Miracle-dz/UniFAR-FTUs huggingface dataset:
Characterization of the Biological Roles and Biochemical Properties of Triphosphate Tunnel Metalloenzyme Superfamily Members in Plants

The triphosphate tunnel metalloenzyme (TTM) superfamily comprises a group of enzymes that hydrolyze organophosphate substrates in a metal-dependent manner. Members of this family have diverse biological functions in different organisms. Arabidopsis encodes three TTM genes, called AtTTM1, AtTTM2, and AtTTM3. Previous work showed that AtTTM3 is a tripolyphosphatase requiring Mg where its crystal structure reveals the signature TTM catalytic tunnel. In this thesis, I present my findings on the biological and biochemical characterization of AtTTM1 and AtTTM2. A reverse genetics approach using T-DNA insertion knockout lines revealed that AtTTM2 is a negative regulator of the SA amplification loop in defense responses. ttm2 plants exhibit enhanced defense responses to virulent and avirulent pathogens, enhanced hypersensitive response (HR), elevated SA, and enhanced SAR. ttm2-mediated enhanced resistance requires the key defense regulators, PAD4, ICS1, and NPR1. Furthermore, AtTTM2 is transcriptionally downregulated in response to pathogen infection and flg22, SA, and BTH treatment. While ttm2 exhibits enhanced resistance, it is not an autoimmune mutant, suggesting that it is not a conventional negative regulator of defense responses. Phenotypic characterization of ttm1 did not reveal any alterations in defense responses. Instead, ttm1 exhibited delayed senescence by showing
Oxidative enzymes and functional quality of minimally processed grape berries sanitised with ozonated water

Thompson Seedless (TS) and Black (BS) grapes sanitised with 2, 4, 6, 8 mg L 1 O3 or NaOCl (100 mg L ) were stored 21 days at 5 °C. Ozonated water stimulated the respiration rate, especially after 5 days of storage, and increased superoxide dismutase and catalase activity compared to NaOCl-sanitised grapes. Total polyphenol content (TPC) was 23–50% higher in TS and 18.5–28% higher in BS samples sanitised with ozonated water. Twofold higher total antioxidant capacity (TAC) was registered in TS at all of the evaluated O3 doses while the doses of 6 and 8 mg L 1 increased TAC by 19–30% in BS. The use of ozonated water as a sanitising method, especially at 6 and 8 mg L 1 doses, improved the functional quality and maintained low microbial counts on fresh-cut grapes being a good alternative for the industry.
Insufficient fumarase contributes to generating reactive oxygen species in Dahl salt sensitive rats

Dahl SS rats exhibit greater levels of renal medullary oxidative stress and lower levels of fumarase activities. Fumarase insufficiencies can increase reactive oxygen species (ROS), the mechanism of which, however, is not clear. A proteomic analysis indicated fumarase knockdown in HK-2 cells resulted in changes in the expression or activity of NADPH oxidase, mitochondrial respiratory chain complex I and III, ATP synthase subunits, and α-oxoglutarate dehydrogenase, all of which are sites of ROS formation. Meantime, the activities of key antioxidant enzymes such as G6PD, 6PGD, GR, GPx and GST increased significantly too. The apparent activation of antioxidant defense appeared insufficient as glutathione precursors, glutathione and GSH/GSSG ratio were decreased. SS rats exhibited changes in redox metabolism similar to HK-2 cells with fumarase knockdown. Supplementation with fumarate and malate, the substrate and product of fumarase, increased and decreased, respectively, blood pressure and the levels of H2O2 and MDA in kidney tissues of SS rats. These results indicate fumarase insufficiencies cause a wide range of changes at several sites of ROS production and antioxidant mechanisms.
Cultivares de milho submetidas ao tratamento de sementes com bioestimulantes fertilizantes líquidos e Azospirillum sp.

RESUMO - Objetivou-se verificar o desempenho agronomico da cultura do milho em funcao do tratamento de semen-tes com o inoculante Azo Total® composto de Azospirillum sp. , com o bioestimulante Stimulate® e com o fertilizante liquido Cellerate®, individualmente e em combinacao. O experimento foi conduzido a campo em Sete Lagoas, MG, utilizando-se o delineamento de blocos casualizados com quatro repeticoes e tratamentos dispostos em esquema fatorial 2x8, sendo duas cultivares de milho (P30F53 e P30F53 YH) e sete tratamentos de sementes mais a testemeunha (T1 = Testemunha; T2 = Azo Total®; T3 = Stimulate®; T4 = Cellerate®; T5 = Azo Total® + Stimulate®; T6 = Azo Total® + Cellerate®; T7 = Stimulate® + Cellerate®; T8 = Azo Total® + Cellerate® + Stimulate®). Para a analise do desempenho agronomico, foram avaliadas as caracteristicas: altura de planta; altura de espiga; numero de espigas; produtividade; diâmetro do colmo; analise foliar; estande final; indice de espiga; e peso de 1.000 graos. Nas condicoes de realizacao deste trabalho, a cultivar P30F53YH proporciona maior produtividade de graos quando tratada com os produtos Azo Total®, Stimulate® e Cellerate®. Tratamentos de sementes de milho com os produtos comerciais Azo Total®, Stimulate® e Cellerate® nao incrementam significativamente a produtividade de graos. Tratamento de sementes com Azo Total®, Stimulate® e Cellerate® nao influenciam os teores foliares de nutrientes em plantas de milho. Palavras-chave: Zea mays; produtividade; qualidade fisiologica; tratamento de sementes. PRODUCTIVITY OF MAIZE CULTIVARS SUBMITTED TO SEED TREATMENT WITH BIOSTIMULANTS LIQUID FERTILIZERS AND Azospirillum sp. ABSTRACT - The objective of this work was to investigate the agronomic performance of maize after the treatment of seeds with the inoculant Azo Total ® associated to Azospirillum sp, with the biostimulant Stimulate ® and the liquid fertilizer Cellerate ®. The experiment was conducted under field conditions in Sete Lagoas – MG,, using a randomized complete block design ,in a 2x8 factorial design with four replications, with two maize cultivars (P30F53 and P30F53 YH) and seven seed treatments and one control (T1 = Control; T2 = Azo Total ® ; T3= Stimulate ®, T4 = Cellerate ® , T5 = Azo Total ® + Stimulate ®, T6 = Azo Total ®+ Cellerate ®, T7 = Stimulate ® +Cellerate ®, T8 = Azo Total ® + Cellerate ® + Stimulate ®) . For the analysis of agronomic performance were evaluated the characteristics plant height, ear height, number of ears, productivity, stem diameter, leaf analysis, final stand, ear index and 1000 grain weight. The cultivar P30F53YH showed higher grain yield when treated with Azo Total ®, Stimulate ® and Cellerate ®. Treatment of maize seeds with Azo Total ®, Stimulate ® and Cellerate ® did not increase significantly grain productivity. Seed treatment with Azo Total ®, Stimulate ® and Cellerate ® did not affect the concentration of foliar nutrients in maize plants. Key words: Zea mays; productivity; physiological quality; seed treatment.
First report of an exceptional monoecious type of Pistacia atlantica ssp. atlantica in Algeria (North Africa)

The Pistachio Atlas tree ( Pistacia atlantica Desf.) is a dioecious specie that belongs to the Anacardiaceae family. Recently, some researchers have found a monoecious species which belongs to this family in Turkey ( P. atlantica Desf.), ( P. terebinthus L.), Bulgaria and China ( P. Chinensis ). No study has reported the case of monoecious species in Pistacia atlantica Desf. in North Africa. However, our research describes for the first time the phenomen on that takes place in Algeria. During our observation, the tree exhibited seeds and a vestige of pistillate inflorescence. In general, pollen shedding started in staminate clusters as vegetative buds broke. Cluster distribution of both sexes on the tree appeared highly complex and variable. This discovery also proves that there are subjects of this species - a monoecious species - in northern Africa and especially in Rechaiga, Tiaret.
A comparison of the effects of water-level policies on the availability of walleye spawning habitat in a boreal reservoir

ABSTRACT Papenfuss JT, Cross T, Venturelli PA. 2018. A comparison of the effects of water-level policies on the availability of walleye spawning habitat in a boreal reservoir. Lake Reserv Manage. 34:321–333. Water levels in reservoirs can affect the quantity and quality of the habitat that is available for spawning fish and their eggs. We studied how a change in the water-level management policy (“rule curve”) in 2000 affected the availability of walleye (Sander vitreus) spawning habitat in 3 lakes (Kabetogama, Namakan, and Sand Point) that make up a large, boreal reservoir between Canada and the United States. According to observed water-level data, available spawning habitat on known Lake Kabetogama spawning sites increased 95% (P < 0.01) with the 2000 rule curve, but did not change on Namakan or Sand Point lake spawning sites. However, when using modeled water-level data to control for confounding weather events, habitat availability at known spawning sites increased significantly (P < 0.01) on all 3 lakes (179%, 92%, and 93%, respectively). Habitat availability improved because the 2000 rule curve increased mean spring water levels by 0.5 m, and water levels rose more slowly (2.2 vs. 3.0 cm/d) during egg incubation. Our findings suggest that, although water-level management on large reservoirs can be a challenge, carefully designed policies can improve walleye spawning habitat conditions and help to achieve fisheries management goals.
Morpho-genetic diversity and anti-bacterial activity in root extracts of nine solanaceous species

The family Solanaceae is immensely important because it has many species with food and medicinal values. There are nine major Solanaceous spp. Namely S. Melongena L. (Wambatu and Elabatu), S. virginianum L. (Katuwelbatu), S. torvum Sw. (Thibbatu), S. violaceum Ortega (Thiththathibbatu), S. trilobatum L. (Welthibbatu), S. hispidum Pers. (Gonabatu), S. pubescens Willd. (Walthibbatu), S. nigrum sensu Trimen (Small Kalukenweriya) and Datura stramonium L. (Sudu aththana) collected from Uva Province, Sri Lanka, a prominent area of growing these species. Currently these species are underutilized in spite of their medicinal importance. No detailed morphogenetic and medicinal level characterization of these species has been reported to promote their economic use. Therefore, the present study was conducted to assess the morphogenetic diversity and the antibacterial activity of these Solanaceous spp. The plant height, canopy width and leaf and fruit morphology were highly variable among these species. DNA barcoding using locus matK revealed a total of eight haplotypes. The polymorphism in matK locus is not diverse enough to set the species limit of the genotypes within S. melongena and to distinguish Thiththathibbatu from Walthibbatu. The antibacterial activity assay using ethanol extracts of roots demonstrated that all these species have inhibitory activity against Gram positive Staphylococcus aureus (NCTC4838) and Gram negative Escherichia coli (JM109).
Nocturnal lemur diversity at Masoala National Park

Approximately 3,000 base pairs of mitochondrial DNA sequence data were utilized as part of a phylogenetic analysis to investigate the taxonomic relationships of the nocturnal lemurs (genera Avahi and Lepilemur) of Masoala National Park. the molecular data distinguished all currently described Avahi and Lepilemur species, but it also revealed previously unrecognized biodiversity within these genera at Masoala National Park. Diagnoses of a new species of woolly lemur and a new species of sportive lemur from Masoala National Park are presented. these results demonstrate that cryptic species can be revealed through molecular data and the importance of initiating further detailed studies in previously unstudied sites to confirm the distributions of all species, particularly nocturnal lemur species.
Etude du mutant E255L de l'ATPase Ca2+ SERCA1a de lapin et de l'ATPase Ca2+ PfATP6 de Plasmodium falciparum

Le puissant anti-paludeen, l'artemisinine a ete decrit comme inhibiteur de l'activite ATPasique de PfATP6 apres son expression dans des ovocytes de Xenope. PfATP6 est l'unique ATPase Ca2+ du reticulum endo/sarcoplasmique de P. falciparum, le parasite responsable du paludisme. Quand un acide amine de SERCA1a de lapin (E255) est mute en son equivalent dans PfATP6 (L), l'activite de ce mutant exprime en ovocyte de Xenope est inhibee en presence d'artemisinine. Apres expression de ce mutant et de PfATP6 dans S. cerevisiae puis leur purification, nous avons constate qu'aucune de ces deux proteines n'etait sensible a l'artemisinine. En parallele, nous montrons que PfATP6 purifiee est sensible aux principaux inhibiteurs de SERCA mais elle est moins sensible a la thapsigargine que ne l'est SERCA1a. Les resultats presentes ici suggerent que le mechanisme d'action de l'artemisinine est complexe et ne peut pas etre du a une interaction directe entre l'artemisinine et PfATP6. D'autre part, la purification de PfATP6 laisse entrevoir l'opportunite de mieux caracteriser cette proteine voire meme de developper de nouveaux anti-paludeens en recherchant des inhibiteurs de cette proteine.
Inhibition of mycobacterial CYP125 enzyme by sesamin and β-sitosterol: An in silico and in vitro study

Background: Cholesterol degradation pathway is one of the important pathways in survival of Mycobacterium tuberculosis (Mtb) bacilli, and steroid C26-monooxygenase (CYP125) enzyme of Mtb associated with this pathway is reported to be novel drug target. This study aims to find out novel, safe, and effective inhibitors against CYP125 from natural phytochemicals with reported anti-tubercular activity. Methods: Bioinformatics approach such as homology modeling, virtual screening, and molecular dynamics (MD) simulation was applied to identify best hits among all the shortlisted 148 compounds. The Mtb H37Ra bacilli growth was measured at optical density at 600 nm in minimal media supplemented with cholesterol and monitored for 10 days. Two promising compounds, namely, sesamin and β-sitosterol, were studied to determine their effective minimum inhibitory concentrations (MICs) in Mtb H37Ra bacilli culture. Results: In virtual screening, 15 compounds showed comparatively better binding affinity than natural substrate (choletst-4-en-3-one). In MD simulation study, the protein structure was observed to be stable in alls the interaction complexes, i.e., with choletst-4-en-3-one, sesamin, and β-sitosterol. The MICs of sesamin and β-sitosterol were observed to be 2 μg/ml, inhibiting the growth of the Mtb bacilli by 51% and 53%, respectively. Conclusions: From the above experimental findings, sesamin and β-sitosterol may be proposed as safe and potential inhibitors of CYP125 resulting in diminished growth of Mtb bacilli.
Translocations of the RARa gene in acute promyelocytic leukemia

Acute promyelocytic leukemia (APL) has been recognized as a distinct clinical entity for over 40 years. Although relatively rare among hematopoietic malignancies (approximately 10% of AML cases), this disease has attracted a particularly good share of attention by becoming the first human cancer in which all-transretinoic acid (ATRA), a physiologically active derivative of vitamin A, was able to induce complete remission (CR). ATRA induced remission is not associated with rapid cell death, as in the case of conventional chemotherapy, but with a restoration of the ‘normal’ granulocytic diAerentiation pathway. With this remarkable medical success story APL has overnight become a paradigm for the diAerentiation therapy of cancer. A few years later, excitement with APL was further enhanced by the discovery that a cytogenetic marker for this disease, the t(15:17) reciprocal chromosomal translocation, involves a fusion between the retinoic acid receptor alpha (RARa) gene and a previously unknown locus named promyelocytic leukemia (PML). Consequence of this gene rearrangement is expression of the PML‐RARa chimeric oncoprotein, which is responsible for the cellular transformation as well as ATRA response that is observed in APL. Since this initial discovery, a number of diAerent translocation partner genes of RARa have been reported in rarer cases of APL, strongly suggesting that disruption of RARa underlies its pathogenesis. This article reviews various rearrangements of the RARa gene that have so far been described in literature, functions of the proteins encoded by the diAerent RARa partner loci, and implications that these may have for the molecular pathogenesis of APL. Oncogene (2001) 20, 7186‐7203.
In vitro antiplasmodial properties of selected plants of Sabah

The antiplasmodial activity of the crude extracts of thirty plant species collected from Sabah was evaluated using chloroquine-sensitive strain (D10) and chloroquine-resistant strain (Gombak A) of Plasmodium falciparum. Significant activities were observed for the bark extract of Polyalthia insignis (IC50 3.89 and 11.89 µg/ml against Gombak A and D10, respectively), the leaf extracts of Kopsia dasyrachis (4.62 µg/ml against Gombak A) and Litsea elliptibacea (IC50 8.88 µg/ml against Gombak A), as well as the leaf and bark extracts of Neouvaria acuminatissima (IC50 6.90-10.08 and 0.69 µg/ml against Gombak A and D10, respectively), and the bark extract of Polyalthia microtus (IC50 9.0 and 12.12 µg/ml against Gombak A and D10, respectively).
A probabilistic procedure for estimating an optimal echo-integration threshold using the Expectation-Maximisation algorithm

To obtain reliable fish biomass estimates by acoustic methods, it is essential to filter out the signals from unwanted scatterers (e.g. zooplankton). When acoustic data are collected at more than one frequency, methods that exploit the differences in reflectivity of scatterers can be used to achieve the separation of targets. These methods cannot be applied with historical data nor recent data collected on board fishing vessels employed as scientific platforms, where only one transducer is available. Instead, a volume backscattering strength (S v ) threshold is set to separate fish from plankton, both for echogram visualisation or, more importantly, during echo-integration. While empirical methods exist for selecting a threshold, it often depends on the subjective decision of the user. A−47 dB threshold was empirically established in 2008 at the beginning of a series of surveys conducted by Mexico's National Fisheries Institute to assess the biomass of Pacific sardine in the Gulf of California. Until 2012, when a 120 kHz transducer was installed, only data collected at 38 kHz are available. Here, we propose a probabilistic procedure to estimate an optimal S v threshold using the Expectation-Maximisation algorithm for fitting a mixture of Gaussian distributions to S v data sampled from schools associated with small pelagic fish and their surrounding echoes. The optimal threshold is given by the Bayes decision function for classifying an S v value in one of the two groups. The procedure was implemented in the R language environment. The optimal threshold found for 38 kHz data was −59.4 dB, more than 12 dB lower than the currently used value. This difference prompts the need to revise the acoustic biomass estimates of small pelagics in the Gulf of California.
Sonochemical synthesis, structural and magnetic properties of air-stable Fe/Co alloy nanoparticles

Nanoparticles of the Fe/Co alloy have been prepared by sonolysis of a Fe(CO)5 and Co(NO)(CO)3 mixture in diphenylmethane solution under argon. The as-prepared product is an amorphous material having 10 nm diameter particles. Upon annealing in argon at 600 °C for 5 h, an air-stable Fe/Co alloy is formed with an increased particle size to ∼40 nm. The Fe/Co alloy nanoparticles have been characterized by XRD, TEM, TGA, DSC, XPS, EPR, MES and magnetic susceptibility measurements. Materials obtained under appropriate conditions possess a very high saturation magnetization of about 150–238 emu g−1 and good, soft magnetic properties (Hc = 70 − 30 G). The nanocrystalline particles have a core-shell structure in which the iron–cobalt core is surrounded by a carbon surface layer. The stability of the nanocrystalline particle has been discussed, based on the core-shell structure.
Broad geographic sampling reveals predictable, pervasive, and strong seasonal adaptation in Drosophila

To advance our understanding of adaptation to temporally varying selection pressures, we identified signatures of seasonal adaptation occurring in parallel among Drosophila melanogaster populations. To study these evolutionary dynamics, we estimated allele frequencies genome-wide from flies sampled early and late in the growing season from 20 widely dispersed populations. We identify parallel seasonal allele frequency shifts across North America and Europe, demonstrating that seasonal adaptation is a general phenomenon of temperate fly populations. The direction of allele frequency change at seasonally variable polymorphisms can be predicted by weather conditions in the weeks prior to sampling, linking the environment and the genomic response to selection. The extent of allele frequency fluctuations implies that seasonal evolution drives substantial (5-10%) allele frequency fluctuations at >1% of common polymorphisms across the genome. Our results suggest that fluctuating selection is an important evolutionary force affecting the extent and stability of linked and functional variation.
Presence, absence, and roosting ecology of the southeastern myotis and Rafinesque's big-eared bat in the Cache River National Wildlife Refuge

Several studies have been conducted on the bats of Arkansas’ bottomlands. However, none have focused exclusively on one of Arkansas’ largest bottomlands habitats, the Cache River National Wildlife Refuge. The objectives of this study were to 1) inventory bat species present throughout the Cache River National Wildlife Refuge via mist-netting and bioacoustics, and 2) estimate the occupancy of bats among five habitat types (cypress-tupelo, emergent wetland, mature forest, reforestation, and managed hardwood). I mist-netted throughout the boundaries of the refuge from sunset for 5 hours and deployed bioacoustic devices from May–August 2014 and 2015. In addition, separate bioacoustics devices were deployed throughout the aforementioned habitat types from May through August, 2015. Four hundred and sixty bats were capture via mist-netting with Rafinesque’s big-eared bats (Corynorhinus rafinesquii; n = 156) being the most common capture, followed by eastern red bats (Lasiurus borealis; n = 104), southeastern myotis (Myotis austroriparius; n = 91), evening bats (Nycticeius humeralis; n = 58), tri-colored bats (Perimyotis subflavus; n = 54), and a bigbrown bat (Eptesicus. fuscus; n = 1). Evening bats and big-brown bats tended to occupy managed hardwood forests more than any other habitat with the occupancy probability = 0.81 and 0.58, respectively, tri-colored bats tended to be more present in mature forest habitats ( = 0.89), and Myotis species tended to have highest occupancy rates at cypress-tupelo stands ( = 0.59).
Short Introduction of Dna Barcoding

DNA barcoding is a system for fast and accurate species identification. It’s creates ecological system more accessible by using short DNA sequence instead of whole genome and is used for eukaryotes and prokaryotes. The short DNA sequence is generated from standard region of genome known as marker. This marker is different for various species like CO1 cytochrome c oxidase 1 for animals, matK and rbcL for plants and Internal Transcribed Spacer (ITS) for fungus. It has many uses in various fields such as agriculture, sustaining natural resources, protecting endangered species, water quality, preserving natural resources, identification of medicinal plants.