Miracle-dz/UniFAR-FTUs huggingface dataset:
Regulation of growth and metabolism in rice (Oryza sativa L.) by arsenic and its possible reversal by phosphate

Abstract The effect of arsenate with or without phosphate on the growth and metabolism in rice seedlings cv. MTU1010 was studied. In the test, cv. arsenic was more toxic for root growth, than for shoot growth, where root hairs were fewer and short, roots were characteristically stubby, brittle and root tips gradually turned brown. Arsenic caused damage to the root epidermal cells and aerenchymatous cortex. The level of total chlorophyll, chlorophyll-a, chlorophyll-b and fluorescence intensity were decreased in arsenic treated rice seedlings. Arsenic toxicity affected the activities of different antioxidant scavenging enzymes in the test seedlings. Activities of superoxide dismutase and ascorbic acid oxidase were increased, whereas catalase and catechol peroxidase activities were decreased by arsenic application. In these seedlings, the oxidative stress has been observed with arsenic treatments and the level of proline, H2O2 and malondialdehyde contents were increased. Joint application of phosphate with arsenic showed significant alterations on all parameters tested under the purview of arsenic treatment alone leading to better growth and metabolism in rice seedlings. Thus the use of phosphorus enriched fertilizers in arsenic contaminated soil may improve the production of healthy rice plants.
Protection From Influenza by Intramuscular Gene Vector Delivery of a Broadly Neutralizing Nanobody Does Not Depend on Antibody Dependent Cellular Cytotoxicity

Cross-subtype neutralizing single domain antibodies against influenza present new opportunities for immunoprophylaxis and pandemic preparedness. Their simple modular structure and single open reading frame format are highly amenable to gene therapy-mediated delivery. We have previously described R1a-B6, an alpaca-derived single domain antibody (nanobody), that is capable of potent cross-subtype neutralization in vitro of H1N1, H5N1, H2N2, and H9N2 influenza viruses, through binding to a highly conserved epitope in the influenza hemagglutinin stem region. To evaluate the potential of R1a-B6 for immunoprophylaxis, we have reformatted it as an Fc fusion for adeno-associated viral (AAV) vector delivery. Our findings demonstrate that a single intramuscular injection in mice of AAV encoding R1a-B6 fused to Fc fragments of different isotypes equipped either, with or without antibody dependent cellular cytotoxicity (ADCC) activity, was able to drive sustained high-level expression (0.5–1.1 mg/mL) in sera with no evidence of reduction for up to 6 months. R1a-B6-Fc fusions of both isotypes gave complete protection against lethal challenge with both pandemic A/California/07/2009 (H1N1)pdm09 and avian influenza A/Vietnam/1194/2004 (H5N1). This data suggests that R1a-B6 is capable of cross-subtype protection and ADCC was not essential for R1a-B6 efficacy. Our findings demonstrate AAV delivery of cross-subtype neutralizing nanobodies may be an effective strategy to prevent influenza infection and provide long-term protection independent of a host induced immune response.
Stem–Mesenchymal Signature Cell Genes Detected in Heterogeneous Circulating Melanoma Cells Correlate With Disease Stage in Melanoma Patients

During the process of metastasis, cancer cells dissociate from primary tumors, migrate to distal sites, and finally colonize, eventually leading to the formation of metastatic tumors. These cancer cells, defined circulating tumor cells (CTCs) spreading through the blood stream, may develop metastatic lesions or remain dormant. Some emerging clinical evidence supports that some tumor cells may possess metastatic properties already in the earlier stages of tumorigenesis. Because the initiation and progression of vertical growth in human melanoma is fundamental to the notion of tumor virulence and progression, we decided to immune-magnetic collect and molecularly characterize circulating melanoma cells (CMCs) from melanoma patients AJCC staged = pT1b (i.e., transition from radial to vertical phase). CMCs are phenotypically and molecularly heterogeneous, thus we performed a “home-made Liquid-Biopsy,” by targeting the melanoma-associated-antigen, MCAM/MUC18/CD146, and/or the melanoma-initiating marker, ABCB5. We assessed a biomarker qualitative expression panel, contemplating the angiogenic-potential, melanoma-initiating and melanoma-differentiation drivers, cell-cell adhesion molecules, matrix-metallo-proteinases, which was performed on three enriched subpopulations from a total of 61 blood-samples from 21 melanoma patients. At first, a significant differential expression of the specific transcripts was documented between and within the CMC fractions enriched with MCAM-, ABCB5-, and both MCAM/ABCB5-coated beads, when analyzing two distinct groups: early AJCC- (stage I–II) and advanced- staged patients (stage II–IV). Moreover, in the early-AJCC staged-group, we could distinguish “endothelial,” CD45–MCAM+ enriched-, “stem” S-CMCs, CD45–ABCB5+ enriched- and a third hybrid bi-phenotypic CD45–MCAM+/ABCB5+ enriched-fractions, due to three distinct gene-expression profiles. In particular, the endothelial-CMCs were characterized by positive expression of genes involved in migration and invasion, whilst the stem CMC-fraction only expressed stem and differentiation markers. The third subpopulation isolated based on concurrent MCAM and ABCB5 protein expression showed an invasive phenotype. All three distinct CMCs sub-populations, exhibited a primitive, “stem-mesenchymal” profile suggesting a highly aggressive and metastasizing phenotype. This study confirms the phenotypic and molecular heterogeneity observed in melanoma and highlights those putative genes involved in early melanoma spreading and disease progression.
Responses of ant communities to dry sulfur deposition from mining emissions in semi‐arid tropical Australia, with implications for the use of functional groups

The impact of dry deposition of SO2 emissions on ant abundance, diversity and composition was investigated at Mount Isa in the semiarid tropics of northern Australia. Forty plots were sampled, stratified at two levels: sulfur deposition zones (high, medium, low, and two control zones) and habitat (Ridge and Plain). The two habitats supported distinctly different ant communities. Ants had clear responses to SO2 emissions. Ant abundance was lowest in the high and medium sulfur zones in both habitats. Species richness in high SO2 plots (up to 5 km from the source) was approximately half that of control plots in Ridge habitat, and was substantially less than controls in the Plain habitat. Ant community composition in the high sulfur zone was clearly separated from those of other zones in ordinations. Vector fitting showed soil SO4 concentration as a primary correlative factor in this separation. Ant abundance and richness were both negatively correlated with soil SO4 concentration, and positively correlated with plant species richness and distance away from the smelters. The abundance of 10 of the 21 most common species showed significant responses to emissions. Five species showed positive responses, and all belong to species-groups known to be abundant at disturbed sites throughout northern Australia. Relative abundance and richness of Eyrean (arid adapted) taxa collectively responded positively to sulfur, and Torresian (tropical) and Widespread species responded negatively. Despite large changes in species composition and abundances, there was relatively little change in the abundance of functional groups that have been widely used in studies of Australian ant communities. Ants are sensitive to SO2 emissions and appear to be good candidates as an indicator group in this context. However, an alternative functional group framework is required for the identification of recurrent responses of arid zone ant communities to disturbance.
Real-time PCR for the detection and quantitative analysis of IHNV in salmonids

The rapid identification and quantification of virus in diseased fish is a goal both conservationists and commercial aquaculturists have struggled to attain. Recently a technique for the detection of viral mRNA particles that uses fluorescent tagging and amplification has been developed. Utilizing primers and fluorescent labelled probes generated for the specific identification of the nucleocapsid (N) and glycoprotein (G) genes of infectious haematopoietic necrosis virus (IHNV), and an instrument that measures cyclic emittance of fluorescence, the presence or absence of virus can be easily and rapidly confirmed. This method is not only useful in confirming viral presence but is effective in measuring the relative or absolute quantity of virus present within the sample. This allows for the determination of the health status of a carrier fish by measuring the quantity of viral genomes or transcribed viral genes present. Because this method is based on sequence detection, instead of virus isolation in cell culture, it is also effective in determining the presence of pathogenic organisms from water, fish feeds, or other potential reservoirs of infection.
Enzyme phenotypes of Meloidogyne spp. populations

Enzyme phenotypes, specifically esterases (EST), malate dehydrogenase (MDH), superoxide dismutase (SOD) and glutamate-oxaloacetate transaminase (GOT) were used to characterise different species of Meloidogyne, mostly from Brazil and from some American countries. Esterase activity was highly polymorphic and was the most useful in the identification of the different species. Using this enzyme it is possible to characterise and identify the four major species: M. javanica, M. incognita, M. arenaria and M. hapla from a large collection of 111 populations of Meloidogyne spp. Another seven less common species (M. coffeicola, M. paranensis, M. konaensis, M. exigua, M. graminicola, M. oryzae, M. mayaguensis), with only one or a few populations of each, were studied and exhibited species-specific EST phenotypes. The two enzymes (EST and MDH) differentiated M. graminicola and M. oryzae. It was possible to detect atypical (unidentified) phenotypes: three from Brazil, one from the USA and another from Chile. The minor bands of esterase profiles provided information to detect intraspecific variability among some populations of M. incognita and six populations of M. exigua. Profiles of MDH permitted separation of two isolates of M. javanica from Brazil. Phenotypes enzymatiques de populations de Meloidogyne - Les phenotypes enzymatiques de l'esterase (EST), la malate deshydrogenase (MDH), la superoxide dismutase (SOD) et la glutamate-oxaloacetate transaminase (GOT) ont ete utilises de maniere systematique afin de caracteriser plusieurs especes de Meloidogyne provenant principalement du Bresil et de quelques pays des regions americaines. C'est l'activite esterasique qui a presente le plus grand polymorphisme et s'est montree la plus utile dans la caracterisation des especes. A l'aide de cette enzyme il a ete possible de caracteriser et d'identifier les quatre especes majeures de Meloidogyne: M. javanica, M. incognita, M. arenaria, et M. hapla au sein d'une collection de 111 populations de Meloidogyne spp. Sept autres especes moins frequentes (M. coffeicola, M. paranensis, M. konaensis, M. exigua, M. graminicola, M. oryzae, M. mayaguensis) comportant seulement quelques populations de chaque especes ont ete etudiees et ont egalement montre des phenotypes esterasiques specifiques. Les deux enzymes (EST et MDH) ont permis la differenciation de M. graminicola et de M.oryzae. Il a ete egalement possible de detecter des phenotypes atypiques non encore identifies chez trois populations originaires du Bresil, une des USA et une du Chili. Par ailleurs, les bandes mineures des profils esterasiques ont apporte des informations sur la variabilite intra-specifique chez quelques populations de M. incognita et six populations de M. exigua, tandis que l'observation des profils enzymatiques de la malate deshydrogenase (MDH) a permis la distinction de deux populations de M. javanica du Bresil.
Leaf senescence and lipid peroxidation: Effects of some phytohormones, and scavengers of free radicals and singlet oxygen

During in vitro senescence (chlorophyll loss) of oat (Avena sativa L. cv. Victory) leaf segments and of leaf discs of Rumex obtusifolius L, the activity of catalase decreases and lipid peroxidation increases. The activity of superoxide dismutase (SOD) decreases in Rumex leaf discs but changes little in oat leaf segments. Kinetin treatment of oat leaf segments, and GA3 treatment of Rumex leaf discs, inhibit decline in the enzyme activities and increase in the level of lipid peroxidation and strongly inhibit senescence. In either leaf tissue a treatment with ethanol or vitamin E (scavengers of free radicals) or with diphenylisobenzofuran (scavenger of singlet oxygen) results in a strong inhibition of lipid peroxidation and senescence, but does not affect much the decline in the SOD and catalase activities. It is concluded that, i) senscence-associated lipid peroxidation is induced by free radicals and singlet oxygen; and, ii) kinetin and GA3 inhibit senescence mainly by a modulation of lipid peroxidation through maintaining high levels of such cellular scavengers as SOD and catalase.
Hybrid Porous Silicon Biosensors Using Plasmonic and Fluorescent Nanomaterials: A Mini Review

During the last two decades, porous silicon (PSi) has been proposed as a high-performance biosensing platform due to its biocompatibility, surface tailorability, and reproducibility. This review focuses on the recent developments and progress in the area related to hybrid PSi biosensors using plasmonic metal nanoparticles (MNPs), fluorescent quantum dots (QDs), or a combination of both MNPs and QDs for creating hybrid nanostructured architectures for ultrasensitive detection of biomolecules. The review discusses the mechanisms of sensitivity enhancement based on Localized Surface Plasmon Resonance (LSPR) of MNPs, Fluorescence Resonance Energy Transfer (FRET) in the case of MNPs/QDs donor-acceptor interactions, and photoluminescence/fluorescence enhancement resulting from the embedded fluorescent QDs inside the PSi microcavity. The review highlights the key features of hybrid PSi/MNPs/QDs biosensors for dual-mode detection applications.
Toward “English” Phonetics: Variability in the Pre-consonantal Voicing Effect Across English Dialects and Speakers

Recent advances in access to spoken-language corpora and development of speech processing tools have made possible the performance of “large-scale” phonetic and sociolinguistic research. This study illustrates the usefulness of such a large-scale approach—using data from multiple corpora across a range of English dialects, collected, and analyzed with the SPADE project—to examine how the pre-consonantal Voicing Effect (longer vowels before voiced than voiceless obstruents, in e.g., bead vs. beat) is realized in spontaneous speech, and varies across dialects and individual speakers. Compared with previous reports of controlled laboratory speech, the Voicing Effect was found to be substantially smaller in spontaneous speech, but still influenced by the expected range of phonetic factors. Dialects of English differed substantially from each other in the size of the Voicing Effect, whilst individual speakers varied little relative to their particular dialect. This study demonstrates the value of large-scale phonetic research as a means of developing our understanding of the structure of speech variability, and illustrates how large-scale studies, such as those carried out within SPADE, can be applied to other questions in phonetic and sociolinguistic research.
Analysis of Genetic Alteration Signatures and Prognostic Values of m6A Regulatory Genes in Head and Neck Squamous Cell Carcinoma

Genetic alteration involving N6-methyladenosine (m6A) regulatory genes is a frequent characteristic of multiple tumors. Nevertheless, little is known regarding their genetic alteration signatures and prognostic values in head and neck squamous cell carcinoma (HNSCC). In this study, RNA sequence profiles and copy number variation (CNV) data of 506 HNSCC patients were downloaded from The Cancer Genome Atlas (TCGA) database. Correlation analysis involving alteration of m6A regulatory genes, clinicopathological characteristics, and patient survival was performed using R language. The results suggest that alteration of m6A regulatory genes was correlated with clinical staging. Patients with high expression of ALKBH5, FTO, METTL14, WTAP, YTHDC1, YTHDF1, and YTHDF2 had poor overall survival (OS) than those with low expression. Univariate and multivariate Cox regression analyses showed that ALKBH5 and YTHDC2 were independent risk factors for OS. However, patients with high YTHDC2 expression had better OS. Moreover, according to machine learning results, YTHDC2 was found to be the most important gene among the 10 m6A regulators. Additionally, high expression of YTHDC2 was correlated with activation of apoptosis and ubiquitin-mediated proteolysis. Here, we identified alterations to m6A regulatory genes in HNSCC for the first time and found that seven m6A regulators were associated with poor prognosis, especially ALKBH5, whereas YTHDC2 was associated with better prognosis. These m6A-related regulators could act as novel prognostic biomarkers for HNSCC. Our findings provide clues for understanding RNA epigenetic modifications in HNSCC.
Integrative Analysis of the Doxorubicin-Associated LncRNA–mRNA Network Identifies Chemoresistance-Associated lnc-TRDMT1-5 as a Biomarker of Breast Cancer Progression

Increasing evidence has revealed close relationships between long non-coding RNAs (lncRNAs) and chemoresistance in multiple types of tumors; however, functional lncRNAs in breast cancer (BC) have not been completely identified. In this study, we aimed to identify novel lncRNAs that might play critical roles in doxorubicn resistance, which could reveal potential biomarkers of BC. Using a BC dataset (GSE81971), we identified 452 lncRNAs that were upregulated and 659 that were downregulated; furthermore, there were 1896 differentially expressed mRNAs, of which 1137 were upregulated and 758 were downregulated in MCF-7/ADR cells compared with the expression in MCF-7 cells. We constructed an lncRNA–mRNA network by integrating probe reannotation and regulatory interactions. To elucidate the key lncRNAs in BC, we further analyzed dysregulated lncRNA–mRNA crosstalk, and six candidate lncRNAs (lnc-TRDMT1-5, ZNF667-AS1, lnc-MPPE1-13, DSCAM-AS1:5, DSCAM-AS1:2, and lnc-CFI-3) were identified. Notably, the expression level of lnc-TRDMT1-5 was significantly upregulated in resistant cells compared with sensitive cells, and its levels were increased in BC tissues compared with adjacent tissues. Levels were positively associated with estrogen receptor (ER) and human epidermal growth factor receptor 2 (HER2) expression levels. High expression of lnc-TRDMT1-5 predicted poor prognosis in ER-positve and HER2-positive BC patients, especially in patients with chemoresistance. Bioinformatic and functional analysis revealed that lnc-TRDMT1-5 was involved in many crucial pathways in cancer, such as the PI3K/AKT and Wnt signaling pathways. Subcellular localization predicted that lnc-TRDMT1-5 was located in the cytoplasm, and the lncRNA–miRNA–mRNA network showed that lnc-TRDMT1-5 might serve as a regulator in BC. Here, our results demonstrated a dysregulated lncRNA–mRNA network that might provide new treatment strategies for chemoresistant BC, and the results identified a new lncRNA, lnc-TRDMT1-5, with oncogenic and prognostic functions in human BC.
Cytotoxic Granule Trafficking and Fusion in Synaptotagmin7-Deficient Cytotoxic T Lymphocytes

Granules of cytotoxic T lymphocytes (CTL) are derived from the lysosomal compartment. Synaptotagmin7 (Syt7) appears to be the calcium sensor triggering fusion of lysosomes in fibroblasts. Syt7 has been proposed to control cytotoxic granule (CG) fusion in lymphocytes and mice lacking Syt7 have reduced ability to clear infections. However, fusion of CG persists in the absence of Syt7. To clarify the role of Syt7 in CTL function, we have examined the fusion of cytotoxic granules of CD8+ T-lymphocytes from Syt7 knock-out mice. We have recorded granule fusion in living CTL, using total internal reflection microscopy. Since Syt7 is considered a high affinity calcium-sensor specialized for fusion under low calcium conditions, we have compared cytotoxic granule fusion under low and high calcium conditions in the same CTL. There was no difference in latencies or numbers of fusion events per CTL under low-calcium conditions, indicating that Syt7 is not required for cytotoxic granule fusion. A deficit of fusion in Syt7 KO CTL was seen when a high-calcium solution was introduced. Expressing wild type Syt7 in Syt7 KO lymphocytes reversed this deficit, confirming its Syt7-dependence. Mutations of Syt7 which disrupt calcium binding to its C2A domain reduced the efficacy of this rescue. We counted the cytotoxic granules present at the plasma membrane to determine if the lack of fusion events in the Syt7 KO CTL was due to a lack of granules. In low calcium there were no differences in fusion events per CTL, and granule numbers were similar. In high calcium, granule number was similar though wild type CTL exhibited significantly more fusion than Syt7 KO CTL. The modest differences in granule counts do not account for the lack of fusion in high calcium in Syt7 KO CTL. In Syt7 KO CTL expressing wild type Syt7, delivery of cytotoxic granules to the plasma membrane was comparable to that of wild type CTL. Syt7 KO CTL expressing Syt7 with deficient calcium binding in the C2A domain had significantly less fusion and fewer CG at the plasma membrane. These results indicate that Syt7 is involved in trafficking of CG to the plasma membrane.
Changes of the Gastric Mucosal Microbiome Associated With Histological Stages of Gastric Carcinogenesis

The changes of gastric microbiome across stages of neoplastic progression remain poorly understood, especially for intraepithelial neoplasia (IN) which has been recognized as a phenotypic bridge between atrophic/intestinal metaplastic lesions and invasive cancer. The gastric microbiota was investigated in 30 healthy controls (HC), 21 non-atrophic chronic gastritis (CG), 27 gastric intestinal metaplasia (IM), 25 IN, and 29 gastric cancer (GC) patients by 16S rRNA gene profiling. The bacterial diversity, and abundances of phyla Armatimonadetes, Chloroflexi, Elusimicrobia, Nitrospirae, Planctomycetes, Verrucomicrobia, and WS3 reduced progressively from CG, through IM, IN to GC. Actinobacteria, Bacteriodes, Firmicutes, Fusobacteria, SR1, and TM7 were enriched in the IN and GC. At the community level, the proportions of Gram-positive and anaerobic bacteria increased in the IN and GC compared to other histological types, whereas the aerobic and facultatively anaerobic bacteria taxa were significantly reduced in GC. Remarkable changes in the gastric microbiota functions were detected after the formation of IN. The reduced nitrite-oxidizing phylum Nitrospirae together with a decreased nitrate/nitrite reductase functions indicated nitrate accumulation during neoplastic progression. We constructed a random forest model, which had a very high accuracy (AUC > 0.95) in predicating the histological types with as low as five gastric bacterial taxa. In summary, the changing patterns of the gastric microbiota composition and function are highly indicative of stages of neoplastic progression.