Miracle-dz/UniFAR-FTUs huggingface dataset:
Regulation of transcription termination by FUS and TDP-43

The carboxy-terminal domain (CTD) of the RNA polymerase II (RNAPII) subunit POLR2A is a platform for modifications specifying the recruitment of factors that regulate transcription, mRNA processing, and chromatin remodelling. We previously found that symmetrical dimethylation (me2s) of a CTD Arginine residue (R1810 in human) causes recruitment of the Tudor domain of SMN, which interacts with Senataxin. SMN is mutated in spinal muscular atrophy (SMA), and Senataxin is sometimes mutated in Amyotrophic Lateral Sclerosis (ALS). R1810me2s and SMN, like Senataxin, are important for resolving R-loops (DNA:RNA hybrids) at transcription terminators. FUS and TDP-43 (TARDBP) are DNA/RNA binding proteins that are sometimes mutated in ALS and FTD (Frontotemporal dementia). Here we show that TDP-43 and, to some extent, FUS are recruited by the R1810me2s-SMN pathway. Defects in FUS and TDP-43 recruitment influence RNAPII termination and R-loop accumulation, leading to elevated DNA damage at terminators that may contribute to neurodegenerative disorders like ALS and FTD.
Varying degrees of running incline: Implications for chronic injury aetiology and rehabilitation

There has yet to be a combined analysis of the kinetics and three-dimensional kinematics of running at various degrees of inclination. The aim of the current study was to investigate the influence of treadmill running at various inclines (flat, 5, 10 and 15 degrees) on three-dimensional kinematics of the lower extremities and accelerations measured at the tibia. Ten male participants ran at 4.0 m/s at the four different inclinations. Three-dimensional lower extremity kinematics and tibial accelerations were quantified and contrasted using repeated measures ANOVA's. Tibial acceleration parameters were reduced significantly as a function of running incline, whilst tibial internal rotation was significant greater at 15° compared to flat. This study confirms that differences in both kinetics and kinematics are mediated through alterations in running inclination. From a clinical perspective, those who are susceptible/ recovering from injury may wish to utilise an incline in their training.
Computational Docking of Uric Acid and Allopurinol Derivatives That Can Bind to Xanthine Oxidase

This project is to seek a uric acid and allopurinol derivative compound that will be able to bind XOD with high affinity, which could possibly be used as an inhibitor against the XOD activity. A computer was used to design several compounds and employed the program Autodock Vina to perform dockings of those compounds to see if they can bind XOD. The uric acid structure contains a six-membered and a five-membered rings fused together with three carbonyl groups on the periphery. The allopurinol structure also contains the two membered rings as uric acid but instead only has a single carbonyl group attached to it. We sequentially replaced each peripheral carbonyl group by a sulfur atom (a less polar atom), follow by an aldehyde, a fluorine and carboxylic acid groups (more polar groups) to obtain different derivatives of uric acid. Oxygen atoms and fluorine atoms were also added to allopurinol on the peripheries. The results showed that the most polar groups, carboxylic acid and fluorine should have a higher affinity than the other groups. After the analysis of data and results we concluded that for the uric acid derivative the carboxylic#8’ and the allopurinol derivative fluorine#2’,6’ could be potential inhibitors for XOD.
Mineral iron dissolution in Trichodesmium colonies: The role of O2 and pH microenvironments

Colonies of the N2‐fixing cyanobacterium Trichodesmium can harbor distinct chemical microenvironments that may assist the colonies in acquiring mineral iron from dust. Here, we characterized O2 and pH gradients in and around Trichodesmium colonies by microsensor measurements on > 170 colonies collected in the Gulf of Eilat over ∼ 2 months. O2 concentrations and pH values in the center of single colonies decreased in the dark due to respiration, reaching minimum values of 70 μmol L−1 and 7.7, whereas in the light, O2 and pH increased due to photosynthesis, reaching maximum values of 410 μmol L−1 and 8.6. Addition of dust and bacteria and increasing colony size influenced O2 and pH levels in the colonies, yet values remained within the range observed in single natural colonies. However, lower values down to 60 μmol L−1 O2 and pH 7.5 were recorded in the dark in dense surface accumulations of Trichodesmium. Using radiolabelled ferrihydrite, we examined the effect of these conditions on mineral iron dissolution and availability to Trichodesmium. Dark‐incubated colonies did not acquire iron from ferrihydrite faster than light‐incubated colonies, indicating that the dark‐induced decrease in pH and O2 within single colonies is too small to significantly increase mineral iron bioavailability. Yet, ligand‐promoted dissolution of ferrihydrite, a mechanism likely applied by Trichodesmum for acquiring mineral iron, did increase at the lower pH levels observed in surface accumulations. Thus, Trichodesmium surface blooms in their final stage may harbor chemical conditions that enhance the dissolution and bioavailability of mineral iron to the associated microbial community.
Complete mitochondrial genome sequence of grey-headed parrotbill (Paradoxornis gularis) and its phylogenetic analysis

Abstract Grey-headed Parrotbill, Paradoxornis gularis, has significant economic and scientific value in China. Length of the complete mitochondrial genome of grey-headed parrotbill is 17,743 bp, and it contains 13 protein-coding genes (PCGs), 2 ribosomal RNA genes (12S rRNA and 16S rRNA), 22 transfer RNA genes (tRNA), and a D-loop sequence. The overall base composition of the mitochondrial sequence was 29.47% A, 14.68% G, 24.33% T, 31.52% C. All tRNAs have the typical cloverleaf structure, except for tRNASer. All PCGs start with ATG codons, except for COXI and NADH6, which are initiated by GTG and CTA, respectively.
Neurobiological successor features for spatial navigation

The hippocampus has long been observed to encode a representation of an animal’s position in space. Recent evidence suggests that the nature of this representation is somewhat predictive and can be modelled by learning a successor representation (SR) between distinct positions in an environment. However, this discretisation of space is subjective making it difficult to formulate predictions about how some environmental manipulations should impact the hippocampal representation. Here we present a model of place and grid cell firing as a consequence of learning a SR from a basis set of known neurobiological features – boundary vector cells (BVCs). The model describes place cell firing as the successor features of the SR, with grid cells forming a low-dimensional representation of these successor features. We show that the place and grid cells generated using the BVC-SR model provide a good account of biological data for a variety of environmental manipulations, including dimensional stretches, barrier insertions, and the influence of environmental geometry on the hippocampal representation of space.
Genetic diversity and population structure of burbotLota lotain Germany: Implications for conservation and management

The genetic structure of the gadiform fish species, burbot Lota lota L. , was investigated across Germany to derive management options for facilitating the preservation of genetic diversity. Sequence analysis of the mitochondrial control region (n = 244) and microsatellite analysis (n = 861) of specimens from 20 sites revealed genetic structuring between major river basins, and particularly between lake and river habitats. The admixture zone between the Eurasian and West European phylogenetic clades in Lake Constance was confirmed and expanded to include the drainage basins of the rivers Rhine and Schlei/Trave. Haplotype distribution and private haplotypes in single river basins indicated population differentiation and imply that German burbot constituted an important part of the entire species' diversity. The derived genetic structuring has implications for future stocking programmes and the preservation of the adaptive potential of burbot, a guiding species for oligotrophic lakes in Europe.
Fermentation characteristics and in vitro ruminal digestion of yacon residue silage with lactic acid bacteria inoculant or beet pulp

ABSTRACT In this study, we examined the effects of lactic acid bacteria (LAB) inoculant and beet pulp (BP) on the quality of yacon (Smallanthus sonchifolius) residue silage. Yacon silage was prepared using a small-scale system of silage fermentation, and the treatments were as follows: control silage without any additive and silages with LAB inoculant Chikuso-1 (Lactobacillus plantarum, 5 mg/kg, fresh matter basis), BP (30% fresh matter basis), and LAB+BP. Silages were opened on days 3, 5, 7, 15, 30, and [. ]
An evaluation of stringent filtering to improve species distribution models from citizen science data

Citizen science data are increasingly used for modelling species distributions because they offer broad spatiotemporal coverage of local observations. However, such data are often collected without experimental design or set survey methods, raising the risk that bias and noise will compromise modelled predictions. We tested the ability of species distribution models (SDMs) built from these low‐structure citizen science data to match the quality of SDMs from systematically collected data and tested whether stringent data filtering improved predictions.
Recharacterization of the Canine Adenovirus Type 1 Vaccine Strain based on the Biological and Molecular Properties

©This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/ license/by-nc/3.0/). Canine adenovirus type 1 (CAV-1) infection results in hepatitis in dogs. In this study, we investigated the biologic and genetic characteristics of the CAV-1 vaccine strain (CAV1V) to improve quality control about CAV vaccine. The identity of CAV1V as CAV-1 was confirmed based on its cytopathic effects and the results of hemagglutination (HA) and immunofluorescence assays, and electron microscopy. The CAV1V strain reached 10 7.5 TCID50/mL in MDCK cells at 4 days post-inoculation and exhibited hemmagglutination activity of 256 U using guinea pig erythrocytes. Intranuclear fluorescence in the infected cells was observed and typical adenoviruses were observed in electon microscope. CAV1V strain was identified as a CAV-1 strain by nucleotide sequence analysis. In a comparison of the nucleotide sequences of the fiber genes of several CAV strains, CAV1V showed the highest similarity (99.8%) with the GLAXO strain, which was isolated in Canada. Our biological characterization of CAV1V will facilitate quality control of the canine hepatitis vaccine.
An abundant quiescent stem cell population in Drosophila Malpighian tubules protects principal cells from kidney stones

Adult Drosophila Malpighian tubules have low rates of cell turnover but are vulnerable to damage caused by stones, like their mammalian counterparts, kidneys. We show that Drosophila renal stem cells (RSCs) comprise a unique, unipotent regenerative compartment. RSCs respond only to loss of nearby principal cells (PCs), cells critical for maintaining ionic balance. Perhaps due to the large size of PCs they are outnumbered by RSCs, which replace each lost cell with multiple PCs of lower ploidy. RSCs share a developmental origin with highly active intestinal stem cells (ISCs), and like ISCs generate daughters by asymmetric Notch signaling, yet RSCs remain quiescent in the absence of damage. Nevertheless, the capacity for RSC-mediated repair extends the lifespan of flies carrying kidney stones. We propose that abundant, RSC-like stem cells exist in other tissues with low rates of turnover where they may have been mistaken for differentiated tissue cells.
transendothelial neutrophil migration

We explored the effect of leukotriene B4 (LTB4) on endothelial cells in LTB4-induced transen- dothelial migration (TEM) ofneutrophils as an in vitro model of neutrophil extravasation. Chemotactic re- sponse of human neutrophils to LTB4 was significantly lower than that in response to N-formyl-methionyl- leucyl-phenylalanine (fMLP), whereas the extent of ThM in response to LTB4 was significantly higher than that to fMLP. The study on random migration induced by LTB4 and fMLP also showed similar results, which indicated that LTB4 might affect the human umbili- cal cord vein endothelial cell (HUVEC) barrier. Neutro- phil TEM was induced by pretreatment of HUVEC monolayer with LTB4 but not with fMLP. Treatment of endothelial cells by ONO-4057, a LTB4 recep- tor antagonist, abolished the effect of LTB4 almost completely whereas neutrophils treated with ONO- 4057 could transnilgrate through HUVEC treated with LTB4. These findings indicated that LTB4 could in- duce neutrophil TEM by acting on HUVEC. J. Leu- koc. Biol. 62: 203-209; 1997.
MANAGEMENT OF INFLAMMATORY BOWEL DISEASE AND EXPERIMENTAL MODELS ESTABLISHED FOR EVALUATION- AN UPDATE

Inflammatory bowel diseases (IBD) include Ulcerative colitis (UC), an inflammatory disease of the large intestine and Crohn‟s disease (CD). Ulcerative colitis is ulcers form in the inner lining or mucosa of the colon or rectum, often resulting in diarrhea, blood, and pus. The use of conventional steroids, glucocorticoids TNF-α inhibitors are found highly effective in treating IBD but their use is associated with some adverse effects. Therefore, the importance of using natural products has increased, as they have interest in discovering efficient new drugs with less adverse effects. Natural drugs are desirable for the treatment of inflammatory bowel diseases, such as ulcerative colitis and Crohn's disease. However, there are limited controlled evidences indicating the efficacy of traditional Chinese medicines, such as aloe vera gel, wheat grass juice, Boswellia serrata etc., in the treatment of UC. Many experimental models such as TNBS model, hapten induced colitis etc. are established for the evaluation of drugs in IBD. This review focuses on the management of IBD by using medicinal plants, synthetic drugs and methods established for the evaluation of drugs in IBD.
Pennisetum ciliare: a review of treatment efficacy, competitive traits, and restoration opportunities

Abstract Buffelgrass [Pennisetum ciliare (L.) Link] is a drought-tolerant invasive grass that is a threat to native biodiversity in the drylands of the Americas and Australia. Despite efforts from land managers to control P. ciliare, management approaches tend to have mixed success, treatment results can be poorly communicated among entities, and there are few long-term controlled studies. In this literature review, we synthesize data from both peer-reviewed and “gray” literature on the efficacy of management techniques to control P. ciliare and the secondary impacts to native plant communities. Our search resulted in 42 unique sources containing a total of 229 studies that we categorized into 10 treatment types, which included herbicide, seeding, manual removal, fire, grazing, biocontrol, fire + additional treatments, manual removal + additional treatments, herbicide + additional treatments, and herbicide + manual removal. We found that treatments that used multiple techniques in tandem along with followup treatments were the most effective at controlling P. ciliare. Fewer than one-third of the studies reported impacts of management on native species, and the most commonly studied treatment (herbicide, N = 130) showed detrimental impacts on native plant communities. However, the average time between treatment and outcome measurement was only 15 mo; we suggest the need for more long-term studies of treatment efficacy and secondary impacts of treatment on the ecosystem. Finally, we conducted a second literature review on P. ciliare biology and traits for mechanisms that allows P. ciliare to alter the invaded environment to facilitate a competitive advantage over native species. We found evidence of self-reinforcing feedbacks of invasion being generated by P. ciliare through its interactions with water availability, nutrient cycling, and disturbance regimes. We developed a conceptual model of P. ciliare based on these feedback loops and offer management considerations based on its invasion dynamics and biology.
Circular RNA ZNF827 tunes neuronal differentiation by facilitating transcriptional repression of Neuronal Growth Factor Receptor

Circular RNAs (circRNAs) comprise a large class of conserved non-coding RNAs that regulate a number of biological processes, including transcription, alternative splicing, translation and mRNA decay. circRNAs are enriched in the brain and mammalian cells subjected to neuronal differentiation markedly change their circRNA transcriptomes. Here, we have mapped high-confidence circRNA inventories of mouse embryonic stem cells, neuronal progenitor cells and in differentiated glutamatergic neurons and identify hundreds of differentially expressed circRNAs. Among several candidate circRNAs, knockdown of circZNF827 significantly induces expression of key neuronal markers, suggesting that this molecule negatively regulates neuronal differentiation. Using Nanostring analyses we demonstrate that among 770 tested genes linked to known neuronal pathways and neuropathological states, knockdown of circZNF827 deregulates expression of several genes including a robust upregulation of neuronal growth factor receptor (NGFR). We show that NGFR becomes transcriptionally upregulated and that this functionally enhances NGF signalling. Our results suggest that circZNF827, although being highly enriched in the cell cytoplasm, can elicit transcriptional changes, which in turn balances proliferation and neuronal differentiation signalling.
Future Changes in Rice Bioclimatic Growing Conditions in Portugal

Rice is a historically important crop in Portugal. This crop development and production strongly depend on atmospheric conditions in the growing season. Given the strong dependence of climatic conditions, climate change may pose a significant risk for future rice production. In the present study, a high spatial resolution bioclimatic characterization over the main rice producing region in Portugal was performed for the recent past (1950–2000) and for the future (2041–2060) under four different anthropogenic forcing scenarios (RCP2.6, RCP4.5, RCP6.0, and RCP8.5). This zoning is performed by using eight bioclimatic indices, based on temperature and precipitation, using a very high resolution gridded dataset (Worldclim). For the future period, an 11-member global climate model ensemble was used, also taking into account model/scenario uncertainties and bias. Additionally, a new index was developed to incorporate the main features of temperature and precipitation at each rice field level. Under recent past climates, a clear north–south gradient in temperature and precipitation is apparent, with the regions of Tejo and Sado presenting higher temperatures and lower precipitation than the Mondego and Vouga regions. Additionally, there is a coastal–inland effect due to the Atlantic Ocean influence. Under anthropogenic climate change, all indices point to annual higher temperatures and lower precipitations across all rice producing regions, accompanied by increased seasonality. Furthermore, the rise of summertime temperatures may substantially increase water demands, which, when unmitigated, may bring physiological problems in the crop development. We conclude that climate change may negatively impact the viability of rice production in Portugal, particularly taking into account the national grown varieties. Thus, adequate and timely planning of suitable adaptation measures are needed to ensure the sustainability of this historically important food sector.
The pollen morphological diversity of Ziziphora clinopodioides (Lamiaceae)

A cogent medicinal and aromatic plant, Ziziphora clinopodioides (Lamiaceae) is a perennial herb, its aerial parts is used as a wild vegetable or additive in foods to proffer pleasant aroma and flavour. There are many discussions about the intraspecific classification of this species and several subspecies have been introduced for it in different flora. These subspecies are morphologically very similar and identification of them is very difficult and in some cases, impossible. Therefore, in the present study, the pollen grains morphology of nine subspecies (32 specimens) of Z. clinopodioides were probed and documented in details utilising the scanning electron microscopy (SEM). In total, eleven pollen morphological characteristics were investigated and analysed by PAST software. The obtained results showed that pollen grains were hexacolpate and their equatorial views were sub-oblate to prolate. The exine ornamentation types of the pollen grains are bireticulate, microreticulate, reticulate and bireticulate-reticulate. The ANOVA test did not show significant difference for the studied quantitative traits. Although, the results of the multivariate analysis revealed a high diversity amongst the specimens even in the specimens of a single subspecies; it did not confirm the separation of subspecies in Z. clinopodioides.
t-SNE transformation: a normalization method for local features of single-cell RNA-seq data

Single-cell RNA sequencing has been widely used by biology researchers. There are many analysis tools developed accordingly. However, almost all of them use log transformation in the process of normalization, which may result in system bias on global features of datasets. It is considered that they may not be suitable for researchers who expect local and detailed features of datasets, such as rare cell population and independent expressed genes. In this study, we developed a method called t-SNE transformation to replace log transformation. We found that it can well respond to some specific bio-markers in real datasets. When the cluster number was changed, t-SNE transformation was steadier than log transformation. Further study showed that clustering after t-SNE transformation detected the residual cells more accurately after majority cells of one type were removed manually. It was also sensitive to a highly-variated independent gene added artificially. In conclusion, t-SNE transformation is an alternative normalization for detecting local features, especially interests arouse in cell types with rare populations or highly-variated but independently expressed genes.