Miracle-dz/UniFAR-FTUs huggingface dataset:
Conservación genética de tres endemismos vegetales canarios amenazados: "Bethencourtia spp.", "Sambucus palmensis" y "Viola cheiranthifolia"

En esta Tesis Doctoral se ha procedido a la caracterizacion genetica de tres taxones vegetales amenazados y endemicos del archipielago canario con diferentes problematicas y necesidades de actuacion desde el punto de vista de la Biologia de la Conservacion. La metodologia empleada incluyo el desarrollo y caracterizacion de marcadores microsatelites hipervariables especifico para cada taxon de estudio. En primer lugar, se procedio a la caracterizacion y diferenciacion genetica de las 3 especies del genero endemico Bethencourtia: B. hermosae, B. rupicola y B. palmensis. Los resultados revelan que los tres taxones se encuentran diferenciados geneticamente y albergan unos escasos niveles de variabilidad genetica intrapoblacional. Debido a la baja diversidad genetica encontrada en B. hermosae y B. rupicola, se sugieren medidas de conservacion a implementar por parte del Parque Nacional de Garajonay. En segundo lugar, en el caso del sauco canario (Sambucus palmensis), se estudiaron los efectos de las traslocaciones sobre la estructura poblacional y diversidad genetica en el Parque Nacional de Garajonay, despues de 30 anos de reforzamiento. Para ello se analizaron ejemplares representativos de todas las localidades restauradas, ademas de todos los individuos naturales. Mediante el genotipado de estas muestras se pudo estimar el numero de genotipos clonicos presentes. Por otro lado, se detecto que las translocaciones no han disminuido la diversidad genetica de S. palmensis en la isla, y se ha homogeneizado la estructura genetica debido al trasvase de genotipos. En tercer lugar, para la violeta del Teide (Viola cheiranthifolia), se estudio la estructura, variabilidad genetica e historia demografica de las poblaciones. Ademas, mediante la modelizacion del nicho climatico, se proyectaron posibles variaciones en la distribucion altitudinal de las poblaciones de V. cheiranthifolia debido al cambio climatico. Estos resultados, junto a la simulacion de la perdida de heterocigosidad esperada, han permitido confirmar la vulnerabilidad de V. cheiranthifolia ante el cambio global.
Investigation of the toxicity of ethanol extracts obtained from six different Satureja L. species on Colorado Potato Beetle, Leptinotarsa decemlineata (Say, 1824), (Coleoptera: Chrysomelidae)

In the present study, ethanol extracts obtained from Satureja cilicica P. H. Davis , Satureja cuneifolia Ten, Satureja hortensis L. , Satureja spicigera (C. Koch) Boiss. , Satureja thymbra L . and Satureja montana L. were tested against on the adults and larvae of Colorado potato beetle ( Leptinotarsa decemlineata (Say, 1824)). The experiments were conducted in glass Petri dishes and vacuum desiccators including 15 individual for each period with three replicates under laboratory conditions. 10, 15 and 20 mg/mL doses of ethanol extracts conducted in the Petri dishes and the desiccators showed that depending on concentration increase and duration of exposure time resulted between 2.22-100% toxic effects on the potato beetle larvae and adults. In Petri trials, the highest mortality rate was recorded as 100% for the second larval stage at the 20 mg/mL dose of S. spicigera ethanol extract after 96 hours the treatment. In desiccator experiments, the highest toxicity rate was determined as 100% for first larval stage at the 20 mg/mL dose of S. thymbra ethanol extract after 96 hours of the application. In addition to, when LD values of the ethanol extracts ​​were taken into account the highest toxicity of adult period was determined for S. thymbra extract (LD 25 : 0.000, LD 50 : 0.010 μL/insect), the lowest toxicity was determined for S. cilicica extract (LD 90 : 436.020 μL/insect). The results obtained from this study suggested that the ethanol extracts of tested Satureja L. species could be used for L. decemlineata larvae and adults as bio-larvicides and insecticides.
EED-Related Overgrowth

Clinical characteristics EED-related overgrowth is characterized by fetal or early childhood overgrowth (tall stature, macrocephaly, large hands and feet, and advanced bone age) and intellectual disability that ranges from mild to severe. To date, EED overgrowth has been reported in eight individuals. Diagnosis/testing The diagnosis of EED overgrowth is established in a proband with suggestive findings and a heterozygous germline EED pathogenic variant by molecular genetic testing. Management Treatment of manifestations: Developmental delay / intellectual disability requires early referral for developmental support and educational interventions tailored to the child's needs. Seizures, cervical spine instability, palatal abnormalities, kyphoscoliosis, congenital heart defects, cryptorchidism, and ophthalmologic findings are treated per standard practice. Surveillance: Routine assessment of the following: development; spine for scoliosis or deformities; joint range of motion for joint contractures; and eyes for refractive errors, myopia, and strabismus. Agents/circumstances to avoid: Activities that involve rapid neck motion and/or possible trauma to the head and neck region (e.g., contact sports or thrill rides at amusement parks) because of the possible increased risk for cervical spine instability. Genetic counseling EED overgrowth is inherited in an autosomal dominant manner. To date all probands whose parents have undergone molecular genetic testing have the disorder as a result of a de novo EED pathogenic variant. The risk to the sibs of the proband depends on the genetic status of the proband's parents: if the EED pathogenic variant found in the proband cannot be detected in the leukocyte DNA of either parent, the recurrence risk to sibs is estimated to be 1% because of the theoretic possibility of parental germline mosaicism. Once a family member has a confirmed molecular diagnosis of EED overgrowth, prenatal testing for pregnancies at increased risk and preimplantation genetic diagnosis are possible.
STRUCTURE AND FUNCTION OF THE FRUIT MICROBIOME IN HEALTHY AND DISEASED KIWIFRUIT

The fruit surface is an infection court where foodborne pathogens compete with indigenous microbiota for microsites to invade the fruits for nutrients acquisition. However, our current understanding of the structure and functions of fruit microbiome visa-vis postharvest pathogen infection is still nascent. Here, we sequenced the metagenomic DNA to understand the structural and functional attributes of healthy and diseased kiwifruit microbiome. The healthy fruits exhibited higher microbial diversity and distinct microbiome composition compared with diseased fruits. The microbiome of diseased fruit was dominated by fungal pathogens Neofusicoccum parvum and Diplodiaseriata, while the microbiome of healthy fruits were enriched by bacteria from Methylobacteriaceae, Sphingomonadaceae, Nocardioidaceae and fungi in Pleosporaceae. Importantly, the healthy fruit microbiome had a higher relative abundance of genes related to ABC transporter, two-component system, bacterial chemotaxis, bacterial secretion system, but had a lower relative abundance of genes associated with polycyclic aromatic hydrocarbon degradation, amino sugar and nucleotide sugar metabolism, glycine, serine and threonine metabolism compared with diseased fruits. Our results indicate that pathogen infection disrupts the fruit microbiome. The changes in microbiome composition and functions could also increase the possibility of secondary pathogen infection as the reduced microbial diversity may demonstrate less resistance to pathogens infection. Therefore, monitoring the microbiome dynamics and their functions using metagenomic approaches could be useful to build a predictive understanding of accurate postharvest disease diagnosis and management in the future
Expanding functional protein sequence space using generative adversarial networks

De novo protein design for catalysis of any desired chemical reaction is a long standing goal in protein engineering, due to the broad spectrum of technological, scientific and medical applications. Currently, mapping protein sequence to protein function is, however, neither computationionally nor experimentally tangible 1,2. Here we developed ProteinGAN, a specialised variant of the generative adversarial network 3 that is able to ‘learn’ natural protein sequence diversity and enables the generation of functional protein sequences. ProteinGAN learns the evolutionary relationships of protein sequences directly from the complex multidimensional amino acid sequence space and creates new, highly diverse sequence variants with natural-like physical properties. Using malate dehydrogenase as a template enzyme, we show that 24% of the ProteinGAN-generated and experimentally tested sequences are soluble and display wild-type level catalytic activity in the tested conditions in vitro, even in highly mutated (>100 mutations) sequences. ProteinGAN therefore demonstrates the potential of artificial intelligence to rapidly generate highly diverse novel functional proteins within the allowed biological constraints of the sequence space.
P. falciparum gametocyte density and infectivity in peripheral blood and skin tissue of naturally infected parasite carriers

Transmission of Plasmodium falciparum depends on the presence of mature gametocytes that can be ingested by mosquitoes taking a bloodmeal when feeding on human skin. It has long been hypothesised that skin sequestration contributes to efficient transmission. Although skin sequestration would have major implications for our understanding of transmission biology and the suitability of mosquito feeding methodologies to measure the human infectious reservoir, it has never been formally tested. In two populations of naturally infected gametocyte carriers from Burkina Faso, we assessed transmission potential to mosquitoes and directly quantified male and female gametocytes and asexual parasites in: i) finger prick blood, ii) venous blood, iii) skin biopsies, and in pools of mosquitoes that fed iv) on venous blood or, v) directly on the skin. Whilst more mosquitoes became infected when feeding directly on the skin compared to venous blood, concentrations of gametocytes in the subdermal skin vasculature were identical to that in other blood compartments. Asexual parasite densities, gametocyte densities and sex ratios were identical in the mosquito blood meals taken directly from the skin of parasite carriers and their venous blood. We also observed sparse gametocytes in skin biopsies from legs and arms of gametocyte carriers by microscopy. Taken together, we provide conclusive evidence for the absence of significant skin sequestration of P. falciparum gametocytes. Gametocyte densities in peripheral blood are thus informative for predicting onward transmission potential to mosquitoes. Quantifying this human malaria transmission potential is of pivotal importance for the deployment and monitoring of malaria elimination initiatives. IMPORTANCE Our observations settle a long-standing question in the malaria field and close a major knowledge gap in the parasite cycle. By deploying mosquito feeding experiments and stage-specific molecular and immunofluorescence parasite detection methodologies in two populations of naturally infected parasite carriers, we conclusively reject the hypothesis of gametocyte skin sequestration. Our findings provide novel insights in parasite stage composition in human blood compartments, mosquito bloodmeals and their implications for transmission potential. We demonstrate that gametocyte levels in venous or finger prick blood can be used to predict onward transmission potential to mosquitoes. Our findings thus pave the way for methodologies to quantify the human infectious reservoir based on conventional blood sampling approaches to support the deployment and monitoring of malaria elimination efforts for maximum public health impact.
Prediksi DNA Primer gen PGC-1α cecak (Hemidactylus platyurus) dengan metoda phylogenetic, multiple alignment, dan qPCR

The role of genes in tissue regeneration process of house gecko ( Hemida c tylus platyurus ) tail is very important to study. However, the PGC-1α gene that plays a role in mitochondrial biogenesis in the tissue regeneration process of house gecko tail has not been studied before. The phylogenetic method can be used to track the determinant species closest to kinship. Multiple alignment method is software that can align the conserved gene sequences from several species that have sequence identities highly. The phylogenetic analysis is used to track the determinant species closest to kinship. Basic Local Alignment Software Tools (BLAST) is used to analyze the identity of gene sequences from several species. Alignment the conserved sequences of gene was using to multiple alignment methods in MEGA7 software. Primary DNA predicted of PGC-1α gene was made using Primer3 software that based on gene sequences conserved from MEGA7 multiple alignment process. The specification of gene expression was tested by Real Time PCR. The results of phylogenetic analysis the species closest to H. platyurus are Gecko japonicus . BLAST results and multiple alignments obtained by sequences as a basis for the design of primary DNA. The primary design of the DNA predicted PGC-1α H.platyurus gene was successfully amplified with Real Time PCR and produced one peak, which indicates the specific gene expression. Predicted primary DNA PGC-1α gene of Hemidactylus platyurus that has not been previously studied, can be designed using phylogenetic to determinant species closest to kinship and multiple alignment methods.
Dietary digestible lysine levels and environmental temperature for growing broiler chickens

This study was aimed to evaluate the effects of the dietary digestible lysine levels and environmental temperature on performance and carcass characteristics of broiler chickens from 22 to 42 days-old. Six hundred seventy two males Ross® broiler chickens with an average weight of 726 g were allotted to a completely randomized design, in a 4 × 4 factorial arrangement with six replicates and seven birds per experimental unit. The chickens were fed with different digestible lysine levels in the diet [. ]
Factors that Affect Nonmarket Fruit and Vegetable Receptions: Analyses of Two Cross-Sectional Surveys in Gunma, Japan

In this study, we identified the factors that affect the frequency of receiving nonmarket fruit and vegetables (FV). For Survey 1, we conducted a cross-sectional survey using a self-administered questionnaire for men aged 50–74 living in city (A) in Gunma, Japan. Participants were asked questions on FV receiving frequency, FV gardening, social cohesion (4–20 points), and basic characteristics. For Survey 2, a similar survey was conducted for residents aged 20–74 in three areas in city (B) in Gunma, but we included more variables. Ordinal logistic regression models were used for the analysis. In Survey 1, the responses of 243 participants were analyzed. The results showed that the FV receiving frequency was positively associated with non-gardeners and social cohesion. In Survey 2, the responses of 791 participants were analyzed. Vegetable receiving frequency was positively associated with rural and suburban areas, family structure, employment status, and non-farmers. The relationship between receiving frequency and social cohesion was similar to that found in Survey 1. In conclusion, in areas with flourishing FV cultivation, it seems to be easy to obtain FV through the social networks of reception, even for individuals who are not cultivating FV themselves.
Integrative taxonomy of Xiphinema histriae and Xiphinema lapidosum from Spain

Abstract Three populations of Xiphinema non-americanum group species were detected in agricultural and natural ecosystems, during routine surveys for plant-parasitic nematodes in Spain. Based on morphological and molecular analyses, the species were identified as Xiphinema histriae and Xiphinema lapidosum, being this the first record and molecular characterization of both species in Spain. The morphometrics and morphology of the Spanish populations agree with those of the original description and paratype specimens and the present study provided a first description of the second to fourth juvenile stages of both species. A detailed study on the morphology in the Spanish populations of X. histriae, as well as in paratypes, showed a pseudo-Z-organ with weakly muscularized wall and containing numerous small dense granular bodies, which was different to the original description by Lamberti et al. (1993). This new finding suggests that X. histriae must be considered a member of the morphospecies Group 5 of X. non-americanum. Phylogenetic analysis based on D2 to D3 expansion segments of 28S gene, ITS1 and partial CoxI gene indicated that X. histriae and X. lapidosum are phylogenetically related with other Xiphinema non-americanum group spp. reported from Spain. Considering the pathological and economic importance of this group of nematodes, the combination of morphological characters, measurements, and molecular analysis is crucial for accurate identification of these species.
Therapeutic effect of P-coumaric acid in the experimentally infected rats with Salmonella typhi

Salmonella enterica subspecies enteric serotype typhi which infect the human and cause typhoid fevers (systemic infection). Experimental infection with Salmonella typhi are very important because they explains the pathogenicity of Salmonella typhi through a histopathological findings. The herbal inhibitors like P-Coumaric acid explain anti-inflammatory effect and have a selective effect against type III secretion system formation of Salmonella typhi. our study includes 15 adult male albino rats were divided into three groups each group composed from 5 rats. A group: were orally challenged with 1ml of 3X106 CFU of Salmonella typhi for one day. Group B: were also orally administered with 1ml of 3X106 CFU of Salmonella typhi, additionally, they also orally received 5ml of 100mg/kg of P-Coumaric acid for three consecutive days. Group C: serving as control group, they orally administered with 5ml of normal saline. All the animals are sacrificed after five days post infection, liver, small intestine and colon specimens were taken for histopathological investigation. the histological sections of liver and small intestine of group A animals showed pathological changes like degeneration of hepatic cells and inflammatory cell infiltration of the lamina properia in small intestine, while the group B animals showed normal liver and small intestine sections like the control group
Known and estimated distribution in Mexico of Batrachochytrium dendrobatidis, a pathogenic fungus of amphibians

Chytridiomycosis caused by fungus Batrachochytrium dendrobatidis (Bd) is one of the decline global causes of amphibians. Currently, it is distributed throughout a broad range of climates and ecosystems around the world. An epidemic wave of chytridiomycosis began in North America, resulting in population decline and local extinction of many species, reconfiguring species composition of amphibian communities in the Americas. In Mexico, Bd has caused an amphibian population decrease, and its potential distribution area has not been determined. We reviewed the number of species infected, obtaining Bd frequency of infection by land use and vegetation type, and by elevation range. We examined the known distribution of Bd, estimated the potential distribution, and obtained the bioclimate variables relevant for Bd. Our results indicate that in Mexico, Bd has been detected in 78 species of amphibians in 10 families, from 29 different land use and vegetation types, with cloud forest having the highest number of cases (139) and infected species (15). Bd occurs over an elevation range of 1–3,300 m asl and is most frequent at 1,200–1,500 m asl (36%). In addition to the regions previously described as suitable for Bd, our model included desert, coastal, and tropical forest regions, revealing an increase in the area where amphibians could be at risk of infection. Distribution of Bd is mainly associated with temperature of the wettest quarter and potential evapotranspiration of the warmer quarter. We offer an estimate of the ideal conditions for Bd in Mexico, also information for future studies on Bd and the conservation of amphibians.
The Changing Face of Inflammatory Bowel Disease: Etiology, Physiopathology, Epidemiology

Context The term inflammatory bowel disease (IBD) classically includes ulcerative colitis (UC) and Crohn’s disease (CD). An abnormally increased mucosal permeability seems to underlie UC, whereas CD is thought to be the result of an immune deficiency state. Evidence Acquisition While these phenomena may well be labeled as genetic factors, the environment has its role as well. Drugs (chiefly, antibiotics and non-steroidal anti-inflammatory molecules, with proton pump inhibitors recently joining the list) and smoking habits are all being scrutinized as IBD causative factors. Results Once almost unknown, the prevalence of IBD, in the Eastern World and China, is now increasing by manifold, therefore arousing warning signals. Conclusions A multidisciplinary approach will soon be necessary, to face the tenacious behavior of IBD, on a global perspective.
Angioplastyka przewlekłego zamknięcia gałęzi międzykomorowej przedniej z użyciem stentu. Badanie porównawcze oceniające wpływ zastosowania abciximabu na wyniki wczesne i odległe

Wstep: Pomimo zastosowania stentow zabiegi udrazniania przewlekle zamknietych tetnic wiencowych są nadal obarczone wyzszym odsetkiem restenoz i reokluzji w porownaniu z angioplastyką droznych tetnic. Celem badania byla ocena bezpośrednich i odleglych efektow zastosowania abciximabu podczas udrazniania przewlekle zamknietej galezi miedzykomorowej przedniej (LAD). Material i metody: Spośrod 55 pacjentow z przewlekle zamknietą LAD, u ktorych podjeto probe udroznienia, u 41 (75%) udalo sie przeprowadzic prowadnik poza miejsce okluzji. Zostali oni losowo przydzieleni do grupy leczonej abciximabem (21 chorych) i grupy kontrolnej (20 osob). Abciximab (bolus + wlew iv.) podawano po umieszczeniu prowadnika w dystalnej cześci naczynia. Dwoch chorych (po 1 z obydwu grup) wykluczono z badania z powodu braku mozliwości implantacji stentu. Koncowej analizie poddano 20 chorych z grupy leczonej abciximabem i 19 osob z grupy kontrolnej. Obserwacje odleglą (kliniczną i angiograficzną) przeprowadzono średnio po 9,8 ± 3,6 miesiąca u wszystkich badanych. Wyniki: Wyjściowa charakterystyka grup byla porownywalna. Koncowy przeplyw TIMI 3 i zwezenie mniejsza niz 50% uzyskano u wszystkich chorych. Odsetki restenoz (ok. 40%) i reokluzji (ok. 15%) byly podobne w obu grupach. Parametry kliniczne w obserwacji odleglej byly porownywalne w obu grupach: nawrot niedokrwienia - 30% vs. 32%, ponowny zawal - 10% vs. 0%, zgon - 0% vs. 0%, odpowiednio w grupach osob leczonych abciximabem i kontrolnej (p = NS). Stwierdzono istotny wzrost frakcji wyrzutowej lewej komory u wszystkich chorych (przed zabiegiem 47,4 ± 7,4%; w obserwacji odleglej 51,0 ± 9,2%; p = 0,025). Wnioski: Zastosowanie abciximabu w trakcie zabiegu stentowania przewleklego zamkniecia LAD nie wplywa na wyniki bezpośrednie i odlegle. Wykazano korzystny wplyw zabiegu na wzrost frakcji wyrzutowej lewej komory w obserwacji odleglej. ( Folia Cardiol. 2003; 10: 279–287 )