Miracle-dz/UniFAR-FTUs huggingface dataset:
Neuroprotection Comparison of Different Nutraceutical Compounds Against Mechanistically Distinct Cell Death Inducing Agents

Neurodegenerative diseases like Alzheimer’s disease (AD), Parkinson’s disease (PD), and amyotrophic lateral sclerosis (ALS), include the progressive loss of structure and function of neurons leading to neuronal death. All of these diseases are fatal, as there is no cure for them. The causes of these diseases are unknown; however, there are many proposed mechanisms that lead to neurodegenerative diseases. Oxidative stress is the leading cause of cell death in neurodegenerative diseases, in addition to other mechanisms including endoplasmic reticulum stress, proteasome inhibition, nitrosative stress, inflammation and excitotoxicity. More understanding of the death mechanisms at work in neurodegeneration is necessary to find ways to block those mechanisms in order to slow or stop the progress of these disorders. Interest in nutraceutical compounds has increased recently because of the discovery their bioactive properties. Many studies have suggested that nutraceutical compounds have the ability to inhibit the different death
Survival and Virulence of Campylobacter spp. in the Environment

Campylobacter spp. is the most common cause of bacterial diarrhoea in humans worldwide. Therefore, rapid and reliable methods for detection and quantification of this pathogen are required. In this study, we have developed a reverse transcription quantitative real-time PCR (RT-qPCR) for detection and quantification of viable Campylobacter jejuni directly from chicken faecal samples. The results of this method and a DNA-based quantitative real-time PCR (qPCR) method were compared with those of a bacterial culture method. Using bacterial culture and RT-qPCR methods, viable C. jejuni cells could be detected for up to 5 days in both the C. jejuni spiked and the naturally contaminated faecal samples. We found that no RT-qPCR signals were obtained when viable C. jejuni cells could not be counted by the culture method. In contrast, using a DNA-based qPCR method, dead or non-viable Campylobacter cells were detected, and all tested samples were positive, even after 20 days of storage. The developed method for detection and quantification of viable C. jejuni cells directly from chicken faecal samples can be used for further research on the survival of Campylobacter in the environment. 2011 Institut Pasteur. Published by Elsevier Masson SAS. All rights reserved.
Genetic Diversity in Roselle (Hibiscus sabdariffa L.) for Fiber Yield Traits in North Coastal Zone of Andhra Pradesh, India

Roselle (Hibiscus sabdariffa L.) is an annual or perennial plant belonging to the large family Malvaceae and is cultivated in Tropical and Sub-Tropical regions for bast fiber, paper pulp or edible calyces, leaves and seeds (Osman et. al., 2011). In India, roselle is one of the most important bast fiber crops which occupies second place in area and production after jute and is mainly used for manufacturing of sacs, twines, carpets etc. (Satyanarayana et al., 2015). In India, the major growing states of roselle crop are Andhra Pradesh, Bihar, Orissa, West Bengal and Maharastra with an area of 84 thousand ha (during 2012-13) that produced 6.16 lakh bales (1bale = 180 kg) with an average productivity of about 13.20 q/ha (Sen and Karmakar, 2014). Raw jute, the fiber of commerce is extracted from the stem of two cultivated species of jute (tossa & white jute) and mesta (roselle & kenaf). Raw jute (jute and mesta) occupying only 0.55% of the International Journal of Current Microbiology and Applied Sciences ISSN: 2319-7706 Volume 6 Number 9 (2017) pp. 2335-2341 Journal homepage: http://www.ijcmas. com
Energy coefficients of plant foods for broiler chickens at different ages

In order to determine the apparent metabolizable energy (AME), the AME corrected for nitrogen balance (AMEn), the apparent coefficients of metabolization (ACM) of gross energy and the ACM corrected for nitrogen balance (ACMn), an experiment was conducted to evaluate five different plant foods (corn, soybean meal, deactivated full-fat soybean, wheat bran and soybean oil) for broilers at different ages (1-8, 11-18, 21-28, 31-38 and 41-48 days). The method of total excreta collection was used, divided into five metabolism assays. The birds were housed in metabolic cages in a completely randomized design, with five treatments and five replicates per treatment, totaling 25 experimental units. The AME and AMEn values increased with the age of the birds for most foods, except soybean meal. The smaller AMC and AMCn of gross energy were obtained for wheat bran. There was adjustment of the equation to the linear response plateau model for the ACM of corn, soybean meal and deactivated full-fat soybean. The wheat bran and soybean oil were adjusted to the linear regression model. The equations show that the digestibility of energy tends to increase with age, except for soybean meal, which had higher metabolization with younger birds. We conclude that the age of the birds influences the determination of the metabolizable energy of feed.
Translational profiling of adipocytes within adipose depots and intermuscular adipose tissues

The imbalance between energy intake and energy expenditure elicited a worldwide problem, which is obesity. Obesity is associated with wide array of medical disorders not only limited to cardiovascular diseases, but also extended to include immune disorders, as well as some types of cancer. Hence, there is an indispensible need for identifying new therapies for tackling this serious health burden. The pathophysiological aspects of obesity include the storage of excess energy as fat droplets in adipocytes within adipose depots. Another less studied aspect of obesity is the increased fat storage ectopically in other organs such as skeletal muscle, liver, pancreas, bone marrow and heart. In this study, we performed an adipocyte-specific RNAseq using a translating ribosomal affinity purification (TRAP) by crossing the transgenic TRAP mice with Adiponectin-Cre mice where Adiponectin is a mature fat cell protein. Using this approach, we have selectively isolated polysomes from Adiponectin-positive cells from brown, subcutaneous, visceral adipose depots and quadriceps muscle in mice. Using differential gene expression analysis (DEseq), we identified S100B as a BAT enriched protein whose role in fat metabolism has not been elucidated before. Here, we describe the role of S100B in inducing thermogenesis through activating lipolysis pathways. In vivo studies using overexpression adenovirus systems showed that S100B improved obesity-induced glucose intolerance and enhanced respiration capacity of mice. Moreover, loss of function experiments demonstrated a physiological role of S100B in stimulating lipolysis and ultimately in activating thermogenesis. We also applied the TRAP model for characterizing the transcriptomic make up of inter/intra-muscular adipose tissue (iMAT). IMAT represents one of the ectopic adipose tissues linked with insulin resistance. Identifying the transcriptomic pattern of iMAT represented a major challenge owing to their location. We demonstrate the close relationship between iMAT and subcutaneous fat cells both in their genetic signature and their ability to respond to cold. Collectively, the TRAP approach is a powerful tool for characterizing transcripts of mature adipocytes that can be utilized for discovering new regulators of adipose tissues. In addition, it can be used for deciphering other ectopically embedded adipocytes within organs such as the heart, pancreas and bone marrow.
Does habitat specialization shape the evolutionary potential of wild bird populations

Because specialist species evolved in more temporally and spatially homogeneous environments than generalist species, they are supposed to experience less fluctuating selection. For this reason, we expect specialists to show lower overall genetic variation as compared to generalists. We also expect populations from specialist species to be smaller and more fragmented, with lower neutral genetic diversity. We tested these hypotheses by investigating patterns of genetic diversity along a habitat specialization gradient in wild birds, based on estimates of heritability, coefficients of variation of additive genetic variance, and heterozygosity available in the literature. We found no significant effect of habitat specialization on any of the quantitative genetic estimators but generalists had higher heterozygosity. This effect was mainly a consequence of the larger population size of generalists. Our results suggest that evolutionary potential does not differ at the population level between generalist and specialist species, but the trend observed in heterozygosity levels and population sizes may explain their difference in susceptibility to extinction.
Amanita glarea , a new species in section Vaginatae from Pakistan

A new species, Amanita glarea , is described and illustrated from Pakistan. Molecular phylogenetic data derived from internal transcribed spacer (ITS) and nuclear ribosomal large subunit (LSU) regions along with morphological characters make it distinct from other currently known Amanita species. Amanita glarea is characterized by a grayish brown, slightly umbonate, pileus having universal veil remnants and striate margins, a long ringless stipe with a saccate volva bearing yellowish brown patches on the verrucose surface, inamyloid globose to subglobose basidiospores, and a filamentous pileipellis with some inflated round to elongated cells. Phylogenetic analysis of nuclear ribosomal ITS and LSU nucleotide sequences resolve A . glarea with other taxa in Amanita section Vaginatae .
Impact of medium pH regulation on biohydrogen production in dark fermentation process using suspended and immobilized microbial cells

ABSTRACT The effect of pH regulation on biohydrogen production was studied using suspended and immobilized mixed cultures. Four sets of dark fermentation processes were carried out using suspended cells under regulated pH (Sus_R) and non-regulated pH conditions (Sus_N), the nalginate-immobilized cells under pH regulated (Imm_R) and non-pH regulated conditions (Imm_N). Sus_R showed a peak hydrogen fraction of 44% and complete glucose degradation, compared to Sus_N with a peak hydrogen fraction of 36% and a glucose degradation of 37%. Imm_R experiments showed a peak biohydrogen fraction of 35%, while the peak hydrogen fraction observed with Imm_N was 22%. The highest hydrogen fraction was observed using Sus_R conditions. A 100% glucose degradation was observed in both pH regulated and non-regulated processes using immobilized cells. The rate of pH change was slower for immobilized cells compared to suspended cells suggesting a better buffering capacity under non-pH regulated conditions. The study showed that biohydrogen production with suspended cells in a non-regulated pH environment resulted in early termination of the process and lower productivity.
QUANTITATIVE CHANGES IN ANTIOXIDANT ENZYME ACTIVITIES, GLUTATHIONE CONTENT AND MALONDIALDEHYDE IN A FRESHWATER FISH, ANABAS TESTUDINEUS (BLOCH), EXPOSED TO SEWAGE

In the present study, the effect of sewage on the antioxidant enzymes such as superoxide dismutase (SOD), glutathione-S-transferase (GST), catalase (CAT) were studied along with Glutathione content (tGSH), and lipid peroxidation product, Malondialdehyde (MDA) in the liver, brain and kidney of a freshwater fish, Anabas testudineus. Exposure to sewage significantly decreased the activity of liver SOD and GST for 7 and 14 days. But after 21 days of exposure, the activities of liver SOD and GST were restored. Liver CAT activity was increased on 7 and 14 days but restored on 21st day of sewage exposure. While the level of tGSH and MDA were increased after sewage exposure. In kidney, sewage exposure significantly inhibited SOD and CAT activity and inhibited the level of tGSH but GST was increased on 7th and 14th days and restored to control on the 21st day. MDA level was significantly increased only on the 7th day and thereafter found to be decreased. In brain, tGSH was found to be decreasing while, the activities of SOD was significantly increasing on the 14th day and CAT on 7th and 21st days. Brain MDA was found to be significantly elevated from control. Alterations in the antioxidant enzyme activity and amelioration in lipid peroxidation products in the present study reveals that the fish experienced oxidative stress.
Analysis of substitutions of glutamate 90 and glutamate 120 in the multidrug resistance regulator QacR reveal new modes of ligand binding

The repressor QacR regulates the expression of the multidrug exporter QacA, which mediates antiseptic resistance of Staphylococcus aureus to a wide variety of molecules. The ligands of both of QacR and QacR are lipophilic cations. In crystal structures of wild-type-QacR-ligand complexes, glutamates 90 and 120 appear to be critical for binding rhodamine-6G, ethidium, malachite green, and dequalinium (1). In order to determine if the negative charges of these glutamates plays a role in ligand binding, these residues were substituted with glutamines. The interactions of these substituted proteins with the structurally characterized QacR ligands: ethidium, malachite green, dequalinium, and rhodamine-6G were studied. The affinities of the substituted QacR to each ligand were measured with tryptophan fluorescence quenching, fluorescence polarization, and isothermal titration calorimetry. The structures of the protein ligand complexes were studied with X-ray crystallography The structures of the E90Q-QacR-R6G complex and E120Q-QacR-Et complex indicated two binding positions were available to each of the ligands in the substituted proteins compared to the one binding position observed in the WT -QacR. As the binding affinity of the substituted proteins for these ligands did not dramatically change from that of the WT, these new binding positions must be accessible in the WT-QacR. Furthermore, the structures of the WT-QacR with DB75 and DB359 indicate that there may be many equivalent binding positions for these ligands as well. This research further demonstrates how the QacR binding pocket binds a multitude of disparately shaped ligands. Not only does this research confirm that the binding pocket changes to accommodate various ligands, but it illustrates that the same ligand can interact with the protein in more than one way.
The brown alga Saccharina japonica features distinct vanadium-dependent bromoperoxidases and iodoperoxidases

Marine algae have an extraordinary ability to absorb halogens which provide algae with an inorganic antioxidant impacting atmospheric chemistry. Although brown algal Laminariales species are the most efficient iodine accumulators among all living systems, and Saccharina japonica is the primary material used for iodine extraction, the functions and regulatory mechanisms of these species have not been fully documented. In this study, a functional genomics analysis of the algal vanadium-dependent haloperoxidase (vHPO) gene family was conducted; there genes can introduce halogen atoms into organic compounds. The comprehensive analyses regarding the bioinformatics and phylogenetics of novel genomic and transcriptomic sequencing data of 21 Rhodophyta and 19 Ochrophyta marine algal species revealed that brown algal vHPOs have two gene types, vanadium-dependent bromoperoxidase (vBPO) and vanadium-dependent iodoperoxidase (vIPO), with secondary endosymbiotic host origin. The enzyme activity of S. japonica vBPO and vIPO were verified for the first time and were quite stable in a wide range of temperature and pH values. However, the specific activity and optimal conditions were considerably different between vBPO and vIPO. The transcript expression analysis in different S. japonica tissues (including rhizoids), generations (sporophytes and gametophytes), sexes (male and female), and stress conditions (hyposaline and hyperthermia) also showed great differences between vBPOs and vIPOs. Most of the vBPOs were constitutively expressed with higher expression dose, which may be responsible for basal halogen metabolism. On the contrary, vIPOs mainly showed specific expression, which may be involved in tissue differentiation, generation differentiation, sex differentiation, and stress regulation. Comprehensive analysis of gene family evolution, enzyme biochemical characteristics, and complex transcriptional mechanisms were conducive to the environmental adaptation and sophisticated system evolution of Laminariales. The successful bromination of small-molecule compound substrate by SjavBPO provided high activity and efficient enzymatic tools for artificial synthesis of halogenated compounds.
IBA AND MICROCUTTING COLLECTIONS IN THE MICROPROPAGATION OF Eucalyptus spp HYBRID CLONES.1

This study aims to evaluate the effect of IBA concentrations and microcuttings successive collections in the micropropagation of Eucalyptus grandis x E. urophylla and Eucalyptus urophylla x E. globulus clones. Clumps containing six to eight buds of clones established in vitro were transferred to a 250 mL glass flask in JADS semisolid medium. Successive collections were performed every 20 days for Eucalyptus grandis x E. urophylla clone and every 30 days for Eucalyptus urophylla x E. globulus clone. The following variables were evaluated under in vitro conditions: number of shoots > 0.5 cm, number of microcuttings > 2 cm, length of the longest microcutting, and shoots vigor. Under ex vitro conditions, in the greenhouse and shade house, the following variables were evaluated: seedling height, percentage of survival, stem diameter, percentage of root observed at the lower end of the tube, and seedling vigor. In full sun (ex vitro), the following variables were analyzed: seedling height, stem diameter, survival, number of roots, root volume, seedling vigor, and shoot and root dry matter. Good in vitro microcuttings productivity was observed over the successive collections. IBA levels were adjusted for each clone, ranging from 0.25 to 0.50 mg L for Eucalyptus grandis x E. urophylla clone, and from 0.75 to 1.0 mg L for Eucalyptus urophylla x E. globulus clone. IBA concentrations led to residual effects under ex vitro conditions, providing good rooting and survival for Eucalyptus grandis x E. urophylla and Eucalyptus urophylla x E. globulus clones at IBA concentrations between 0.25 and 0.50 mg L and between 0.50 and 1.0 mg L, respectively.
Isolasi Bakteri Termofilik Sumber Air Panas Gedongsongo dengan Media Pengaya MB (Minimal Broth) dan TS (Taoge Sukrosa) serta Identifikasi Fenotip dan Genotip

Bakteri termofilik merupakan bakteri yang mampu bertahan hidup pada suhu tinggi di mana salah satu habitatnya adalah sumber air panas. Indonesia memiliki banyak sumber air panas yang potensial sebagai habitat bakteri termofilik. Dalam penelitian ini dilakukan isolasi bakteri termofilik sumber air panas gedongsongo dengan menggunakan pendekatan minimal media MB ( Minimal Broth ) dan TS (Taoge Sukosa) serta identifikasi fenotip dengan uji mikrobiologi yang meliputi pewarnaan gram dan morfologi dan identifikasi genotip dengan menggunakan urutan nukleotida gen 16S rRNA dan konstruksi pohon filogenetik dengan menggunakan program Phylip 3.68 ed. metode Distance matrix (Neighbour joining) . Identifikasi enzim ekstraseluler secara kualitatif dilakukan dengan menggunakan media selektif yang meliputi uji selulase, uji a-amilase, uji protease dan uji P-galaktosidase. Dari penelitian diperoleh dua isolat tunggal bakteri termofilik yaitu isolat GS_MBan dan isolat GS_TSan. Isolat GS_MBan memiliki kemiripan dengan bakteri kelompok Anoxybacillus sp. sebesar 94-99%, berbentuk batang, bakteri gram positif, memiliki enzim ekstraseluler a-amilase, protease dan P-galaktosidase serta tidak menunjukkan potensi adanya enzim ekstraseluler selulase. Isolat GS_TSan memiliki kemiripan dengan bakteri kelompok Thermoanaerobacterium sp. sebesar 78-86%, berbentuk batang, bakteri gram negatif, memiliki enzim ekstraseluler a-amilase dan protease serta tidak menunjukkan potensi adanya enzim ekstraseluler P-galaktosidase dan selulase.
Karakteristik Gen Cytochrome Oxidase subunit I (COI) Tiram Daging dari Genus Crassostrea sebagai Identitas Jenis di Delta Cimanuk, Jawa Barat

Oysters belong to the Crassostrea, which is a type of shellfish that lives as benthos in waters under the same substrate and environmental conditions will exhibit similar morphological changes in response. There are many types of oysters that have a similar shape are often an obstacle to differentiate of Crassostrea species through morphological identification. The purpose of this research was to identify the types of oysters found in the waters of Delta Cimanuk through analysis of the morphology and nucleotide diversity of Cytochrome Oxidase subunit I (COI) gene, as basic information on proper management and conservation. The morphological identification results show that there were two species of the Crassostrea. Identification of species through the Barcoding DNA technique shows that there is one type of oyster: Crassostrea iredalei with an accuracy of 99.5%. Key word : COI gene, Crassostrea, Delta Cimanuk, molecular identification, morphology ABSTRAK Tiram termasuk ke dalam Genus Crassostrea yang merupakan jenis kerang-kerangan yang hidup sebagai bentos di perairan pada kondisi substrat dan lingkungan yang sama akan menunjukkan respon berupa perubahan morfologi yang hampir mirip. Banyaknya jenis tiram yang memiliki bentuk yang mirip seringkali menjadi hambatan untuk membedakan jenis Crassostrea melalui identifikasi secara morfologi. Tujuan dari penelitian ini adalah untuk mengidentifikasi jenis tiram yang terdapat di perairan Delta Cimanuk melalui analisis morfologi dan keragaman nukleotida gen Cytochrome Oxidase subunit I (COI), sebagai informasi dasar dalam pengelolaan dan konservasi yang tepat sasaran. Hasil identifikasi secara morfologi menunjukkan bahwa terdapat dua spesies dari Genus Crassostrea yakni Crassostrea iredalei dan Crassostrea gigas. Identifikasi spesies melalui teknik DNA Barcoding menunjukkan bahwa terdapat satu jenis tiram dari Genus Crassostrea yakni Crassostrea iredalei dengan tingkat keakuratan sebesar 99,5%. Kata kunci : Crassostrea, Delta Cimanuk, gen COI, identifikasi molekuler, morfologi
Mycobacterium avium subsp. paratuberculosis infection in dairy cattle: development, optimization and evaluation of cell-mediated immune based assays: Development, optimization and evaluation of cell-mediated immune based assays

Although the interferon-gamma (IFN) assay for measurements of cell-mediated immune (CMI) responses to paratuberculosis PPD (johnin) has been available for close to 20 years, the assay has not yet emerged as the long desired test to identify infected animals at an early time point. Among other issues, this relates to problematic interpretation of the test results and maybe an over-expectation of what can be deducted from this kind of test given the chronic nature and slow development of infection of paratuberculosis. Over a number of years a modified IFNassay with addition of recombinant bovine IL-12 to the PPDj stimulation of blood samples from the heifer group in more than 20 Danish dairy herds which also perform surveillance of MAP antibodies in milk have been performed. The results indicate that IFNassay results are specific for paratuberculosis, but the IFNassay result of an individual animal cannot establish whether the animal is infected or predict the future progression of disease in this animal. The IFNassay should thus be used on a group of animals to test the level of exposure to paratuberculosis bacteria the animals have experienced, and thereby assist in maintaining rational in-herd management procedures and in the establishment of paratuberculosis status of a given herd. Indeed, for any diagnostic test applied in paratuberculosis, both the diagnostic target condition and the purpose of the diagnostic testing must be considered before any meaningful estimates of sensitivity or specificity can be given. © 2011 Elsevier B.V. All rights reserved.