Miracle-dz/UniFAR-FTUs huggingface dataset:
Designer Pasture Plants: From Single Cells to the Field

Pasture occupies more land area than any other crop and it is of tremendous value as livestock feed. Ryegrasses (Lolium spp.) and white clover (T. repens) are among the most important forage plants in the world. The demand for high quality forages continues to grow. Elite pasture plants need to demonstrate tolerance to both biotic and abiotic stresses, including drought-stress, low temperatures, diseases and insect pests, without compromising their forage quality and productivity. Generation of these advanced forages is beyond the scope and speed of conventional plant breeding. Functional genomics has greatly increased our understanding of mechanisms that determine the genetic, molecular and biochemical basis of economically important traits in forage plants and allow plants to develop and adapt to a dynamic environment. In the post-genomics era, we need to convert this information into practical benefits for farmers and the agricultural sector. This has required multi-disciplinary approaches that exploit advances in molecular genetics, functional genomics and computational biology as well as close collaboration with plant breeders. This review discusses recent progress in finding the molecular and biochemical bases of quality traits in white clover and ryegrass which will enable the development of transgenic ‘designer’ cultivars with improved forage quality, yield and stress tolerance.
The distribution of Athetis lepigone and prediction of its potential distribution based on GARP and MaxEnt

Athetis lepigone (Möschler) is a new agronomic pest which has caused serious damages to summer maize in China. In order to effectively monitor it, it is necessary to carry‐out a worldwide investigation on its potential geographical distribution. In this study, we give two ecological niche models, Genetic Algorithm for Rule‐set Production and Maximum Entropy (MaxEnt), to predict the potential geographical distribution of A. lepigone. The results indicate that the suitable areas for A. lepigone are mainly in China (Beijing, Tianjin, central and southern Hebei, northern Jiangsu, Shandong, most of Henan, northern Anhui, central and southern Shanxi, central and southern Shaanxi, small parts of north‐west in Hubei, eastern Gansu, parts of Ningxia, western of Xinjiang and Dandong, and Liaoning) and other Asian countries (South Korea, North Korea and Japan). Parts of Europe (south‐western Russia, Ukraine, Moldova, Romania, Hungary, Bulgaria, Slovenia, and Croatia, Bosnia and Herzegovina, Serbia, parts of Austria, western Poland, the Czech Republic, Germany, northern Italy, Denmark, western Lithuania, Latvia, Estonia, southern Finland and Sweden) are also highly suitable for A. lepigone. In addition, in the states of the USA including Michigan, New York, Chicago, Missouri, Ohio, Illinois and Indiana are also favourable for its occurrence although till now no reports about of this species has been recorded. A jackknife test in MaxEnt showed that the mean temperature of the driest quarter was the most important environmental variable affecting the distribution of this pest.
Insilico Functional Annotation of Hypothetical ORFs in Human Chromosome2

The high-throughput genome projects have resulted in a rapid accumulation of genome sequences for a large number of organisms and large number of genes with unknown function (Hypothetical). To fully realize the value of the data, scientists need to identify proteins encoded by these genes and understand how these proteins function in making up a living cell. With experimentally verified information on protein function lagging far behind, computational methods are needed for reliable and large-scale functional annotation of proteins. Functional annotation is the process of identifying for a given gene its biological function, interaction with other elements, involvement in metabolic pathways, and any other piece of information that helps in understanding when and how a gene influences the overall system. On the other hand, many Biological Processes and Disease mechanisms are still unknown due to lack of knowledge about the function of the Hypothetical genes in Human. Once its function is revealed the so called hurdle of unknown mechanism of the Human Genome can be mastered. Hence, the present study aims to use computational approaches to annotate the function of hypothetical genes in Chromosome 2 of Human. The annotation of the hypothetical genes in human chromosoem2 was done both at the nucleotide and protein level. Among the 41 uncharacterized hypothetical genes in Human chromosome 2, the functions of 27 of them were successfully annotation. Further, experimental validation is essential to confirm the predicted function.
Ecosystem indicators—accounting for variability in species' trophic levels

&NA; Trophic level (TL)‐based indicators are commonly used to track the ecosystem effects of fishing as the selective removal of organisms from the food web may result in changes to the trophic structure of marine ecosystems. The use of a fixed TL per species in the calculation of TL‐based indicators has been questioned, given that species' TLs vary with ontogeny, as well as over time and space. We conducted a model‐based assessment of the performance of fixed TL‐based indicators vs. variable TL‐based indicators for tracking the effects of fishing pressure. This assessment considered three TL‐based indicators (the trophic level of the landed catch (TLc), the marine trophic index (MTI) and the trophic level of the surveyed community (TLsc)), three fishing scenarios that targeted specific model groups (the low TL scenario (LTL), the high TL scenario (HTL) and a scenario encompassing broad‐scale exploitation (ALL)) and ten contrasting marine ecosystems with four types of ecosystem modelling approaches that differ in their structure and assumptions. Results showed that, overall, variable TL‐based indicators have a greater capacity for detecting the effects of fishing pressure than fixed TL‐based indicators. Across TL‐based indicators, TLsc displayed the most consistent response to fishing whether fixed or variable species' TLs were used, as well as the highest capacity for detecting fishing effects. This result supports previous studies that promote the use of survey‐based indicators over catch‐based indicators to explore the impacts of fishing on the structure of marine ecosystems. Across fishing scenarios, the low trophic level fishing scenario (LTL) resulted in the lowest consistency between fixed and variable TL‐based indicator responses and the lowest capacity of TL‐based indicators for detecting fishing effects. Overall, our results speak to the need for caution when interpreting TL‐based indicator trends, and knowledge of the broader context, such as fishing strategies and exploitation history.
Micropropagation of date palm (Phoenix dactylifera L.) CV khadrawy using tissue culture technique

Micropropagation of date palm (Phoenix dactylifera L.) CV khadrawy using tissue culture technique , Micropropagation of date palm (Phoenix dactylifera L.) CV khadrawy using tissue culture technique , مرکز فناوری اطلاعات و اطلاع رسانی کشاورزی
Manipulations of black bear and coyote affect caribou calf survival

The population of woodland caribou (Rangifer tarandus) in Newfoundland declined from approximately 94,000 to 32,000 animals between 1996 and 2013. Poor calf survival was the primary cause of the population decline, largely because of predation of newborn calves by American black bear (Ursus americanus) and the non-native coyote (Canis latrans). This situation offered an opportunity to test the efficacy of preventative management options such as diversionary feeding and lethal removal of predators for improving calf survival. We monitored caribou calves (n = 536) in 4 calving areas (3 untreated, 1 treatment) for 2 years (2008–2009) followed by diversionary feeding of black bears and coyotes in 2010–2011 and lethal removal of coyotes in 2012–2013. We estimated calf survival for 70 days, the period calves and females remain on the calving grounds, and for 182 days, after which calves were considered recruited into the population. Calf survival was nearly constant over the 6-year study period on the untreated areas. Calf survival was initially lower on the treatment area compared to the untreated areas but increased substantially on the treatment area during the lethal removal period, especially during the initial 70-day period. Predation on calves by coyote decreased substantially during the lethal removal period. Diversionary feeding had little influence on survival rates. This study suggests that lethal removal of coyotes could be a viable management option for improving calf survival, but it is expensive and logistically challenging in remote field settings. © 2016 The Wildlife Society.
Vitellogenin as a biomarker for environmental estrogens

Much recent interest has focused on “xenoestrogens” in the environment. The potential for these chemicals to disrupt hormonal function in wildlife has led to the development of techniques to monitor the effects of discharges of these compounds particularly in aquatic environments. Increases in the concentration of the egg yolk precursor protein, vitellogenin (Vtg), in the plasma of fish and other vertebrates have been identified as a potentially useful biomarker of exposure to and the effects of chemicals with estrogen like properties. Here, we review the mechanisms underlying Vtg production, methods for the analysis of Vtg, and studies that have measured Vtg production in response to chemical or effluent exposure. These studies indicate that the production of Vtg may be a useful biomarker of exposure to estrogenic chemicals but that a greater understanding of the mechanism of action of these chemicals is required. In cyprinid fishes reproductive endpoints are more sensitive to exposureto xenoestrogens than Vtg induction. These observations indicate that Vtg induction is of more use as a biomarker of exposure to xenoestrogens rather than a predictor of adverse effects.
Evaluation of the Water Stress-Inducible Promoter Wsi18 in the Model Monocot Brachypodium distachyon

ii Acknowledgments iii List of Tables vii List of Figures viii List of Appendices ix List of Abbreviations x Chapter 1: Introduction 1 1.1 Water deficit stresses 1 1.2 Mechanisms of water deficit tolerance 2 1.2.1 Osmotic stress and cellular dehydration 3 1.2. 2 Salt stress 5 1.3 Promoters 6 1.3. 1 Promoter classification 7 1.3. 2 Transcription initiation at the core promoter 8 1.3. 3 Gene expression patterns are established in the proximal and distal promoter regions 10 1.3. 4 Water deficit-inducible promoters 14 1.4 The Wsi18 promoter 17 1.5 Brachypodium distachyon, a model monocot 19 1.6 Research objective 21 Chapter 2: Materials and Methods 23 2.1 Preparation of media and solutions 23 2.1.1 Brachypodium distachyon seed germination medium 23 2.1.2 B. distachyon transformation media 23
Screening and characterization of amylase enzyme in sweet orange (Citrus sinensis) juice clarification

Abstract. Utami R, Widowati E, Christy A. 2016. Screening and characterization of amylase enzyme in sweet orange (Citrus sinensis) juice clarification. Nusantara Bioscience 8: 268-272. The amylum compound of sweet orange cloudify the produced juice. Clarification by amylase could remove the cloudiness. The aimed of this study were screening the amylolytic bacteria from spoiled potato which are potential in clarification of sweet orange juice, and characterization of the resulted amylase (optimum pH and temperature, pH and thermal stability, KM and Vmax). The results showed that from thirteen bacterial isolates, three isolates (K-7, K-8, and K-11) produced enzymes that showed the best clarification activity on the sweet orange juice. The optimum pH of the isolate K-7, K-8, and K-11 enzymes were found to be 7, 7 and 6, respectively. The optimum temperature of the isolate K-7, K-8, and K-11 enzymes were found to be 35, 40 and 35°C, respectively. Enzymes of isolate K-7, K-8, and K-11 were stable in the pH range 3-6, 5-6, and 7-8, respectively. The enzyme of isolate K-7 and K-11 were stable at temperature 40-60°C while enzyme of isolate K-8 stable at temperature 40-70° C. Km values of isolate K-7, K-8, and K-11 enzymes were 0.2756 mg/mL, 0.0888 mg/mL, and 0.0956 mg/mL, respectively. Vmax values of isolate K-7, K-8, and K-11 enzyme were 0.0325 U/mL, 0.0164 U/mL, and 0.0134 U/mL.
Identification and Characterization of Potential Phenol Degrading Bacterial strains Isolated from Municipal Sewage, Bilaspur, Chhattisgarh

Phenol and its derivatives are consistently causing harmful effects to an aquatic ecosystem. The present study focused on the isolation and characterization of potential phenol degrading bacterial strains and subsequently optimization of media ingredients for efficient phenol degradation by potential bacterial strains. Bacterial strains were isolated from municipal sewage, Bilaspur (21'47 and 23'8 N 81'14 and 83'15 E). After optimization phenol degradation rate was increased by 1.84 fold for PDB 5 (from 40.37% to 74.67%) and 1.39 fold for PDB 11 (from 58.62% to 81.51%) at 500mg/l initial phenol concentration. PDB 5 and PDB 11 were identified as Streptococcus sp. PDB 5 and Pseudomonas sp. PDB 11 respectively as potential phenol degrading bacterial strains. These strains can further be used in microbially assisted phenol degradation to remove phenol derivatives present in industrial wastewater. Int J Appl Sci Biotechnol, Vol 4(3): 288-293
Molecular dynamic studies of amyloid-beta interactions with curcumin and Cu2+ ions

Amyloid-beta (Aβ) peptide readily forms aggregates that are associated with Alzheimer’s disease. Transition metals play a key role in this process. Recently, it has been shown that curcumin (CUA), a polyphenolic phytochemical, inhibits the aggregation of Aβ peptide. However, interactions of Aβ peptide with metal ions or CUA are not entirely clear. In this work, molecular dynamics (MD) simulations were carried out to clear the nature of interactions between the 42-residue Aβ peptide (Aβ-42) and Cu2+ ions and CUA. Altogether nine different models were investigated, and more than 2 µs of the simulation data were analyzed. The models represent the possible modes of arrangement between Aβ-42 and Cu2+ ions and CUA, respectively, and were used to shed light on the Aβ-42 conformational behavior in the presence of Cu2+ ions and CUA molecules. Obtained data clearly showed that the presence of a CUA molecule or a higher concentration of copper ions significantly affect the conformational behavior of Aβ-42. Calculations showed that the change of the His13 protonation state (Aβ(H13δ)-Cu2+, Aβ(H13δ)-Cu2+ -CUA models) leads to higher occurrence of the Asp23-Lys28 salt bridge. Analyzes of trajectories revealed that C-terminal β-sheet structures occurred significantly less frequently, and CUA promoted the stabilization of the α-helical structure. Further, calculations of the Aβ-42 complex with CUA and Cu2+ ions showed that CUA can chelate the Cu2+ ion and directly interact with Aβ, which may explain why CUA acts as an inhibitor of Aβ aggregation.
Primary Neuron-glia Culture from Rat Cortex as a Model to Study Neuroinflammation in CNS Injuries or Diseases

1Department of Nursing, Hsin Sheng Junior College of Medical Care and Management, Taoyuan, Taiwan; 2Graduate Institute of Medical Sciences and Department of Physiology, College of Medicine, Taipei Medical University, Taipei, Taiwan; 3Graduate Institute of Medical Sciences and Department of Physiology, College of Medicine, Taipei Medical University, Taipei, Taiwan *For correspondence: jywang2010@tmu.edu. tw
Comparison of the non-linear models defining the growth of Thalli sheep under desert conditions.

The aim of this study was to estimate growth curve parameters of Thalli sheep using different nonlinear models. To achieve the aim, Thalli lambs (n= 130) maintained at Livestock Experiment Station, RakhGhulaman, district Bhakkar (Pakistan) were used to detect the best non-linear model identifying the growth of Thalli sheep. In the present study, seven non-linear regression models such as Gompertz, Brody, Bertalanffy, Monomolecular, Logistic, Richards, and Weibull models were fitted to body weight-age data of Thalli sheep. The most suitable model which determines the growth pattern of these sheep was identified with determination coefficient (R2) and Root of Mean Square Error (RMSE) criteria. The values of parameter ‘a’, which is the asymptotic weight for all the models, were estimated as: 28.2, 33.1, 28.9, 33.1, 27.1, 28.2 and 28.0, respectively. The values of the turning point (point of inflection), ‘b’ were 1.304, 1.123, 0.822, 0.165, 2.535, -3.630 and 27.017, respectively. The corresponding values for parameter ‘c’, which is the growth rate for each model, were 0.398, 0.165, 0.325, 0.701, 0.609, 0.400 and 0.060, respectively. The determination coefficients (R2 %) obtained for these models had a narrow range of 96.8 to 97.9%. Among these models, Gompertz and Richards models produced slightly higher estimates compared to other models in the identification of growth pattern of Thalli sheep. It was concluded that Gompertz model with three parameters would be used for modeling growth curve in Thalli sheep.
Trehalase Activity in Arabidopsis thaliana Optimized for 96-well Plates

[Abstract] Trehalose is a nonreducing disaccharide. It is a common sugar in bacteria, fungi and yeast, where it functions as a carbon source and stress protectant. In contrast, plants, although encoding large trehalose biosynthesis gene families, contain only small amounts of trehalose. The intermediate compound of trehalose, trehalose-6-phosphate (T6P), is a signaling molecule in plants, regulating metabolism, growth, and development. Most plants contain only a single trehalase, the enzyme that specifically hydrolyzes trehalose into two glucose molecules. High trehalase activity has been suggested to be part of the defense mechanism in plants hosting mycorrhizal fungi, rhizobia, and the plant pathogen Plasmodiophora brassica. Recently, it was shown in Arabidopsis thaliana that high trehalase activity is associated with an increase in drought stress tolerance and that trehalase fulfills an important role in stomatal regulation. Here we describe a protocol for measuring trehalase activity in Arabidopsis tissues, optimized for 96well plates. Dialyzed protein extracts will be incubated with trehalose, followed by the quantitation of the released glucose using glucose oxidase-peroxidase.
Strongyloides stercoralis found in imported dogs, household dogs and kennel dogs in Iceland

The aim of this paper is to report cases of the intestinal parasitic nematode Strongyloides stercoralis in dogs in Iceland. The nematode was diagnosed in 20 (0.6%) of imported dogs in quaratine in Iceland during 19892016. Household dogs: The first case of S. stercoralis infection diagnosed outside quaratine in Iceland was in an unhealthy household puppy purchased from an Icelandic breeding kennel (Kennel A) in 2012. A total of nine puppies purchased from Kennel A, and two dogs which had contact with dogs from the kennel, were diagnosed with S. stercoralis. Kennel dogs: In 2012 S. stercoralis was confirmed in dozens of dogs in Kennel A. Follow-up examinations after anthelmintic treatments indicated a successful removal of worms in imported and household dogs. In spite of more than a dozen anthelmintic treatment actions and other arrangements in Kennel A since 2012, recurrent infections have repeatedly been confirmed, the last one in 2015. The nematode is believed to have been introduced to the breeding kennel with an imported dog, in spite of anthelmintic treatments in quarantine. YFIRLIT Sníkjuþráðormurinn Strongyloides stercoralis staðfestur á Íslandi í innfluttum hundum, heimilishundum og í hundaræktunarstöð. Markmið þessa yfirlits er að greina frá tilfellum sem greinst hafa af sníkjuþráðorminum Strongyloides stercoralis í hundum á Íslandi. Ormurinn hefur greinst í saursýnum úr 20 (0.6%) hundum sem fluttir voru til landins um einungrunarstöðvar á árunum 1989-2016. Heimilishundar: Fyrsta tilfelli utan einangrunarstöðva greindist í veikum heimilishvolpi sem keyptur var á íslenskri hundaræktunarstöð 2012. Ormurinn greindist í alls níu hvolpum sem keyptir voru á stöðinni og í tveimur heimilishundum sem höfðu haft samgang við hunda frá stöðinni. Hundaræktunarstöðin: S. stercoralis greindist í tugum hunda í stöðinni í byrjun árs 2012, bæði í hvolpum og fullorðnum hundum. Innfluttu hundarnir og heimilishundarnir fengu ormalyfjameðferð og eftirfylgnirannsóknir bentu til að tekist hefði að uppræta ormana. Margendurteknar ormalyfjagjafir á árunum 2012 -2016 og aðrar aðgerðir í hundaræktunarstöðinni virðast hafa borið umtalsverðan árangur en ormurinn hefur þó greinst í stökum saursýnum á undanförnum árum, síðast í nóvember 2015. Talið er að þráðormurinn hafi borist inn í hundaræktunarstöðina með innfluttum hundi, þrátt fyrir endurteknar ormalyfjagjafir í einangrunarstöð, smitast milli hunda í ræktunarstöðinni og borist þaðan út með seldum hundum.
Fasting in α1-antitrypsin deficient liver: consultative activation of autophagy

Antitrypsin (α 1 -AT) deficiency causes severe liver injury in a subgroup of patients. Liver injury is thought to be caused by retention of a polymerized mutant α 1 -ATZ molecule in the endoplasmic reticulum (ER) of hepatocytes and is associated with an intense autophagic response. However, there is limited information about what physiologic stressors might influence liver injury. In this study, we examined the effect of fasting in the PiZ mouse model of α 1 -AT deficiency, because fasting is a well-characterized physiological stressor and a known stimulus for autophagy. Results show that there is a marked increase in fat accumulation and in α 1 -AT-containing globules in the liver of the PiZ mouse induced by fasting. Although fasting induced a marked autophagic response in wild-type mice, the autophagic response was already activated in PiZ mice and did not further increase with fasting. PiZ mice also had a significantly decreased tolerance for prolonged fasting compared with wild-type mice (PiZ mice 0% survival of 72-h fast; wild-type 100% survivial). These results demonstrate an altered response to stress in the α 1 -AT-deficient liver, including inability to further increase an activated autophagic response, a developmental state-specific increase in α 1 -AT-containing globules, and increased mortality.
Computational Identification of MicroRNA-targeted Nucleotide-Binding Site-Leucine-Rich Repeat Genes in Plants

[Abstract] Plant genomes harbor dozens to hundreds of nucleotide-binding site-leucine-rich repeat (NBS-LRR, NBS for short) type disease resistance genes (Shao et al., 2014; Zhang et al., 2015). Proper regulation of these genes is important for normal growth of plants by reducing unnecessary fitness costs in the absence of pathogen infection. Recent studies have revealed that microRNAs are involved in regulation of NBS genes in plants (Zhai et al., 2011; Shivaprasad et al., 2012). This protocol describes computational methods for the genome-wide identification of plant NBS genes potentially regulated by microRNAs.