Miracle-dz/UniFAR-FTUs huggingface dataset:
Genomic stability of self-inactivating rabies

Transsynaptic viral vectors provide means to gain genetic access to neurons based on synaptic connectivity and are essential tools for the dissection of neural circuit function. Among them, the retrograde monosynaptic ΔG-Rabies has been widely used in neuroscience research. A recently developed engineered version of the ΔG-Rabies, the non-toxic self-inactivating (SiR) virus, represents the first tool for open-ended genetic manipulation of neural circuits. However, the high mutational rate of the rabies virus poses a risk that mutations targeting the key genetic regulatory element in the SiR genome could emerge and revert it to a canonical ΔG-Rabies. Such revertant mutations have recently been identified in a SiR batch. To address the origin, incidence and relevance of these mutations, we investigated the genomic stability of SiR in vitro and in vivo. We found that “revertant” mutations are rare and accumulate only when SiR is extensively amplified in vitro, particularly in suboptimal production cell lines that have insufficient levels of TEV protease activity. Moreover, we confirmed that SiR-CRE, unlike canonical ΔG-Rab-CRE or revertant-SiR-CRE, is non-toxic and that revertant mutations do not emerge in vivo during long-term experiments. Highlights Revertant mutations are rare and do not accumulate when SiR is produced in high-TEVp expressing production cell lines SiR is non-toxic in vivo Revertant SiR mutations do not accumulate during in vivo experiments
Dinámica poblacional y estructura de la comunidad de metazoarios parásitos de Menticirrhus ophicephalus (Pisces: Sciaenidae) en la costa peruana

En 1988. se estudio 237 ejemplares del pez Menticirrhus ophicephalus de la costa central peruana, siendo identificados dos trematodes, tres monogeneos, un nematode, cuatro copepodos y un isopodo parasitos. La comunidad parasitaria estaba compuesta por dos especies centrales, tres secundarias y seis satelites. Estos parasitos mostraron el tipico patron de sobredispersion, excepto Neobrachiella menticirrhi (distribucion uniforme). El tamano de las infrapoblaciones aumento con el tamano del hospedador para Rhamnocercoides menticirrhi. Cynoscionicola americana. Ascaropms sp. , Bomolochus peruensis y Lernanthropus huamani. El aspidobotrio Lobatostoma. veranoi presento un patron opuesto. Rhamnocercoides menticirrhi. H. menticirrhi, C. americana, Ascaroprus sp. y C. dilalata preflrieron los peces hembras, mientras L. veranoi mostro mayor prevalencia en los machos. La prevalencia e intensidad de los siguientes parasitos tuvieron variacion estacional: Rhamnocercoides menticirrhi, C. americana, B. peruensis y C. dilatata (mas alta en verano y otofto), L. verano; y H.fasciata (mas alta en invierno y primavem). El monogeneo R. mentic;"hi prefirio el segundo par de bmnquias y el copepodo L. huamani el primer par. Como en otros peces marinos escienidos del Peru, la comunidad parasitaria de M. ophicephalus es dominada por ectoparasitos y especies satelites, y esta caracterizada por la ausencia de estadios larvales de parasitos comunes en el ecosistema marino. El numero de componentes de las infracomunidades parasitarias y su intensidad fueron tambien similares.
Inducible expression of human C9ORF72 36× G4C2 hexanucleotide repeats is sufficient to cause RAN translation and rapid muscular atrophy in mice

ABSTRACT The hexanucleotide G4C2 repeat expansion in the first intron of the C9ORF72 gene accounts for the majority of frontotemporal dementia (FTD) and amyotrophic lateral sclerosis (ALS) cases. Numerous studies have indicated the toxicity of dipeptide repeats (DPRs), which are produced via repeat-associated non-AUG (RAN) translation from the repeat expansion, and accumulate in the brain of C9FTD/ALS patients. Mouse models expressing the human C9ORF72 repeat and/or DPRs show variable pathological, functional and behavioral characteristics of FTD and ALS. Here, we report a new Tet-on inducible mouse model that expresses 36× pure G4C2 repeats with 100-bp upstream and downstream human flanking regions. Brain-specific expression causes the formation of sporadic sense DPRs aggregates upon 6 months of dox induction, but no apparent neurodegeneration. Expression in the rest of the body evokes abundant sense DPRs in multiple organs, leading to weight loss, neuromuscular junction disruption, myopathy and a locomotor phenotype within the time frame of 4 weeks. We did not observe any RNA foci or pTDP-43 pathology. Accumulation of DPRs and the myopathy phenotype could be prevented when 36× G4C2 repeat expression was stopped after 1 week. After 2 weeks of expression, the phenotype could not be reversed, even though DPR levels were reduced. In conclusion, expression of 36× pure G4C2 repeats including 100-bp human flanking regions is sufficient for RAN translation of sense DPRs, and evokes a functional locomotor phenotype. Our inducible mouse model suggests that early diagnosis and treatment are important for C9FTD/ALS patients. This article has an associated First Person interview with the first author of the paper. Summary: Only 36 C9ORF72 repeats are sufficient for RAN translation in a new mouse model for amyotrophic lateral sclerosis and frontotemporal dementia. Reducing toxic dipeptides can prevent but not reverse the phenotype.
Wing Geometry and Genetic Analyses Reveal Contrasting Spatial Structures between Male and Female Aedes aegypti Populations in Metropolitan Manila, Philippines

Background Many important arboviral diseases (e.g. dengue, chikungunya) are transmitted by the bite of a female mosquito vector, Aedes aegypti. Hence, the population genetic structure of the mosquito has been studied in order to understand its role as an efficient vector. Several studies utilized an integrative approach; to combine genetic and phenotypic data to determine the population structure of Ae. aegypti but these studies have only focused on female populations. To address this particular gap, our study compared the population variability and structuring between male and female Ae. aegypti populations using phenotypic (wing geometry) and genetic (microsatellites) data from a highly-urbanized and dengue-endemic region of the Philippines, Metropolitan Manila. Methods Five mosquito populations comprised of female (n = 137) and male (n = 49) adult Ae. aegypti mosquitoes were used in this study. All mosquito individuals underwent geometric morphometric (26 landmarks), and genetic (11 microsatellite loci) analyses. Results Results revealed that FST estimates (genetic) were 0.055 and 0.009 while QST estimates (phenotypic) were 0.318 and 0.309 in in male and female populations, respectively. Wing shape variation plots showed that male populations were distinctly separated from each other while female populations overlapped. Similarly, discriminant analysis of principal components using genetic data revealed that male populations were also distinctly separated from each other while female populations showed near-overlapping populations. Genetic and phenetic dendrograms showed the formation of two groups in male populations but no groups in female populations. Further analysis indicated a significant correlation (r = 0.68, p = 0.02) between the genetic and phenetic distances of male populations. Bayesian analysis using genetic data also detected multiple clusters in male (K = 3) and female (K = 2) populations, while no clusters were detected using the phenotypic data from both sexes. Conclusions Our results revealed contrasting phenotypic and genetic patterns between male and female Ae. aegypti, indicating that male populations were more spatially structured than female populations. Although genetic markers demonstrated higher sensitivity in detecting population structures than phenotypic markers, correlating patterns of population structure were still observed between the two markers.
Improvement of xylose fermentation of Saccharomyces cerevisiae

The increasing need of oil and the negative impacts of fossil fuels on climate change have motivated the research towards environmental friendly alternatives to diminish the use of fossil resources. Until today, bioethanol production and use has increased worldwide. The raw materials used today compete with food industry and conquently, the ethanol production from lignocellulose has been developed intensively. However, to make the processes economically competitive, also pentoses in lignocellulose should be fermented at high rate. Saccharomyces cerevisiae, alias baker’s yeast has an excellent ethanol production capacity but it can not naturally utilize xylose. Several xylose-utilizing S. cerevisiae strains have been constructed; however the fermentation rate is still lower than that of hexose sugars. The major obstacles are thought to be the xylose transport, ATP depletion during the fermentation and the redox imbalance due to the different cofactor specifities of xylose reductase (XR) and xylitol dehydrogenase (XDH) enzymes in the xylose utilization pathway. This thesis includes three separate studies related to xylose metabolism of recombinant S. cerevisiae. In the first part the aim was to set up a high throughput xylose uptake assay by overexpressing a gene encoding βxylosidase enzyme from Tricoderma reesei in S. cerevisiae. The experimental part included the enzyme activity measurements by using commercial xylose analogue p-nitrophenyl-β-d-xylopyranoside, which creates yellow colour when hydrolyzed with β-xylosidase. In the second study Trypanosoma brucei’s NADH dependent fumarate reductase (FRDg) encoding gene was overexpressed in xylose utilizing S. cerevisiae in order to improve ethanol fermentation by providing intracellular NAD for the XDH reaction. Aerobic and anaerobic shake flask cultivations were carried out with the constructed strains. The xylose utilization and metabolite and ethanol productivities were measured with high pressure liquid chromatography (HPLC). In the third part of the study, XR and XDH activities were measured spectrophotometrically from the xyloseutilizing yeast strains from the VTT Culture collection. The aim of the study was to find new enzymes to be exploited in the engineering of xylose metabolism of S. cerevisiea. The xylose transporter assay was not functional. The BXL1 gene was expressed in yeast, but no β-xylosidase activity was detected. The expression of FRDg slightly improved the xylose fermentation in xylose-utizing S. cerevisiae but the activity measurements did not show FRDg activity. In the XR and XDH activity measurements of strains from the VTT Culture collection a couple of strains with potentially interesting XR and XDH activities were found. These enzymes offer alternatives for S. stipitis XR and XDH enzymes in engineering of baker’s yeast strains for ethanol or xylitol production.
Improving Code Search with Co-Attentive Representation Learning

Searching and reusing existing code from a large-scale codebase, e.g, GitHub, can help developers complete a programming task efficiently. Recently, Gu et al. proposed a deep learning-based model (i.e., DeepCS), which significantly outperformed prior models. The DeepCS embedded codebase and natural language queries into vectors by two LSTM (long and short-term memory) models separately, and returned developers the code with higher similarity to a code search query. However, such embedding method learned two isolated representations for code and query but ignored their internal semantic correlations. As a result, the learned isolated representations of code and query may limit the effectiveness of code search. To address the aforementioned issue, we propose a co-attentive representation learning model, i.e., Co-Attentive Representation Learning Code Search-CNN (CARLCS-CNN). CARLCS-CNN learns interdependent representations for the embedded code and query with a co-attention mechanism. Generally, such mechanism learns a correlation matrix between embedded code and query, and coattends their semantic relationship via row/column-wise max-pooling. In this way, the semantic correlation between code and query can directly affect their individual representations. We evaluate the effectiveness of CARLCS-CNN on Gu et al.'s dataset with 10k queries. Experimental results show that the proposed CARLCS-CNN model significantly outperforms DeepCS by 26.72% in terms of MRR (mean reciprocal rank). Additionally, CARLCS-CNN is five times faster than DeepCS in model training and four times in testing.
Experimental warming reduces gut prokaryotic diversity, survival and thermal tolerance of the eastern subterranean termite, Reticulitermes flavipes (Kollar)

Understanding the effects of environmental disturbances on the health and physiology of insects is crucial in predicting the impact of climate change on their distribution, abundance, and ecology. As microbial symbionts have been shown to play an integral role in a diversity of functions within the insect host, research examining how organisms adapt to environmental fluctuations should include their associated microbiota. Previous studies have shown that temperature affects the diversity of protists in termite gut, but less is known about the bacterial symbionts. In this study, subterranean termites (Reticulitermes flavipes (Kollar)) were exposed to three different temperature treatments characterized as low (15 °C), medium (27 °C), and high (35 °C). Results showed low temperature exposed termites had significantly lower CTmin and significantly higher SCP values compared to termites from medium or high temperature groups. This suggests that pre-exposure to cold allowed termites to stay active longer in decreasing temperatures but caused termites to freeze at higher temperatures. High temperature exposure had the most deleterious effects on termites with a significant reduction in termite survival as well as reduced ability to withstand cold stress. The microbial community of high temperature exposed termites showed a reduction in bacterial richness and decreased relative abundance of Spirochaetes, Elusimicrobia, and methanogenic Euryarchaeota. Our results indicate a potential link between gut bacterial symbionts and termite’s physiological response to environmental changes and highlight the need to consider microbial symbionts in studies relating to insect thermosensitivity.
Comprehensive genomic analysis reveals virulence factors and antibiotic resistance genes in Pantoea agglomerans KM1, a potential opportunistic pathogen

Pantoea agglomerans is a Gram-negative aerobic bacillus causing a wide range of opportunistic infections in humans including septicemia, pneumonia, septic arthritis, wound infections and meningitis. To date, the determinants of virulence, antibiotic resistance, metabolic features conferring survival and host-associated pathogenic potential of this bacterium remain largely underexplored. In this study, we sequenced and assembled the whole-genome of P. agglomerans KM1 isolated from kimchi in South Korea. The genome contained one circular chromosome of 4,039,945 bp, 3 mega plasmids, and 2 prophages. The phage-derived genes encoded integrase, lysozyme and terminase. Six CRISPR loci were identified within the bacterial chromosome. Further in-depth analysis showed that the genome contained 13 antibiotic resistance genes conferring resistance to clinically important antibiotics such as penicillin G, bacitracin, rifampicin, vancomycin, and fosfomycin. Genes involved in adaptations to environmental stress were also identified which included factors providing resistance to osmotic lysis, oxidative stress, as well as heat and cold shock. The genomic analysis of virulence factors led to identification of a type VI secretion system, hemolysin, filamentous hemagglutinin, and genes involved in iron uptake and sequestration. Finally, the data provided here show that, the KM1 isolate exerted strong immunostimulatory properties on RAW 264.7 macrophages in vitro. Stimulated cells produced Nitric Oxide (NO) and pro-inflammatory cytokines TNF-α, IL-6 and the anti-inflammatory cytokine IL-10. The upstream signaling for production of TNF-α, IL-6, IL-10, and NO depended on TLR4 and TLR1/2. While production of TNF-α, IL-6 and NO involved solely activation of the NF-κB, IL-10 secretion was largely dependent on NF-κB and to a lesser extent on MAPK Kinases. Taken together, the analysis of the whole-genome and immunostimulatory properties provided in-depth characterization of the P. agglomerans KM1 isolate shedding a new light on determinants of virulence that drive its interactions with the environment, other microorganisms and eukaryotic hosts.
Short Peptides as Predictors for the Structure of Polyarginine Sequences in Disordered Proteins

Intrinsically disordered proteins (IDPs) and regions (IDRs) are frequently enriched in charged amino acids. IDRs are regularly involved in important biological processes, where one or more charged residues is the driving force behind a protein-biomolecule interaction. Several lines of experimental and computational evidence suggest that polypeptides and proteins that carry high net charges have a high preference for extended conformations with average end to end distances exceeding expectations for self-avoiding random coils. Here, we show that charged arginine (R) residues in even short glycine (G) capped model peptides (GRRG and GRRRG) significantly affect the conformational propensities of each other when compared to the intrinsic propensities of a mostly unperturbed arginine in the tripeptide GRG. A conformational analysis based on experimentally determined J-coupling constants from heteronuclear NMR spectroscopy and amide I’ band profiles from polarized Raman spectroscopy reveals that nearest neighbor interactions stabilize extended β-strand conformations at the expense of polyproline II and turn conformations. The results from MD simulations with an CHARMM36m force field and TIP3P water reproduce our results only to a limited extent. The use of the Ramachandran distribution of the central residue of GRRRG in a calculation of end-to-end distances of polyarginines of different length yielded the expected power law behavior. The scaling coefficient of 0.66 suggests that such peptides would be more extended than predicted by a self-avoiding random walk. Our findings thus support in principle theoretical predictions of Mao et al. (Proc. Natl. Acad. Sci. USA, 107, 8183-8188, 2010). Significance Intrinsically disordered proteins are rich in charged and deficient in hydrophobic residues. High net charges of disordered protein segments favor statistical coil ensembles which are more extended than a self-avoiding random coil. It is unclear whether the chain extension solely reflects the avoidance of non-local interactions or also local nearest neighbor interactions provide significant contributions. The relevance of nearest neighbor interactions, which are neglected in random coil models, has been emphasized in the literature, but only sporadically considered in molecular modellings of disordered proteins and peptides. We determined the Ramachandran distributions of protonated arginine in GRRG and GRRRG peptides. Our results reveal the contribution of nearest neighbor interactions to the extended conformations reported for a variety of poly-arginine protein segments.
Proteomic analysis of metabolic pathways shows chloroplast-mitochondria cross-talk in a Cu-limited diatom

Diatoms are one of the most successful phytoplankton groups in our oceans, being responsible for over 20% of the Earth’s photosynthetic productivity. Their chimeric genomes have genes derived from red algae, green algae, bacteria and heterotrophs, resulting in multiple isoenzymes targeted to different cellular compartments with the potential for differential regulation under nutrient limitation. The resulting interactions between metabolic pathways are not yet fully understood. We previously showed how acclimation to Cu limitation enhanced susceptibility to overreduction of the photosynthetic electron transport chain and its reorganization to favor photoprotection over light-harvesting in the oceanic diatom Thalassiosira oceanica (Hippmann et al., 2017). In order to understand the overall metabolic changes that help alleviate the stress of Cu limitation, we generated comprehensive proteomic datasets from the diatom Thalassiosira oceanica grown under Cu-limiting and -replete conditions. The datasets were used to identify differentially expressed proteins involved in carbon, nitrogen and oxidative stress-related metabolic pathways and to predict the proteins cellular location. Metabolic pathway analysis showed integrated responses to Cu limitation in diatoms. The up-regulation of ferredoxin (Fdx) was correlated with up-regulation of plastidial Fdx-dependent isoenzymes involved in nitrogen assimilation as well as enzymes involved in glutathione synthesis thus integrating nitrogen uptake and metabolism with photosynthesis and oxidative stress resistance. The differential regulation of glycolytic isoenzymes located in the chloroplast and mitochondria enables them to channel both excess electrons and/or ATP between these compartments. Additional evidence for chloroplast-mitochondrial cross-talk is shown by up-regulation of chloroplast and mitochondrial proteins involved in the proposed malate shunt. One sentence summary Diatoms adapt to Cu limitation by regulating their large repertoire of isoenzymes to channel electrons away from the chloroplast, enhance nitrogen uptake, and integrate the oxidative stress response. 123
Evaluation of Phytochemical Constituents of the Fruits of Cucumis Sativus Linn. For their Hepatoprotective Activity by Molecular Docking Studies

Cucumis sativus Linn. (Fam. Cucubitaceae) is commonly known as “Vellari” in Tamil, “Cucumber” in English and “Sakusa” in Sanskrit. Cucumis sativus fruit is shown to possess various activities such as ameliorative, hypoglycemic, hypolipidemic, carminative and ameliorative and antacid properties. It is used in Cosmetics as treatment for skin-inflamation and skin protectant. Pulp of the fruit is useful in dysentery, diarrhea, dropsy, piles and leprosy. It is also used as a liver tonic. Hepatocellular carcinoma is a metabolic disorder which is emerging as a severe problem and is a disease involving liver disorder. In the present study, six phytochemical constituents isolated and identified from the ethanolic extract of the fruits of Cucumis sativus Linn. by GC-MS analysis have been screened for inhibitory activity against Hepatitis B X and Heme oxygenase I using molecular docking studies. The binding affinities of the Phytochemical constituents were compared with that of the known hepatoprotective agent, silymarin.The ACD/Chemsketch tool was used to generate 3D structures of ligands. A molecular file format converter tool has been used to convert the generated data to the protein Data Bank (PDB) and has been used for docking studies. The active site of the target protin was identified using Q-site finder tool. The energy values for docking interactions between the active site and the phytochemical constituents have been studied by using Flex X tool. Out of all inhibitors, silymarin, followed by 2-(2-methyleyclohexylidene)-hydrazinccarboxamide possess the highest energy value indicating them as efficient inhibitors with the target proteins to treat hepatocellular carcinoma. The effective properties may be due to the presence of carbonyl and alholic OH groups present in the ligand molecules. The findings will be discussed in detail.