Miracle-dz/UniFAR-FTUs huggingface dataset:
Identification of the functional states of human vitamin K epoxide reductase from molecular dynamics simulations

In mammalians, the enzymatic activity of vitamin K epoxide reductase (VKORC1) requires a protein conformational reorganisation that includes several transient enzymatic states involving a dynamic electron transfer. Regarding the structurally non-characterised human enzyme (hVKORC1), this process remains poorly explained and the different redox states of the enzyme generated by its biochemical transformation are unknown. Here, we report a 3D model of the fully reduced hVKORC1 at the atomistic level. By exploring this model through molecular dynamics (MD) simulations, we established the most probable intermediate states of the enzyme which were used for generation of the putative functionally-related enzymatic states. Enzymatic functionality of each state was assigned by probing their recognition properties with respect to vitamin K in its quinone and hydroxyquinone forms. Two states were identified as contributing to the two-step vitamin K transformation. The state highly selective for native vitamin K was further validated through analyses of its free energy of binding with vitamin K agonists (VKAs) that showed a high correlation with the experimental inhibiting constants.
The contribution of flight capability to the post‐fledging dependence period of golden eagles

The period prior to an individual emigrating from its natal site and initiating dispersal is important for developing the skills that are ultimately required for surviving natal dispersal. Using a novel method to quantify the early movements of 35 juvenile golden eagles fitted with satellite transmitters, we hypothesised that variation in golden eagles’ post-fledging dependence period (PFDP) was determined by variation in how quickly movement skills were acquired in order to become independent and disperse. Twenty nine young eagles exhibited an initial increase in mobility (“ontogenic phase”) levelling off after a median of 68 days, followed by a period of maintained mobility (“maintained phase”) that lasted a median of 99 days (range 24 - 176). Eagles that developed their mobility more quickly during the ontogenic phase had a correspondingly shorter ontogenic phase. Despite this, most of the inter-individual variation in the length of the PFDP resulted from variation in the length of the “maintained phase”. In general, females (the larger sex) developed more slowly and had a longer ontogenic phase. Males exhibited dispersal strategies around two modes with some dispersing early (mode 1: 89.5 days) and others late (mode 2: 220 days). In contrast females dispersed around a unimodal distribution of timing (mode 167.5 days). Apart from six individuals (mostly males) which dispersed with no discernible maintained phase, most offspring remained in the parental home range after they were fully mobile, even those that developed mobility quickly, suggesting that the PFDP in golden eagles is not simply a function of physical capacity for independence, but also a period when young eagles decide to remain, and are tolerated by parents, in their parental home range before dispersing. We suggest that delaying dispersal may be a beneficial strategy for young raptors facing a competitive environment after PFDP. This article is protected by copyright. All rights reserved.
Efficacy of a Kalanchoe gastonis-bonnieri extract to control bacterial biofilms and dental calculus in dogs

Abdalla S.L. , Costa S.S. , Gioso M.A., Casanova L.M. , Coutinho M.A.S. , Silva M.F. A. , Botelho M.C. S.N. & Dias R.S. G. 2017. Efficacy of a Kalanchoe gastonis-bonnieri extract to control bacterial biofilms and dental calculus in dogs. Pesquisa Veterinária Brasileira 37(8):859-865. Departamento de Cirurgia, Faculdade de Medicina Veterinária e Zootecnia, Universidade de São Paulo, Avenida Prof. Dr. Orlando Marques de Paiva 87, Cidade Universitária, São Paulo, SP 05508-270, Brazil. E-mail: pgcir@usp.br An aqueous leaf extract of the medicinal species Kalanchoe gastonis-bonnieri (here denominated KGB) has been found to be effective as an antimicrobial agent against canine oral cavity bacteria in in vitro assays. In this study, we investigated the effect of topic oral administration of KGB on the development of dental biofilm in Beagle dogs. The experiments were performed with an experimental group (0.2% of KGB extract), a negative control group (0.9% of saline solution) and a positive control group (0.12% chlorhexidine). Each treatment was sprayed into the oral cavity daily for 28 days. Thirty Beagle dogs with similar characteristics and kept under the same management and diet were used. The measurement of dental plaque and calculus was performed using a computerized analytical method. The phenolic profile of KGB extract was analyzed by HPLC-DAD. KGB extract at 0.2% showed efficacy in controlling the formation of plaque compared to the negative control group, and dental calculus in relation to the negative and positive control groups. A significant difference was observed among these three groups. Peaks attributed to flavonoids and phenolic acids were identified in the HPLC-DAD chromatogram of the KGB extract. The presence of these substances could be related to the activity observed. Our findings demonstrate that treatment with KGB is effective in controlling periodontal disease in dogs, providing new insights into the medicinal properties of this plant. KGB extract has a potential use as a supplemental agent in pharmaceutical products for the prevention of periodontal disease.
Phosphorus transfer at a small catchment in southeastern Brazil: distributed modelling in different land use scenarios

Identificar e classificar areas quanto ao risco de perda de nutrientes sao passos importantes para o manejo integrado de bacia hidrografica. O objetivo deste estudo foi aplicar o modelo Indice P na bacia hidrografica das Posses, Extrema-MG. O Indice P foi empregado sobre as condicoes atuais de uso da terra na bacia hidrografica das Posses e na simulacao de dois cenarios: cenario 1, o fertilizante P foi aplicado para todos os usos, exceto para florestas nativas e, cenario 2, alem do fertilizante P ser aplicado da mesma forma que no cenario 1, considerou-se que as Areas de Protecao Ambiental referentes as matas ciliares e nascentes fossem totalmente restituidas. Considerando o uso atual, quase toda a bacia hidrografica (91,4%) apresentou baixo risco de perda de P. O maior Indice de P foi associado a lavouras e plantacoes de eucalipto. No cenario 1, as pastagem apresentaram Indice P baixo (15,1%), medio (45,5%), alto (27,1%) e muito alto (12,3%). No cenario 2, as Areas de Protecao Ambiental promoveram uma reducao de 37,6% no risco de perda de P do cenario 1. Dessa forma, os resultados do modelo indicam que o reflorestamento de matas ciliares pode reduzir o risco de perdas de P no caso do aumento do uso de fertilizantes. O Indice P e uma potencial ferramenta para promocao do uso criterioso de fertilizantes e de praticas conservacionistas na bacia hidrografica das Posses.
Seed depletion and landscape structure affect aggregative response in two wintering passerine birds

ABSTRACT Capsule: Seed abundance but also seed depletion during winter modifies habitat use and aggregation behaviour of Eurasian Sky Lark Alauda arvensis and Meadow Pipit Anthus pratensis. Aims: To investigate the effect of seed abundance on the density of two passerine birds, the Eurasian Sky Larks and the Meadow Pipit, at an agricultural landscape scale during winter. Methods: Bird counts as well as seed density measurements were carried out in winter to quantify the aggregative response of farmland birds to seed abundance from November to March. Results: Seed resources varied by a factor of ten between crop types, but declined so sharply over the winter that seed abundance was low and similar among crop types by late winter. Sky Larks selected for higher seed density plots, but only at the end of winter when the resources were the lowest. Conversely, Meadow Pipits did not show any aggregative response to seed abundance. Conclusion: These results show that an uptake of seed-rich habitats in agricultural landscape would be very beneficial for wintering granivorous birds, by fulfilling the late winter ‘hungry gap’. The inclusion of seed mixtures in habitats that attract high densities of birds and retain seeds until late winter is of primary interest.
The genetic variation of lactase persistence alleles in northeast Africa

Lactase persistence (LP) is a well-studied example of a Mendelian trait under selection in some human groups due to gene-culture co-evolution. We investigated the frequencies of genetic variants linked to LP in Sudanese and South Sudanese populations. These populations have diverse subsistence patterns, and some are dependent on milk to various extents, not only from cows, but also from other livestock such as camels and goats. We sequenced a 316bp region involved in regulating the expression of the LCT gene on chromosome 2, which encompasses five polymorphisms that have been associated with LP. Pastoralist populations showed a higher frequency of LP-associated alleles compared to non-pastoralist groups, hinting at positive selection also in northeast African pastoralists. There was no incidence of the East African LP allele (−14010:C) in the Sudanese groups, and only one heterozygote individual for the European LP allele (−13910:T), suggesting limited recent admixture from these geographic regions. Among the LP variants, the −14009:G variant occurs at the highest frequency among the investigated populations, followed by the −13915:G variant, which is likely of Middle Eastern origin, consistent with Middle Eastern gene-flow to the Sudanese populations. The Beja population of the Beni Amer show three different LP-variants at substantial and similar levels, resulting in one of the greatest frequencies of LP-variants among all populations across the world.
Acoustic communication and reproductive behaviour in the aquatic frog Xenopus laevis (Pipidae), a field study

Abstract We studied the acoustic and reproductive behaviour of the clawed frog, Xenopus laevis, in a pond with clear water in South Africa over a period of two months. It contained 21 adult males and females. Each was marked with a transponder so that the behaviour of individuals could be tracked. The animals inhabited the bottom of the pond. They were active from dusk to midnight. Series of nights in which several males called alternated with series without calling. Simultaneous calls were not synchronised. On nights when males called, several of them established territories on the bottom of the pond that they defended against other males. They delineated the territory by calling along its borders. When meeting a male intruder they emitted an encounter call, followed by a fighting call if they fought. At the end of a fight the loser emitted a release call. Territories could remain constant over several weeks. They were abandoned on nights without calling, but re-established by the same individuals at the same locations on nights with calling. When a female entered a territory, the male approached, started the courtship call and attempted amplexus. The female usually rejected the male while emitting a release call. Females spawned synchronously on one or two nights, with weeks without oviposition in-between. Eggs were laid individually or in small groups on hard structures all over the pond. The adults preyed upon the tadpoles and only a few single tadpoles remained after two weeks. Raising the water level stimulated calling activity.
Regulation of the FGF/ERK Signaling Pathway: Roles in Zebrafish Gametogenesis and Embryogenesis

Signaling cascades, such as the extracellular signal-regulated kinase (ERK) pathway, play vital roles in early vertebrate development. Signals through these pathways are initiated by a growth factor or hormone, are transduced through a kinase cascade, and result in the expression of specific downstream genes that promote cellular proliferation, growth, or differentiation. Tight regulation of these signals is provided by positive or negative modulators at varying levels in the pathway, and is required for proper development and function. Two members of the dual-specificity phosphatase (Dusp) family, dusp6 and dusp2, are believed to be negative regulators of the ERK pathway and are expressed in both embryonic and adult zebrafish, but their specific roles in gametogenesis and embryogenesis remain to be fully understood. Using CRISPR/Cas9 genome editing technology, we generated zebrafish lines harboring germ line deletions in dusp6 and dusp2. We do not detect any overt defects in dusp2 mutants, but we find that approximately 50% of offspring from homozygous dusp6 mutants do not proceed through embryonic development. These embryos are fertilized, but are unable to proceed past the first zygotic mitosis and stall at the one-cell stage for several hours before dying by 10 hours post fertilization. We demonstrate that dusp6 is expressed in the gonads of both male and female zebrafish, suggesting that loss of dusp6 causes defects in germ cell production. Notably, the 50% of homozygous dusp6 mutants that complete the first cell division appear to progress through embryogenesis normally and give rise to fertile adults.
Pigments in Fruits and Vegetables : Genomics and Dietetics

This comprehensive treatise provides insight into pigment biosynthesis and dietetics. The text includes current reviews on the genomics of carotenoid, flavonoid, and betalain biosynthesis in plants and the dietetics of these pigments in humans. Pigments biosynthesized in plants are a source of attractive colors in nature and essential nutrients in our daily fruit, vegetable, and grain diet. Deciphered from general perspectives and specific fruits and vegetables, genomics focuses on enzymatic genes and regulatory molecular mechanisms in the biosynthesis pathways to produce these pigments in plants. Dietetics focuses on the nutritional and medical benefits to human health from these pigments as nutrients, nutraceuticals, and disease prevention agents when they are ingested from pigment-abundant plant food and metabolized in human body. This work contributes to an expanding awareness of the dietetic benefits to the daily consumption of pigment-rich fruit, vegetable, and grain food
Small RNA-Dependent Gene Silencing in the Green Alga Chlamydomonas reinhardtii : Functions and Mechanisms

Microalgae exhibit enormous diversity and can potentially contribute to the production of biofuels and high-value compounds. However, for most species, our knowledge of their physiology, metabolism, and gene regulation is fairly limited. In eukaryotes, gene silencing mechanisms play important roles in both the reversible repression of genes that are required only in certain contexts and the suppression of genome invaders such as transposons. The recent sequencing of several algal genomes is providing insights into the complexity of these mechanisms in microalgae. Collectively, glaucophyte, red, and green microalgae contain the machineries involved in repressive histone H3 lysine methylation, DNA cytosine methylation, and RNA interference. However, individual species often only have subsets of these gene silencing mechanisms. Moreover, current evidence suggests that algal silencing systems function in transposon and transgene repression but their role(s) in gene regulation or other cellular processes remains virtually unexplored, hindering rational genetic engineering efforts.
Efficacy of Ethanolic Leaf Extract of Chromolaena odurata in Controlling Sitophilus zeamais in Stored Maize

Sitophilus zeamais Motschulsky is among the important pests which attack stored maize. It is listed in addition to Prostephanus truncatus as the two most damaging species of maize in West Africa. In Ghana about 15% of maize grains harvested is lost to S. zeamais. A laboratory study was conducted at the Entomology laboratory of the Faculty of Agriculture of Kwame Nkrumah University of Science and Technology, Kumasi, to determine the efficacy of Chromolaena odorata (L) R. M. King and H. Robintson ethanolic leaf extract for Sitophilus zeamais control. The bioactivity of these extracts was assessed under average laboratory conditions of 26°C and relative humidity of 80%. The leaf extract at four dosage levels (0.0, 2.5, 5.0 and 10.0 ml) were mixed with 50 g of disinfested MAMABA maize variety in 750 ml plastic containers and the effect on insect mortality, progeny production and grain damage were assessed. The repellent action of these extracts at 0.0, 5.0, 10.0, 20.0 ml on Sitophilus zeamais was also evaluated. The leaf extract showed significant difference between 10.0 and 5.0 ml on one hand and 2.5 and control on the other hand. The 10.0 Original Research Article Jnr et al.; JEAI, 14(5): 1-10, 2016; Article no.JEAI. 29216 2 ml that recorded the highest mortality could inflict only as low as 8.75% after 7 days. The maize grain treated with the various dosage levels of the leaf extract showed much promise by significantly reducing the number of progeny produced by S. zeamais as compared with the control. Grain weight loss in leaf extract treated grains was dose dependent ranging from 3.51% in the highest dose to 11.34% in the control with significant differences. The leaf extracts was not repellent to the weevil. The correlation between grain weight loss and progeny production was very strongly positively correlated in the leaf extract effect.
Diagnostic utility of an immunochromatography test for the detection of Leptospira IgM antibodies in domestic dogs

Azócar-Aedo L. , Smits H. & Monti G. 2017. Diagnostic utility of an immunochromatography test for the detection of Leptospira IgM antibodies in domestic dogs. Pesquisa Veterinaria Brasileira 37(7):708-712. Facultad de Ciencias Veterinarias, Universidad Austral de Chile, Independencia 641, PO Box 567, Valdivia, Chile. E-mail: luciaazocaraedo@gmail.com A cross-sectional study using 99 serum samples of dogs from southern Chile was conducted to determine the diagnostic utility of a rapid immunochromatography assay for the detection of Leptospira specific IgM antibodies as screening test and as a potential aid in the diagnosis of leptospirosis in animals with and without clinical suspicion of the disease. The Microscopic Agglutination Test (MAT) was used as reference assay. Anti-Leptospira antibodies were detected in 37.3% of the dogs with MAT. Using the immunochromatography test, specific IgM antibodies were found in 13.1% of sampled dogs. The sensitivity of the rapid test as screening assay was 29.7% (95% Confidence Interval=16.4-47.2) and the specificity was 96.7% (95% Confidence Interval=87.8-99.4). 40.0% of the canines with clinical suspicion of leptospirosis and 37.1% of dogs without clinical signs were serological reactors to MAT, but none of MAT reactive dogs with clinical suspicion tested positive in the rapid test. Rapid and user-friendly diagnostic procedures for canine leptospirosis such as this immunochromatography assay could be important tools to use in clinical practice, however, further studies are needed to obtain more information about their utility, considering that diagnostic tests could not have similar performances in different geographic locations, clinical and epidemiological contexts.
Effect of Insect Infestation (C. Chinesis) on the Physio-Chemical Properties of Green Gram (Vigna Radiata L. Wilzeck) During Storage

Abstract The present study was conducted to evaluate the physico-climate changes in insect infested green gram stored for six months. With increase in storage period, insect infestation increased resulting in a decrease in weight, density, embedded larvae (%) true protein and methionine contents, while all other components viz. moisture, ash, crude, fiber, crude protein, curd fat, non-protein nitrogen and uric acid contents increased. The changes in these parameters were significant as compared to control samples and were the highest at the end of six months storage period.
Camel’s wharton jelly mesenchymal stem cell is a novel tool for regeneration of induced diabetes mellitus

Wharton's jelly derived mesenchymal stem cell (WJ-MSC) possesses therapeutic properties. WJ-MSC was nontumorigenic, acquired high rate of proliferation and their immune privileged status make them ideal for both autologous and allogeneic use in regenerative medicine applications. This study examined the possible therapeutic potentials of camel WJ-MSC in regeneration of damaged pancreatic diabetic tissues in rats. Streptozotocin (STZ) induced diabetic rats showed pancreatic tissues degeneration in parallel with suppressed expressions of the insulin, smad-2, PDX-1 and SIRT-1. The infusion of WJ-MSC markedly alleviated the altered induced diabetes by significant increase in quantitative genes expression and significantly enhanced histopathological cellular integrity of islets of Langerhans and pancreatic acini compared to STZ group. The infusion of WJ-MSC enhanced the liver and kidneys functions supported by decrease of ALT, AST and urea levels than diabetic group. These findings shows for the first time the novel valuable therapeutic role of camel WJ-MSC on pancreatic tissue regeneration with function retrieval and reduced the side effects of STZ on the liver and kidneys.
Antibacterial activity of essential oil from Wedelia trilobata leaves against Propionibacterium granulosum

This study reports on the in vitro antibacterial activity of hydro-distilled essential oil from Wedelia trilobata (L.) Hitchc leaves against Propionibacterium granulosum. The percentage yield of this essential oil via hydrodistillation was 0.21±0.01% (v/w). A total of 112 chemical components present in the essential oil from W. trilobata leaves representing 62% of the total oil were identified by gas chromatography-mass spectrometry. The main bioactive constituents were monoterpenes, α-pinene (19.5%), α-phellandrene (7.4%), limonene (3.6%), oxazine (3.3%), and β-pinene (3.1%). This essential oil showed the moderate antioxidant capacity of 1,1-diphenyl-2-picrylhydrazyl (DPPH) compared to the trolox equivalent antioxidant capacity and gallic acid equivalent, and possessed anti-P. granulosum activity from the inhibition zone from the disc diffusion method. The minimum inhibitory concentration (MIC, 595±206 μg/ml) and minimum bacterial concentration (MBC, 1191±413 μg/ml) values of this essential oil were higher than the MIC (1.30±0.37 μg/ml) and MBC (2.61±0.91 μg/ml) values of commercial clindamycin gel and the MIC (52±18 μg/ml) and MBC (104±36 μg/ml) values of commercial benzoyl peroxide gel. The results provide new information on the hydro-distilled essential oil from W. trilobata leaves, which may be important for developing new alternative anti-acne products.