Miracle-dz/UniFAR-FTUs huggingface dataset:
Microbial ecology of Ixodes scapularis from Central Pennsylvania, USA

(1) Background: Native microbiota represent a potential resource for biocontrol of arthropod vectors. Ixodes scapularis are mostly inhabited by the endosymbiotic Rickettsia buchneri, but the bacterial communty composition varies with life stage, fed status, and/or geographic location. We investigated sex-specific bacterial community diversity from I. scapularis collected from central Pennsylvania between populations within a small geographic range. (2) Methods: We sequenced the bacterial 16S rRNA genes from individuals and pooled samples and investigated the abundance or infection frequency of key taxa using taxon-specific PCR and/or qPCR. (3) Results: Bacterial communities were more diverse in pools of males than females. When R. buchneri was not the dominant taxon, Coxiellaceae was dominant. We determined that the infection frequency of Borrelia burgdorferi ranged between 20 to 75%. Titers of Anaplasma phagocytophilum were significantly different between sexes. High Rickettsiella titer in pools were likely due to a few heavily infected males. (4) Conclusion: Bacterial 16S sequencing is useful for establishing the baseline community diversity and focusing hypotheses for targeted experiments. However, care should be taken not to overinterpret data concerning microbial dominance between geographic locations based on a few individuals as this may not accurately represent the bacterial community within tick populations.
Exploring the microbial community structure and metabolic gene clusters during silage fermentation of paper mulberry, and developing the high-protein woody plant as ruminant feed

To develop a new high-protein woody forage resource for livestock, we applied PacBio single-molecule, real-time (SMRT) sequencing technology to explore the community structure, species diversity, and metabolic gene clusters of nature microbes associated with paper mulberry (PM) silage fermentation. The microbial diversity and abundance were rich in PM raw material and decreases with the progress of silage fermentation. Woody ensiling is process that the dominant bacteria shifted from Gram-negative pathogenic Proteobacteria to Gram-positive beneficial Firmicutes. Lactic acid bacteria became the most dominant bacteria that affected fermentation quality in the terminal silages. Global and overview maps, carbohydrate metabolism and amino acid metabolism were the important microbial metabolic pathways that impact final fermentation product of silage. PM is rich in nutrients and preserved well during ensiling, indicating PM can develop as new woody resources suitable for ruminants. PacBio SMRT sequencing revealed specific microbial-related information about silage. IMPORTANCE In the tropics, there is often a shortage of forage during the dry season. Failure to obtain high-quality feed will reduce the milk and meat production of ruminants. Therefore, it is essential to maximize the use of land and biomass resources through strategic development of alternative feed. Paper mulberry (PM) is a perennial deciduous tree in tropics, with a variety of nutrients and biologically active ingredients, and it adapts to various soils and climates, with high production capacity, and low cultivation costs. In order to develop new potential woody forage, we firstly used PacBio single-molecule real-time (SMRT) sequencing technology to explore the community structure, species diversity and metabolic gene clusters of natural microorganisms related to the fermentation of silage. PacBio SMRT revealed information about specific microorganisms related to silage, indicating PM can prepare as good-quality silage, and will become a new potential woody feed resources for livestock.
GuidePro: A multi-source ensemble predictor for prioritizing sgRNAs in CRISPR/Cas9 protein knockouts

The efficiency of CRISPR/Cas9-mediated protein knockout is determined by three factors: sequence-specific sgRNA activity, frameshift probability, and the characteristics of targeted amino acids. A number of computational methods have been developed for predicting sgRNA efficiency from different perspectives. We propose GuidePro, a two-layer ensemble predictor that enables the integration of multiple predictive methods and feature sets. GuidePro leverages information from DNA sequences, amino acids, and protein structures, and reduces the impact of dataset-specific biases. Tested on independent datasets, GuidePro demonstrated consistent superior performance in predicting phenotypes caused by protein loss-of-function. GuidePro is implemented as a web application for prioritizing sgRNAs that target protein-coding genes in human, monkey and mouse genomes, available at https://bioinformatics.mdanderson. org/apps/GuidePro.
Disruption of a Hedgehog-Foxf1-Rspo2 signaling axis leads to tracheomalacia and a loss of Sox9+ tracheal chondrocytes

ABSTRACT Congenital tracheomalacia, resulting from incomplete tracheal cartilage development, is a relatively common birth defect that severely impairs breathing in neonates. Mutations in the Hedgehog (HH) pathway and downstream Gli transcription factors are associated with tracheomalacia in patients and mouse models; however, the underlying molecular mechanisms are unclear. Using multiple HH/Gli mouse mutants, including one that mimics Pallister–Hall Syndrome, we show that excessive Gli repressor activity prevents specification of tracheal chondrocytes. Lineage-tracing experiments show that Sox9+ chondrocytes arise from HH-responsive splanchnic mesoderm in the fetal foregut that expresses the transcription factor Foxf1. Disrupted HH/Gli signaling results in (1) loss of Foxf1, which in turn is required to support Sox9+ chondrocyte progenitors, and (2) a dramatic reduction in Rspo2, a secreted ligand that potentiates Wnt signaling known to be required for chondrogenesis. These results reveal an HH-Foxf1-Rspo2 signaling axis that governs tracheal cartilage development and informs the etiology of tracheomalacia. This article has an associated First Person interview with the first author of the paper. Summary: Genetic and molecular analyses of mutant mouse embryos reveal a HH-Foxf1-Rspo2 signaling axis that informs the mechanistic basis of tracheomalacia in individuals with Hedgehog pathway mutations.
Individual differences in frontal midline theta activity during visuomotor adaptation are related to execution noise

Frontal midline EEG activity has been found to correlate with error magnitude during motor adaptation. We replicated a previous visuomotor adaptation experiment with very small perturbations, likely to invoke implicit adaptation, in a new group of 60 participants and combined it with EEG recordings. We used this data to explore 1) whether frontal midline activity will be evoked in the absence of awareness of the perturbation; 2) whether frontal midline activity is related to implicit adaptation; 3) whether individual differences in frontal midline activity are related to individual differences in motor learning. The results showed that frontal midline theta activity (FMΘ) is also present during small perturbations, does not drive between-trial error correction, and that the sensitivity of FMΘ to error magnitude was smaller for participants with greater execution noise. This relation between FMΘ-error-sensitivity and execution noise could be fully explained by looking at the relationship between FMΘ and error probability. This implies that frontal midline theta activity represents a surprise-like saliency signal, potentially driving awareness and cognitive control in situations with more salient errors.
SEASONAL CHANGES IN REPRODUCTIVE TRAITS OF THE CRAB SESARMA RECTUM (GRAPSOIDEA: SESARMIDAE) ON THE NORTHERN COAST OF SÃO PAULO STATE, BRAZIL

Abstract This paper describes seasonal changes (summer vs. winter) in reproductive traits (fecundity in relation to female body size and dry mass, egg size, egg weight and reproductive output) of the semiterrestrial crab Sesarma rectum from a mangrove area (23°29′S, 45°09′W) on the northern coast of the State of São Paulo, Brazil. Regression analyses using log-transformed data were used to test size-dependent relationships, which were compared between the breeding periods by means of ANCOVA. During winter, the eggs produced were heavier and larger; therefore, no trade-off between egg number and female size was observed. The mean size of ovigerous females remained fairly constant across the seasons. In contrast, the reproductive output and mean dry weight of females decreased in summer. These trends may indicate the seasonal variation of energy allocate for reproduction. The ecological implications of the observed seasonal trends are discussed in the context of the temporal variation of environmental and biological factors in the region.
Characterization of swine stress gene by DNA testing using plucked hair as a source of DNA

O gene do estresse suino (hal) em homozigose recessiva (nn) ocasiona a sindrome do estresse porcino (PSS), e esta relacionado com a ocorrencia da carne palida, mole e exudativa (PSE). Em heterozigose (Nn) esta associado com diminuicao da qualidade de carcaca. Um total de 179 suinos (86 Large White, 69 Landrace, 12 Duroc e 12 Pietrain) foram caracterizados como homozigotos normais (NN), heterozigotos e homozigotos recessivos por analise do DNA usando a reacao de polimerizacao em cadeia (PCR), seguida de um ensaio com endonuclease de restricao. Foi utilizado foliculo piloso como fonte de DNA genomico. O produto do PCR foi digerido com a enzima de restricao CfoI, seguindo-se analise dos fragmentos por eletroforese em gel de agarose. Dentre os 179 animais analisados, 126 (70,0%) foram caracterizados como NN, 50 (28,0%) como Nn, e 3 (2,0%) caracterizados como nn. A frequencia de heterozigotos foi maior (P < 0,05) em animais da raca Landrace do que em animais da raca Large White. Nove animais da raca Pietrain foram classificados como heterozigotos e tres como homozigotos recessivos. Estes resultados podem estar relacionados com a incidencia de PSS e PSE nestas racas, as quais sao largamente utilizadas em programas de cruzamento. A utilizacao de foliculo piloso como fonte de DNA genomico foi um metodo rapido e nao-invasivo que viabiliza a execucao da caracterizacao do gene hal.
Statistically correcting dynamical electron scattering improves the refinement of protein nanocrystals, including charge refinement of coordinated metals

Electron diffraction allows protein structure determination when only nanosized crystals are available. Nevertheless, multiple elastic (or dynamical) scattering, prominent in electron diffraction, is a concern. Current methods for modeling dynamical scattering by multi-slice or Bloch wave approaches are not suitable for protein crystals because they are not designed to cope with large molecules. Here, we limited dynamical scattering of nanocrystals of insulin, thermolysin, and thaumatin by collecting data from thin crystals. To accurately measure the weak diffraction signal from the few unit cells in the thin crystals, we used a low-noise hybrid-pixel Timepix electron counting detector. The remaining dynamical component was further reduced in refinement using a likelihood-based correction, which we introduced previously for analyzing electron diffraction data of small molecule nanocrystals and adapted here for protein crystals. We show that the procedure notably improved the structural refinement, allowing in one case the location of solvent molecules. It also allowed the refinement of the charge state of bound metal atoms, an important element in protein functions, through B-factor analysis of the metal atoms and their ligands. Our results clearly increase the value of macromolecular electron crystallography as a complementary structural biology technique.
Bioinformatic and Reactivity-Based Discovery of Linaridins

Linaridins are members of the ribosomally synthesized and post-translationally modified peptide (RiPP) family of natural products. Five linaridins have been reported, which are defined by the presence of dehydrobutyrine, a dehydrated threonine residue. This work describes the development of a linaridin specific scoring module for Rapid ORF Description and Evaluation Online (RODEO), a genome-mining tool tailored towards RiPP discovery. Upon mining publicly accessible genomes available in the NCBI database, RODEO identified 561 (382 non-redundant) linaridin biosynthetic gene clusters (BGCs). Linaridin BGCs with unique gene architectures and precursor sequences markedly different from previous predictions were uncovered during these efforts. To aid in dataset validation, two new linaridins, pegvadin A and B, were detected through reactivity-based screening (RBS) and isolated from Streptomyces noursei and Streptomyces auratus, respectively. RBS involves the use of a reactive chemical probe that chemoselectively modifies a functional group present in the natural product. The dehydrated amino acids present in linaridins as α/β-unsaturated carbonyls were appropriate electrophiles for nucleophilic 1,4 addition using a thiol-functionalized probe. The data presented within significantly expands the number of predicted linaridin BGCs and serves as a road map for future work in the area. The combination of bioinformatics and RBS is a powerful approach to accelerate natural product discovery.
Controllability over stressor decreases responses in key threat-related brain areas

Controllability over stressors has major impacts on brain and behavior. In humans, however, the effect of controllability on responses to stressors is poorly understood. Using functional magnetic resonance imaging (fMRI), we investigated how controllability altered responses to a shock-plus-sound stressor with a between-group yoked design, where participants in controllable and uncontrollable groups experienced matched stressor exposure. Employing Bayesian multilevel analysis at the level of regions of interest and voxels in the insula, and standard voxelwise analysis, we found that controllability decreased stressor-related responses across threat-related regions, notably in the bed nucleus of the stria terminalis and anterior insula. Posterior cingulate cortex, posterior insula, and possibly medial frontal gyrus showed increased responses during control over stressor. Our findings support the idea that the aversiveness of stressors is reduced when controllable, leading to decreased responses across key regions involved in anxiety-related processing, even at the level of the extended amygdala. Limbachia et al conduct a fMRI study in which participants are shown stressful stimuli that is either controllable or not. They show that the ability to control a stressor results in reduced activity in key areas of the brain that coordinate responses to a perceived threat.
Analysis of neuronal Ca2+ handling properties by combining perforated patch clamp recordings and the added buffer approach

Ca2+ functions as an important intracellular signal for a wide range of cellular processes. These processes are selectively activated by controlled spatiotemporal dynamics of the free cytosolic Ca2+. Intracellular Ca2+ dynamics are regulated by numerous cellular parameters. Here, we established a new way to determine neuronal Ca2+ handling properties by combining the ‘added buffer’ approach (Neher and Augustine, 1992) with perforated patch-clamp recordings (Horn and Marty, 1988). Since the added buffer approach typically employs the standard whole-cell configuration for concentration-controlled Ca2+ indicator loading, it only allows for the reliable estimation of the immobile fraction of intracellular Ca2+ buffers. Furthermore, crucial components of intracellular signaling pathways are being washed out during prolonged whole-cell recordings, leading to cellular deterioration. By combining the added buffer approach with perforated patch-clamp recordings, these issues are circumvented, allowing the precise quantification of the cellular Ca2+ handling properties, including immobile as well as mobile Ca2+ buffers.
STING Promotes Breast Cancer Cell Survival by an Inflammatory-Independent Nuclear Pathway Enhancing the DNA Damage Response

STING (Stimulator of Interferon Genes) is a well-known endoplasmic reticulum-anchored adaptor of the innate immunity that triggers the expression of inflammatory cytokines in response to pathogen infection. In cancer cells, this pro-inflammatory pathway can be activated by genomic DNA damage potentiating antitumor immune responses. Here we report that STING promotes cancer cell survival and resistance to genotoxic treatment in a cell-autonomous manner. Mechanistically, we show that STING partly localizes at the inner nuclear membrane in various breast cancer cell lines and clinical tumor samples, and interacts with several proteins of the DNA damage response (DDR). STING overexpression enhances the amount of chromatin-bound DNA-dependent Protein Kinase (DNA-PK) complex, while STING silencing impairs DDR foci formation and DNA repair efficacy. Importantly, this function of STING is independent of its canonical pro-inflammatory pathway. This study highlights a previously unappreciated cell-autonomous tumor-promoting mechanism of STING that opposes its well-documented role in tumor immunosurveillance. Graphical abstract
Cancer-Associated Fibroblasts in Pancreatic Ductal Adenocarcinoma Determine Response to SLC7A11 Inhibition

This study demonstrates that SLC7A11 in PDAC stromal cells is important for the tumor-promoting activity of CAFs and validates a clinically translatable nanomedicine for therapeutic SLC7A11 inhibition in PDAC. Cancer-associated fibroblasts (CAF) are major contributors to pancreatic ductal adenocarcinoma (PDAC) progression through protumor signaling and the generation of fibrosis, the latter of which creates a physical barrier to drugs. CAF inhibition is thus an ideal component of any therapeutic approach for PDAC. SLC7A11 is a cystine transporter that has been identified as a potential therapeutic target in PDAC cells. However, no prior study has evaluated the role of SLC7A11 in PDAC tumor stroma and its prognostic significance. Here we show that high expression of SLC7A11 in human PDAC tumor stroma, but not tumor cells, is independently prognostic of poorer overall survival. Orthogonal approaches showed that PDAC-derived CAFs are highly dependent on SLC7A11 for cystine uptake and glutathione synthesis and that SLC7A11 inhibition significantly decreases CAF proliferation, reduces their resistance to oxidative stress, and inhibits their ability to remodel collagen and support PDAC cell growth. Importantly, specific ablation of SLC7A11 from the tumor compartment of transgenic mouse PDAC tumors did not affect tumor growth, suggesting the stroma can substantially influence PDAC tumor response to SLC7A11 inhibition. In a mouse orthotopic PDAC model utilizing human PDAC cells and CAFs, stable knockdown of SLC7A11 was required in both cell types to reduce tumor growth, metastatic spread, and intratumoral fibrosis, demonstrating the importance of targeting SLC7A11 in both compartments. Finally, treatment with a nanoparticle gene-silencing drug against SLC7A11, developed by our laboratory, reduced PDAC tumor growth, incidence of metastases, CAF activation, and fibrosis in orthotopic PDAC tumors. Overall, these findings identify an important role of SLC7A11 in PDAC-derived CAFs in supporting tumor growth. Significance: This study demonstrates that SLC7A11 in PDAC stromal cells is important for the tumor-promoting activity of CAFs and validates a clinically translatable nanomedicine for therapeutic SLC7A11 inhibition in PDAC.
Enthalpy efficiency of the soleus muscle explains improvements in running economy

During human running, the soleus, as the main plantar flexor muscle, generates the majority of the mechanical work through active shortening. The fraction of chemical energy that is converted into muscular work (i.e. the enthalpy efficiency) depends on the muscle shortening velocity. Here, we investigated the soleus muscle fascicle behavior during running with respect to the enthalpy efficiency as a mechanism that could explain previously reported improvements in running economy after exercise-induced increases of plantar flexor strength and Achilles tendon stiffness. Healthy amateur runners were randomly assigned to a control (n=10) or intervention group (n=13), which performed a specific 14-week muscle-tendon training. Significant increases in plantar flexor maximum strength (10%) and Achilles tendon stiffness (31%) yet reduced metabolic cost of running (4%) was found only in the intervention group (p<0.05). Following training, the soleus fascicle velocity profile throughout stance was altered, with the fascicles operating at a higher enthalpy efficiency during the phase of muscle-tendon unit lengthening (15%) and in average over stance (7%, p<0.05). These findings show that the improvements in energetic cost following increases in plantar flexor strength and Achilles tendon stiffness can be attributed to increased enthalpy efficiency of the operating soleus. This provides the first experimental evidence that the soleus enthalpy efficiency is a determinant of human running economy. Furthermore, the current results imply that the soleus energy production in the first part of the stance phase were the muscle-tendon unit is lengthening is crucial for the overall metabolic energy cost of running.
Activation of endogenous retroviruses during brain development causes neuroinflammation

Endogenous retroviruses (ERVs) make up a large fraction of mammalian genomes and are thought to contribute to human disease, including brain disorders. In the brain, aberrant activation of ERVs is a potential trigger for neuroinflammation, but mechanistic insight into this phenomenon remains lacking. Using CRISPR/Cas9-based gene disruption of the epigenetic co-repressor protein Trim28, we found a dynamic H3K9me3-dependent regulation of ERVs in proliferating neural progenitor cells (NPCs), but not in adult neurons. In vivo deletion of Trim28 in cortical NPCs during mouse brain development resulted in viable offspring expressing high levels of ERV expression in excitatory neurons in the adult brain. Neuronal ERV expression was linked to inflammation, including activated microglia, and aggregates of ERV-derived proteins. This study demonstrates that brain development is a critical period for the silencing of ERVs and provides causal in vivo evidence demonstrating that transcriptional activation of ERV in neurons results in neuroinflammation.
Analysis of a photosynthetic cyanobacterium rich in internal membrane systems via gradient profiling by sequencing (Grad-seq)

Regulatory sRNAs in photosynthetic cyanobacteria have been reported, but the lack of plausible RNA chaperones involved in this regulation appears enigmatic. Here, we analyzed the full ensemble of cellular RNAs and proteins using gradient profiling by sequencing (Grad-seq) in Synechocystis 6803. Complexes with overlapping subunits such as the CpcG1-type versus the CpcL-type phycobilisomes or the PsaK1 versus PsaK2 photosystem I pre(complexes) could be distinguished supporting a high quality of the approach. Clustering of the in-gradient distribution profiles followed by several additional criteria yielded a short list of potential RNA chaperones that include a YlxR homolog and a cyanobacterial homolog of the KhpA/B complex. The data suggest previously undetected complexes between accessory proteins and CRISPR-Cas systems, such as a Csx1-Csm6 ribonucleolytic defense complex. Moreover, the exclusive association of either RpoZ or 6S RNA with the core RNA polymerase complex and the existence of a reservoir of inactive sigma-antisigma complexes is suggested. The Synechocystis Grad-seq resource is available online at https://sunshine.biologie. uni-freiburg.de/GradSeqExplorer/, providing a comprehensive resource for the functional assignment of RNA-protein complexes and multisubunit protein complexes in a photosynthetic organism. One-sentence summary We provide the first global analysis of a cyanobacterium using Grad-seq, providing a comprehensive resource for the in-depth analysis of the complexome in a photosynthetic organism.