Miracle-dz/UniFAR-FTUs huggingface dataset:
Population Isolation and Genetic Subdivision of Timber Rattlesnakes (Crotalus horridus) in the New Jersey Pine Barrens

Abstract: Timber Rattlesnakes, Crotalus horridus, are an endangered species in New Jersey, where high human population density places extraordinary pressures on natural populations. Disjunct populations are found in both the northern part of the state and a few scattered locations in the southern Pine Barrens. The Pine Barrens populations were previously shown to have reduced levels of genetic diversity compared to other populations in the Mid-Atlantic region. In this study, we used microsatellite DNA to examine the remaining six known C. horridus populations in the Pine Barrens and two in the northern part of the state. Bayesian analysis, genetic distance analysis, and factorial component analysis were performed, and the results indicated that the sampled populations represented four genetic subgroups, the two northern populations comprised one subgroup and the remaining six Pine Barrens populations comprised the other subgroups. Although there was evidence for isolation by distance among the Pine Barrens populations, geographic distance alone did not account for a substantial amount of among-group variation. The combined analyses implicated paved roads as primary isolating barriers between populations. Given their geographic isolation and reduced levels of genetic diversity, intensive efforts may be required to ensure the persistence of the behaviorally and genetically unique C. horridus populations of the New Jersey Pine Barrens.
The genetic characterization of Myrmelachista spp. Roger (Hymenoptera: Formicidae) specimens collected in the Atlantic Forest of southeastern Brazil

Arboreal ants of the genus Myrmelachista , which have ecologically important relationships with different vegetable species, are found exclusively in the Neotropical region. These ant species are difficult to identify, and their taxonomy remains controversial; moreover, little is known regarding their biology. The objective of the present work is to assess the genetic similarities and dissimilarities between and within Myrmelachista species, with the goal of expanding knowledge of the relationships among the taxa of this genus. Sample collection in selected regions of the dense ombrophile forest of southeastern Brazil yielded 256 nests, which were found in vegetation or among scattered twigs in the leaf litter; eight species were recorded. A total of 180 specimens were analyzed, producing 123 molecular characters. Data analyses revealed similarity relationships that allowed the examined species to be classified into the following groups: (1) Myrmelachista sp. 4, M. nodigera , M. ruszkii and M. gallicola ; (2) M. catharinae and M. arthuri ; (3) M. reticulata ; and (4) Myrmelachista sp. 7. The study results also revealed the existence of two morphological variants of M. catharinae ; M. arthuri was more closely related to one of these M. catharinae variants than to the other variant. The present work provides important information regarding genetic variation among Myrmelachista species that may contribute to interpreting the complex morphology of this genus.
EXPRESSION OF REOVIRUS STRUCTURAL PROTEIN MU1 LEADS TO ACTIVATION OF THE INTRINSIC AND EXTRINSIC APOPTOTIC PATHWAYS

Mammalian orthoreoviruses induce apoptosis in vivo and in vitro; however, the specific mechanism by which apoptosis is induced is not fully understood. Previous studies have identified the reovirus M2 gene segment as a determinant for apoptosis induction. Furthermore the μ1 protein, encoded by the M2 gene segment, has been shown to induce apoptosis and localize to intracellular membranes when expressed in cells. Here, I report that expression of μ1 in cells activated both the intrinsic and extrinsic apoptotic pathways. I found that similar to reovirus infection, μ1 expression alone induced release of cytochrome c and smac/DIABLO from the mitochondrial intermembrane space into the cytosol. In addition, expression of μ1 activated the initiator caspases, -8 and -9. Inhibition of either caspase-8 or caspase-9 abolished effector caspase-3 activation in μ1-expressing cells; however, the presence of broadspectrum caspase inhibitors augmented cytochrome c release indicating that activation of upstream caspases was not required for μ1-induced release of cytochrome c. Based on these findings, I hypothesize that μ1 plays a primary role in the activation of the intrinsic and extrinsic apoptotic pathways during reovirus infection.
Ni(Ge 1− x − y Si x Sn y ) Ohmic Contact Formation on p-type Ge 0.86 Si 0.07 Sn 0.07

A single-crystalline Ge0.86Si0. 07Sn0.07 alloy was grown on double Ge1− x Sn x and Ge buffers on Si (100) using magnetron sputtering. The temperature-dependent contact resistivity ( $\rho _{\mathrm {c}})$ of Ni/p-type Ge0.86Si0. 07Sn0.07 structure was investigated in detail. Good ohmic contacts with $\rho _{\mathrm {c}}$ of $\sim 1.96 \times 10^{\mathrm {-6}}\Omega \cdot {\rm cm}^{\mathrm {-2}}$ have been demonstrated on p-type Ge0.86Si0. 07Sn0.07 after annealing at 350 °C. The low contact resistivity is attributed to the formation of Ni(Ge1− x − y SixSny) complex, and the hole Schottky barrier height of Ni(Ge1− x − y SixSny)/p-type Ge0.86Si0. 07Sn0.07 is measured.
Psychosomatic disorder may be related to circadian rhythms in physically healthy students

Students suffering from subjective psychosomatic disorder often have basic lifestyle problems. We examined 30 healthy students aged 21–22 years old. Salivary samples were collected from the subjects at home five times per day (20:00, 24:00, 04:00, 08:00 and 12:00 h). We assessed melatonin secretion patterns by fluorescence enzyme immunoassay and cortisol secretion by ELISA. We assigned the subjects to regular, semi-regular and irregular circadian rhythm groups based on whether melatonin secretion was high until midnight. A self-assessment questionnaire addressing psychosomatic disorder was completed by the same students. The subjects rated their psychosomatic symptoms twice per day (08:00 and 20:00 h). The irregular group showed lower cortisol awakening response, but high cortisol concentrations at 12:00 h; this group also reported more subjective health complaints related to psychosomatic stress compared with the regular group. Our findings suggest that psychosomatic disorder is associated with circadian rhythms in Japanese students.
Endolithic thraustochytrid marine fungi from planted shell fragments

A thraustochytrid zoosporic fungus with characteristics of the genus Schizochytrium is a common member of an assemblage of different endolithic marine microorganisms found in carbonate shell fragments. We used clean shell fragments as bait in various subtidal marine locations on the coasts of Maine, Georgia and Jamaica. Heterotrophs (including fungi) were selected by covering each bait panel with a stainless steel shade that allowed sea water to circulate easily over the shell fragments. Shell fragments were recovered after six months. Details of the cytology of the endolithic organisms were revealed by a technique which produced a resin cast of the endoliths, or their traces, after fixed and embedded shells were decalcified. Scanning electron microscope observations were of the resin casts and transmission electron microscope observations were of sections of reembedded resin casts. Thraustochytrids were particularly abundant in fragments of mussel shells, which have more organic matrix than clam or oyster shells. Within the shells the thraustochytrids formed unusual elongated, tapered, and sometimes branched thalli that are divided into many vegetative cells, a characteristic feature of Schizochytrium. The cell nearest the shell surface typically was a zoosporangium containing biflagellate zoospores. Ultrastructural evidence for the thraustochytrid nature of the endoliths included a layered wall of dictyosome-derived thin scales and the production of an ectoplasmic network from bothrosomes on the cell surface. This role of thraustochytrid fungi in bioerosion is new and unexpected.
Evaluation of inbreeding and relationship coefficients in Hovawart dogs and analysis of trends in coat colour changes / Ocena stopnia zinbredowania i spokrewnienia psów rasy hovawart oraz analiza tendencji zmian umaszczenia

Abstract Analyses were conducted on pedigrees of 845 animals registered at the Hovawart Club in Poland (113 dogs and their ancestors). The degree of inbreeding was calculated for the whole population (0.0026) and separately for male dogs (0.0021) and bitches (0.0031), and the coefficient of mean relationship was calculated for the entire population (0.0064), among male dogs (0.0064), among females (0.0073) and between males and females (0.0061). The inbreeding and relationship coefficients obtained are lower than those estimated for Polish populations of other dog breeds. The calculated effective number of founders (268) and ancestors (233) may indicate rather low genetic diversity. Preferences of breeders concerning coat colour were discussed. Black and tan coat dogs dominated at first, followed by blond ones, and over the last five of the analysed years black coat dogs emerged. Streszczenie Analizowano rodowody 845 osobników należących do Klubu Hovawarta w Polsce (113 osobników oraz ich przodków). Obliczono współczynnikinbredu dla całej populacji (0,0026) oraz oddzielnie dla psów (0,0021), suk (0,0031); średnie spokrewnienie dla całej populacji (0,0064), pomiędzy samicami (0,0073) oraz pomiędzy samcami a samicami (0,0061). Uzyskane wartości współczynników inbredu oraz spokrewnienia są niższe niż obliczone dla polskich populacji psów innych ras. Obliczono także efektywną liczbę założycieli (268) oraz przodków (233), co może wskazywać na niezbyt dużą różnorodność genetyczną. Prześledzono preferencje hodowców dotyczące umaszczenia zwierząt. Początkowo dominowały zwierzęta o umaszczeniu czarnym podpalanym, następnie o umaszczeniu blond, a w ciągu ostatnich pięciu analizowanych lat pojawiły się psy o nowym umaszczeniu - czarnym.
Occurrence of aflatoxin in some liver curative herbal medicines

Fifty herbal medicine samples of seven different taxa known to cure liver disorders were analysed for aflatoxin contamination. Twenty‐three samples, out of 50, were contaminated with various levels of aflatoxins. Amongst the 23 contaminated samples the maximum level of aflatoxin B1 recorded was 2.23 μg g‐1 in Asparagus racemosus and the minimum 0.28 μg g‐1 in Emblica officinalis. Aflatoxin G1 was only found in one species, Terminalia belarica. Aflatoxin production of the isolates of Aspergillus flavus was also examined and the highest levels were produced by isolates from A. racemosus (1.07‐2.47 μg ml‐1). Aflatoxin contamination of herbal drugs may be a risk for patients because the level of aflatoxins is much higher than the tolerance level fixed by the WHO for foods.
Vibrio cholerae hemolysin

Vibrio cholerae hemolysin (HlyA), a water-soluble protein with a native monomeric relative molecular mass of 65 000, forms transmembrane pentameric channels in target biomembranes. The HlyA binds to lipid vesicles nonspecifically and without saturation; however, self-assembly is triggered specifically by cholesterol. Here we show that the HlyA partitioned quantitatively to amphiphilic media irrespective of their compositions, indicating that the toxin had an amphiphilic surface. Asialofetuin, a β1-galactosyl-terminated glycoprotein, which binds specifically to the HlyA in a lectin-glycoprotein type of interaction and inhibits carbohydrate-independent interaction of the toxin with lipid, reduced effective amphiphilicity of the toxin significantly. Resistance of the HlyA to proteases together with the tryptophan fluorescence emission spectrum suggested a compact structure for the toxin. Fluorescence energy transfer from the HlyA to dansyl-phosphatidylethanolamine required the presence of cholesterol in the lipid bilayer and was synchronous with oligomerization. Phospholipid bilayer without cholesterol caused a partial unfolding of the HlyA monomer as indicated by the transfer of tryptophan residues from the nonpolar core of the protein to a more polar region. These observations suggested: (a) partitioning of the HlyA to lipid vesicles is driven by the tendency of the amphiphilic toxin to reduce energetically unfavorable contacts with water and is not affected significantly by the composition of the vesicles; and (b) partial unfolding of the HlyA at the lipid–water interface precedes and promotes cholesterol-induced oligomerization to an insertion-competent configuration.
SHORT COMMUNICATION Genetic Diversity of Cucumber Mosaic Virus Strain Soybean from Several Areas

Cucumber mosaic virus strain soybean (CMV-S) is one of economically important virus infecting soybean in Indonesia. However, it is very few information related with the CMV-S Indonesia isolates. Thus, the aim of present work is to detect and identify CMV-S isolates from different origin. Leaf samples collected from six different soybean fields in Java and North Sumatera. Molecular detection was carried out by reverse transcription polymerase chain reaction (RT-PCR) using specific primer of the coat protein (CP) gene and DNA sequencing. RT-PCR were successfully amplified the entire CP gene size ~657 bp from all samples and encoded 218 amino acids. Analysis of nucleotide and amino acid sequences showed high homology among isolates ranging from 99.5% and 100%. However isolate from Sindang Laut either nucleotides or amino acids showed lower homology to that of five isolates ranging from 89.4-89.6% and 91.7%, respectively. The differences between CMV-S with other non legume strain found in six amino acid positions in the CP gene, suggesting the differences might related with host specificity. Phylogenetic analysis of amino acid of six isolates to other CMV strain showed that the five CMV-S isolates were in the same cluster, while Sindang Laut isolate was in different cluster together with the non-legume CMV from India. It is indicating the present of genetic variability among CMV-S isolates in Java.
Desempenho produtivo e econômico do confinamento de bovinos zebuínos alimentados com três dietas de alto concentrado

The production performance and economic viability of a feedlot of 24 cattle, with an average age of 23 months, 12 Nellore (NEL) and 12 F1 Nellore x Brahman (NBR), divided into three diets: SIL - corn silage and concentrate diet; PEL - exclusive of pellets; GRN - corn and whole grain pellets were studied. The experiment was conducted in a completely randomized scheme in a 2x3 factorial with four replications. The NBR animals showed similar results to the NEL in performance and economic viability for all variables analyzed. Among the diets, the PEL diet, although not the highest diet cost in R$/kg, had the lowest performance with higher TOC/kg, lower TR and lower net margins. The SIL diet had the lowest TOC/kg and cost/kg of carcass, with higher revenues and net margins. The economic results obtained for the GRN diet were similar to SIL, but had lower ADG compared to SIL and highest diet cost (R$/kg) among all. The diets were economically viable at the end of the trial, with average net margin/kg carcass of 2.12, 0.35 and 1.09 for SIL, FEP and GRN, respectively; however the SIL diet presented better productive and economical performance.
Comparison of microbial community structures in four Black soils along a climatic gradient in northeast China

Mi, L. , Wang, G. , Jin, J., Sui, Y. , Liu, J. and Liu, X. 2012. Comparison of microbial community structures in four Black soils along a climatic gradient in northeast China. Can. J. Soil Sci. 92: 543-549. Surveys of microorganisms across climatic gradients provide important information about their biodiversity and spatial distribution, which is linked to fundamental ecological functions. The present study investigated the bacterial communities, including total and culturable communities, and fungal communities in Black soils collected from Lishu (lat. 43°20'N, long. 124°28'E), Dehui (lat. 44°12'N, long. 125°33'E), Hailun (lat. 47°26'N, long. 126°38'E) and Beian (lat. 48°17'N, long. 127°15'E) in northeast China. Bacterial and fungal communities were evaluated by polymerase chain reaction (PCR)-denaturing gradient gel electrophoresis (DGGE) banding patterns of partial 16S rDNA and fungal rDNA internal transcribed spacer regions (ITS), respectively. Bacterial and fungal diversity, based on the number of DGGE bands, were similar among the locations, but cluster analysis of banding patterns showed distinct microbial communities along the climatic gradient. A closer relationship was found among soil bacterial (total and culturable) and fungal communities in neighboring locations than those at greater distance, which suggested that the spatial distribution of microbial community existed in the Black Soil Zone. Comparison of DGGE profiles among the four locations showed that the changes of fungal community and culturable bacterial community were greater than that of bacterial community, suggesting that fungal community and culturable bacterial community are more suitable to study microbial biogeographic distribution in Black soils.
Discrimination among cultivars of cabbage using randomly amplified polymorphic DNA markers.

Randomly amplified polymorphic DNA (RAPD) markers were used to discriminate among 16 commercial cultivars of cabbage (Brassica oleracea L. Capitata Group). A set of 18 decamer primers was selected from 100 random sequences and used to characterize cultivars and to evaluate distances. The selected primers produced 105 (54%) polymorphic bands ranging in size from 100 and 2500 base pairs, out of a total of 195 bands, which allowed for discrimination of all cultivars. Similarity indices between cultivars were computed from RAPD data, and ranged from 0.72 to 0.87 with an average of 0.82. Unweighted pair-group method with arithmetic average (UPGMA) cluster analysis revealed two groups, one formed by two cultivars recommended for summer cropping, and the other by 14 cultivars. This large group was additionally divided into two subgroups. RAPD analysis provides a quick and reliable alternative for the identification of cabbage cultivars and for determination of the relationships among them.
Improvement of Antioxidant Activities in Red Cabbage Sprouts by Lactic Acid Bacterial Fermentation

In the present study, the influence of three types of lactic acid bacteria (Lactobacillus plantarum ATCC 8014, Lactobacillus acidophilus NCFM, Danisco, and Lactobacillus rhamnosus GG E522 (ATCC 53103)) on antioxidant activities of fermented red cabbage sprouts was determined and compared with those of their unfermented/control counterparts. The fermentation resulted in a significant increase (p < 0.05) of antioxidant functionalities as measured by four assays: 1,1-diphenyl-2-picrylhydrazyl (DPPH) radical-scavenging, Trolox equivalent antioxidant capacity (TEAC), superoxide dismutase (SOD)-like, and β-carotene/linoleic bleaching. The most considerable shift in the antioxidant activities was observed after 24 h of fermentation. These increases were followed by a decrease in total phenolic compounds, anthocyanins, and L-ascorbic acid and by an increase in flavonoids, flavonols, and several phenolic acids (gallic, chlorogenic, caffeic, syringic, p-coumaric, trans-3-hydroxy-4-methoxycinnamic, and trans-o-hydroxycinnamic acid) content. The relationship between the antioxidant activities and the compositional changes in antioxidant compounds due to LAB fermentation was observed. Fermented red cabbage sprouts inoculated with L. plantarum had the highest antioxidant activities (DPPH scavenging: 70.92%; TEAC: 1.94 mM Trolox equivalent; SOD-like activity: 63.40%, and β-carotene/linoleic bleaching: 44.33%), which was almost two-fold higher than those of unfermented treatments. These results indicated that LAB fermentation could be applied as a method to improve the potent antioxidant activities of red cabbage sprouts.
Preference among four Bactrocera species (Diptera: Tephritidae) by Diachasmimorpha kraussii (Fullaway) (Hymenoptera: Braconidae)

Diachasmimorpha kraussii is an endoparasitoid of larval dacine fruit flies. To date, the only host preference study done on D. kraussii has used fruit flies from outside its native range (Australia, Papua New Guinea, Solomon Islands). In contrast, this paper investigates host preference for four fly species (Bactrocera cacuminata, Bactrocera cucumis, Bactrocera jarvisi and Bactrocera tryoni), which occur sympatrically with the wasp in the Australian component of the native range. D. kraussii oviposition preference, host suitability (parasitism rate, number of progeny, sex ratio) and offspring performance measures (body length, hind tibial length, developmental time) were investigated with respect to the four fly species in the laboratory in both no-choice and choice situations. The parasitoid accepted all four fruit fly species for oviposition in both no-choice and choice tests; however, adult wasps only emerged from B. jarvisi and B. tryoni. Through dissection, it was demonstrated that parasitoid eggs were encapsulated in both B. cacuminata and B. cucumis. Between the two suitable hosts, measurements of oviposition preference, host suitability and offspring performance measurements either did not vary significantly or varied in an inconsistent manner. Based on our results, and a related study by other authors, we conclude that D. krausii, at the point of oviposition, cannot discriminate between physiologically suitable and unsuitable hosts.
Phylogenetic relationships of some economically important cereal plants based on genome characterization using molecular markers

Genomes of 14 cereal germplasms (three barley cultivars: G124, G128, and G2000; two maize cultivars: Hybrid 10, and Hybrid 311; three rice cultivars: Sakha 101, Sakha 102, and G 182; two sorghum cultivars: white sorghum, and red sorghum; and four wheat cultivars: Sakha 95, Gemmizah 9, G 168, and Sakha 93) were characterized using two molecular markers: inter simple sequence repeat polymerase chain reaction (ISSR-PCR) and randomly amplified polymorphic DNA PCR (RAPD-PCR) to address the genetic relationships among them. Ten ISSR primers were used for fingerprinting the 14 cereal cultivars. A total of 109 ISSR markers of 400–3000 bp were scored as a result of ISSR-PCR markers. In addition, 130 RAPD markers were scored as a result of fingerprinting the same cultivars using 15 RAPD primers. ISSR-PCR and RAPD-PCR data were analyzed separately and together using the numerical taxonomy system of multivariate statistical (NTSYS-pc) program to address the genetic relationships among the 14 cereal cultivars under study. All the resulting dendrograms showed that the cereal germplasms under study were grouped into two clusters; the first one consists of maize and sorghum cultivars that appeared closely related to each other, whereas the second cluster consists of rice, wheat and barley. In the second cluster, barley and wheat cultivars appeared closer to each other than rice. This study showed that both ISSR and RAPD markers succeeded in characterizing the genomes of the cereal crop cultivars under study and succeeded in addressing their phylogenetic relationships.