Miracle-dz/UniFAR-FTUs huggingface dataset:
Phylogeny of Ononis in Iran using nuclear ribosomal DNA and chloroplast sequence data

The genus Ononis,embraces more than 85 species worldwide. In the present study, materials of two subspecies of O. spinosa from different localities of Iran alongside some other native species of the genus were included in phylogenetic analyses. In addition, over 50 accessions were obtained from GenBank. In order to clarify the exact number of subspecies of O. spinosa in Iran, datasets were obtained from sequencing of nuclear ribosomal ITS (nr DNA ITS) and trnL-F plastid (cp DNA) regions and analysed. Three taxa belonging to O. spinosa L. complex (O. spinosa subsp. leiosperma, O. spinosa subsp. antiquorum, and O. arvensis=O. spinosa subsp. arvensis) were previously reported from Iran. Based on Maximum Parsimony and Bayesian analyses of the molecular datasets, it is shown that, unlike the previous reports, Iranian O. spinosa complex belongs to only two subspecies (i.e. leiosperma and arvensis subspp.). In addition, we also found that, O. spinosa subsp. antiquorum is not present in Iran. It was also demonstrated that, seed sculpturing does not provide valuable characters in diagnosing different subspecies of O. spinosa.
The influence of transportation stress on serum cortisol, thyroid hormones, and some serum biochemical parameters in Iranian cashmere (Raini) goat.

________________________________________________________________________________________ TaJIk, J., S. NazIfI, R. EShTRakI: The influence of transportation stress on serum cortisol, thyroid hormones, and some serum biochemical parameters in Iranian cashmere (Raini) goat. Vet. arhiv 86, 795-804, 2016. aBSTRaCT In this study the effect of transportation stress on serum concentrations of cortisol, thyroid hormones, β-hydroxybutyrate, nonesterified fatty acids, glucose and plasma total protein in Iranian cashmere (Raini) goats were evaluated. On the first day, blood samples from 10 Raini goats (5 males and 5 non-lactating nonpregnant females) were collected at 8 A.M. (T1), and after 3h food and water deprivation (T2). On the second day, samples were collected at 8 A.M. (T3), and after 3h transport (T4). Final blood sample was taken 24 h after transport ended (T5). Food and water deprivation caused a significant decrement in serum cortisol, and a significant increase between T2 and T3 was evident. Transportation caused a significant increase in serum cortisol, and the increase continued until T5. Serum T3 showed a marginally significant decrease due to the food and water deprivation. Serum T4 and NEFA significantly increased between T2 and T3. No significant change in serum concentrations of glucose, fT3, fT4, T3/T4 ratio and BHBA in different samplings was observed. The current study showed that short road transport had a significant effect on some stress biomarkers in cashmere goats, however, it takes a longer time before hormonal control of metabolism can be affected. key words: transportation stress, cashmere goat, cortisol, thyroid hormones, serum, biochemical parameters ________________________________________________________________________________________
MicroED Structures from Micrometer Thick Protein Crystals

Theoretical calculations suggest that crystals exceeding 100 nm thickness are excluded by dynamical scattering from successful structure determination using microcrystal electron diffraction (MicroED). These calculations are at odds with experimental results where MicroED structures have been determined from significantly thicker crystals. Here we systematically evaluate the influence of thickness on the accuracy of MicroED intensities and the ability to determine structures from protein crystals one micrometer thick. To do so, we compare ab initio structures of a human prion protein segment determined from thin crystals to those determined from crystals up to one micrometer thick. We also compare molecular replacement solutions from crystals of varying thickness for a larger globular protein, proteinase K. Our results indicate that structures can be reliably determined from crystals at least an order of magnitude thicker than previously suggested by simulation, opening the possibility for an even broader range of MicroED experiments. Summary Atomic resolution protein structures can be determined by MicroED from crystals that surpass the theoretical maximum thickness limit by an order of magnitude.
Alpha EEG power reflects the suppression of Pavlovian bias during social reinforcement learning

Socially appropriate behavior involves learning actions that are valued by others and those that have a social cost. Facial expressions are one way that others can signal the social value of our actions. The rewarding or aversive properties of signals such as smiles or frowns also evoke automatic approach or avoidance behaviors in receivers, and a Pavlovian system learns cues that predict rewarding or aversive outcomes. In this study, we examined the computational and neural mechanisms underlying interactions between Pavlovian and Instrumental systems during social reinforcement learning. We found that Pavlovian biases to approach cues predicting social reward and avoid cues predicting social punishment interfered with Instrumental learning from social feedback. While the computations underlying Pavlovian and Instrumental interactions remained the same as when learning from monetary feedback, Pavlovian biases from social outcomes to approach or withdraw were not significantly correlated with biases from money. Trial-by-trial measures of alpha (8-14Hz) EEG power was associated with suppression of Pavlovian bias to social outcomes, while suppression of bias from money was associated with theta (4-7Hz) EEG power. Our findings demonstrate how emotional reactions to feedback from others are balanced with the instrumental value of that feedback to guide social behavior. Significance statement A smile from another can be a signal to continue what we are doing, while an angry scowl is a sure sign to stop. Feedback from others such as this plays an important role in shapeing social behavior. The rewarding nature of a smile (or the aversive nature of a scowl) can also lead to automatic tendencies to approach (or avoid), and we can learn situations that predict positive or negative social outcomes. In this study, we examined the brain mechanisms that come into play when the instrumental demands of a situation are in conflict with our automatic biases to approach or withdraw, such as when we have to approach someone who is scowling at us or withdraw from someone who is smiling.
Molecular Approaches to Improvement of Biocontrol Agents of Plant Diseases

Biological control holds out the prospect of an attractive proposition against plant diseases. Hitherto, a host of microorganisms have been identified as biocontrol agents while only a few have been able to be successfully commercialized. A major difficulty faced while translating the efficacious biocontrol agents into merchandise was that the efficacy of the developed strains was largely unstable under diverse environmental conditions in which the finished product of organismal origin was to tread before reaching the farmer's field. To add to the problem, desirable properties of a given biocontrol agent are not usually determined by a single attribute; on the contrary desirable biocontrol behavior of the agent is decided by its competitive ability, nature of antibiosis involved, lysis of the target pathogen and induced systemic resistance of the host plant, if any. Yet, a comprehensive understanding of the nature of genes encoding various observable biocontrol mechanisms of action and their putative role at molecular level is still elusive. A detailed characterization of gene(s) encoding biocontrol properties of a given biocontrol agent with respect to individual mechanism of action is a sine qua non for further improvement of biocontrol agents with a view to getting the most out of the individual biocontrol agent. With the advent of molecular biology, several approaches have been made towards achieving the following goals: i) Identification and characterization of genes encoding the specific biocontrol property against a given pathogen and ii) Designer biocontrol strains with potential genes responsible for superior biocontrol properties This review tries to focus on the recent developments on the above areas while bringing out a list of promising biocontrol agents so far worked upon with respect to individual target diseases of major crop plants.
Modulation of primary meristem activity by gibberellins through DELLA-TCP interaction in Arabidopsis

Plant development is an iterative process of organ formation from the primary meristems of the plant. Meristem activity is driven by dynamic transcriptional programs that determine cell fate and identity as cells are displaced trough the meristematic tissue to initiate organ primordia. This regulatory network includes members of the TCP and KNOX family of transcription factors, and integrates external and intrinsic cues to efficiently adapt meristem activity to an ever-changing environment. However, how this integration occurs is not clear yet. DELLA proteins have been proposed to modulate transcriptional circuits in plants in response to environmental signals. Although they do not show DNA binding capacity, DELLAs regulate transcription through physical interaction with a large number of DNA-binding transcription factors and other transcriptional regulators. Given the observed interaction between DELLAs and several members of the TCP family of transcription factors, we have explored the relevance of this interaction in the regulation of primary meristems. We have confirmed that DELLAs interact with members of both Class I and Class II TCPs, and prevent their ability to regulate downstream targets. In the embryonic roots, DELLAs maintain a dormant meristem by impairing TCP14/15-dependent activation of cell-cycle genes. On the other hand, DELLAs participate in the establishment of the shoot apical meristem domain that keeps an indeterminate fate, through the control of KNAT1 gene expression by the TCP2/4-AS1 regulatory module. In summary, this Thesis provides a mechanistic framework to eventually explain environmental regulation of meristem activity.
Dissection of the interaction between human holo-transferrin and ciprofloxacin in the presence of silver nanoparticles: spectroscopic approaches

Abstract The binding of ciprofloxacin (CIP) to human holo-transferrin (HTF) in the presence of silver nanoparticles (AgNPs) has been investigated by fluorescence quenching and circular dichroism (CD) techniques as well as resonance light scattering under physiological conditions. It was determined that the intrinsic fluorescence of HTF was quenched by CIP in the presence of AgNPs through static quenching, thus confirming that a CIP-HTF complex was formed in both the binary and ternary systems. However, the analysis of HTF fluorescence quenching in these binary and ternary systems indicated that the AgNPs were affected upon complex formation between CIP and HTF and that the binding affinity between them became more substantial when the AgNPs coexisted with the drug. Fluorescence quenching proved that HTF had one class of binding sites for CIP in both binary and ternary systems. CD spectra indicated that the secondary structure of HTF changed when increasing the CIP concentration and during the simultaneous presence of CIP and AgNPs, which led to decreased contents of α-helix and, β-sheet structures in HTF, inducing destabilization of the protein.
Winter Diet in Correlation to Sexual Dimorphism in Pennsylvania Coyotes ( Canis latrans )

Coyotes (Canis latrans) have been rapidly expanding into the Northeastern Region of the United States since the mid 1900’s most likely due to anthropogenic changes in their habitat. Several studies suggest that in addition to being top predators, coyotes are opportunistic feeders and are able to switch prey based on availability and density. Their generalist predation approach allows variation in their diets, and a widespread impact on the ecosystems in which they reside. In this paper, one hundred and seventy seven coyote stomachs were obtained throughout Pennsylvania from 2009-2012 and were dissected to define coyote winter diet. The contents were identified using ad hoc reference bone collections and a set of SEM hair images. Stomach contents were used to identify any correlation between sexual dimorphism and winter diets. It is hypothesized that if Pennsylvania’s coyotes show sexual dimorphism, male diets may differ from females. Being able to hunt larger animals may provide males the benefit of a higher caloric return. As a by-product of this research we are detailing a list of prey items found in the winter diet of C. latrans arranged by sex and location.
MHC: Polimorfismos genéticos en autoinmunidad

Autoimmune diseases are characterized by inflammation and by the development and maintenance of antibodies and T lymphocytes against “self” antigens. Although the etiology of these diseases is unknown, they have a number of cellular and molecular mechanisms in common. A strong genetic association exists between a number of autoimmune diseases such as rheumatoid arthritis, multiple sclerosis, and insulindependent diabetes mellitus (IDDM) and the expression of certain alleles or haplotypes of the major histocompatibility complex (MHC). The current explanation for this association proposes that disease-associated MHC molecules efficiently bind autoantigens involved in the pathophysiology of the disease. This results in a peripheral T cell-mediated immune response to the autoantigens and autoimmune sequelae. Individual susceptibility to autoimmune diseases may be determined by a combination of specific polymorphisms of genes encoding multiple cytokines, MHC antigens, adhesion molecules, and cellular proteins. This condition may lead to abnormal expression of immunoregulatory molecules and finally result in the development or exacerbation of the disease. Recently, the role of viral sequences in the pathogenesis of autoimmunity has been discussed, mainly involved in molecular mimicry.
A concise review of poultry vaccination and future implementation of plant-based vaccines

Every year the growth of the poultry industry is severely threatened by a number of infectious viral, bacterial and parasitic diseases. There are a number of vaccines to control these diseases including inactivated virus vaccines, attenuated virus vaccines, live virus vaccines, and subunit vaccines, but they are often relatively expensive and require cold storage and trained people to administer them, especially in developing countries. Plant-based vaccines provide a better option to control these diseases in low profit margin poultry industry. Still there are some challenges in the field of plant-based, so called ‘green’ vaccines. Injection-based oral priming is a big challenge for commercialisation of green vaccines so, new techniques are needed in the field of plant-based vaccine to pass these barriers for commercialisation. This discusses the potential for plant-based vaccines and whether they are good option to control poultry diseases.
Entomopathogenicity of Metarhizium anisopliae and some fungi toward the filbert aphid, Myzocallis coryli Goetze (Hemiptera: Aphididae)

The Filbert Aphid is one of the pests of hazelnut growing area of Turkey. This study was carried out all fungal isolates caused significant mortality against third instar nymphs of filbert aphid after 3, 6 and 10 days of conidial treatments at 18, 22 and 25 °C temperatures under laboratory conditions. The results showed that third instar nymphs of M. coryli were more susceptible to the entomopathogenic fungi at 25 °C than 18 °C. M. anisopliae was highly and statically equally effective against nymphs of M. coryli at 18, 22 and 25 °C (80.8%, 93.8%, and 100%) after 10 days of conidial treatment. The other isolates; TR-05 and TR-78.07 weren’t as effective as M. anisopliae on nymphs of M. coryli at 25 °C (67.8 and 62.6%). This study showed that isolate of M. anisopliae has virulent and highly potential for biological control on nymphs of Myzocallis coryli.
Effect of Catechin on Serum Levels of Inflammatory Cytokines, Antioxidant Enzymes Activity and DNA Oxidative Damage of Ovarian Tissue in Polycystic Ovarian Syndrome Rat Model

Women with polycystic ovary syndrome (PCOS) suffer anovulation due to hormonal disorders, oxidative stress and ovarian tissue inflammation. Catechin is the most important green tea flavonoids (Camellia sinensis) with antioxidant properties. This study aimed to determine the effects of catechin on serum levels of inflammatory cytokines, antioxidant enzymes activity and DNA oxidative damage of ovarian tissue in polycystic ovarian syndrome rat model. (saline solution, days, non-treated (saline solution, 24 and PCOS treated with catechin (50 and 100 mg/kg, 24 days, Polycystic ovarian syndrome was induced by single intramuscular injection of estradiol valerate (4 mg/kg). levels of TNF-α, IL-1β, IL-6, SOD, CAT, GPX and levels of MDA and HOdG-8 in ovarian tissue were measured by ELISA. of catechin, serum levels of TNF-α, IL-1β and IL-6 significantly decreased dose-dependently (p<0.05), levels of SOD, CAT, GPX in ovarian tissue significantly increased dose-dependently (p<0.05) and levels of MDA and HOdG-8 significantly decreased dose-dependently (p<0.05). Conclusion: Catechin decreases serum levels of cytokines, increases activity of antioxidant enzymes, decreases lipid peroxidation and DNA oxidative damage of ovarian tissue in polycystic ovarian syndrome rat model.
Does serum bilirubin prevent cardiovascular disease

Bilirubin possesses potent antioxidant, anti-inflammatory, anti-platelet, anti-hypercholesterolemic and anti-adiposity properties. Cross-sectional studies have demonstrated negative associations between serum bilirubin and metabolic syndrome (MetS), diabetes and atherosclerotic cardiovascular diseases (CVDs). However, longitudinal studies show conflicting results. Serum bilirubin levels are determined both genetically and environmentally, and fluctuate throughout one’s life. Longitudinal data suggest that some genetically hyperbilirubinemic individuals may have a lower CVD risk than the general population. However, the reverse may be also true; that is, postnatal metabolic or atherosclerotic diseases may cause oxidative stress and reduce serum bilirubin levels. Therefore, baseline serum bilirubin levels may not always be associated with future metabolic or atherosclerotic diseases. This situation resembles a phenomenon called antioxidant paradox; that is, randomized controlled trials have failed to confirm a role for antioxidant supplementation in CVD prevention, although oxidative stress is involved in the pathogenesis of CVD. Further prospective studies are required to confirm whether serum bilirubin prevents metabolic and atherosclerotic diseases.
Rearing temperature effect on the skeletal muscle fibres of Acipenser baerii yolk-sac larvae

Siberian sturgeon farming is important because it provides an alternative source of caviar and meat, but also for the conservation of the endangered natural stocks. Farmed fish is continuously subjected to stress factors, of which, water temperature is considered a major one (Schram et al., 2006). It has been demonstrated that physiological stress may have serious negative consequences on growth (Wendelaar Bonga, 1997) and that fish larvae appear less tolerant than adults to temperature variations (Stefanovich et al., 2016). The present study aims at investigating the stress response and development in precocious stages of siberian sturgeon when subjected to different rearing temperatures, by analysing ontogeny, growth and stress response of yolk-sac larvae. This study was approved by the Ethic Committee of the University of Milan (OPBA_20_2016). Fertilized Siberian sturgeon eggs were reared at 16°C, 19°C and 22°C until complete yolk-sac absorption. Sampling timepoints were: hatching, schooling and complete yolk-sac absorption stage. Water parameters and larvae development data were registered. Histological, histochemical and immunohistochemical analyses were performed in order to assess ontogeny and stress biomarkers and whole body cortisol was measured by a specific microtitre radioimmunoassay (RIA). Statistical analysis was performed with SAS software (v. 9.3, Cary Inc., NC). Larvae subjected to the highest water temperature showed a faster yolk-sac absorption and larvae body weight significantly increased from hatching onwards. Structural normal development considering the three different temperatures investigated from hatching until the end of the trial was observed. Significant differences were found between temperatures regarding body weight and cortisol levels (P<0.01). A qualitative stronger expression of stress markers was noticed in larvae subjected to the lower temperature. Even if this study indicates that lower rearing temperatures would appear more suitable for Siberian sturgeon rearing, further studies would be necessary to evaluate the temperature effect on a mid-long term basis.
Insert restriction enzyme cutting-free cloning strategy for expression plasmid construction

ABSTRACT Plasmids are important tools for producing biological reagents and performing molecular biological investigations. They are often constructed by the traditional restriction digestion/ligation cloning method. However, there are some drawbacks of this method due to its nature. It is time-consuming; sometimes there are no suitable restrictive digestion sites and the efficiency of digestion of the polymerase chain reaction (PCR) products is low. To address these problems, we employed an insert cutting-free cloning (ICFC) method in this work. Two kinds of DNA fragments containing the same gene but different terminal sequences were amplified by PCR. Inserts with desired cohesive ends were generated by successively mixing, denaturing and re-annealing these DNA fragments. Finally, they were ligated to the restriction-endonuclease digested vectors. Using this method, we successfully constructed a STAT3 (signal transducer and activator of transcription 3) expression plasmid. The method proved to be simple and efficient. It made the selection of restriction endonucleases and vectors easier, as well as simplified and shortened the cloning process.
Effect of Heat Stress and Ascorbic Acid on Gut Morphology of Broiler Chicken

The experiment was conduct d to evaluate the effect of heat stress and ascorbic acid (AA) on the gut morphology of broiler chickens. In this regard, macro and micromorphomatric study of the three segment of intestine such as duodenum, jejunum, ilium were performed along with the nutrients retention in the intestine. For this purpose 180 birds were purchased and divided into four equal groups i.e. normal temperature with and without AA, high temperature with and without AA supplementation. Our finding showed that birds reared under heat stress free environment and provided with AA showed significantly higher weight gain and size of intestinal parts along with higher nutrient retention than all other groups (P<0.05). Moreover, weight and length of Duodenum, jejunum and ileum was observed significantly (P<0.05) lower in heat stress control group than the AA supplemented group. Thus it was concluded that AA supplementation improves the villi size and nutrients digestibility when supplemented in normal temperature, whereas significantly (P<0.05) improves the weight and length of intestine when supplemented under higher temperature.