Miracle-dz/UniFAR-FTUs huggingface dataset:
DNA repair systems

This paper provides detailed insight into the mechanisms of repair of different types of DNA damage and the direct molecular players (enzymes repairing the damage or tagging the damaged site for further processing; damage sensor molecules; other signalling and effector molecules). The gene c bases of diseases and condi ons associated with defec ve DNA repair are comprehensively reviewed, from the 'classic' severe diseases such as xeroderma pigmentosum and Cockayne syndrome to the much more subtle UV sensi vity syndromes. The review analyses the basic molecular mechanisms underlying the rela vely rare monogenic diseases of DNA repair and management of genome integrity as well as the common mul factorial diseases and condi ons with late onset that are associated with increased levels of oxida ve stress (metabolic syndrome, diabetes type 2, cardiovascular disease) and with accumula on of 'errors' in DNA (normal and pathological ageing phenotypes, various cancers). The role of cell cycle checkpoints in dividing cells and the mechanisms of decision-making for the fate of a damaged cell are discussed with regards to the cell homeostasis in normal and cancerous ssues. The role of major DNA damageassociated signalling and effector molecules (p53, ATM, poly-(ADP-ribose)-polymerase, DNA-dependent protein kinase, BRCA proteins, re noblastoma protein, and others) is discussed and illustrated with examples in the context of health and disease. DNA repair and programmed cell death are viewed together as a unified mechanism for limi ng the presence of damaged cells and cells with poten ally oncogenic transforma on in mul cellular organisms. Special a en on is paid to ageing as a natural phenomenon and an adap ve evolu onary mechanism, with a brief outline of 'successful ageing'. The differen al rates of repair of DNA in transcribed and nontranscribed regions of the genome and the specifici es of DNA repair profile in some types of cells (terminally differen ated cells, pluripotent stem cells, etc.) and in certain taxonomic groups (e.g. 'the rodent repairadox') are discussed with regards to replica ve ageing and the evolu onary processes on microand macroscale. The role of mutagenesis as a 'hit and miss' mechanism and the 'leakiness' of DNA repair for increasing gene c diversity in the course of individual life and on evolu onary scale and the phenomenology of ongoing molecular evolu on are extensively reviewed. Cita on: Chakarov S, Petkova R, Russev GCh. DNA repair systems. Biodiscovery 2014; 13: 2; DOI: 10.7750/BioDiscovery.2014. 13.2 1* 2 3
Phylogenetic Positions of the Bothitrematidae and Neocalceostomatidae (Monopisthocotylean Monogeneans) Inferred from 28S rDNA Sequences

Abstract A molecular phylogeny was inferred from newly obtained partial (D1 domain) 28S rDNA gene sequences of Bothitrema bothi (Bothitrematidae), Neocalceostoma sp. (Neocalceostomatidae), Bravohollisia sp. (Ancyrocephalidae), and other already available sequences of Ancyrocephalidae, Anoplodiscidae, Pseudodactylogyridae, and Sundanonchidae, with the Diplectanidae as outgroup. Bothitrema, Anoplodiscus, and Sundanonchus formed a very robust clade that was the sister group to a group that included all other species examined. In this latter group, Neocalceostoma and Thaparocleidus were basal to a clade in which the Ancyrocephalidae and Pseudodactylogyridae were sister groups. Molecular results that suggest inclusion of the families Bothitrematidae, Anoplodiscidae, and Sundanonchidae in the same group partially contradict a previous morphological analysis of Boeger and Kritsky in which the first 2 were placed in the Gyrodactylidea and the third in the Dactylogyridea.
Systematics and mating systems of two fungal pathogens of opium poppy: the heterothallic Crivellia papaveracea with a Brachycladium penicillatum asexual state and a homothallic species with a Brachycladium papaveris asexual state

This paper presents a systematic revision of the fungal opium poppy (Papaver somniferum L.) pathogens for- merly known as Pleospora papaveracea (de Not.) Sacc. , along with allied asexual states formerly placed in Dendryphion. The revision is based on analysis of phylogenetic relationships, comparative morphology, and analysis of mating systems. Using morphology, 18S and ITS rDNA, we established that these species belong to the Alternaria group rather than to Pleospora, a conclusion supported by the Shimodaira-Hasegawa test. For these fungi, we erect the new genus Crivellia, with Crivellia papaveracea as type. ITS rDNA analyses suggested with moderate support Alternaria brassicicola (Schw.) Wiltshire, Alternaria japonica Yoshii, and Ulocladium alternariae (Cooke) Simmons as Crivellia's closest relatives. Com- bined ITS, partial GPD and EF-1 alpha analyses confirmed earlier studies that show that asexual isolates in the Crivellia lineage of poppy pathogens represent two closely related species. Because Dendryphion was determined to be polyphyletic, the former genus Brachycladium was resurrected for B. penicillatum Corda and B. papaveris (K. Sawada) Shoemaker & Inderbitzin, the Crivellia asexual states that had been in Dendryphion. Molecular and morphological comparison with iso- lates from field-collected ascomata and morphological comparison with the type specimen of P. papaveracea indicated that B. penicillatum, and not B. papaveris, is the anamorph of C. papaveracea. The mycelia from single conidium or sin- gle ascospore isolates, including mycelia from 14 single ascospores from one field-collected C. papaveracea ascoma, ei- ther have a MAT1-1 or MAT1-2 gene and are thus heterothallic. In contrast, each single-conidium isolate of B. papaveris has an incomplete MAT1-2 gene fused to a MAT1-1 region and is inferred to be homothallic. We speculate that ancestral MAT fusion might have led to speciation in Crivellia.
Laparoscopic Access Techniques: Experience in a Developing Country, Sudan

Background: Minimal access surgery has revolutionized the field of surgery. Access to the abdominal cavity represents a critical step in laparoscopic procedures. Various techniques have been used to obtain safe access into the abdominal cavity, with no apparent superiority of one technique over another. Aim: This study was conducted to assess the different types of laparoscopic access techniques used at Almak Nimir University Hospital in the period from January to December 2019. Methodology: This descriptive cross-sectional study compared the use and outcomes of different laparoscopic access techniques in various laparoscopic procedures performed at Almak Nimir University Hospital, (Shendi University, Shendi, Sudan). Results: The study included 324 patients with a mean age of 26.2±15.3 years (range 1–85 years). Most of the patients were female (266 patients, 82.1%). Of the laparoscopic procedures, 77.2% were laparoscopic appendicectomy while 18.8% were laparoscopic cholecystectomy. The Veress needle technique was used in 158 patients (49.7%), the open technique was used in 97 patients (29.9%) and direct trocar insertion was used in 66 patients (20.4%). Direct trocar insertion showed a statistically shorter procedure duration (mean 2.9±0.9 min) compared to the other techniques (p=0.001). Access-related complications occurred in five patients (0.6%), but there was no statistically significant difference between the three access techniques. Conclusion: This study confirms the safety of various access techniques used in laparoscopic procedures; however, the choice of access type should be individualized.
Taxonomy of Hawaiian Sphagna

Abstract Two Sphagnum species are reported for Hawaii: S. palustre L. (section Sphagnum) and S. wheeleri C. Müll. (section Rigida). Sphagnum henryense Warnst. (section Sphagnum) is excluded. Additional evidence supporting the exclusion of Sphagnum vitjianum Schimper and S. perichaetiale Hampe (both in section Sphagnum) is also presented. The type of S. lonchocladum C. Müll. is shown to be a Hillebrand collection (in section Sphagnum) from Hawaii and not a Kirk collection (in section Rigida) from New Zealand. The description of S. palustre is revised, in large part to reflect the incorporation of S. japonicum Warnst. , S. pseudocymbifolium C. Müll, and S. sulphureum Warnst.
Centesimal composition and fatty acids of meat from lambs fed diets containing soybean hulls

The objective of this study was to evaluate the centesimal composition and fatty acids in meat from animals fed diets containing levels of soybean hulls. The experiment was conducted at UESB in Itapetinga-BA, Brazil. Twenty-five confined Santa Ines rams were used. Treatments consisted of different levels of substitution of corn by soybean hulls (0, 25, 50, 75 and 100%) and elephant grass silage as forage. The design was completely randomized. Samples of concentrate and silage were collected to evaluate the fatty acid composition. The experimental period lasted 110 days. After this period, the animals were slaughtered and samples of the longissimus muscle were collected and vacuum-packed for further analysis. The levels of total lipid and protein showed quadratic effect with the increase of soybean hulls in the diet, as the moisture increased linearly with inclusion. There was no effect of treatments on the percentage of ash. The composition of saturated fatty acids (SFA), monounsaturated fatty acids (MUFA), polyunsaturated fatty acids (PUFA), PUFA/SFA and omega 6 (n-6) did not change, but increases in n-3 and reduction in the n-6:n-3 ratio were observed when the the amount of soybean hulls in the diet increased. The content of fatty acid conjugated linoleic acid (CLA) ranged from 3.0 to 4.0 g/kg at levels of substitution. The inclusion of soybean hulls in the diet increased CLA, the n-3 and decreased the n-6:n-3 ratio.
Growth, photosynthesis, nodule nitrogen and carbon fixation in the chickpea cultivars under salt stress

Four cultivars of chickpea, two of them of Mediterranean origin (kabuli), CSG 9651, BG 267 and two Indian (desi) types, CSG 8962, DCP 92-3, differing in their salt sensitivities were identified after screening ten genotypes in saline soils. The cultivars CSG 9651 and CSG 8962 were salt tolerant while BG 267 and DCP 92-3 were salt sensitive, respectively. The seeds of different cultivars were inoculated with Mesorhizobium ciceri, strain F: 75 and the plants were grown in the greenhouse. After the establishment of symbiosis, 15-day-old seedlings were administered doses of saline at varying concentrations (0, 4, 6, 8 dSm-1 NaCl, Na2SO4, CaCl2). Plants were harvested at 40, 70 and 100 days after sowing, for analyses. The main aim was to compare the relative salt tolerance of both desi and kabuli cultivars in terms of nitrogen fixation and carbon metabolism, as well as to ascertain whether the negative effects of saline stress on nitrogen fixation were due to a limitation of photosynthate supply to the nodule or to a limitation on the nodular metabolism that sustains nitrogenase activity. Plant growth, nodulation and nitrogenase activity was more severely affected in BG 267 and DCP 92-3 under salinity treatments (6 and 8 dSm-1) compared with CSG 9651 and CSG 8962. Nodule number as well as nodule mass increased under salt stress in CSG 9651 and CSG 8962 which might be responsible for their higher nitrogen fixation. Salinity reduced leaf chlorophyll and Rubisco activities in all cultivars. However, tolerant cultivars CSG 9651 and CSG 8962 showed smaller declines than the sensitive ones. Phosphoenolpyruvate carboxylase (PEPCase) activity increased significantly in the nodules of tolerant cultivars under salt stress at all harvests, and this was clearly related to salt concentrations. Our results suggest that in salt-affected soils tolerant cultivars have more efficient nodulation and support higher rates of symbiotic nitrogen fixation than the sensitive cultivars.
Clava multicornis (Forsskål, 1775): rediscovery of a North Atlantic hydroid (Cnidaria, Hydrozoa, Anthoathecata) on the Pacific coast of North America

The shallow-water hydroid Clava multicornis is reported from the west coast of North America for the first time in nearly six decades. A North Atlantic species often occurring on intertidal fucoid algae, it had been found elsewhere only in heavily-invaded San Francisco Bay, California, with records dating from the late 19 th to mid-20 th centuries. The species has not been reported from the Bay Area since 1954, in spite of intensive recent collecting, and it is presumed to no longer exist there. During the winter and summer of 2013, robust colonies (which were fertile in the winter) were discovered in fouling communities on floating docks further north in Coos Bay, Oregon. This estuary harbours a large number of introduced species from both the western Pacific and the North Atlantic. We suspect that C. multicornis was introduced to Coos Bay in one of two ways. One means of transport might have been in hull fouling on ships, either directly from the North Atlantic or possibly from another Pacific coast estuary where the species remains undetected. A second possibility is on fucoid algae used in the shipment of polychaete bait worms from the State of Maine, on the Atlantic coast of the United States.
Fowl play: identification and management of hybridisation between wild and domestic Helmeted Guineafowl (Numida meleagris) in South Africa

This study investigates the possibility of hybridisation between introduced domestic Helmeted Guineafowl Numida meleagris, derived from the West African subspecies N. m. galeata, and South African guineafowl, N. m. coronata. There is putative morphological evidence of such hybridisation in wild populations and it is known that domestic guineafowl do not survive well in the wild. Molecular analysis of the control region of mtDNA confirmed the occurrence of the domestic guineafowl haplotype in individuals present in wild populations from KwaZulu-Natal, but not in birds from populations from the Free State. Thus, despite the absence of the availability of bi-parentally inherited nuclear DNA marker, the presence of the domestic haplotype in individuals of both wild and intermediate phenotype (between wild and domestic birds) suggests that there is hybridisation in the wild between domestic and wild guineafowl. To avoid potential negative affects associated with outbreeding depression, we argue for careful control of releases of domestic guineafowl into the wild. This study investigates the possibility of hybridisation between introduced domestic Helmeted Guineafowl Numida meleagris, derived from the West African subspecies N. m. galeata, and South African guineafowl, N. m. coronata. There is putative morphological evidence of such hybridisation in wild populations and it is known that domestic guineafowl do not survive well in the wild. Molecular analysis of the control region of mtDNA confirmed the occurrence of the domestic guineafowl haplotype in individuals present in wild populations from KwaZulu-Natal, but not in birds from populations from the Free State. Thus, despite the absence of the availability of bi-parentally inherited nuclear DNA marker, the presence of the domestic haplotype in individuals of both wild and intermediate phenotype (between wild and domestic birds) suggests that there is hybridisation in the wild between domestic and wild guineafowl. To avoid potential negative affects associated with outbreeding depression, we argue for careful control of releases of domestic guineafowl into the wild.
Morphology, morphogenesis, and molecular phylogeny of a new marine urostylid ciliate (Ciliophora, Stichotrichia) from the South China Sea, and a brief overview of the convergent evolution of the midventral pattern within the Spirotrichea

The morphology, infraciliature, morphogenetic events, and small subunit ribosomal RNA (SSU rRNA) gene-based phylogeny of a stichotrich ciliate, Bergeriella ovata gen. et sp. nov., found in coastal waters off Daya Bay, Guangdong, South China, were investigated. The new taxon has an atypical midventral pattern, and is characterized by several rather unusual morphological features: frontal cirri forming an irregular tricorona; one nonmigratory row located right of the midventral rows, which is morphogenetically derived from the posteriormost fronto-ventral-transverse (FVT) streak; conspicuously enlarged postoral ventral cirri, whereas the left ventral cirri are delicate and arranged in oblique rows. Based on both the morphological and morphogenetical data, a new family, Bergeriellidae fam. nov., is proposed. In the SSU rRNA phylogenetic trees, B. ovata gen. et sp. nov. groups with the classic urostylids (urostylids s.s.) with high nodal support. Our phylogenetic analyses have revealed at least seven separate clades for midventral pattern-bearing taxa (e.g. Pattersoniella, Neokeronopsis, Rigidothrix, urostylids s.s., Uroleptidae, Holostichidae + Psammomitridae, and Pseudoamphisiellidae), suggesting that the order Urostylida Jankowski, 1979 sensu Lynn, 2008 is a polyphyletic assemblage, and that the convergent evolution of the urostylid midventral pattern might have occurred more times among the spirotrichs than has previously been recognized.
Loss of heterozygosity and microsatellite instability in the 3p24.2~3pter region in papillary thyroid carcinoma

Introduction: The aim of this study was to analyse the loss of heterozygosity (LOH) and microsatellite instability (MSI) at the thyroid hormone receptor beta (THRB) locus (3p24.3) and in the 3p24.2~3pter region in human papillary thyroid carcinoma (PTC). Material and methods: Polymorphic cleaved amplified polymorphic sequence (CAPS) markers were used for cleaved amplified polymorphic sequence analysis to examine the THRB locus and microsatellite markers D3S1435, THRB, D3S1597 and D3S1304 were used to perform the innovative, PCR-based WAVE® Nucleic Acid Fragment Analysis to evaluate LOH/MSI presence in the 3p24.2~3pter region. Results: Twenty-three (23) PTC samples were used. Interestingly enough, only one (1) among 18 informative cases (1/18) presented with LOH at the THRB locus, while none of the same 18 cases revealed any trace of MSI. Moreover, we also observed a single polymorphism at the THRB gene, restricted to one of the used CAPS markers. Conclusions: Our results suggest that LOH and MSI in the 3p24.2~3pter region are not characteristic features in sporadic PTC.
VARIABLE RESPONSE OF BUTTERFLIES AND VEGETATION TO ELK HERBIVORY: AN EXCLOSURE EXPERIMENT IN PONDEROSA PINE AND ASPEN-MIXED CONIFER FORESTS

Abstract Herbivory by wild ungulates influences the structure and composition of plant communities, but less is known about how such changes affect species richness and abundance of insect herbivores. In Bandelier National Monument, New Mexico, 1999 to 2002, we used ungulate exclosures and reference sites to measure the response of butterflies to herbivory by high numbers of elk (Cervus elaphus) in ponderosa pine (Pinus ponderosa) grassland and aspen-mixed conifer forests. At each site, we measured butterfly abundance, species richness, and selected environmental variables. Butterfly abundance and species richness significantly differed among dates in ponderosa pine-grassland sites and differed significantly for date, treatment, and date*treatment interaction in aspen-mixed conifer sites in 2001, the year of greatest butterfly abundance and richness. Environmental variables differed little between treatments in either habitat, with the exception of the distribution of aspen stem densities, which significantly differed among height classes and treatments in 2001 and 2002. Results of nonmetric, multidimensional scaling ordination indicated that butterfly community composition in late summer was best explained by non-woody biomass, blooming forb species richness and abundance, and aspen saplings excluded from elk in the aspen-mixed conifer sites. Although elk were only excluded for 4 y, our results indicated that, at high densities, they browse non-woody vegetation and young aspen, which in turn has a cascading affect on adult butterfly community composition in some habitats during some years.
RESPONSE OF A FOURTH RATOON SUGARCANE CROP TO NITROGEN, SILICON, AND LIME FERTILIZATION

La eficiencia maxima de nitrogeno (N) se alcanza cuando el fertilizante de N se usa con silicio (Si). Por tanto, el objetivo de este estudio fue evaluar los atributos quimicos del suelo, el estado nutricional, la produccion de tallos y la acumulacion de N y Si en el cuarto cultivo de soca de cana (Saccharum sp.), y la influencia de la dosis de N en presencia y ausencia de Si y cal. El estudio se realizo en la granja experimental del campus UNESP-Jaboticabal, estado de Sao Paulo, Brasil. El diseno experimental fue de bloques completos al azar con un arreglo factorial de 5x2: cinco dosis de N (0, 40, 80, 120 y 160 kg ha-1), y dos materiales correctivos, silicato y cal; con cuatro repeticiones por tratamiento. El suelo se clasifico como Latosol Rojo distrofico y la variedad de cana de azucar fue RB855156. Durante el experimento se midieron el contenido de N (N-NH4+ y N-NO3-) y Si en el suelo, el contenido de N y Si en la hoja, la produccion de tallos y la acumulacion de N y Si en las hojas y tallos. La fertilizacion con N asociada con silicato y caliza aumento los niveles de N-NO3- y Si en el suelo, lo cual mejoro el estado nutricional y la acumulacion de N y Si en las hojas y tallos de la cana de azucar, pero la produccion de tallos fue menor al usar silicato, comparado con cal
The Perturbation Toxic Effect of Graphene on HepG2 Cell

How to accurately and comprehensively unveil the toxic effect of graphene on the cells have always received extensive attention by many researchers. Owing to the opposition results in classical assay approaches, some researchers have attempted to adopt advanced analysis techniques. Our group successful performed mass spectrometry-based metabolomics to investigate the toxic effect of graphene on the HepG2. In this analysis platform, by pattern recognition and metabolism analysis, we acquired twelve potential biomarkers and two main disturbed metabolism pathway involving in glutathione metabolism and arginine and proline metabolism. Our findings demonstrated that the graphene stimulate the HepG2 cell and results in breaking the homeostasis and perturbation the metabolism pathway, we should focus on this disturbance from the graphene.
Azorean aphid fauna (Homoptera, Aphidoidea): comments on some species and an updated list

Specific biological comments are made about the following four aphid species from the Azores: Brachycaudus persicae (Passerini) [Aphididae], Macrosiphoniella tanacetaria (Kaltenbach) [Aphididae], Melanaphis donacis (Passerini) [Aphididae] and Saltusaphis scirpus Theobald [Drepanosiphidae]. Using the known literature an updated list of the aphids of the Azores is presented, with indication of each first reference record for the Archipelago.
Analysis of Biometric Systems in Mobile devices

: Authentication techniques and biometric systems have occupied a major industrial area today. People have moved from big devices to small portable devices like mobile phones. Ample amount of systems requires relaibility as an important factor as they want that the access should be given only to the genuine users. Technology revolution has bought biometric systems to become more secure and highly user friendly. This paper is highlighting on various biometric technology available and their comparative analysis, strength, and related privacy issues with biometric system.
In vitro germination and structure of hard seed testa of natural tetraploid Trifolium pratense L.

Scarified and non-scarified seeds of natural tetraploid Trifolium pratense L. were germinated on in vitro and ex vitro germination media. The medium producing the best outcome was determined and germination media were compared. Additionally, testa of normal and hard seeds were examined. The media producing the best outcomes in both seed groups (scarified and non-scarified) were hormonefree MS medium, filter paper and soil respectively. Macrosclereid layer of normal seed testa was thicker than that of hard seed testa due to imbibitions. Whereas, epidermis walls in the macrosclereid layer of hard seed testa were thicker when compared to those of normal seed testa.