Miracle-dz/UniFAR-FTUs huggingface dataset:
Male germline stem cells in non-human primates

Abstract Over the past few decades, several studies have attempted to decipher the biology of mammalian germline stem cells (GSCs). These studies provide evidence that regulatory mechanisms for germ cell specification and migration are evolutionarily conserved across species. The characteristics and functions of primate GSCs are highly distinct from rodent species; therefore the findings from rodent models cannot be extrapolated to primates. Due to limited availability of human embryonic and testicular samples for research purposes, two non-human primate models (marmoset and macaque monkeys) are extensively employed to understand human germline development and differentiation. This review provides a broader introduction to the in vivo and in vitro germline stem cell terminology from primordial to differentiating germ cells. Primordial germ cells (PGCs) are the most immature germ cells colonizing the gonad prior to sex differentiation into testes or ovaries. PGC specification and migratory patterns among different primate species are compared in the review. It also reports the distinctions and similarities in expression patterns of pluripotency markers (OCT4A, NANOG, SALL4 and LIN28) during embryonic developmental stages, among marmosets, macaques and humans. This review presents a comparative summary with immunohistochemical and molecular evidence of germ cell marker expression patterns during postnatal developmental stages, among humans and non-human primates. Furthermore, it reports findings from the recent literature investigating the plasticity behavior of germ cells and stem cells in other organs of humans and monkeys. The use of non-human primate models would enable bridging the knowledge gap in primate GSC research and understanding the mechanisms involved in germline development. Reported similarities in regulatory mechanisms and germ cell expression profile in primates demonstrate the preclinical significance of monkey models for development of human fertility preservation strategies.
Gender Determination in Mature Gila Monsters, Heloderma suspectum, and Mexican Beaded Lizards, Heloderma horridum, by Ultrasound Imaging of the Ventral Tail

ABSTRACT In a single blind study the gender of nine adult Mexican beaded lizards, Heloderma horridum and 35 adult Gila monsters, Heloderma suspectum of known sex was determined by two dimensional ultrasound imaging of the ventral tail just distal to the cloaca. In each case subjects could be sorted into two distinct morphologic groups. Group 1 animals had large, variably hypoechoic, paired soft tissue structures in the ventral aspect of the tail spanning 2 cm distal to the vent, while the distal tail lacked these structures. Group 2 animals lacked this characteristic altogether, giving the ventral tail a much more consistent ultrasonic complexion along the entire length. The most logical conclusion for this difference was the presence of paired hemipenes in group 1 animals. Using this premise, subjects in group 1 were declared males, while group 2 animals were declared females. The predictions matched the known sexes of each individual in every case for adult lizards. One juvenile Gila monster could not b.
‘Insight’ into Molecular Genetic Testing in Retinoblastoma

Abstract Retinoblastoma is an intraocular tumor with hereditary and sporadic forms. Tumor develops when both alleles of the tumor suppressor gene, RB1 is inactivated in the embryonal retinal cells. Clinical screening for retinoblastoma is most often done on examination under anesthesia for proband and closely related infants. Genetic testing in retinoblastoma could avoid unwanted ophthalmic surveillance for infants who do not have mutations in the gene. However establishing a single genetic test is not possible due to the multiple RB1 inactivation mechanisms like gene mutations, deletions and also hypermethylation of the gene promoter. The review focuses on the application of molecular screening methods-multiplex PCR, sequencing of 27 exons of RB1 gene, methylation analysis of promoter region and peripheral blood karyotyping in retinoblastoma. The cost benefit analysis of genetic testing compared to conventional clinical management of retinoblastoma is also discussed. Clinical management of retinoblastoma could be aided by coordinated application of the molecular genetic testing.
Effets des bioinsecticides à base de Bacillus thuringiensis sur la physiologie intestinale de la Drosophile

Le tube digestif est la premiere barriere contre les agresseurs presents dans la nourriture (virus, bacteries, produits chimiques, pesticides etc.). Il doit donc maintenir au mieux son integrite structurale et fonctionnelle tout au long de la vie de l'individu. Bien que l'impact deletere d'une intoxication aigue puisse etre surmonte par la capacite de defense et de regeneration de la muqueuse digestive, une agression prolongee ou repetee peut compromettre l'equilibre physiologique (l'homeostasie) du tube digestif. Parmi les agresseurs pouvant etre ingeres avec la nourriture, on trouve la bacterie Bacillus thuringiensis (Bt) et represente 70% des ventes de bioinsecticides. Bt est une bacterie Gram+ sporulante qui produit, pendant la sporulation, des toxines nommees Cry. Parmi les differentes souches de Bt, certaines ont ete selectionnees pour la specificite d'action de leurs toxines Cry contre des nuisibles et sont commercialisees sous forme de sporanges. Certaines de ces souches sont utilisees en agriculture biologique en France et l'accroissement de leur utilisation fait qu'elles sont de plus en plus presentes dans la nourriture, source de contamination potentielle pour l'homme et l’environnement. La question qui se pose maintenant est de savoir si un tel accroissement de l’utilisation de Bt peut avoir des impacts sur des especes non cibles. Mon projet de these a consiste en l’etude des consequences de l'ingestion de Bt (sous forme vegetative ou de sporanges) sur la physiologie intestinale de la drosophile (animal non sensible a Bt en termes de toxicite aigue
Focused issue on KATP channels K ATP channel therapeutics at the bedside

The family of potassium channel openers regroups drugs that share the property of activating adenosine triphosphate-sensitive potassium (KATP) channels, metabolic sensors responsible for adjusting membrane potential-dependent functions to match cellular energetic demands. KATP channels, widely represented in metabolically-active tissue, are heteromultimers composed of an inwardly rectifying potassium channel pore and a regulatory sulfonylurea receptor subunit, the site of action of potassium channel opening drugs that promote channel activity by antagonizingATP-induced pore inhibition. The activity of KATP channels is critical in the cardiovascular adaptive response to stress, maintenance of neuronal electrical stability, and hormonal homeostasis.Thereby, KATP channel openers have a unique therapeutic spectrum, ranging from applications in myopreservation and vasodilatation in patients with heart or vascular disease to potential clinical use as bronchodilators, bladder relaxants, islet cell protector, antiepileptics and promoters of hair growth. While the current experience in practice with potassium channel openers remains limited, multitude of ongoing investigations aims at defining the benefit of this emerging family of therapeutics in diverse disease conditions associated with metabolic distress. © 2005 Elsevier Ltd. All rights reserved.
An in vitro investigation of Malaysian Phytophthora palmivora isolates and pathogenicity study on oil palm

Bud rot disease affecting oil palm in South American countries is reported to be caused by Phytophthora palmivora. P. palmivora is a local pathogen affecting various crops in Malaysia, and this finding caused an alarm, which prompted an investigation of pathogenicity using Malaysian P. palmivora to assess the potentials of this Oomycete to infect oil palm in Malaysia. A total of 11 P. palmivora isolates were obtained from cocoa and durian for the study. Leaf bioassays via artificial inoculation using 50,000 zoospores/ml and mycelial agar disc showed severe necrotic lesions on the infection spot of oil palm (DxP) spear leaves. Mild infection was observed in oil palm spear leaves of OxG hybrids indicating lower susceptibility against P. palmivora infection. Phylogenetic analysis using internal transcribed spacer (ITS) data revealed that Malaysian isolates were genetically similar to Colombian isolates supported by significant bootstrap values. The leaf bioassay results revealed that Malaysian oil palm materials are susceptible towards local P. palmivora infection. The Colombian P. palmivora isolates causing bud rot incidence may have evolved over a long period of time, undergone sequential genetic shift to become more virulent towards Colombian oil palm planting materials.
The halophilic fairy shrimp, Phallocryptus spinosa (Milne-Edwards, 1840) (Crustacea: Branchiopoda: Anostraca) from southeast, Iran

Phallocryptus spinosa (Milne-Edwards, 1840) was previously recorded in Iran from a shallow salty pond close to Tabriz, occurring sympatrically with Branchinecta orientalis Sars, 1901; Second and third locations were reported from similar habitats in central area and south of Iran from Bafq and Lar, respectively. Here, a forth population was found during sampling in a pool, about 2000 Km to the south of the first recorded locality. A global distribution map for P. spinosa is presented.
Brain region-specific genome-wide deoxyribonucleic acid methylation analysis in patients with Alzheimer’s disease

Objective Alzheimer’s disease (AD) is a neurodegenerative disease characterized by neuropathology and cognitive decline and associated with age. The comprehensive deoxyribonucleic acid methylation (DNAm)-transcriptome profile association analysis conducted in this study aimed to establish whole-genome DNAm profiles and explore DNAm-related genes and their potential functions. More appropriate biomarkers were expected to be identified in terms of AD. Materials and methods Illumina 450KGSE59685 dataset AD (n = 54) and HC (n = 21) and ribonucleic-acid-sequencing data GSE118553 dataset AD patients (n = 21) and HCs (n = 13) were obtained from the gene expression omnibus database before a comprehensive DNAm-transcriptome profile association analysis, and we performed functional enrichment analysis by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analyses (KEGG). Three transgenic mice and three wild-type mice were used to validate the hub genes. Results A total of 18,104 DNAm sites in healthy controls (n = 21) and AD patients (n = 54) were surveyed across three brain regions (superior temporal gyrus, entorhinal cortex, and dorsolateral prefrontal cortex). With the addition of the transcriptome analysis, eight hypomethylated-related highly expressed genes and 61 hypermethylated-related lowly expressed genes were identified. Based on 69 shared differentially methylated genes (DMGs), the function enrichment analysis indicated Guanosine triphosphate enzymes (GTPase) regulator activity, a synaptic vesicle cycle, and tight junction functioning. Following this, mice-based models of AD were constructed, and five hub DMGs were verified, which represented a powerful, disease-specific DNAm signature for AD. Conclusion The results revealed that the cross-brain region DNAm was altered in those with AD. The alterations in DNAm affected the target gene expression and participated in the key biological processes of AD. The study provides a valuable epigenetic resource for identifying DNAm-based diagnostic biomarkers, developing effective drugs, and studying AD pathogenesis.
Comparative Study Of DNA Preservation Under Various Conditions On Local Egyptian Cowpea Germplasm

This study were to study the impact of storage conditions on DNA quality in different materials, the integrity and quality of stored DNA; as well as determining the best way to store of DNA extracts in some Cowpea plants collected from different sites in Egypt. Ten germplasm representing Vigna radiata and V. unguiculata, procured from local regions by National Gene Bank (NGB), Agricultural Research Centre (ARC), Giza, Egypt. The DNA from each treatment was stored in different buffers for at least a year at LN, –20°C, –80°C and room temperature (RT) without special control of temperature or humidity. In order to simulate and evaluate the long-term storage samples subjected to high temperature over a period of time by extrapolation could correspond to 100 years at 25°C. These ex periments were conducted on the samples of ten samples of Vigna at 65°C for one day in hot-plate. The obtained results, the protectant trehalose were the highest value of DNA concentration (43.6±1.1 ng/µL) at room temperature, following by PVA scored 43.5±1.0 ng/ µL at RT and TE buffer showed 43.5±0.7 ng/µL at -20°C, for stored DNA. The average mean of PVA and trehalose were 43.5±1.1 ng/ µL more than TE-buffer. For stored tissue, the high mean (43.5±0.8 ng/µL) value of DNA concentration scored with the silica-gel and herbarium specimens, respectively. DNA samples of ten samples under study were also subjected to PCR analysis using SSR to determine whether the DNA was degraded. While no degradation was observed for DNA stored under different conditions, special in dry conditions (≤ 5% humidity). To assess its effects on DNA stability during storage at different conditions under controlled humidity. It was very interesting to note that DNA samples stored in the presence or absence of protectant additives exhibited no detectable degradation, whereas in the absent of, DNA was degraded and appeared as a smear on an agarose gel.
Systematic analysis and prediction for disease burden of ovarian cancer attributable to hyperglycemia: a comparative study between China and the world from 1990 to 2019

Background Ovarian cancer is one of the most common female malignancies worldwide, and metabolic factors, such as hyperglycemia, are becoming potential risk factors. This study aimed to analyze the disease burden and its changing trend of ovarian cancer attributable to hyperglycemia in the Chinese population from 1990 to 2019. Methods Using the data released by the Global Burden of Disease study 2019 (GBD 2019), we analyze the disease burden of ovarian cancer attributable to hyperglycemia in Chinese from 1990 to 2019 via morbidity, death, disability-adjusted life years (DALY); compare it with the global population; and predict the incidence and death trend in Chinese women for the next 10 years (2020–2029). Results The incidence, death cases, and DALY numbers of ovarian cancer attributable to hyperglycemia in Chinese in 2019 were 2,751, 1,758, and 44,615 person-years, respectively, with an increase of 352.5%, 356.6%, and 329.0% compared with 1990, and the growth rate was higher than the global level. The age-standardized incidence rate (ASIR), age-standardized mortality rate (ASMR), and age-standardized DALY rate (ASDR) in 2019 were 0.270/100,000, 0.164/100,000, and 4.103/100,000, respectively. Moreover, the average annual percent changes (AAPCs) were 2.3%, 2.0%, and 2.0%, respectively, all higher than the global average. The disease burden of ovarian cancer attributable to hyperglycemia increased with age, reaching a peak in the 45–75 age group. The prediction of the neural network model showed that the incidence and death of the disease would remain high and rise in the next 10 years. Conclusion The disease burden caused by ovarian cancer attributable to hyperglycemia in Chinese accounts for a large proportion globally, and the ASIR, ASMR, and ASDR are increasing year by year. We should continue to pay attention to the role of metabolic factors, such as hyperglycemia, in the occurrence and development of ovarian cancer, perform a good job in tertiary prevention, and strive to reduce health losses.
DNP NMR of carbohydrate converting enzymes

Dissolution dynamic nuclear polarization (DNP) NMR can be used to increase the sensitivity of 13 C NMR signal by up to four orders of magnitude [1]. This allows for real time monitoring of reactions and observation of intermediates [2]. The biggest drawback of the method is the loss of polarization with T 1 relaxation, but even with this limitation, it is possible to obtain detailed reaction parameters in less than one minute. The enzyme investigated was β -galactosidase from E. coli (E.C. 3.2.1.23). It is well described and the mechanism is generally accepted to be a double displacement with a covalently bound intermediate, however, this evidence is based on mutant of X-ray crystallography and simulations [3]. As the natural substrate lactose does not have any quaternary carbon with long T 1, the unnatural substrate o - nitrophenyl β -D-galactopyranoside was used (figure 1) as the quaternary positions have T 1 relaxations of ca. 15 s instead of <2 s.
Mécanismes de propagation du roseau commun envahisseur au Québec

III TABLE DES MATIÈRES . V LISTE DES TABLEAUX . X LISTE DES FIGURES . XII LISTE DES ANNEXES . XIV LISTE DES SIGLES ET DES ABRÉVIATIONS . XV REMERCIEMENTS . XVII CHAPITRE I : INTRODUCTION GÉNÉRALE . 1 1.1. Les invasions végétales . 2 1.1.1. Les étapes et les filtres . 2 1.1.2. Les composantes et les hypothèses . 4 1.2. Le roseau commun . 7 1.2. 1. La génétique du roseau . 8 1.2. 2. La stratégie vitale de l'espèce . 12 1.2. 3. L'écologie de l'espèce . 17 1.3. La problématique, les objectifs et les hypothèses . 22 1.3. 1. Les trois projets du doctorat . 22 1.3. 2. Les considérations générales . 24
Database-integrated genome screening (DIGS): exploring genomes heuristically using sequence similarity search tools and a relational database

A significant fraction of most genomes is comprised of DNA sequences that have been incompletely investigated. This genomic ‘dark matter’ contains a wealth of useful biological information that can be recovered by systematically screening genomes in silico using sequence similarity search tools. Specialized computational tools are required to implement these screens efficiently. Here, we describe the database-integrated genome-screening (DIGS) tool: a computational framework for performing these investigations. To demonstrate, we screen mammalian genomes for endogenous viral elements (EVEs) derived from the Filoviridae, Parvoviridae, Circoviridae and Bornaviridae families, identifying numerous novel elements in addition to those that have been described previously. The DIGS tool provides a simple, robust framework for implementing a broad range of heuristic, sequence analysis-based explorations of genomic diversity. Availability http://giffordlabcvr.github. io/DIGS-tool/ Contact robert.gifford@glasgow.ac. uk Supplementary information Supplementary data are available at Bioinformatics online.
Complete mitochondrial genome of Haematopus ostralegus (Charadriiformes: Haematopodidae)

Abstract The Eurasian oystercatcher (Haematopus ostralegus), Near Threatened in the IUCN red list, was designated classified endangered species II by the Ministry of Environment of Korea and a Natural Monument (No. 326) by the Cultural Heritage Administration of Korea. In this study, the complete mitochondrial genome (16,798 bp) of H. ostralegus was determined for the first time, including 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes, and 1 non-coding region. The overall base composition was A (31.4%), C (31.3%), G (13.8%), and T (23.5%), so the percentage of A and T (54.9%) was slightly higher than that of G and C. A phylogenetic analysis using concatenated mitogenomes revealed that the family Haematopodidae has a closer relationship with the family Recurvirostridae and H. ostralegus and H. ater clustered together. The results are expected to provide useful resources for species identification and further phylogenetic studies of genus Haematopus.
Thymidylate synthase maintains the de-differentiated state of aggressive breast cancers

Cancer cells frequently boost nucleotide metabolism (NM) to support their increased proliferation, but the consequences of elevated NM on tumor de-differentiation are mostly unexplored. Here, we identified a role for thymidylate synthase (TS), a NM enzyme and established drug target, in cancer cell de-differentiation and investigated its clinical significance in breast cancer (BC). In vitro, TS knockdown increased the population of CD24+ differentiated cells, and attenuated migration and sphere-formation. RNA-seq profiling indicated a repression of epithelial-to-mesenchymal transition (EMT) signature genes upon TS knockdown, and TS-deficient cells showed an increased ability to invade and metastasize in vivo, consistent with the occurrence of a partial EMT phenotype. Mechanistically, TS enzymatic activity was found essential for the maintenance of the EMT/stem-like state by fueling a DPYD-dependent pyrimidine catabolism. In patient tissues, TS levels were found significantly higher in poorly differentiated and in triple negative BC (TNBC), and strongly correlated with worse prognosis. The present study provides the rationale to study in-depth the role of NM at the crossroads of proliferation and differentiation, and depicts new avenues for the design of novel drug combinations for the treatment of BC.
Self-monitoring microbiological criteria for the assessment of hygienic procedures during chicken slaughtering

Self-monitoring procedures are adopted by food industries to ensure the quality and safety of final products, considering hygiene and processing criteria. This study aimed to evaluate contamination in chicken processing, considering the microbiological criteria proposed by self-monitoring systems. Environmental samples from reception, slaughtering and processing were collected from three chicken slaughterhouses (Sl1, Sl2, Sl3), and subjected to microbiological analysis to enumerate hygiene indicators microorganisms: mesophilic aerobes, enterobacteriaceae, coliforms and Escherichia coli. The obtained counts were converted to log10, compared by ANOVA (p<0.05) and self-monitoring microbiological criteria for each slaughterhouse were considered. In reception, the mean counts of hygiene indicator microorganisms in Sl3 were significantly higher than mean counts observed in Sl1 and Sl2 (p<0.05). During slaughtering, the chilling was enough to decrease the mean counts of all hygiene indicator microorganisms in Sl1, Sl2 and Sl3 (p<0.05). Based on self-monitoring criteria, in the first stages of slaughtering the facilities presented higher frequencies of chicken carcasses with counts above their respective reference values. Sl02 presented carcasses with higher counts after final washing, resulting in environmental samples with higher counts when compared to Sl1 and Sl3 (p<0.05). Even considering the high counts observed in the initial steps of chicken processing and slaughtering, the results indicated the efficacy of hygienic procedures in providing chicken carcasses and cuts with low microbiological contamination. Self-monitoring criteria supported these results, and the high levels of microbial contamination during the initial steps of slaughtering require subsequent antimicrobial hygienic procedures.