Miracle-dz/UniFAR-FTUs huggingface dataset:
GENOMIC PERSPECTIVES ON AMPHIBIAN EVOLUTION ACROSS MULTIPLE PHYLOGENETIC SCALES

OF DISSERTATION GENOMIC PERSPECTIVES ON AMPHIBIAN EVOLUTION ACROSS MULTIPLE PHYLOGENETIC SCALES Genomes provide windows into the evolutionary histories of species. The recent accessibility of genome-scale data in non-model organisms and the proliferation of powerful statistical models are now providing unprecedented opportunities to uncover evolutionary relationships and to test hypotheses about the processes that generate and maintain biodiversity. This dissertation work reveals shallow-scale species boundaries and population genetic structure in two imperiled groups of salamanders and demonstrates that the number and information content of genomic regions used in species delimitation exert strong effects on the resulting inferences. Genome scans are employed to test hypotheses about the mechanisms of genetic sex determination in cryptobranchid salamanders, suggesting a conserved system of female heterogamety in this group. At much deeper scales, phylogenetic analyses of hundreds of protein-coding genes across all major amphibian lineages are employed to reveal the backbone topology and evolutionary timescales of the amphibian tree of life, suggesting a new set of hypotheses for relationships among extant amphibians. Yet, genomic data on their own are no panacea for the thorniest questions in evolutionary biology, and this work also demonstrates the power of a model testing framework to dissect support for different phylogenetic and population genetic hypotheses across different regions of the genome.
Taxonomy of the Genus Blacodatus Koch, 1963 with Description of a New Species from South Africa (Coleoptera: Tenebrionidae: Opatrini)

Abstract. Blacodatus szutkowskii, sp. nov. from South Africa is described, illustrated and compared with its relative — Blacodatus vertagus (Mulsant et Rey, 1859). A new generic concept of the previously monotypic Blacodatus is proposed. The distribution map is presented.
Occurrence of Idiosepius (Mollusca: Cephalopoda) in Indonesian Waters

ABSTRAK Jenis Idiosepius (Mollusca: Cephalopoda) di perairan Indonesia. Informasi dan penelitian tentang sotong mini “pygmy squid” marga Idiosepius yang ada di Indonesia sangat kurang, meskipun pernah dilaporkan setidaknya ada tiga jenis dijumpai di Ambon, Ternate, Banda, Balikpapan, Sibolga dan Lombok. Dalam tulisan ini diuraikan karakter morfologi, habitat dan distribusi empat jenis sotong mini jenis I. picteti, I. pygmaeus, I. biserialis dan I. pygmaeus herbereri. Karena ukurannya yang sangat kecil, jenis sotong ini tidak diminati oleh para nelayan, sehingga hanya sedikit data yang diketahui mengenai pertumbuhan, reproduksi dan siklus hidupnya. Penelitian ini bertujuan untuk memberikan gambaran ringkas tentang sistematik, habitat, siklus hidup dan distribusi Idiosepius. Hasil studi ini mencatat lokasi baru (new record) ditemukannya sotong mini jenis I. biserialis dan I. pygmaeus khusus dari perairan pantai di Lombok. Hasil penelitian juga menunjukkan bahwa beberapa jenis Idiosepius memiliki sebaran yang luas di perairan Indonesia kecuali jenis I. picteti hingga saat ini hanya dijumpai di Ambon. Hasil studi diharapakan menambah khasanah pengetahuan tentang sotong mungil ini sekaligus memacu para peneliti untuk lebih memperhatikan genus ini. Keywords: Cephalopoda, distribution, habitat, Idiosepiidae, Indo-Pacific Kata kunci: Cephalopoda, distribusi, habitat, Idiosepiidae, Indo-Pacific
Genetic variation in two African Euprepis species (Reptilia, Scincidae), based on maximum-likelihood and Bayesian analyses: taxonomic and biogeographic conclusions

In the present study we applied Bayesian and maximum likelihood methods of phylogenetic inference to mitochondrial 12S rRNA and I6S rRNA gene fragments to examine the degree of genetic variation within the West African Euprepis affinis and the widespread African Euprepis maciililabris. We found considerable genetic differentiation in Euprepis affinis, revealing a cryptic species. Similarly, we could show that Euprepis maciililabris is comprised of at least two distinct species, with the nominotypic form being distributed in West Africa, and a cryptic species in East Africa. We discuss biogeographical aspects and outline the relevant evolutionary processes, which probably led to allopatric speciation in Euprepis luaculilabris. Evaluating the systematic status of Euprepis comorensis and Euprepis casuarinae, two species formerly recognized as subspecies of E. maculilabris, we underlined the need of further studies to clarify their taxonomic status.
Phytochemical, antioxidant and antimicrobial assay of mushroom metabolite from Pleurotus pulmonarius –LAU 09 (JF736658)

The phytochemical, antioxidant and antimicrobial in vitro assay of Pleurotus pulmonarius-LAU09 (JF736658) was evaluated. The metabolite obtained from Pleurotus pulmonarius was characterized by IR analysis. It revealed the absorption of O-H, C-H, C-O bonds and hydrated water peaks (1650.6cm-1), without no absorption at uronic acid peak (1730cm-1). 1HNMR spectrum analysis of the metabolite has anomeric carbon peaks of 5.10 and 4.51ppm, characterized as α and β linkages of glucan compoumd. The phytochemical screening of the mushroom extract revealed the presence of alkaloids, saponins, steroids, phlobatannins, flavonoids and anthraquinones. The metabolite was active against all tested pathogens except Pseudomonas aeruginosa with percentage activity of 85.75%. The highest zone of inhibition was obtained against Staphylococcus aureus (30mm), while the lowest zone size obtained was against E. coli (7mm). The antioxidant activity of evaluated mushroom extracts gave positive results with free radical scavenging activity found to be higher in all used in vitro methods. The result obtained from this study has shown the potential of mushroom extract as a potent therapeutic agent and a food supplement. Keywords: phytochemical, antioxidant, antimicrobial, metabolite, mushroom.
APLICAÇÃO DE FUNGICIDAS EM DIFERENTES ESTÁDIOS FENOLÓGICOS DA CULTURA DO MILHO (Zea mays) NO CONTROLE DE DOENÇAS

O objetivo deste trabalho foi avaliar os efeitos da epoca de aplicacao dos fungicidas piraclostrobin + epoxiconazole e azoxystrobin + ciproconazole na cultura do milho no controle da mancha foliar de phaeosphaeria (Phaeosphaeria maydis), ferrugem comum (Puccinia sorghi), mancha foliar de cercospora (Cercospora zea-maydis), mancha de diplodia (Diplodia macrospora) e a podridao de colmo. Foram instalados tres experimentos, no delineamento de blocos ao acaso com 4 repeticoes, em parcelas medindo 3,2 x 5,0 metros. No experimento 1, foi aplicado o fungicida piraclostrobin + epoxiconazole na dose de 99,75 + 37,5 g i.a. ha-1, mais oleo mineral (Assist) na dose de 500 mL p.c. ha-1 e nos experimentos 2 e 3 foi aplicado o fungicida azoxystrobin + ciproconazole na dose de 70 + 28 g.i.a. ha-1, mais oleo mineral parafinico (Nimbus) na dose de 600 mL p.c. ha-1. No experimento 1, as aplicacoes foram realizadas nos estadios fenologicos V8; V16; V8 e V16; V12; V15; VT e R2, sendo avaliada a severidade da mancha foliar de phaeosphaeria e mancha foliar de cercospora nos estadios R3, R4 e R5 e a podridao de colmo no estadio R6. Com os dados de severidade calculou-se a area abaixo da curva de progresso da doenca para a mancha foliar de phaeosphaeria. Os menores valores de AACPD ocorreram nos tratamentos com uma aplicacao em V16, com duas aplicacoes em V8 e V16, com controles de 74 a 80%. Nos experimentos 2 e 3, as aplicacoes dos fungicidas foram realizadas em V8; V16; R2; V8 e V16; V8 e R2; V16 e R2; V8, V16 e R2. Avaliou-se no experimento 2 a mancha foliar de cercospora, mancha foliar de phaeosphaeria e a podridao de colmo. No controle da mancha foliar de cercospora os melhores tratamentos foram as aplicacoes no estadio fenologico V8, os quais coincidiram com a ocorrencia da doenca na cultura. Para mancha foliar de phaeosphaeria, os menores valores na AACPD foram os com duas aplicacoes em V8 e V16, V16 e R2 e as tres aplicacoes em V8, V16 e R2, com controle variando de 25 a 40%. No experimento 3, foram avaliadas a ferrugem comum, mancha foliar de phaeosphaeria, mancha de diplodia e a podridao de colmo. Para ferrugem comum os tratamentos que continham aplicacao em V8 foram os mais eficientes com porcentagem de controles acima de 80%. Em relacao a mancha foliar de phaeosphaeria, o melhor tratamento para AACPD foi o com tres aplicacoes (V8, V17 e R2) com 27% de controle. Os tratamentos nao controlaram a mancha de diplodia. Nos tres experimentos avaliou-se tambem graos ardidos, peso de mil sementes e produtividade, constatando-se somente no experimento 2, diferenca significativa quanto ao numero e estadio fenologico de aplicacao, para as variaveis peso de mil sementes e produtividade, destacando as 3 aplicacoes em V8, V16 (17), R2 e as 2 aplicacoes em V16 (17), R2 e V8, V17.
Genetic variability and character association for seed yield in chickpea ( Cicer arietinum L.)

The present investigation was conducted to estimate the genetic variability and character association existing among 18 chickpea genotypes including one local check which were evaluated during Rabi 2016-17 under randomized block design having three replications. The data was recorded for days to 50% flowering, plant height, number of primary branches per plant, number of pods per plant, days to maturity, biological yield per plant, harvest index, seed-index and seed yield per plant. Analysis of variance revealed significant differences among the genotypes for all the characters studied. Number of pods per plant followed by days to maturity and seed-index exhibited high estimates of heritability (bs) as well as genetic advance. Seed-index and number of pods per plant exhibited high estimates of genetic advance expressed as percent of mean. Correlation coefficient analysis revealed that seed yield per plant exhibited significant and positive correlation both at genotypic and phenotypic level with biological yield per plant, harvest-index and only at genotypic level with number of pods per plant. Hence, these characters may serve as effective selection criterion for yield improvement in chickpea.
PyBoost: A parallelized Python implementation of 2D boosting with hierarchies

Motivation: Gene expression is controlled by networks of transcription factors that bind specific sequence motifs in regulatory DNA elements such as promoters and enhancers. GeneClass is a boosting-based algorithm that learns gene regulatory networks from complementary paired feature sets such as transcription factor expression levels and binding motifs across conditions. This algorithm can be used to predict functional genomics measures of cell state, such as gene expression and chromatin accessibility, in different cellular conditions. We present a parallelized, Python-based implementation of GeneClass, called PyBoost, along with a novel hierarchical implementation of the algorithm, called HiBoost. HiBoost allows regulatory logic to be constrained to a hierarchical group of conditions or cell types. The software can be used to dissect differentiation cascades, time courses or other perturbation data that naturally form a hierarchy or trajectory. We demonstrate the application of PyBoost and HiBoost to learn regulators of tadpole tail regeneration and hematopoeitic stem cell differentiation and validate learned regulators through an inducible CRISPR system. Availability: The implementation is publicly available here: https://github.com/kundajelab/boosting2D/.
Reproduction and Trypanosoma congolense in Nigerian West African Dwarf ewes:I. Effects on the estrous cycle

: Ten cycling Nigerian West African Dwarf (WAD) ewes were used to determine the effect of Trypanosoma congolense infection on the estrous cycle. The estrus of ewes were synchronized using intravaginal progesterone sponges and divided into 2 groups (A and B) of 5 ewes each after 54 days (3 cycles). The ewes in group A were inoculated with blood containing approximately 5 × 10 5 trypanosomes per ml of blood while ewes in group B served as the uninfected control. All the ewes were monitored from infection till the end of the study (56 days). Ewes in the infected group had silent estrus with clinical trypanosomosis that was characterized by undulating parasitemia, intermittent pyrexia, anemia and weight loss. There was no statistical (p > 0.05) difference between the mean estrous cycle length of the infected and the control groups. Estrus behavior of seeking the male, tail wagging, bleating, restlessness, edema of the vulva and mucus discharge from the vulva were observed in both groups at estrus, the basal progesterone profile corresponded with a true estrus rate of 60 % and 90 % for the infected and control groups respectively. However, there were statistical (p < 0.05) differences in the duration and intensity of estrus between the infected and control groups. The study shows that T. congolense infection affects the estrous cycle of Nigerian WAD but not detrimental to cause serious infertility.
Bakteri Entomopatogen Sebagai Agen Biokontrol Terhadap Larva Spodoptera Litura (F.) [Entomopathogenic Bacteria as Biocontrol Agent Against Spodoptera Litura (F.) Larvae]

Spodoptera litura (F.) (Lepidoptera: Noctuidae) is one of the agricultural pests that attacking almost all kinds of herbaceous plants, especiallyvegetables. Insect control using entomopathogenic bacteria is an alternative strategy that is effective and has a lower environmental impact than the use of synthetic insecticides. The purpose of this research was to explore entomopathogenic bacteria that have insecticidal activity against S. litura larvae at various stages of instars. The result showed that 25% of total number of isolated bacteria have potency as entomopathogenic bacteria. Isolate Staphylococcus sciuri strain BLSP-3 and isolate Serratia sp. strain BLSP-4 showed the highest larvicidal activity against the first and second instar larvae of S. litura 83% and 86%, respectively. The activity against on the third instar larvae however was only by 40%. However, the mortality caused by both isolates was lower than that of Bacillus thuringiensis (more than 90% mortality to the first and second instars and 80 % of the third instar larvae). It is suggested that both of isolates are potential to be developed further as a biocontrol agent to control S. litura population.
The Role of Ethanolic Extracts of Leaves and Roots of Lantana camara (L.) in the Management of Pests of Okra Abelmoschus esculentus (L.) Moench

The cultivation of many crops in Africa is negatively affected by a number of constraints, the most important of which is the incidence of pests and diseases. In many areas of the world, the most preferred option in the management of pests is the application of synthetic chemical pesticides. Due to the negative effects of pesticides on humans and the environment as a whole, efforts are being made to find alternatives for pest management. Ethanolic extracts of the leaves and roots of Lantana camara were tested against the major pests of okra, Abelmoschus esculentus. The plant extracts were compared with a standard chemical insecticide, Mektin (a.i 18 g/L abamectin) in a randomly complete block design with four treatments and three replications. Parameters studied included the major pests of the plant and the damage caused, leaf area, plant height as well as yield of okra. Cotton aphids, Aphis gossypii, the tobacco whitefly Bemisia tabaci and the cotton flea beetle, Podagrica puncticollis were the major pests encountered on okra plants. Aphis gossypii and B. tabaci populations were significantly lower on the L. camara-sprayed plots compared with the control plots. Similarly, P. puncticollis numbers were significantly smaller on the L. camara-sprayed plots than the control plots. There were no significant differences between the treatments and the control for plant height, leaf area and yield. The significant reduction in pests numbers on the L. camara-sprayed plots indicates its potential as an alternative to chemical insecticides, thereby reducing the reliance on chemical insecticides in the management of insect pests.
Correlation and path analysis in rainy season sorghum [Sorghum bicolour (L.) Moench]

Association and path analysis was attempted for five traits viz . , days to 50% flowering, plant height, panicle length, days to maturity, test weight and grain yield per plant. Thirty sorghum hybrids their respective parents and three checks were studied. Grain yield had expressed highly significant and positive correlation with plant height, panicle length, days to maturity and test weight at both genotypic and phenotypic levels. The characters that had positive direct effects on grain yield at both phenotypic and genotypic levels were test weight (0.543, 0.557), panicle length (0.352, 0.354) days to 50%flowering (0.169, 0.206) and days to maturity (0.113, 0.084). Plant height (-0.108,-0.0829) had direct effect in negative direction at both phenotypic level and genotypic level. The inter-relationship among these characters might be used in the breeding programme to exploit the yield potential and to develop high yielding improved varieties with ease and target oriented research.
Insulin-Like Growth Factor-Binding Protein

NEW MATERIAL: An insulin-like growth factor-binding protein comprising an amino acid sequence at least 85% homologous to the amino acid sequence beginning with position 1 and ending at position 289 represented by the formula or to any fragment thereof containing more than 20 amino acid residues. USE: A remedy for mammary cancer, renal cancer, diabetic proliferative retinopathy, abnormal growth of tall children, etc. PREPARATION: An adult liver cDNA library, for example, is introduced into Escherichia coli to transform it, which is cultured and screened by using a probe to select a clone which produces an insulin-like growth factor-binding protein, from which clone DNA is collected and treated with a restriction enzyme to obtain a fragment, which fragment is bonded to a vector and introduced into a eucaryotic cell to transform it and subsequently the cell line transformed is cultured to obtain an insulin-like growth factor-binding protein. COPYRIGHT: (C)1991,JPO
Effects of Zinc Foliar Nutrition on ‘Gala’ Apple (Malus Domestica Borkh) Fruit Quality

Gianguzzi, G. , G. Liguori, G. Sortino, G. Piva and V. Farina, 2017. Effects of zinc foliar nutrition on ‘Gala’ apple (Malus domestica Borkh) fruit quality. Bulg. J. Agric. Sci., 23 (2): 213–218 To improve fruit color features research has focused on the use of foliar nutrition with zinc. There is a lack of know about apples. The aim of this trial was to evaluate the effects of foliar zinc treatment on the qualitative characteristics of ‘Gala’ apple. Apple trees Cv ‘Gala’ were submitted to a foliar spray application of Zn in the form of aqueous solution of 0.2% and 0.4% zinc sulfate (ZnSO4) for three times. Fruit was harvested at commercial ripening and physicochemical parameters, yield, crop load, yield effi ciency and zinc leaf content were measured. Results revealed that yield, crop load, fruit weight, cover color index and cover color percentage of the observed trees was infl uenced by zinc foliar spray treatment in each harvest date. The foliar fertilization using zinc infl uenced yield and several fruit quality traits. Since the ZN1 and ZN2 treatments do not differ signifi cantly in the effect, the choice may lie in the adoption of the fi rst treatment as it yields more economic and sustainable outcomes.
Comprehensive analysis of intrinsically disordered protein content in organisms exposed to extreme ambient conditions

In this thesis, we analyzed the content of intrinsically disordered proteins (IDPs) in prokaryotic organisms adapted to extreme habitats. We conclude that the extremity of the organism environment has a considerable influence on the total content of IDPs, significantly more than phylogeny. Motivated by these results, we analyzed the protein disorder content in a culture of Saccharomyces cerevisiae (baker’s yeast) experimentally exposed to high temperatures by duplicating specific chromosomes.
Monitoring the threatened brush-tailed phascogale (Phascogale tapoatafa tapoatafa) at Sugarloaf Reservoir, Victoria

The brush-tailed phascogale (Phascogale tapoatafa tapoatafa) is a marsupial threatened in Victoria by habitat fragmentation and modification. As part of the development of infrastructure in phascogale habitat, Melbourne Water was required to improve habitat for the phascogale. We aimed to develop and test a method for monitoring phascogales on Melbourne Water land, and to assess the effectiveness of habitat improvements. Trapping, nest boxes, and cameras were all successful in detecting phascogales; however, cameras had the highest detection per unit effort. We suggest that future monitoring should favour camera surveys with trapping potentially every 3–5 years for acquisition of physical data.
Pelagic behavior of adult Greenland halibut (Reinhardtius hippoglossoides)

It is evident from several field experiments with vertical longlines and archival tags, as well as concurrent studies of predator-prey relationships, that adult specimens of the deep-water flatfish Greenland halibut (Reinhardtius hippoglossoides) make regular excursions several hundred meters through the water column. The distribution of longline catches within the water column is confined to a well-defined depth layer overlapping with the distribution of blue whiting (Micromesistius poutassou), an important prey species, and depth recordings from archival tags overlap with Atlantic herring (Clupea harengus), the other major fish prey. The degree of pelagic use varies with fish size as well as seasons. Smaller individuals are found further off the bottom, and pelagic activity is greatest during early autumn. Interaction with pelagic prey species can influence results from bottom trawl surveys.
Characterization of Gentamicin Resistance in Enteric Bacteria Isolated From Pseudomys Scripta-Elegans From Commercial Turtle Farms.

Several genera of aminoglycoside resistant enteric bacteria were isolated from commercial turtle farms. Citrobacter freundii and Proteus vulgaris were the most prevalent organisms. Gentamicin resistance, measured by minimum inhibitory concentrations (MIC), ranged as high as 100 /Ltg/ml. While resistance to other antibiotics was detected in gentamicin-resistant isolates, no correlation was observed between antibiotic resistance and plasmid content. Spontaneous mutation to gentamicin could not account for the high levels of gentamicin resistance found in the original isolates. Regions of chromosomal DNA encoding gentamicin resistance of 100 fig/ml were obtained from two Citrobacter freundii, two Proteus vulgaris, and two Salmonella enteritidis strains. These recombinant plasmids imparted a level of gentamicin resistance to Escherichia coli similar to that observed in the resistant isolates. The resistance gene was located on a 858 base pair DNA fragment. This fragment was common to both Citrobacter strains and hybridized with chromosomal DNA from several gentamicin-resistant enterics. The nucleotide sequences of the resistance genes obtained from Citrobacter freundii, Proteus vulgaris and Salmonella enteritidis shared complete homology.