Miracle-dz/UniFAR-FTUs huggingface dataset:
Prevalence and Antibiotic Resistance Pattern among the Mastitis Causing Microorganisms

Mastitis is one of the most commonly occurring diseases of dairy animals. It is the most important cause of economic losses to the dairy industry in India and throughout the world. In the present study prevalence of microorganisms isolated from mastitic milk and their antibiotic resistance was studied. A total of sixty nine milk samples from mastitic animals (clinical and subclinical) were tested using sodium lauryl sulphate test and those positive were selected and transported to the laboratory for isolation and identification of the causative agent. Out of these samples fifty samples yielded bacterial growth when tested on selective/non selective medium. Of these fifty samples, seven samples had single bacterial growth whereas rest of the 43 samples had mixed growth. Among the bacterial isolates it was found that the highest prevalence was of Streptococcus agalactiae and Staphylococcus aureus followed by E. coli and Klebsiella pneumoniae. Antibiotic sensitivity test revealed that Streptococcus agalactiae revealed the highest sensitivity to ofloxacin, ciprofloxacin, gentamicin and resistance to amoxicillin and doxycycline; Staphylococcus aureus revealed the highest sensitivity to ciprofloxacin, doxycycline, azithromycin and sparfloxacin and resistance to amoxycillin and gentamicin. Similarly, E. coli revealed the highest sensitivity to azithromycin and chloramphenicol and resistance to amoxicillin and teicoplanin, and Klebsiella pneumoniae revealed highest sensitivity to azithromycin, gentamicin and resistance to amoxicillin, teicoplanin and erythromycin. Thus, from the present study it could be concluded that Streptococcus agalactiae, Staphylococcus aureus, E. coli and Klebsiella pneumoniae were the most frequently isolated organisms from mastitic animals and azithromycin and the third generation fluoroquinolones (ciprofloxacin, sparfloxacin and ofloxacin) were the most sensitive drugs.
Genetic relationships in wild olives (Olea europaea ssp. oleaster) by ISSR and RAPD markers

ABSTRACT Wild olives or oleaster (Olea europaea ssp. oleaster) are found naturally in the Mediterranean basin. The changes in climate and environmental conditions have been gradually accelerating in the last decades. Since oleasters are more resistant to diseases, pests and unfavorable environmental conditions, they have become a very important source for resistance breeding studies that would be required in the future. Twelve inter simple sequence repeat (ISSR) and 12 random amplified polymorphic DNA (RAPD) markers were used; the effectiveness of these markers was studied and different parameters such as effective multiplex ratio, marker index, resolving power, and polymorphic information content, Shannon information index (I), effective allele number (ne), and Nei's genetic distance (h) were used in the determination of genetic varieties of 18 oleasters grown in Turkey. When both marker systems were analyzed in this study, it was observed that MI, RP and EMR parameters in ISSR gave higher values than RAPD while ne, I, and h were lower in ISSRs. Neighbour-joining dendrograms were developed by using Nei's genetic distance matrix, and principal coordinate analysis was performed.
Impact of genetic and nutritional disturbances in one-carbon metabolism on brain function and structure in mice

Homocystinuria can be caused by severe deficiency in either methylenetetrahydrofolate reductase (MTHFR) or methionine synthase reductase (MTRR). Patients present with neurological symptoms, some of which include developmental delays, mental retardation, motor abnormalities and brain atrophy. Biochemically patients have reduced enzyme activity, hyperhomocysteinemia and decreased levels of serum folic acid, methionine and S-adenosylmethionine (SAM). Mouse models for genetic deficiencies in MTHFR and MTRR have been developed to investigate the in vivo effects of these deficiencies. Young BALB/c Mthfr-/- mice have elevated levels of plasma homocysteine as well as decreased methylation and SAM levels in brain tissue. Mtrr is expressed in the developing neural tube and Mtrr expression is increased in brain tissue of MTRR-deficient mice. The first two objectives of this thesis will examine the brain function of MTHFR and MTRR in adult male mice. Adult C57BL/6 Mthfr-/- male mice have elevated plasma homocysteine levels, impaired memory function along with changes in hippocampus, including morphology, global DNA hypomethylation, altered choline metabolites and increased levels of choline acetyltransferase (ChAT) and glucocorticoid receptor (GR). In the cerebellum of Mthfr-/- mice we confirmed morphological changes and increased apoptosis previously described in young BALB/c Mthfr-/- mice. Additionally, we identified changes in function, decreased volume and alterations in choline metabolites in the cerebellum. Adult mice deficient in MTRR have mildly elevated plasma homocysteine levels, short-term memory impairments, gait and affective behavior changes along with reduced methylation in hippocampus and cerebellum and reduced hippocampal volume. Changes in choline metabolism in hippocampus, cerebellum, liver and plasma were also identified.Maternal contributions of MTHFR, folic acid and choline during fetal and early neonatal brain development are essential. The last two objectives of this thesis will investigate the effects of maternal deficiencies in MTHFR, folic acid or choline on brain function and structure of 3-week-old Mthfr+/+ offspring. Preliminary data suggests that maternal deficiencies in MTHFR can lead to impaired short-term memory and motor function in Mthfr+/+ offspring. Elevated maternal plasma homocysteine and increased apoptosis in cerebellum and hippocampus of Mthfr+/+ offspring may be responsible for these behavioural changes. Maternal folic acid (FADD) or choline (ChDD) deficient diets result in impaired short-term memory in Mthfr+/+ offspring. Maternal ChDD results in impaired motor function, whereas maternal FADD changes affective behaviors in Mthfr+/+ offspring. Both maternal FADD and ChDD result in increased apoptosis, alterations in choline metabolites and increased ChAT protein levels in the cerebellum and hippocampus of Mthfr+/+ offspring.These behavioural, morphological and biochemical results suggest that MTHFR, MTRR and maternal folate and choline are critical for brain development, maturation…
Beneficial effect of edible blue-green alga Nostoc flagelliforme (Cyanophyceae) on blood glucose level and serum lipid concentrations in spontaneously non-insulin-dependent diabetic rats

The edible blue-green alga Nostoc flagelliforme was evaluated for beneficial effect on blood glucose level and serum lipid concentrations in an experiment with SHR rats used as model animals for spontaneously non-insulin-dependent diabetes mellitus. In both of N. flagelliforme powder administered rats and N. flagelliforme extract administered rats, the fasting glucose levels on 21st day, 35th day, 49th day and 63rd day were significantly lower than control rats. The concentrations of triglyceride in the serum of N. flagelliforme powder administered rats and total cholesterol and triglyceride in the serum of N. flagelliforme extract administered rats were significantly lower than those of control rats. The concentrations of triglyceride and total cholesterol in the liver of both of N. flagelliforme powder administered rats and N. flagelliforme extract administered rats were significantly lower than those of control rats. These results indicate that N. flagelliforme has beneficial effects on blood glucose level and serum lipid concentrations in spontaneously non-insulin-dependent diabetic rats.
Mycorrhizal colonization, P uptake and yield of older and modern wheats under organic management

Kirk, A. P., Entz, M. H. , Fox, S. L. and Tenuta, M. 2011. Mycorrhizal colonization, P uptake and yield of older and modern wheats under organic management. Can. J. Plant Sci. 91: 663-667. Arbuscular mycorrhizal fungi (AMF) are important for plant nutrient uptake, and mycorrhizal dependence varies between wheat genotypes. Cultivar selection under fertilized conditions may have reduced mycorrhizal associations in modern cultivars. This study investigated AMF colonization, tissue P and grain yield of five modern (post 1990) and five older (pre 1970) spring wheat cultivars over 4 site-years in Manitoba. Older cultivars actually had significantly lower AMF colonization and grain yield than modern cultivars, but no tissue P concentration differences were observed. The two highest yielding lines were released after 2004, and one of these (FBC Dylan) was selected for suitability in organic farming systems.
Actin impacts the late stages of prion formation and prion propagation

In yeast, the [PSI+] and [PIN+] prions are aggregated forms of the Sup35 and Rnq1 proteins, respectively. The cellular mechanisms that underlie the formation and propagation of these prion states are not clearly understood. Our previous work suggested that actin networks play a role in early and late steps of the formation of [PSI+]. To further explore how actin impacts yeast prions, we turned to a set of actin point mutants. We found that the disruption of actin cables, either by an actin destabilizing drug or the act1-101 mutant, can enhance prion formation during the later stages of prion formation. Our data suggest that under normal conditions, actin cables play a role in limiting the inheritance of newly made prion particles to daughter cells. We also found actin can impact prion propagation. The act1-122 mutant, which contains a substitution in the fimbrin binding region, destabilized the [PIN+] prion over time. This is the first evidence that actin has a role in [PIN+] propagation. Taken together, our findings reveal novel roles for actin in the formation and propagation of prions.
Detection of sustained signals and its relation to coherent feedforward loops

Many studies have shown that cells use temporal dynamics of signaling molecules to encode information. One particular class of temporal dynamics is sustained and transient signals, i.e. signals of long and short durations respectively. This paper formulates a detection problem for distinguishing sustained signals from transient ones. The solution of the detection problem is to compute the likelihood ratio of observing a sustained signal to a transient signal. We show that, if the logarithm of this likelihood ratio is positive (i.e. when the signal is likely to be sustained), then this log-likelihood ratio can be approximately computed by a coherent feedforward loop. Although the capability of coherent feedforward loops to discriminate sustained signals is known, its statistical information processing interpretation has not been pointed out before.
Grating coupled-surface plasmon resonance and fluorescent plasmonics biosensor for diagnosis of Lyme disease

Infection with the spirochete Borrelia burgdorferi leads to Lyme disease, the most common tick-borne disease in North America, Europe, and Asia. Currently, Lyme disease is diagnosed using a two-tiered approach of ELISA/immunofluorescence, followed by Western blot analysis. These assays measure serological immune response to the infection, namely levels of IgG or IgM antibodies that bind to B. burgdorferi antigens. However, the existing approach is non-quantitative, lacks sensitivity, and may contribute to delayed diagnosis. In this study, grating-coupled fluorescence plasmonics (GC-FP) was used for rapid, highly-multiplexed detection of antibodies that bind B. burgdorferi proteins in human and mouse blood serum. GC-FP is an optical plasmonic method that enables quantitative detection of molecular interactions and can be incorporated into microfluidic format for highly multiplexed testing. We have demonstrated that this technique allows us to use only three microliters of blood serum to quantitatively detect multiple target antibodies within 30 minutes. We have also shown that GC-FP is faster and more sensitive than the traditional two-tiered Lyme disease testing scheme, making it attractive for diagnostic purposes. This proof-of-concept study provides foundations to develop GC-FP as a highly sensitive diagnostic tool to enhance the efficiency of assessment for Lyme disease patients, which will ultimately improve treatment outcomes.
Genetic and Genomic Tools for Cannabis sativa

ABSTRACT The Cannabis industry is currently one of the fastest growing industries in the United States. Given the changing legal status of the plant, and the rapidly advancing research, updated information on the advancement of Cannabis genomics is needed. This versatile plant is used as medicine and for food, fiber, and bioremediation. Insights from modern, high-throughput genomic technology are revolutionizing our understanding of the plant and are providing new tools to further improve our knowledge and utilization of this unique species. This review quantifies and evaluates the currently available genomic resources for Cannabis research, including six whole-genome assemblies, two transcriptomes, and 393 other substantial genomic resources, as well as other smaller publicly available genetic and genomic resources. The open-source approaches followed by many leading scientists in the field promote collaboration and facilitate these rapid advances.
In vitro Efficacy of Different Botanicals and Fungicides on Brinjal Leaf Mold Pathogen

The diseases leaf mold disease is now causing the considerable yield losses in Manipur state. The symptoms of the leaf mold disease are characterized by the appearance of brown cottony growth in patches on the abaxial side of the leaf and the patches become dark brown when the disease advances and all leads to defoliation (Prashant et al., 2017). Pandey and Pandey (2001) identified Cladosporium fulvum from diseased plants and fruits of aubergines. Mishra and Mishra (2012) reported that Cladosporium fulvum was present on both plant and fruit of eggplant and generally occurred during November to May.
A 1-deoxy-d-xylulose 5-phosphate reductoisomerase gene probably involved in the synthesis of terpenoids in Chrysanthemum indicum var. aromaticum

Abstract: Terpenoids are important secondary metabolites in plants. The synthesis of terpenoids involves a key enzyme, 1-deoxy-d-xylulose 5-phosphate reductoisomerase (DXR). In an aromatic ornamental plant, Chrysanthemum indicum var. aromaticum, terpenoids were found to be an important component in leaf secretions. To study the regulatory mechanism of terpenoid synthesis in C. indicum var. aromaticum, we cloned the DXR gene from C. indicum var. aromaticum, named CiDXR, based on transcriptome data. CiDXR is 1419 bp, encoding a polypeptide chain of 472 amino acids. Comparative and bioinformatic analysis showed that CiDXR was highly similar to DXRs from other plant species. The protein product of CiDXR was analyzed for physical and chemical properties, and secondary and tertiary structures. Methyl jasmonate (MeJA) is an effective exogenous elicitor that can impact the synthesis of secondary metabolites by regulating the expression of a series of specific key enzymes. In our study, MeJA treatment was used to study the relationship between CiDXR expression and terpenoid metabolism. The expression pattern of CiDXR was analyzed by quantitative real-time polymerase chain reaction. Leaves expressed the highest level of CiDXR mRNA. In addition, CiDXR expression was found to be activated by MeJA, up to 20-fold at 24 h post induction. The MeJA treatment significantly affected the relative contents of the secretion products, and the induction effect was maximal at 24 h, consistent with the expression of CiDXR. This study shows that CiDXR may play a key regulatory role in the control of terpenoid synthesis in C. indicum var. aromaticum.
Changes in the chemical compositions of leaf litter in the canopy of a Japanese cedar plantation

ABSTRACT Canopy leaf litter is typically unevenly distributed due to interception by branches and epiphytes and/or due to attachment to branches and tree trunks. Japanese cedar (Cryptomeria japonica) trees hold a large amount of canopy litter that stays attached to foliage and branches for several years before litterfall. Litter retention in the canopy is predicted to affect the chemical composition of litterfall and throughfall. We analyzed the chemical compositions of water-soluble materials washed from the leaves and those of the leaf residues with different leaf litter ages to clarify the effect of leaf-litter retention in the canopy of Japanese cedar trees. Chemical components of the leaf litter after the washing procedure show temporal changes in total carbon, total nitrogen, and carbon/nitrogen ratio just after senescence and prior to litterfall. Higher inorganic ion concentrations in soluble materials from old dead leaves (ODL) dead for more than 2 years suggest the importance of ODL in leaching and catching chemical components in the canopy. Our results show that Japanese cedar canopies retain the various qualities of leaf litter, which are produced by senescence, leaching, and catching dry deposition, and that a large amount of dissolved components leach from dead leaves that are still attached to the canopy.
Gaze Bias Differences Capture Individual Choice Behavior

How do we make simple consumer choices (e.g., deciding between an apple, an orange, and a banana)? Recent empirical evidence suggests a close link between choice behavior and eye movements at the group level, with generally higher choice probabilities for items that were looked at longer during the decision process. However, it is unclear how variable this effect is across individuals. Here, we investigate this question in a multialternative forced-choice experiment using a novel computational model that can be easily applied to the individual participant level. We show that a link between gaze and choice is present for most individuals, but differs considerably in strength, namely, the choices of some individuals are almost independent of gaze allocation, while the choices of others are strongly associated with gaze behavior. Accounting for this variability in our model allows us to explain and accurately predict individual differences in observed choice behavior.
Estimating the Annual Spawning Run Size and Population Size of the Southern Distinct Population Segment of Green Sturgeon

The Southern Distinct Population Segment of Green Sturgeon Acipenser medirostris spawns in the Sacramento River, California, and is listed as a threatened species under the U.S. Endangered Species Act. We estimated the spawning run size and population size in 2010–2015 by using dual-frequency identification sonar (DIDSON) sampling, underwater video camera species identification, and acoustic tag detections. Spawning run size varied from 336 to 1,236 individuals. We estimated the total population size to be 17,548 individuals (95% confidence interval [CI] = 12,614–22,482). The estimated number of adults was 2,106 (95% CI = 1,246–2,966), the estimated number of juveniles was 4,387 (95% CI = 2,595–6,179), and the estimated number of subadults was 11,055 (95% CI = 6,540– *Corresponding author: ethan.mora@noaa.gov Received June 17, 2017; accepted November 14, 2017 Transactions ofthe American Fisheries Society 147:195–203, 2018 © 2017 American Fisheries Society ISSN: 0002-8487 print / 1548-8659 online DOI: 10.1002/tafs.10009
Insertion of a Retrotransposon into a Flavonoid 3'-hydroxylase Homolog Confers the Red Root Character in the Radish (Raphanus sativus L. var. longipinnatus L. H. Bailey)

Flavonoid 3'-hydroxylase (F3'H) has an important role in determining anthocyanin patterns in plants. Here, we analyzed root coloration characteristics in the radish by investigating anthocyanidin and expression of F3'H genes in cultivars with purple, red, or white roots. Cyanidin was detected in the roots of the purple radish, while pelargonidin was found in the red radish; however, neither of these anthocyanidins was detected in white radish. We isolated the RsF3'H gene of the purple root radish and found that it showed a relatively higher level of expression compared to the RsF3'H of the red radish. Moreover, we identified a retrotransposon, gypsy-Ty3 , in the first exon of the F3'H homolog in the red radish. These results suggested that the F3'H enzyme may determine cyanidin-based anthocyanin in the purple radish, and that the lack of F3'H function due to the retrotransposon insertion, contributed to pelargonidin-based anthocyanin accumulation in the red radish.
Foliar Spray with Different Agrochemicals on Fruit Quality and Exportability of ‘Washington’ Navel Orange Fruit (Citrus sinensis L.)

ABSTRACT The present study was carried out to improve fruit set, yield, quality, marketability, and exportability of ‘Washington’ Navel orange. Pre-harvest foliar sprays of GA3, K, and Ca, either alone or combined, were applied at full bloom. The following treatments were applied: {control (T1), 25 mg/L GA3 (T2), 2% K2SO4 (T3), 25 mg/L GA3 + 2% K2SO4 (T4), 25 mg/L GA3 + 2% Ca Cl2 (T5), 2% K2SO4 + 2% Ca Cl2 (T6), and 25 mg/L GA3 + 2% K2SO4 + 2% Ca Cl2 (T7). All treatments improved fruit set, yield, physical and chemical characteristics, mineral content of leaves and fruit rind, and the percentage of exportable fruit in comparison to the control. Fruit set, fruit detachment force, peel firmness, and the mineral content of leaves and fruit rind were enhanced significantly with the combination of GA3 + K2SO4 + Ca Cl2 (T7) in comparison to all other treatments and the control. Results indicated that all foliar combination treatments improved fruit quality and marketability, and increased the percentage of exportable fruit and reduced the defects of non-exportable fruit.
Laser-triggering of electric breakdown in liquids

A laser-triggering device for the study of electric breakdown in liquids is described. Triggered breakdown can be used to study the propagation of the breakdown after initiation. It is important that the triggering method used be as flexible as possible, for example, that the trigger pulse can be applied at various points in a gap and that the trigger pulse energy can be varied. Laser triggering provides such flexibility. The technique has been shown to trigger DC breakdowns for pulse energies down to about 50 mJ for 8-ns-long 1064-nm Q-switched laser pulses. It is concluded that electrical breakdown at semihomogeneous field strengths much below spontaneous breakdown can be induced by laser-produced plasmas, thereby allowing direct study of the propagation field.
Full light and soil drought constrain plant growth in Mediterranean cliffs: the case of Primula palinuri Petagna

Abstract In any biogeographical region, cliffs shelter a larger number of relict species than do the surrounding areas. To develop effective conservation strategies, experimental studies are needed. We focused on Mediterranean coastal cliffs and on Primula palinuri Petagna, an endangered narrow-endemic plant, included in the IUCN Red List and chosen as a key species. The hypothesis was that light intensity and soil water availability could affect survival and growth of juvenile plants. To avoid the bias of other cliff environmental factors and to overcome problems of cliff site inaccessibility, we performed an ex-situ experiment. The effect of two light regimes and two soil water availability conditions on survival and morpho-functional traits were analysed. Plants grown under reduced light intensity and wet soil showed no reduction in survival and performed very well in terms of growth and storage accumulation. By contrast, full light and dry soil proved to be detrimental conditions. Overall results suggested that cliff environmental conditions play an important role in conservation of narrow-endemic species. The decreasing trend of the already severely fragmented populations of P. palinuri and the ongoing increasing aridity is likely to contribute to a further reduction of the already narrow distribution this cliff relict species.