Miracle-dz/UniFAR-FTUs huggingface dataset:
PD-L1 expression at tumor invasive front is associated with EMT and poor prognosis in esophageal squamous cell carcinoma.

Abstract Programmed death-ligand 1 (PD-L1) plays a crucial role in the host immune system in cancer progression. The gene promoter region of PD-L1 also contains a binding site for ZEB1, a transcription factor related to epithelial-mesenchymal transition (EMT). The purpose of this study was to clarify the relationship between PD-L1 and EMT and its clinical importance in esophageal squamous cell carcinoma (ESCC). PD-L1 and ZEB1 expression at the tumor invasive front was examined by immunohistochemistry in resected specimens from 90 patients with ESCC who underwent surgery without preoperative therapy, and their expression and clinicopathological factors were compared. ZEB1 and PD-L1 expression was determined in TE8 cells, which demonstrate the EMT phenotype, following ZEB1 knockdown by siZEB1. TE5, TE6 and TE11 cells with non-EMT phenotype were also used for studies of TGF-β1-dependent EMT induction and ZEB1 and PD-L1 expression. In cases of high PD-L1 expression at the invasive front, significantly greater depth of tumor invasion, EMT, and less CD8(+) lymphocyte infiltration were observed. High PD-L1 expression was also associated with worse overall and relapse-free survival. A correlation was observed between PD-L1 and ZEB1 expression. In TE8 cells, siZEB1 suppressed PD-L1 and promoted E-cadherin mRNA and protein expression. TGF-β1 induced EMT and surface expression of PD-L1 in TE5, TE6 and TE11 cell lines. PD-L1 expression at the ESCC invasive front was related to ZEB1 expression, EMT and poor prognosis. We suggest that a cooperative mechanism bridging between tumor immune avoidance and EMT contributes to tumor malignancy in ESCC. This article is protected by copyright. All rights reserved.
Cysteine residues of the mammalian GET receptor: Essential for tail-anchored protein insertion?

Tail-anchored proteins integrate into lipid bilayers via a single transmembrane segment at their extreme C-terminus. The membrane insertion step is mediated by a heterodimeric receptor complex formed by WRB and CAML in higher eukaryotes and Get1 and Get2 in yeast. The transmembrane domains of the receptor complex form an integration site at the endoplasmic reticulum membrane and interact transiently with the transmembrane domain of an integrating TA protein prior to its membrane embedding. Cysteine residues are absent in yeast Get1 and Get2 whereas the mammalian homologues WRB and CAML contain three and five cysteines respectively. I aimed to investigate the role of the cysteine residues of WRB and CAML and test whether they are essential for TA protein targeting. Mutants of WRB and CAML in which the cysteine residues were mutated to serine were generated and I used a yeast-based complementation assay in which cells depleted of Get1 and Get2 were transformed with plasmids encoding either wild type or mutant WRB and CAML. Mutants were still able to create a receptor complex as assayed by yeast two-hybrid and did not impair the targeting of a substrate TA protein. Moreover, mutants rescued growth phenotypes of GET mutants confirming the formation of a functionally active receptor. In line with the absence of cysteines in the yeast GET receptor, cysteines in WRB and CAML seem to be not essential for TA protein targeting and may be required for potential still unknown regulation of TA protein targeting such as receptor stoichiometry, substrate quality control and chaperone function.
A thermophilic nitrate-reducing bacterium isolated from production water of a high temperature oil reservoir and its inhibition on sulfate-reducing bacteria

A thermophilic spore-forming facultative anaerobic bacterium, designated as Njiang2, was isolated from the production water of a high temperature oil reservoir (87°C). The physiological, biochemical and 16S rRNA gene based phylogenetic analysis indicated that Njiang2 belonged to the genus Anoxybacillus. Njiang2 could significantly inhibit H2S production when co-cultured with Desulfotomaculum sp under laboratory conditions, which implied its great potential in mitigation of brine souring in the oil reservoir and in control of biocorrosion caused by sulfate-reducing bacteria. As far as we know, this might be the first report of Anoxybacillus sp. isolated from high temperature oilfield
Simulation of Transmembrane Potential Propagation in Normal and Ischemic Tissue Using Aliev-Panfilov Model

Mathematical modelling of heart's electrical activity is useful for understanding the details of heart's function, and developing methods for prediction, diagnosis and treatment of various heart diseases. In this work, we modelled the electrical activity of the heart in the three dimensional (3D) ventricular geometry based on transmembrane potential (TMP) distributions. The main intention in this study is to simulate TMP distributions using heart geometry obtained from Magnetic Resonance (MR) Images, and corresponding fiber structure obtained from Diffusion Weighted Images (DWI). Aliev-Panfilov model was used to describe electrical activity of the heart at tissue level, which focuses on the potential wavefront propagation. Using this model, it is also possible to include the anisotropy of the heart muscle in the calculations. Here, we first simulated 3 dimensional mapping of transmembrane distribution and propagation due to an ectopic stimulation on a normal ventricular geometry of the heart. Then, based on action potential morphology changes in a tissue with ischemia, we derived ischemic weight values and equation parameters for our model. By introducing ischemic regions on the ventricular geometry and applying ischemic weight values and parameters, we simulated TMP distribution and propagation in ventricular geometry with partial ischemia.
THE WOODY VEGETATION OF QUARTZITE SOILS IN A MOUNTAIN LANDSCAPE IN THE ATLANTIC FOREST DOMAIN (SOUTH-EASTERN BRAZIL): STRUCTURE, DIVERSITY AND IMPLICATIONS FOR CONSERVATION

The Serra Negra belongs to the Mantiqueira mountain complex, Minas Gerais, Brazil. It has a vegetation mosaic dominated by ombrophilous and seasonal forest and grassland formations. Woody physiognomies occur on patches of quartzite soils. The aim of the present study was to investigate the patterns of structure and diversity of woody vegetation on quartzite soils in Serra Negra. Ten plots (20 × 50 m) were randomly placed in patches of woody vegetation on quartzite soils along the landscape. The diameter and height of all woody plants with a diameter of ≥ 3 cm at 30 cm from the soil were measured. The 1899 individuals sampled represented 30 plant families and 68 species. A strong ecological dominance was found, with about 30% of individuals belonging to a single species, Eremanthus incanus (Asteraceae). The Shannon diversity index ( H ′) was 2.74 nats/individual and evenness ( J ) 0.65. The two most abundant and ecologically important species in this vegetation type, Eremanthus incanus and Eremanthus erythropappus , called ‘candeias’, are exploited in the region, mainly for firewood. This exploitation, combined with other factors (e.g. increased tourism), can pose risks to the conservation of the whole flora of the region.
Development of human skin equivalents to unravel the impaired skin barrier in atopic dermatitis skin

The studies in this thesis describes the barrier defects in Atopic Dermatitis (AD) skin and various techniques to develop AD Human Skin Equivalents (HSEs) which can be used to better understand the role of several factors in the pathogenesis of AD skin. The results described show that Inflammation plays a pivotal role in the development of epidermal and SC features of AD skin and that AD epidermal features can be maintained in vitro when AD skin biopsies are used to generate explant-HSEs. These AD-HSEs can also serve as a tool to screen potential therapeutics for AD and skin barrier repair. However, limitations exist in the complexity and full representation of all possible factors known to influence the development of AD e.g. FLG mutations, other aspects of inflammatory micro-environment, microbe colonization etc.
Electrochemical-Nucleic Acid Detection with Enhanced Specificity and Sensitivity

Development of a rapid and label-free Electrochemical Impedance Spectroscopy (EIS) biosensor for nucleic acid detection based on sensitivity and specifies was proposed to fill the technology gap between rapid and portable detection of DNA sequences. Current biosensors have inherent limitations to sensitivity and specificity due to the monovalent character of the detection method. These limitations were significantly improved upon by constructing cooperative probes, called Tentacle Probes™ (TP), which utilize divalent binding to achieve both high sensitivity as well as extremely high specificity. Immobilization of Tentacle Probe onto gold disk electrode produced statistical significance, with p<3.0*10-13. Tentacle Probe with EIS detection was able to detect a difference between the B. AnthracisgyrA gene and B. Cereus gyrA Single Nucleotide Polymorphism sequence at a lower limit of detection of 20nM. Furthermore, B. Cereus gyrA is a common soil bacterium that causes false positives for B. AnthracisgyrA. This method of detection is current a model system for DNA detection; other genes could be detected with this system. With the potential to be transformative by providing a platform technology for both DNA and protein detection with high sensitivity this system offers extremely low rates of false positives. There is a high capacity for the technology to be multiplexed for high-throughput applications or quick diagnostic tests for medical purposes. Thus, the biomarker development will also have the potential to be assessed through noninvasive methods.
Zebra Mussels in the Neosho River Basin: Ecology and Economics

In rivers of the upper Neosho basin, Kansas, USA, lowhead dams are facilitating the downstream dispersal of zebra mussels (Dreissena polymorpha). I quantified densities of planktonic and settled zebra mussels in this recently-invaded riverreservoir system to examine potential effects of lowhead dams on dispersal dynamics of this invasive species. Although populations declined with distance from reservoir sources, densities repeatedly increased at sites inundated by lowhead dams compared to free-flowing areas, resulting in colonization along nearly 200 river-km. The pattern of zebra mussel dispersal in these rivers is best described by the downstream-march model, facilitated by lowhead dams acting as stepping stones. In rivers with lowhead dams, control of zebra mussel metapopulations may not be accomplished solely by limiting source-sink dynamics from upstream infested lakes.
Modelling and analysis of oscillations in gene expression through neural development

The timing of differentiation underlies the development of any organ system. In neural development, the expression of the transcription factor Hes1 has been shown to be oscillatory in neural progenitors, but at a low steady state in differentiated neurons. This change in the dynamics of expression marks the timing of differentiation. We previously constructed a mathematical model to test the experimental hypothesis that the topology of the miR-9/Hes1 network and specifically the accumulation of the micro-RNA, miR-9, could terminate Hes1 oscillations and account for the timing of neuronal differentiation, using deterministic delay differential equations.However, biochemical reactions are the result of random encounters between discrete numbers of molecules, and some of these molecules may be present at low numbers. The finite number of molecules interacting within the system leads to inherent randomness, and this is known as intrinsic stochasticity. The stochastic model predicts that low molecular number causes the time to differentiation to be distributed, which is in agreement with recent experimental evidence and considered important to generate cell type diversity. For the exact same model, fewer reacting molecules causes a decrease in the average time to differentiation, showing that the number of molecules can systematically change the timing of differentiation.Oscillations are important for a wide range of biological processes, but current methods for discovering oscillatory genes have primarily been designed for measurements performed on a population of cells. We introduce a new approach for analysing biological time series data designed for cases where the underlying dynamics of gene expression is inherently noisy at a single cell level. Our analysis method combines mechanistic stochastic modelling with the powerful methods of Bayesian nonparametric regression, and can distinguish oscillatory expression in single cell data from random fluctuations of nonoscillatory gene expression, despite peak-to-peak variability in period and amplitude of single cell oscillations.Models of gene expression commonly involve delayed biological processes, but the combination of stochasticity, delay and nonlinearity lead to emergent dynamics that are not understood at a theoretical level. We develop a theory to explain these effects, and apply it to a simple model of gene regulation. The new theory can account for long time-scale dynamics and nonlinear character of the system that emerge when the number of interacting molecules becomes low. Both the absolute length and the uncertainty in the delay time are shown to be crucial in controlling the magnitude of nonlinear effects. %%%%During neural development stem cells produce neurons through the process of differentiation. During differentiation, the expression of key genes controlling the stem cell state change from oscillatory to a low steady state. We use mathematical modelling to understand how the dynamics of this transition is regulated, and how the randomness caused by few…
Comparative Analysis of mecA and nuc Gene Sequences of Staphylococcus aureus Strains Isolated from Human Urine Samples

In the present study twenty five human urine samples of hospital patients were screened for Staphylococcus aureus. Twenty percent of the samples were positive for Staphylococcus aureus as yellow colonies were observed aerobically on mannitol salt agar, out of the five isolates two were catalase positive. On the basis of resistance against methicillin, out of the three catalase positive isolates, two were MSSA and one was MRSA. One MRSA and one MSSA strain was examined using PCR technique, for gene identification. The mecA and nuc gene were amplified using PCR technique. The presence of mecA gene and nuc gene in MRSA and MSSA respectively, confirmed the strains. Comparative gene analysis of mecA gene and nuc gene was performed using BLAST and CLUSTALW tools. Thereafter rooted phylogenetic tree was obtained for both mecA and nuc gene sequences explaining the genetic evolutionary lineage. Present study analyzed the resistance mechanism of MRSA and to identify the gene responsible in order to control the re-emerging methicillin resistant Staphylococcus aureus infection.
Intake, digestibility and nitrogen retention in goats fed ensiled maize stover and supplemented with snake bean (Bobgunnia madagascariensis) pod meal -

Objective: The aim of this study was to assess nutrient intake, digestibility and nitrogen (N) retention in goats fed ensiled maize stover (EMS) when supplemented with snake bean (Bobgunnia madascariensis) pod meal (BMM). Materials and methods: Eight local goats (21±2 Kg) in individual metabolic cages were divided into two groups. One group received a 100 gm BMM daily supplement to basal diet (EMS+50 gm maize bran), while the other group did not receive any supplement. The experimental design was a 2x2 switchback with 7 days of adaptation and 5 days of sampling of orts, feces and urine. Feed intake was recorded and total fecal collection was done to analyze digestibility of dry matter (DM), crude protein (CP), acid detergent fiber (ADF) and neutral detergent fiber (NDF), as well as N balance. Results: Goats receiving BMM supplement had higher (P<0.05) intake and digestibility of the analyzed nutrients than the group without supplementation. BMM supplementation also significantly increased N intake and fecal N output, compared to those without supplementation. BMM-supplemented goats had significantly better N retention than those without supplementation. Conclusion: Thus, supplementing BMM to goats fed EMS induced a higher (P<0.05) intake and digestibility of nutrients as well as better N retention. http://doi.org/10.5455/javar.2017. d207 XML PubReader
Resveratrol Attenuates Bleomycin-İnduced Genotoxicity, Pulmonary Fibrosis and DNA Damage in Balb/C Mice with Ehrlich Ascites Carcinoma

Amaç: Oksidatif stres, bleomisin (BLM) kaynaklı akciğer fibrozis patogenezi ve genotoksisitesinde önemli rol oynamaktadır. Bu çalışmanın amacı, resveratrolün (RES) Ehrlich asit karsinoması (EAT) taşıyan farelerde BLM’ye bağlı gelişen genotoksisite, akciğer fibrozisi ve DNA hasarı üzerindeki koruyucu etkisini araştırmaktır. Yöntemler: Çalışmada 60 adet Balb/c fare rastgele altı gruba ayrıldı. Sham grubu hariç diğer gruplardaki farelere 3x105 canlı EAT hücreleri intraperitonal (ip) olarak enjekte edildikten 24 saat sonra, farelere altı gün boyunca; BLM (10 mg/kg, i.p) tek başına, RES (50 mg/kg, i.p) tek başına, BLM (10 mg/kg, i.p) +RES (25 mg/kg, i.p), BLM (10 mg/kg, i.p) +RES (50 mg/kg, i.p) uygulandı. Serum ve akciğer dokusunda BLM’ye bağlı olarak artan; DNA hasarı (comet assay ve 8-OHdG), malondialdehit (MDA), myeloperoksidaz (MPO), protein karbonil (PC), hidroksiprolin (HPR), total oksidant durum (TOS) ve oksidatif stress indeksi (OSI) gibi oksidant parametreler ile süperoksit dismutaz (SOD), total antioksidant durum (TAS) ve glutatyon (GSH) gibi antioksidan paremetreleri incelenerek, resveratrolün BLM’ye bağlı olarak gelişen, pulmoner toksisite ve genotoksisitenin önlenmesindeki potansiyel rolü araştırıldı. Bulgular: Çalışma sonucunda resveratrolün (RES); bleomisine (BLM) bağlı olarak artış gösteren MDA, PC, TOS, MPO OSI, HPR ve DNA hasar seviyesini azaltırken (p <0.05), GSH, TAS ve SOD gibi antioksidanların aktivitelerini artırmıştır (p<0.05). Ayrıca histolojik bulgularda’da RES’in BLM kaynaklı fibrozisi engellediği tespit edilmiştir. Sonuç: Bu sonuçlar EAT taşıyan farelerde BLM’nin akciğerde neden olduğu DNA hasarı, lipit ve protein oksidasyonu sonucu oluşan fibrozisin RES uygulamasıyla azaltılabileceği ve RES’in akciğerdeki DNA hasarına ve pulmoner fibrozisin konvansiyonel tedavi yöntemlerine destekleyici tedavi sağlayabileceğini göstermektedir. Anahtar kelimeler: Bleomisin, ehrlich asit karsinoma, akciğer fibrozis, resveratrol, DNA hasarı ABSTRACT
CONFIRMATION BY QTL MAPPING OF THE MALUS ROBUSTA ('ROBUSTA 5') DERIVED POWDERY MILDEW RESISTANCE GENE PL1

‘Robusta 5’ (Malus robusta) apple rootstock has been used extensively as a source of resistance to powdery mildew by several breeding programs. A single locus Pl1 has been associated with this resistance and recently mapped on LG12 of the European Apple Framework Map using a qualitative approach. We collected quantitative data on field powdery mildew resistance in 2006 and 2007 on a segregating population made up of 186 individuals from a cross between ‘Ottawa 3’ (a susceptible apple rootstock) and ‘Robusta 5’; the correlation between the two years was 0.84 (P=0.0001). These quantitative data were used in combination with a molecular marker linkage map derived from the same cross to scan the genome using interval and MQM mapping in MapQTL 5 software. Preliminary results show a large effect QTL on the distal end of LG12 with a peak near the SSR marker CH01b12z which coincides with the mapped position of Pl1. Another QTL was detected on LG7 near marker E38M49-265. We are furthering the analysis by increasing the marker density in those regions.
Ewsa-dependent regulation of Runx2 during zebrafish skeletogenesis

Ewing’s sarcoma is the second most common malignant bone cancer found in adolescents, and the genetic hallmark of this disease is the presence of the aberrant chimeric fusion protein EWS/FLI1. This fusion is induced by the t(11; 22) chromosomal translocation of EWS and FLI1, and is the most prominent and common characteristic of Ewing sarcoma tumors found in approximately 85-90% of reported cases. EWS/FLI1 has been shown to directly bind to and inhibit the function of endogenous EWS in a dominant manner. In this study, we seek to increase our understanding of the role of endogenous EWS during development and skeletogenesis to gain insight into the pathogenesis of the disease. Previously, we demonstrated the role of a zebrafish EWS homolog Ewsa by analyzing the phenotype of a maternal zygotic homozygous ewsa/ewsa mutant line (MZ ewsa/ewsa) of zebrafish null for Ewsa protein. Prehypertrophic chondrocytes of Meckel’s cartilage in 4dpf MZ ewsa/ewsa mutants fail to completely differentiate into hypertrophic chondrocytes, followed by structural defects in craniofacial bones (dentary and basihyal bones) at the adult stage. Based on these results, we sought to understand EWS’s involvement in skeletogenesis by asking if Ewsa regulates activity of critical transcription factors involved in chondrocyte development. We have previously shown that Ewsa directs chondrocyte differentiation through modulation of chondrogenesis master transcription factor Sox9. Runx2 is also known to play a critical role in differentiation of both chondrocytes and osteoblasts, so we have addressed whether and how Ewsa regulates Runx2 expression and transcriptional activity. We discovered that Runx2 protein expression dramatically increases in craniofacial chondrocytes of 4-6dpf MZ ewsa/ewsa compared to wt/wt embryos. We have also observed premature mineralization in MZ ewsa/ewsa embryos at 6dpf and 10dpf. MZ ewsa/ewsa fish also display a decrease in expression of collagen10a1, a hypertrophic-specific Runx2 target gene. These data together suggests that Ewsa regulates Runx2 expression and transcriptional activity during chondrogenesis and regulates mineralization of these domains. Additionally, our lab has previously discovered that adult MZ ewsa/ewsa fish display aberrant
Description of Antho ( Plocamia ) bremecae sp. nov. and checklist of Microcionidae (Demospongiae: Poecilosclerida) from Burdwood Bank and neighboring areas, SW Atlantic Ocean

In this contribution, we describe a new Demospongiae species, Antho ( Plocamia ) bremecae sp. nov., from the west slope of Burdwood bank, a poorly studied region in the SW Atlantic Ocean. We also recorded for the first time in the region two other microcionid species, Clathria ( Axosuberites ) nidificata and Clathria ( Microciona ) antarctica. In addition, a regional checklist of Microcionidae from Burdwood Bank and neighboring areas, including Malvinas (Falkland) Islands, Tierra del Fuego Province and the North of the Scotia Arc (South Georgia and Shag Rocks) is provided.