Psychosis via Deep Learning
Authors: Wen Yang , Zhou Chuan , Chen Leiting , Deng Yu , Cleusix Martine , Jenni Raoul , Conus Philippe , Do Kim Q. , Xin Lijing
Published: May 2022

Recent efforts have been made to apply machine learning and deep learning approaches to the automated classification of schizophrenia using structural magnetic resonance imaging (sMRI) at the individual level. However, these approaches are less accurate on early psychosis (EP) since there are mild structural brain changes at early stage. As cognitive impairments is one main feature in psychosis, in this study we apply a multi-task deep learning framework using sMRI with inclusion of cognitive assessment to facilitate the classification EP patients from healthy individuals. Unlike previous studies, we used sMRI as the direct input to perform EP classifications and cognitive estimations. The proposed model does not require time-consuming volumetric or surface based analysis and can provide additionally cognition predictions. Extensive experiments were conducted on a sMRI data set with a total of 77 subjects (38 EP patients and 39 healthy controls), and we achieved 74.9±4.3% five-fold cross-validated accuracy and an area under the curve of 71.1±4.1% on EP classification with the inclusion of cognitive estimations. We reveal the feasibility of automated cognitive estimation using sMRI by deep learning models, and also demonstrate the implicit adoption of cognitive measures as additional information to facilitate EP classifications from healthy controls.
Loss of mitochondrial Chchd10 or Chchd2 in zebrafish leads to an ALS-like phenotype and Complex I deficiency independent of the mt-ISR
Authors: Légaré Virginie Petel , Rampal Christian J. , Aaltonen Mari J. , Janer Alexandre , Zinman Lorne , Shoubridge Eric A. , Armstrong Gary A.B.
Published: May 2022

Mutations inCHCHD10andCHCHD2, coding for two paralogous mitochondrial proteins, have been identified in amyotrophic lateral sclerosis (ALS), frontotemporal lobar degeneration (FTD), and Parkinson’s disease (PD). Here we investigated the biological roles of these proteins during vertebrate development using knockout (KO) models in zebrafish. We demonstrate that loss of either or both proteins leads to a motor impairment, reduced survival, and compromised neuromuscular junction (NMJ) integrity in larval zebrafish. Compensation by Chchd10 was observed in thechchd2-/-model, but not by Chchd2 in thechchd10-/-model. The assembly of mitochondrial respiratory chain Complex I was impaired inchchd10-/-andchchd2-/-zebrafish larvae, but unexpectedly not in the doublechchd10-/-&chchd2-/-model, suggesting that reduced mitochondrial Complex I cannot be solely responsible for the observed phenotypes, which are generally more severe in the double KO. Activation of the mitochondrial integrated stress response (mt-ISR) was only observed in the double KO model, possibly implicating this pathway in the recovery of the Complex I defect, and suggesting that Complex I assembly defect in our single KO is independent of the mt-ISR. Our results demonstrate that both proteins are required for normal vertebrate development, but their precise molecular function in the mitochondrial biology of motor neurons remains to be discovered.
Translational approach to increase phosphate accumulation in two plant species through perturbance of inositol pyrophosphates
Authors: Freed Catherine , Craige Branch , Cridland Caitlin , Donahue Janet , Williams Sarah Phoebe , Kim Jiwoo , Gillaspy Glenda
Published: May 2022

Inorganic phosphate (Pi), while indispensable for all biological organisms and a major agricultural macronutrient, is an increasingly limited and nonrenewable resource. Recent studies demonstrate the importance of inositol pyrophosphates (PP-InsPs) in plant Pi signaling and homeostasis, however the extent to which PP-InsPs impact plant development is not well understood. We report that transgenic expression of the Saccharomyces cerevisiae enzyme Diadenosine and Diphosphoinositol Polyphosphate Phosphohydrolase (DDP1) in Arabidopsis thaliana and Thlaspi arvense (pennycress) provide a unique translational utility for Pi phytoremediation as well as unique germplasm and insight on the long-term impacts of reduced PP-InsPs. Transgenic DDP1 expression in Arabidopsis decreased PP-InsPs, impacted growth and development, and increased Pi accumulation leading to Pi toxicity. Analysis of Pi Starvation Response (PSR) marker genes indicated that the PSR is activated in DDP1 expressing plants. We assessed translational utility through transformation of pennycress, a spring annual cover crop with emerging importance as a biofuel crop, with a DDP1 transgene. Pennycress plants expressing DDP1 showed similar altered Pi accumulation phenotypes, suggesting that these plants could potentially serve to remove Pi from Pi-rich soils. Our study addresses the long-term impacts of PP-InsP reduction on plant growth, as well as establishing a starting material for a unique Pi reclaiming cover crop.

SIGNIFICANCE STATEMENT

A major challenge to food security is the phosphorus (P) crisis. A global P shortage is imminent based on the misuse of current resources and will be further aggravated by climate change and a lack of policy addressing sustainability. Our work addresses this crisis by investigating the sustained impact of altering inositol pyrophosphates to manipulate plant P accumulation, a strategy that could be used to remediate nutrient-polluted environments.
Perchlorate-Specific Proteomic Stress Responses of Debaryomyces hansenii Could Enable Microbial Survival in Martian Brines
Authors: Heinz Jacob , Doellinger Joerg , Maus Deborah , Schneider Andy , Lasch Peter , Grossart Hans-Peter , Schulze-Makuch Dirk
Published: May 2022

If life exists on Mars, it would face several challenges including the presence of perchlorates, which destabilize biomacromolecules by inducing chaotropic stress. However, little is known about perchlorate toxicity for microorganism on the cellular level. Here we present the first proteomic investigation on the perchlorate-specific stress responses of the halotolerant yeast Debaryomyces hansenii and compare these to generally known salt stress adaptations. We found that the responses to NaCl and NaClO4-induced stresses share many common metabolic features, e.g., signaling pathways, elevated energy metabolism, or osmolyte biosynthesis. However, several new perchlorate-specific stress responses could be identified, such as protein glycosylation and cell wall remodulations, presumably in order to stabilize protein structures and the cell envelope. These stress responses would also be relevant for life on Mars, which - given the environmental conditions - likely developed chaotropic defense strategies such as stabilized confirmations of biomacromolecules and the formation of cell clusters.
ATP induced conformational change of axonemal outer dynein arms studied by cryo-electron tomography
Authors: Zimmermann Noemi , Noga Akira , Obbineni Jagan Mohan , Ishikawa Takashi
Published: May 2022

Axonemal dyneins in the outer dynein arm (ODA) generate force for ciliary beating. We analyzed three states of ODA during the power stroke cycle using in situ cryo-electron tomography, subtomogram averaging and classification. These states of force generation depict the pre-power stroke, post-power stroke conformations and an intermediate state. Comparison of these conformations to published in vitro atomic structures of cytoplasmic dynein, ODA and Shulin-ODA complex showed that the orientation and position of the dynein head and linker differs. Our analysis shows that all dynein linkers in the in the absence of ATP interact with AAA3/AAA4, indicating interaction to the adjacent B-tubule direct dynein orientation. For the pre-power stroke conformation, we found changes of the tail anchored on the A-tubule. We built pseudo-atomic models from high-resolution structures to generate a best fitting atomic model to the in-situ pre- and post-power stroke ODA, thereby showing that the Shulin-ODA display similar conformation as the active pre-power stroke ODA conformation in the axoneme.
Two Competing Guilds as a Core Microbiome Signature for Health Recovery
Authors: Wu Guojun , Xu Ting , Zhao Naisi , Lam Yan Y. , Ding Xiaoying , Wei Dongqin , Fan Jian , Shi Yajuan , Li Xiaofeng , Li Mi , Ji Shenjie , Wang Xuejiao , Fu Huaqing , Zhang Feng , Shi Yu , Zhang Chenhong , Peng Yongde , Zhao Liping
Published: May 2022

Summary Paragraph

Over eons of co-evolution, the gut microbiota has become an essential organ for humans1,2. However, it is unclear what core members and their ecological organization ensures the stable provision of this organ’s essential health-relevant functions to the host. With high quality metagenome-assembled genomes as network nodes, here we identified two competing guilds3of the most stably and highly connected bacteria that together correlate with a wide range of host health conditions. Genomes in these two guilds kept their ecological relationship unchanged despite experiencing profound abundance changes during a 3-month high fiber intervention and 1-year follow-up in patients with type 2 diabetes (T2DM). The genomes of one guild harbored more genes for plant polysaccharide degradation and butyrate production, while the other guild had more genes for virulence or antibiotic resistance. A Random Forest regression model showed that the abundance distributions of these genomes were associated with 41 out of 43 bio-clinical parameters in the study cohort. With these genomes as reference, Random Forest modeling successfully classified case and control of T2DM, atherosclerotic cardiovascular disease, liver cirrhosis, inflammatory bowel diseases, colorectal cancer, ankylosing spondylitis, schizophrenia, and Parkinson’s disease in 12 independent metagenomic datasets from 1,816 participants across ethnicity and geography. This core microbiome signature may serve as a common target for health recovery.
Seabird morphology determines operational wind speeds, tolerable maxima and responses to extremes
Authors: Nourani Elham , Safi Kamran , de Grissac Sophie , Anderson David J. , Cole Nik C. , Fell Adam , Grémillet David , Lempidakis Emmanouil , Lerma Miriam , McKee Jennifer L. , Pichegru Lorien , Provost Pascal , Rattenborg Niels C. , Ryan Peter G. , Santos Carlos D. , Schoombie Stefan , Tatayah Vikash , Weimerskirch Henri , Wikelski Martin , Shepard. Emily L. C.
Published: May 2022

Storms can cause widespread seabird strandings and wrecking1,2,3,4,5, yet little is known about the maximum wind speeds that birds are able to tolerate or the conditions they avoid. We analyzed > 300,000 hours of tracking data from 18 seabird species, including flapping and soaring fliers, to assess how flight morphology affects wind selectivity, both at fine scales (hourly movement steps) and across the breeding season. We found no general preference or avoidance of particular wind speeds within foraging tracks. This suggests seabird flight morphology is adapted to a “wind niche”, with higher wing loading being selected for in windier environments. In support of this, wing loading was positively related to the median wind speeds on the breeding grounds, as well as the maximum wind speeds in which birds flew. Yet globally, the highest wind speeds occur in the tropics (in association with tropical cyclones) where birds are morphologically adapted to low median wind speeds. Tropical species must therefore show behavioral responses to extreme winds, including long-range avoidance of wind speeds that can be twice their operable maxima. In contrast, procellariiformes flew in almost all wind speeds they encountered at a seasonal scale. Despite this, we describe a small number of cases where albatrosses avoided strong winds at close-range, including by flying into the eye of the storm. Extreme winds appear to pose context- dependent risks to seabirds, and more information is needed on the factors that determine the hierarchy of risk, given the impact of global change on storm intensity6,7.