Miracle-dz/UniFAR-FTUs huggingface dataset:
Genetic Diversity Analysis of Egyptian Native Chickens Using mtDNA D-loop Region

This study was aimed to evaluate the genetic diversity of Egyptian native chickens by using mtDNA sequence polymorphism. A 546-bp fragment of the mtDNA D-loop region was sequenced for a total of 36 Egyptian native chickens with 14 reference sequences from DNA databank. Of the Egyptian chickens 5 haplotypes were identified. Haplotype diversity and nucleotide diversity of the Egyptian native chickens were 0.5635±0.0845 and 0.00123± 0.00108, respectively. The Egyptian native chickens were distributed within one clade, which were closed to the haplotypes from Indian subcontinent and Southeast Asia. Most of Egyptian native chickens were classified into the haplotype E1, which contains 63.9% of individuals followed by E4 (16.6%), E5 (11.1%), E2 (5.5%) and E3 (2.7%), respectively. These findings indicate that the maternal lineages was involved in the origin of domestic chicken in Egypt may have roots in Indian subcontinent and other Southeast Asia. The genetic information from this study will probably pave the way to further studies for evaluation, preservation and improvement of Egyptian native chickens as genetic resources in the future.
Transcriptome-Wide Comparisons and Virulence Gene Polymorphisms of Host-Associated Genotypes of the Cnidarian Parasite Ceratonova shasta in Salmonids

Abstract Ceratonova shasta is an important myxozoan pathogen affecting the health of salmonid fishes in the Pacific Northwest of North America. Ceratonova shasta exists as a complex of host-specific genotypes, some with low to moderate virulence, and one that causes a profound, lethal infection in susceptible hosts. High throughput sequencing methods are powerful tools for discovering the genetic basis of these host/virulence differences, but deep sequencing of myxozoans has been challenging due to extremely fast molecular evolution of this group, yielding strongly divergent sequences that are difficult to identify, and unavoidable host contamination. We designed and optimized different bioinformatic pipelines to address these challenges. We obtained a unique set of comprehensive, host-free myxozoan RNA-seq data from C. shasta genotypes of varying virulence from different salmonid hosts. Analyses of transcriptome-wide genetic distances and maximum likelihood multigene phylogenies elucidated the evolutionary relationship between lineages and demonstrated the limited resolution of the established Internal Transcribed Spacer marker for C. shasta genotype identification, as this marker fails to differentiate between biologically distinct genotype II lineages from coho salmon and rainbow trout. We further analyzed the data sets based on polymorphisms in two gene groups related to virulence: cell migration and proteolytic enzymes including their inhibitors. The developed single-nucleotide polymorphism-calling pipeline identified polymorphisms between genotypes and demonstrated that variations in both motility and protease genes were associated with different levels of virulence of C. shasta in its salmonid hosts. The prospective use of proteolytic enzymes as promising candidates for targeted interventions against myxozoans in aquaculture is discussed. We developed host-free transcriptomes of a myxozoan model organism from strains that exhibited different degrees of virulence, as a unique source of data that will foster functional gene analyses and serve as a base for the development of potential therapeutics for efficient control of these parasites.
Antibiotic Consumption on Dairy and Beef Cattle Farms of Central Italy Based on Paper Registers

The overuse of antibiotics in livestock contributes to the antibiotic resistance pandemic. The assessment of the actual antibiotic consumption is crucial in limiting the expansion of the problem effectively. The aim of this study was to provide the first qualitative and quantitative analysis of antimicrobial usage using data from paper-based registers on dairy and beef farms located in the Umbria region, Italy. Antimicrobial therapies of a one-year period were collected from 101 farms with at least 50 cattle each. Defined daily doses (DDDvet) and defined course doses (DCDvet) were calculated per administration route and antimicrobial class. The total courses administered were fewer in beef (330.7 × 10−3 DCDvet/year) than in dairy farms (1034.1 × 10−3 DCDvet/year). The use of the highest priority critically important antimicrobials (HPCIAs) was higher (p = 0.0033) in dairy than in beef herds. In terms of DDDvet, the parenteral fluoroquinolone administration ranked second and fourth on dairy and beef farms, respectively; the consumption of beta-lactams was ten times higher on dairy than on beef farms. Our results confirm that intensive dairy management practices are associated with increased antibiotic consumption and highlight the necessity to strengthen the existing stewardship programs by involving all stakeholders in effective antimicrobial resistance reduction plans.
Desenvolvimento de bebida láctea sabor morango utilizando diferentes níveis de iogurte e soro lácteo obtidos com leite de búfala

Este trabalho foi realizado com o objetivo de avaliar as caracteristicas fisico-quimicas, sensoriais e microbiologicas de bebidas lacteas elaboradas com leite de bufala e diferentes niveis de iogurte e soro lacteo. Foram desenvolvidas cinco formulacoes a base de leite de bufala, soro de queijo tipo frescal e iogurte. Os tratamentos foram: T1=10% leite, 10% soro e 80% iogurte; T2=10% leite, 20% soro e 70% iogurte; T3=10% leite, 30% soro e 60% iogurte; T4=10% leite, 40% soro e 50% iogurte; e T5=10% leite, 50% soro e 40% iogurte. Para o leite e soro, foram determinadas acidez titulavel (°D), densidade a 15°C, gordura, EST e ESD. As bebidas lacteas foram avaliadas quanto aos parâmetros: pH, acidez titulavel, gordura, proteina, viscosidade, cor (CIEL*a*b*), teste de aceitacao sensorial com escala hedonica de cinco pontos, ordenacao da preferencia, enumeracao de coliformes a 35 e 45°C e contagem de microrganismos mesofilos aerobios. Os resultados obtidos, submetidos ao teste de ANOVA e teste de medias com nivel de significância a 5%, revelaram que os niveis de soro influenciaram os valores de pH, acidez, gordura, proteina, viscosidade e L* das bebidas lacteas, enquanto as coordenadas de cromaticidade a* e b* nao sofreram influencia. As formulacoes com 10 e 20% de soro foram as mais aceitas no teste de aceitacao sensorial, bem como na preferencia pelos julgadores.
Calyptophyllum longiventre (Verhoeff, 1941) invading houses in Turkey, with the first description of the male (Diplopoda: Julida: Julidae)

A mass occurrence of the millipede Calyptophyllum longiventre (Verhoeff, 1941) in Mardin, south‐east Turkey, is reported. Descriptive notes on this poorly known species are given, including the first description of male characters. Comparison is made with other instances of millipede mass occurrences, previous swarming events of millipedes in Turkey are summarized, and a note on the distribution of the genus Calyptophyllum is given.
Designing Questions for Research Design and Design Research
 in e‑Learning

This paper presents a model for developing research questions that are aligned to research aims for research design in e-learning. The model is proposed as a solution to the on-going problem of heterogeneity of research problems. The model is based on Burrell and Morgan’s four social paradigms, and integrates four research aims, namely, explore, explain, develop and describe; four design positions, namely, formalist, populist, functionalist and conventionist; and four pursuits of (hu)mankind, namely, virtue, value, power and knowledge. Four of Roode’s (1993) research questions are mapped onto each of the consolidated paradigms. The feasibility of the model was tested against eight papers in previous issues of this journal. Two questions drove the study: what are the paradigms in which the selected articles can be classified, and how are these paradigms aligned to the research aims and research questions? The model was found to be useful in aligning the implied research aims and research questions of the selected papers. The model is proposed as a useful tool for supervisors and novice researchers to assist with the development of integrated research aims and research questions. Further research will include the development of generic question stems that can be used as the first few words of the questions that correspond to each aim.
Social status and individual behavioral differences in juvenile Macrobrachium rosenbergii

Adult Macrobrachium rosenbergii males appear in three distinct morphotypes associated with dominance hierarchy. Juveniles can also differ but only in body size. We examined whether juveniles present a size-related dominance hierarchy and whether it could be related to individual behavioral profile. Behaviors were recorded in groups of four prawns for 30 days in the laboratory, four times during light and dark phases of the 24 h cycle. Dominance ranks were analyzed using David’s score method. Observed behaviors differed between light phases. In most groups, two individuals obtained a positive score and the other two a negative score; they were therefore considered dominants and subordinates, respectively. There was no correlation between dominance and general behavioral activities. Dominants had greater weight gain and faster access to food. The precocious relation between growth and dominance suggests dominant juveniles are more likely to become blue claw adult males, the morphotype with greater reproductive success.
The effects of pathogen infection and mutation on life‐history characters in Arabidopsis thaliana

The nature of the interaction among deleterious mutations is important to models in many areas of evolutionary biology. In addition, interactions between genetic and environmental factors may affect the predictions of such models. Individuals of unknown genotypes of Arabidopsis thaliana, ecotype Marburg, were exposed to five levels of chemical (EMS) mutagenesis and three levels of Pseudomonas syringae infection. Survival, growth and flowering characteristics of each individual were measured. The logarithm of fitness is expected to be a linear function of mutation number if mutations act independently. Furthermore, the expected number of mutations should be approximately a linear function of time of exposure to mutagen. Therefore, nonlinear effects of mutagen exposure on the logarithm of fitness characters would suggest epistasis between mutations. Similarly, if pathogen infection and mutation act independently of each other, their effects should be additive on a log scale. Statistical interactions between these factors would suggest they do not act independently; particularly, if highly mutated individuals suffer more when infected than do less mutated individuals, this suggests that pathogens and mutations act synergistically. Pseudomonas‐infected individuals were shown to have an increased probability of flowering under conditions of short day length, but to ultimately produce fewer flowers than uninfected individuals. This suggests a plastic response to stress and, despite that response, an ultimately deleterious effect of infection on fitness. Leaf rosette growth was negatively and linearly related to the expected number of mutations, and the effects of mutation on different life‐cycle stages appeared to be uncorrelated. No significant interactions between pathogen and mutation main effects were found. These results suggest that mutations act multiplicatively with each other and with pathogen infection in determining individual fitness.
The Possible Existence of a Vitamin A-storing Cell System

Vitamin A is stored in the liver. Small amounts of vitamin A are also found in the lungs, intestines, eyes and other areas of the body. Cells responsible for vitamin A storage have long been regarded as a part of the reticuloendothelial cell system (RES) (6, 8), e.g., in the liver, Kupffer cells are thought to be the site of vitamin A storage. However, Nakane (7) first noticed in 1963 by fluorescence microscopy that liver vitamin A was found not in the Kupffer cells but in the "fat-storing cell" described by Ito (4) in 1951. Subsequently, Wake (11) and Kobayashi and Takahashi (5) demonstrated by light and electron microscopy that the lipid granules in the fat-storing cell increased markedly when vitamin A was injected into the animal. Furthermore, Wake (11) clearly demonstrated that the cell described by Kupffer in 1876 (9) was the fatstoring cell of Ito. Kupffer in his second paper in 1899 (10), however, modified his original report and described his stellate cell as the phagocytic endothelial cell of the sinusoidal wall. Since then, this stellate cell has been regarded as a part of the RES. More recently, by means of tritiated vitamin A and electron microscopic radioautography, we showed (1) that vitamin A was incorporated and stored for a considerable period of time in the lipid granules of the liver fat-storing cell. These findings indicated that the fat-storing cell in the liver should be classified as a "vitamin A storing cell" and that vitamin A was not stored in the phagocytic stellate cell described by Kupffer in his second paper. Further observations in the same series of experiments revealed that the septal cell (12) in the lung alveolar wall had characteristics similar to the liver vitamin A-storing cell (2). Subsequently, the same kind of cell was detected in the adrenal glands and intestines (3). The findings were further substantiated as these cells exhibited the specific transient colour of vitamin A under fluorescence microscopy. The colour response of these cells was previously noted by Kudo (6) and by Popper (8), although these investigators regarded the cells as a part of the RES, as mentioned earlier. The examined vitamin A-storing cells showed the following features. (a) Cells were irregular in shape and extended slender, often branched, cell processes. (b) Cells possessed several vitamin A-containing lipid granules. The number of granules increased in hypervitaminosis. (c) No basement lamina was found around the cell surface. (d) Well-developed granular endoplasmic reticulum and Golgi apparatus were found, and the former was frequently dilated in cisternal form. (e) Filaments about 50 A diameter were usually seen along the plasma membrane. Microtubules were frequently present, especially in the cell processes. (f) Cells were located in the connective tissue spaces and had a close relationship to both the endothelium of the vascular vessel and various epithelial tissues. Based on these morphological features, the vitamin Astoring cells were easily distinguishable from macrophages or histiocytes found in
Courtship and Mating Behavior of Bemisia tabaci (Homoptera: Aleyrodidae)

A description of the courtship and mating behavior of Bemisia tabaci (Gennadius) is presented. Upon emergence, both sexes were clear winged and sexually immature. They matured during the next 24 h and their wings were coated with wax. Newly emerged males were attracted to 1-d-old females and sometimes initiated courtship that rarely persisted. Males between 10 and 24 h old readily initiated courtship but failed to complete antennation. Newly emerged adult females were not attractive to males for about 10 h. Females accepted courting males 20–24 h after emergence. The precopulatory, copulatory, and postcopulatory behaviors, including the time spent at each step, are described for mature adults. Unsuccessful sexual encounters included male and female rejection, male–male interference, and misdirected sexual behavior. A comparison of the sexual behavior of B. tabaci and Trialeurodes vaporariorum (Westwood) suggests that B. tabaci , like T. vaporariorum , may use a sex pheromone.
Draft Genome Sequences of Two Potentially Novel Bacillus Isolates from Backyard and Commercial Chicken Gastrointestinal Tracts

Here, we present the draft genome sequences of two Bacillus strains, HF117_J1_D and USDA818B3_A, isolated in Pomona, California, from the gastrointestinal (GI) tract of backyard and commercial broiler chickens, respectively. The draft genomes of both strains appear to represent novel species. ABSTRACT Here, we present the draft genome sequences of two Bacillus strains, HF117_J1_D and USDA818B3_A, isolated in Pomona, California, from the gastrointestinal (GI) tract of backyard and commercial broiler chickens, respectively. The draft genomes of both strains appear to represent novel species.
Transforming growth factor-β1 regulates chemokine and complement production by human proximal tubular epithelial cells

Transforming growth factor-γ1 regulates chemokine and complement production by human proximal tubular epithelial cells. Previously it has been demonstrated that human proximal tubular epithelial cells (PTEC) are able to produce chemokines (such as IL-8 and MCP-1) and complement components (such as C2, C3, C4 and factor H), and that production of these proteins is regulated by pro-inflammatory cytokines such as interleukin-1α (IL-1α), tumor necrosis factor-α (TNF-α) and interferon-γ (IFN-γ). Since TGF-γ is also expressed in the renal interstitium during inflammation, we investigated the effect of TGF-γ on the production of chemokines and complement components by PTEC in culture. Transforming growth factor-γ1 up-regulated IL-8 production by an average of 4.11 ± 1.0-fold. macrophage chemoattractant phagocyte (MCP-1) production, on the other hand, was down-regulated by TGF-γ1 by an average of 2.2 ± 0.7-fold. The production of C3 and C4 was also down-regulated after incubation with TGF-γ1 (1.9 ± 0.3- and 3.0 ± 1.2-fold, respectively). All effects were dose- and time-dependent and were found to be specific for TGF-γ1, as assessed by inhibition of the effect with a neutralizing antibody against TGF-γ1. These data, together with the knowledge that TGF-γ, chemokines and complement components play a role in several types of renal disease, suggest that TGF-γ is involved in the regulation of local expression of chemokines and complement components by tubular cells.
Estimation of growth and yielding of five highbush blueberry (Vaccinium corymbosum L.) cultivars

Abstract In the years 1996-1999, a study was conducted on the estimation of the growth and yielding of northern highbush blueberry on a brown soil developed from loess. The study comprised bushes from five highbush blueberry cultivars - ‘Bluecrop’, ‘Bluejay’, ‘Darrow’, ‘Herbert’ and ‘Jersey’ - aged from six to nine years since planting. ‘Bluecrop’ bushes were the tallest and those of ‘Darrow’ the shortest, but ‘Darrow’ was characterised by the largest number of annual shoots. The best yielding was ‘Darrow’ and its berries were the largest. ‘Bluejay’ and ‘Jersey’ produced the lowest yields. In the study, the highest estimate was awarded to ‘Darrow’ (number of annual shoots, yielding, fruit size), and ‘Bluecrop’ also proved to be a valuable cultivar.
Studying human reproductive biology through single-cell analysis and in vitro differentiation of stem cells into germ cell-like cells.

BACKGROUND Understanding the molecular and cellular mechanisms of human reproductive development has been limited by the scarcity of human samples and ethical constraints. Recently, in vitro differentiation of human pluripotent stem cells into germ cells and single-cell analyses have opened new avenues to directly study human germ cells and identify unique mechanisms in human reproductive development. OBJECTIVE AND RATIONALE The goal of this review is to collate novel findings and insightful discoveries with these new methodologies, aiming at introducing researchers and clinicians to the use of these tools to study human reproductive biology and develop treatments for infertility. SEARCH METHODS PubMed was used to search articles and reviews with the following main keywords: in vitro differentiation, human stem cells, single-cell analysis, spermatogenesis, oogenesis, germ cells and other key terms related to these subjects. The search period included all publications from 2000 until now. OUTCOMES Single-cell analyses of human gonads have identified many important gene markers at different developmental stages and in subpopulations of cells. To validate the functional roles of these gene markers, researchers have used the in vitro differentiation of human pluripotent cells into germ cells and confirmed that some genetic requirements are unique in human germ cells and are not conserved in mouse models. Moreover, transcriptional regulatory networks and the interaction of germ and somatic cells in gonads were elucidated in these studies. WIDER IMPLICATIONS Single-cell analyses allow researchers to identify gene markers and potential regulatory networks using limited clinical samples. On the other hand, in vitro differentiation methods provide clinical researchers with tools to examine these newly identify gene markers and study the causative effects of mutations previously associated with infertility. Combining these two methodologies, researchers can identify gene markers and networks which are essential and unique in human reproductive development, thereby producing more accurate diagnostic tools for assessing reproductive disorders and developing treatments for infertility.
Structural basis of HapEP88L-linked antifungal triazole resistance in Aspergillus fumigatus

The mutation P88L in subunit HapE of the CCAAT transcription factor causes resistance of Aspergillus fumigatus to azole drugs due to altered binding, bending, and transcription of target promoters. Azoles are first-line therapeutics for human and plant fungal infections, but their broad use has promoted the development of resistances. Recently, a pan-azole–resistant clinical Aspergillus fumigatus isolate was identified to carry the mutation P88L in subunit HapE of the CCAAT-binding complex (CBC), a conserved eukaryotic transcription factor. Here, we define the mechanistic basis for resistance in this isolate by showing that the HapEP88L mutation interferes with the CBC’s ability to bend and sense CCAAT motifs. This failure leads to transcriptional derepression of the cyp51A gene, which encodes the target of azoles, the 14-α sterol demethylase Cyp51A, and ultimately causes drug resistance. In addition, we demonstrate that the CBC-associated transcriptional regulator HapX assists cyp51A repression in low-iron environments and that this iron-dependent effect is lost in the HapEP88L mutant. Altogether, these results indicate that the mutation HapEP88L confers increased resistance to azoles compared with wt A. fumigatus, particularly in low-iron clinical niches such as the lung.