Miracle-dz/UniFAR-FTUs huggingface dataset:
Mainly on the Plane: Deep Subsurface Bacterial Proteins Bind and Alter Clathrate Structure

Gas clathrates are both a resource and a hindrance. They store massive quantities of natural gas but also can clog natural gas pipelines, with disastrous consequences. Eco-friendly technologies for controlling and modulating gas clathrate growth are needed. Type I Antifreeze Proteins (AFPs) from cold-water fish have been shown to bind to gas clathrates via repeating motifs of threonine and alanine. We tested whether proteins encoded in the genomes of bacteria native to natural gas clathrates bind to and alter clathrate morphology. We identified putative clathrate-binding proteins (CBPs) with multiple threonine/alanine motifs in a putative operon (cbp) in metagenomes from natural clathrate deposits. We recombinantly expressed and purified five CbpA proteins, four of which were stable, and experimentally confirmed that CbpAs bound to tetrahydrofuran (THF) clathrate, a low-pressure analog for structure II gas clathrate. When grown in the presence of CbpAs, THF clathrate was polycrystalline and plate-like instead of forming single, octahedral crystals. Two CbpAs yielded branching clathrate crystals, similar to the effect of Type I AFP, while the other two produced hexagonal crystals parallel to the [1 1 1] plane, suggesting two distinct binding modes. Bacterial CBPs may find future utility in industry, such as maintaining a plate-like structure during gas clathrate transportation. Table of Contents Graphic
The section Pseudophrys ( Ophrys , Orchidaceae) in the Iberian Peninsula: a morphometric and molecular analysis

Section Pseudophrys is a taxonomically critical species complex that has a history of circumscriptional uncertainty, suggesting the need for further evaluation. Its taxonomy in the Iberian Peninsula has been controversial, with treat- ments ranging from three species and three subspecies to ten species. Extensive observations in the field and anal- ysis of morphological characters based on 50 populations sampled show that most of the characters used by previous authors for distinguishing the species are variable among or even within populations. In the present study, repre- sentatives from the Iberian Peninsula and Morocco were investigated using morphometric and molecular (nuclear ribosomal ITS sequences) analyses. Seventeen floral characters and, in addition, four ratios, were measured from 642 live plants belonging to 50 populations of representatives of sect. Pseudophrys ( Ophrys arnoldii , O. bilunulata , O. dianica , O. fusca and O. lupercalis ). To determine characters distinguishing different species and to examine their circumscription, we performed morphometric analyses on three different subsets of sect. Pseudophrys , one with all the currently recognized species, another containing the closely related O. bilunulata and O. dianica , and finally the populations of O. arnoldii and O. lupercalis . These populations were treated as Operational Taxonomic Units (OTUs) and studied using cluster analysis, principal component analysis (PCA) and canonical discriminant analysis (CDA); box plots of selected quantitative characters were also made. Finally, variation in nrITS sequences among eight members of sect. Pseudophrys was analysed phylogenetically. Our results indicate that sect. Pseudophrys is mono- phyletic and well supported. We maintain the recognition of all taxa studied except O. arnoldii , and do not recognize any new taxa based on our examinations of the different populations of O. lupercalis . © 2005 The Linnean Society of London, Botanical Journal of the Linnean Society , 2005, 148 , 359-375. ADDITIONAL KEYWORDS: ITS sequences - Portugal - Spain - taxonomy - variation gradient.
Cortico-hippocampal morphology and behavioural indices improved in maternal deprivation model of schizophrenia following vitamin B complex supplementation

Maternal deprivation (MD) during early life development has been documented to culminate in long-term alterations in brain function and behavioural manifestations that mimic schizophrenia. This study elucidated the putative neuroprotective roles of vitamin B complex in MD-induced behavioural and neurochemical modifications in hippocampus and prefrontal cortex of Wistar rats. Rat pups were maternally deprived on postnatal day 9 for 24 hours and then treated with or without vitamin B complex for 15 days while a control group was undisturbed during the experimental period. The rats were then subjected to behavioural paradigms to measure memory indices and anxiety levels. The rats were sacrificed to obtain the PFC and hippocampus for histomorphological and biochemical analysis. Behavioural analysis of the animals revealed that MD induced a declination in long- and short-term memory in addition to anxiety-like behaviour in the open field test. Cortico-hippocampal histomorphology of these animals showed an increased astrocytic density and chromatolysis, which were accompanied by reduced levels of superoxide dismutase and catalase enzymes. Vitamin B complex mitigated MD-induced behavioural decline, histomorphological perturbation and oxidative stress by enhancing the intrinsic antioxidant defence, thereby culminating in nootropic behaviour and reduced anxiety. In conclusion, we confirmed the hypothesis that vitamin B complex is neuroprotective against neuropathological alterations induced by maternal deprivation.
Interaction between depth and protection in determining the structure of Mediterranean coastal fish assemblages

Patterns of spatial and temporal variability of coastal fish assemblages were compared between areas subjected to different levels of protection at two different depths using a visual census technique. A no take reserve was compared with recreational fishing areas around a small Mediterranean island at 5 m and 20 m depth. Univariate and multivariate statistical techniques were used to test the hypothesis that protection could have different effects at different depths. A total of 56 species were identified during the survey. The most represented families were Sparidae and Labridae. Results showed an interaction between depth and levels of protection that was not persistent across the study period. This result was consistent for the whole fish assemblage and for the target species; most species showed higher abundance in protected areas at 20 m depth.
Asbestos accelerates disease onset in a genetic model of malignant pleural mesothelioma

Hypothesis Asbestos-driven inflammation contributes to malignant pleural mesothelioma beyond the acquisition of rate-limiting mutations. Methods Genetically modified conditional allelic mice that were previously shown to develop mesothelioma in the absence of exposure to asbestos were induced with lentiviral vector expressing Cre recombinase with and without intrapleural injection of amosite asbestos and monitored until symptoms required euthanasia. Resulting tumours were examined histologically and by immunohistochemistry for expression of lineage markers and immune cell infiltration. Results Injection of asbestos dramatically accelerated disease onset and end-stage tumour burden. Tumours initiated in the presence of asbestos showed increased macrophage infiltration. Single-agent suppression of macrophages in mice with established tumours failed to extend survival. Conclusion Asbestos-driven inflammation contributes to the severity of mesothelioma beyond the acquisition of rate-limiting mutations, however, targeted suppression of macrophages alone in established disease showed no therapeutic benefit.
Macrolichen Indicators of Air Quality for Nova Scotia

Abstract Presence and frequency of epiphytic macrolichens were measured along an air-quality gradient in Halifax City, NS, Canada. Species frequency plots over distance and multidimensional scaling (MDS) suggested lichen-community changes consistent with expected air-quality changes. A provisional list of air-quality indicators was selected based on: 1) demonstrated variation along the air-quality gradient, 2) frequency across the province, 3) literature values of air-quality sensitivity, and 4) ease of field identification. Indicators were placed in one of three classes: 1) pollution tolerant, 2) intermediate pollution tolerance, and 3) pollution sensitive. MDS analysis suggests an elevation gradient in Nova Scotia and this should be investigated with a further study.
IL-6 Regulation on Skeletal Muscle Mitochondrial Remodeling During Cancer Cachexia in the <em>Apc<sup>Min/+</sup></em> Mouse

Background: Muscle protein turnover regulation during cancer cachexia is being rapidly defined, and skeletal muscle mitochondria function appears coupled to processes regulating muscle wasting. Skeletal muscle oxidative capacity and the expression of proteins regulating mitochondrial biogenesis and dynamics are disrupted in severely cachectic Apc mice. It has not been determined if these changes occur at the onset of cachexia and are necessary for the progression of muscle wasting. Exercise and anti-cytokine therapies have proven effective in preventing cachexia development in tumor bearing mice, while their effect on mitochondrial content, biogenesis and dynamics is not well understood. The purposes of this study were to 1) determine IL-6 regulation on mitochondrial remodeling/dysfunction during the progression of cancer cachexia and 2) to determine if exercise training can attenuate mitochondrial dysfunction and the induction of proteolytic pathways during IL-6 induced cancer cachexia. Methods: Apc mice were examined during the progression of cachexia, after systemic interleukin (IL)-6r antibody treatment, or after IL-6 over-expression with or without exercise. Direct effects of IL-6 on mitochondrial remodeling were examined in cultured C2C12 myoblasts. Results: Mitochondrial content was not reduced during the initial development of cachexia, while muscle PGC-1α and fusion (Mfn1, Mfn2) protein expression was repressed. With progressive weight loss mitochondrial content decreased, PGC-1α and fusion proteins were further suppressed, and fission protein (FIS1) was induced. IL-6 receptor antibody administration after the onset of cachexia improved mitochondrial content, PGC-1α, Mfn1/Mfn2 and FIS1 protein expression. IL-6 over-expression in pre-cachectic mice accelerated body weight loss and muscle wasting, without reducing mitochondrial content, while PGC-1α and Mfn1/Mfn2 protein expression was suppressed and FIS1 protein expression induced. Exercise normalized these IL-6 induced effects. C2C12 myotubes administered IL-6 had increased FIS1 protein expression, increased oxidative stress, and reduced PGC-1α gene expression without altered mitochondrial protein expression. Conclusions: Altered expression of proteins regulating mitochondrial biogenesis and fusion are early events in the initiation of cachexia regulated by IL-6, which precede the loss of muscle mitochondrial content. Furthermore, IL-6 induced mitochondrial remodeling and proteolysis can be rescued with moderate exercise training even in the presence of high circulating IL-6 levels.
Sexual signaling and the persistence of alternative reproductive tactics: a test of game theoretic predictions

In many species, males produce signals to attract females. However, in some species and populations, only some males produce these signals with other males competing for and “sneaking” reproductive opportunities. In these systems, at least three tactics are expected: always signal, signal only when others are not (assessors), and never signal. The representation of these tactics within a population is unknown in part because the costs of signaling (C) and the fitness value of a single reproductive bout (V) are unknown. Using a game-theoretic model we predict that the always signal strategy only persists if the fitness value of calling is greater than twice the cost. We also show that always signal males are apparently absent in decorated crickets (Gryllodes sigillatus). Moreover, males of this species were not strict assessors and instead signaled infrequently (30% of the time) when signaling by others was constant. Males also exhibited substantial among-individual variation in the propensity to call when other males were not signaling (τ = 0.3). Our results suggest a high relative cost of signaling (2C > V) in this species. The presence of among-individual variation is indicative of underlying genetic variation and a mixed evolutionary stable strategy.
Improving oligo-conjugated antibody signal in multimodal single-cell analysis

Simultaneous measurement of surface proteins and gene expression within single cells using oligo-conjugated antibodies offers high resolution snapshots of complex cell populations. Signal from oligo-conjugated antibodies is quantified by high-throughput sequencing and is highly scalable and sensitive. In this study, we investigated the response of oligo-conjugated antibodies towards four variables: Concentration, staining volume, cell number at staining, and tissue. We find that staining with recommended antibody concentrations cause unnecessarily high background and that concentrations can be drastically reduced without loss of biological information. Reducing volume only affects antibodies targeting abundant epitopes used at low concentrations and is counteracted by reducing cell numbers. Adjusting concentrations increases signal, lowers background and reduces costs. Background signal can account for a major fraction of the total sequencing and is primarily derived from antibodies used at high concentrations. Together, this study provides new insight into the titration response and background of oligo-conjugated antibodies and offers concrete guidelines on how such panels can be improved. Impact statement Oligo-conjugated antibodies are a powerful tool but require thorough optimization to reduce background signal, increase sensitivity, and reduce sequencing costs.
Linear-time cluster ensembles of large-scale single-cell RNA-seq and multimodal data

A fundamental task in single-cell RNA-seq (scRNA-seq) analysis is the identification of transcriptionally distinct groups of cells. Numerous methods have been proposed for this problem, with a recent focus on methods for the cluster analysis of ultra-large scRNA-seq datasets produced by droplet-based sequencing technologies. Most existing methods rely on a sampling step to bridge the gap between algorithm scalability and volume of the data. Ignoring large parts of the data, however, often yields inaccurate groupings of cells and risks overlooking rare cell types. We propose method Specter that adopts and extends recent algorithmic advances in (fast) spectral clustering. In contrast to methods that cluster a (random) subsample of the data, we adopt the idea of landmarks that are used to create a sparse representation of the full data from which a spectral embedding can then be computed in linear time. We exploit Specter’s speed in a cluster ensemble scheme that achieves a substantial improvement in accuracy across 16 scRNA-seq datasets and that is sensitive to rare cell types. Its linear time complexity allows Specter to cluster a dataset comprising 2 million cells in just 26 minutes. Furthermore, on CITE-seq data that simultaneously measures gene and protein marker expression we demonstrate that Specter is able to utilize multimodal omics measurements to resolve subtle transcriptomic differences between subpopulations of cells. Specter is open source and available at https://github.com/canzarlab/Specter.
Environmental Correlates of the Distribution and Abundance of Microstegium vimineum, in East Tennessee

Abstract We conducted a landscape-level survey of Microstegium vimineum (Trin.) A. Camus (Japanese grass, Nepal grass) at the Oak Ridge National Environmental Research Park to: (1) document the distribution of this species, (2) measure several important characteristics of the populations and invaded habitats, (3) identify biotic and abiotic environmental factors that may limit its distribution, and (4) quantify its response to environmental gradients. We found that M. vimineum exhibits the broad environmental tolerance of many “weedy” species, and it appears that no single variable explains presence or performance. Presence of M. vimineum was correlated only with soil pH, whereas M. vimineum performance was positively correlated with canopy openness and biomass of other species. Explanatory variables differed among sites, which suggests that other factors (such as disturbance or dispersal) may be locally important, or that different factors may interact to control the distribution and performance of this species at any given site. The nearly ubiquitous presence of M. vimineum along roads and trails in the study area, and the frequent incursion of roadside populations into adjacent forested habitat, highlights the importance of early control of source populations at forest edges.
Polyclonal epitope cartography reveals the temporal dynamics and diversity of human antibody responses to H5N1 vaccination

Novel influenza A virus (IAV) strains elicit recall immune responses to conserved epitopes, making them favorable antigenic choices for universal influenza virus vaccines. Evaluating these immunogens requires a thorough understanding of the antigenic sites targeted by the polyclonal antibody (pAb) response, which single particle electron microscopy (EM) can sensitively detect. Here, we employed EM polyclonal epitope mapping (EMPEM) to extensively characterize the pAb response to hemagglutinin (HA) after H5N1 immunization in humans. Cross-reactive pAbs originating from memory B cells immediately bound the stem of HA and persisted for over a year post vaccination. In contrast, de novo pAb responses to multiple sites on the head of HA, which targeted previously determined key neutralizing sites on H5 HA, expanded after the second immunization and waned quickly. Thus, EMPEM provides a robust tool for comprehensively tracking the specificity and durability of immune responses elicited by novel universal influenza vaccine candidates.
Optimized culture of retinal ganglion cells and amacrine cells from adult mice

Cell culture is widely utilized to study the cellular and molecular biology of different neuronal cell populations. Current techniques to study enriched neurons in vitro are primarily limited to embryonic/neonatal animals and induced pluripotent stem cells (iPSC). Although the use of these cultures is valuable, the accessibility of purified primary adult neuronal cultures would allow for improved assessment of certain neurological diseases and pathways at the cellular level. Using a modified 7-step immunopanning technique to isolate for retinal ganglion cells (RGCs) and amacrine cells (ACs) from adult mouse retinas, we have successfully developed a model of neuronal culture that maintains for at least one week. Isolations of Thy1.2+ cells are enriched for RGCs, with the isolation cell yield being congruent to the theoretical yield of RGCs in a mouse retina. ACs of two different populations (CD15+ and CD57+) can also be isolated. The populations of these three adult neurons in culture are healthy, with neurite outgrowths in some cases greater than 500µm in length. Optimization of culture conditions for RGCs and CD15+ cells revealed that neuronal survival and the likelihood of neurite outgrowth respond inversely to different culture media. Serially diluted concentrations of puromycin decreased cultured adult RGCs in a dose-dependent manner, demonstrating the potential usefulness of these adult neuronal cultures in screening assays. This novel culture system can be used to model adult neurons in vivo. Studies can now be expanded in conjunction with other methodologies to study the neurobiology of function, aging, and diseases.
stLFRsv: a germline SV analysis pipeline using co-barcoded reads

Co-barcoded reads originated from long DNA fragment (mean length larger than 50Kbp) with barcodes, maintain both single base level accuracy and long range genomic information. We propose a pipeline stLFRsv to detect structure variation using co-barcoded reads. stLFRsv identifies abnormally large gaps between co-barcoded reads to detect potential breakpoints and reconstruct complex structure variations. The barcodes enabled co-barcoded reads phasing increases the signal to noise ratio and barcode sharing profiles are used to filter out false positives. We integrate the short reads SV caller smoove for smaller variations with stLFRsv. The integrated pipeline was evaluated on the well characterized genome HG002/NA24385 and obtained precision and recall rate of 74.2% and 22.3% for deletion on the whole genome. stLFR found some large variations not included in the benchmark set and verified by means of long reads or assembly. Our work indicates that co-barcoded reads technology has the potential to improve genome completeness.
An Organoid for Woven Bone

Stem cell-based organoids are promising as functional, self-organizing 3D in vitro models for studying the physiology and pathology of various tissues1. Bone formation (osteogenesis) is a complex process in which i) cellular differentiation and ii) the generation of a mineralized organic matrix are synchronized to produce a hybrid hierarchical architecture. To study the molecular mechanisms of osteogenesis in health and disease there is great need for organoids that capture both processes in parallel2, however, for human bone no such functional model system is yet available3. Here, we report the in vitro differentiation of human bone marrow stromal cells into a functional 3D self-organizing co-culture of osteoblasts and osteocytes, creating an organoid for early stage bone (woven bone) formation. We demonstrate that the osteocytes form a network showing cell-cell communication via the expression of sclerostin, embedded within the collagen matrix that is formed by the osteoblasts and mineralized under biological control.
A general theory of coherence between brain areas

What does neuronal coherence tell us about neuronal communication? Does coherence between field potentials (e.g. LFP, EEG, MEG) reflect spiking entrainment or coupling between oscillators? Is it a mechanism for communication between brain areas, or a byproduct of interareal connectivity and spectral power? We hypothesized that interareal coherence is explained by the fact that outputs from one cortical area give rise to synaptic inputs in the same brain area, and correlated synaptic inputs in another area. Our mathematical analysis demonstrates that coherence between a sending and receiving area is precisely predicted from only two parameters: Interareal connectivity and oscillatory synchronization in the sending area. This model predicts narrow-band coherence even in case of a flat transfer function and in the absence of spiking entrainment in a downstream area, and reproduces frequency-specific Granger-causality patterns between brain areas (gamma feedforward, beta feedback). In general, we find that Granger-causality between field potentials is dominated by oscillatory synchronization in the sending area, whereas spiking entrainment is determined by the resonant properties of the receiver. Our model accurately reproduces LFP-LFP beta-coherence between macaque areas 7B and F5 in the absence of beta phase-locking within area F5. Together, these findings uncover a precise mechanistic model of interareal coherence as a (by)product of connectivity and power.