NP Analyst: An Open Online Platform for Compound Activity Mapping

Few tools exist in natural products discovery to integrate biological screening and untargeted mass spectrometry data at the library scale. Previously, we reported Compound Activity Mapping as a strategy for predicting compound bioactivity profiles directly from primary screening results on extract libraries. We now present NP Analyst, an open online platform for Compound Activity Mapping that accepts bioassay data of almost any type, and is compatible with mass spectrometry data from major instrument manufacturers via the mzML format. In addition, NP Analyst will accept processed mass spectrometry data from the MZmine 2 and GNPS open-source platforms, making it a versatile tool for integration with existing discovery workflows. We demonstrate the utility of this new tool for both the dereplication of known compounds and the discovery of novel bioactive natural products using a challenging low-resolution antimicrobial bioassay data set. This new platform is available at www.npanalyst.org.

Comparison of the effects of tylosin and tilmicosin as a systemic treatment of dry Holstein cows

The aim of the present study was to evaluate the efficacy of macrolides to eliminate intramammary infection (IMI) caused by Staphylococcus aureus (S. aureus) and Streptoccus spp. 3 weeks before calving time. Eighty Holstein dairy cows with subclinical mastitis pathogens were divided into three groups. Three weeks before expected parturition time, cows in group 1 received tilmicosin (n = 29), cows in group 2 received tylosin (n = 30) and cows in group 3 were left as negative control (n = 21). Milk samples were obtained on 3 and 7 days after calving. Randomly amplified polymorphic DNA (RAPD) method was determined for all of the S. aureus isolates that had the same isolates before and after parturition. The total cure rate was 63.33, 75.86 and 66.66% for tylosin, tilmicosin and control groups, respectively. Furthermore, cure rates were not significant, when each type of mastitis causing pathogens were considered separately. The incidence of clinical mastitis during 60 days after calving for tylosin, tilmicosin and Control groups was 23.33, 27.58 and 38.09%, respectively. Only four S. aureus isolated before drying-off were similar to post-calving isolate, according to RAPD-PCR method. In conclusion, antibiotic therapy before calving improved the cure rate numerically, however, it was not significant.

Effect of different dry period duration on milk components and serum metabolites, and their associations with the first conception rate in multiparous Holstein dairy cows

The aims of the present study were to evaluate the effects of different dry period (DP) lengths on milk fat to protein ratio (FPR) and metabolic status – blood leptin, adiponectin and non-esterified fatty acids (NEFA) concentrations in dairy cows, and their associations with the result of the first timed artificial insemination (TAI). Cows were blocked either to short DP (SDP; 30±2 days; n=72) or conventional DP (CDP; 60±2 days; n=76). Milk FPR was calculated at 30 and 60 days in milk (DIM). Body condition score (BCS) was recorded at –60, –30, calving, and 60 DIM. Blood samples were obtained at –60, –30, –7, calving, +7, +30, and +60 DIM for serum metabolites measurement. TAI was implemented between 65–75 DIM for all cows. Milk FPR and its changes were statistically analysed using an independent sample t test. To assess the impact of time, the pattern of BCS, and serum metabolites on the result of the first AI, repeated measure ANOVA was used. Only FPR-30 DIM revealed significant difference between pregnant and non-pregnant cows in SDP group (P<0.01). Reduced BCS loss was observed in the SDP group and followed by slightly higher probability of pregnancy at first AI (P=0.19). Leptin was not altered by shortening the DP (P≥0.1). Significant differences were observed in blood adiponectin prepartum (P<0.001) and at +7 DIM (P<0.01), as well as in NEFA at +7 and +30 DIM between the two groups (P<0.05). Pregnant cows following the first AI had significantly high postpartum leptin concentrations (P<0.05), high prepartum adiponectin (P≤0.001), and lower NEFA at +7 DIM (P<0.01) in the SDP group. In conclusion, shortening the dry period caused reduced BCS loss postpartum and variations in serum metabolits that favoured the possibility of pregnancy at first AI.

Evaluating the effectiveness of two bovine mastitis vaccines and their influences on oxidant and antioxidant capacities of milk

The aim of the current study was to investigate the efficacy of two commercial mastitis vaccines (Startvac® and Mastivac®) and their influence on oxidant and antioxidant capacities of milk samples in a dairy farm. A total of 165 Holstein dairy cows were recruited into the study and were divided into Startvac®, Mastivac®, and control groups. The effects on the incidence and severity of clinical mastitis cases, duration of treatment, infection status, bacteriologic culture, somatic cell count, 5-thio-2-nitrobenzoic acid assay and ferric reducing antioxidant power assay, incidence of metritis and endometritis, and milk yield were evaluated within the first 90 days of lactation. The incidence of clinical mastitis was not significantly different among groups. The mean SCCs during the first, second, and third months of lactation did not differ significantly. The percentage of cured cows did not differ significantly. TNB and FRAP assays were used to know whether or not vaccination against mastitis has an effect on oxidant and antioxidant capacity of milk samples, which did not differ significantly. In conclusion, we observed no significant difference in the abovementioned variables. However, it is possible that applying mastitis vaccines within the specific conditions may have positive effects considering the results of previous studies.

Effect of prostaglandin F2α and GnRH administration at the time of artificial insemination on reproductive performance of dairy cows

The present study aimed to determine the effect of administrating prostaglandin F2α (PGF2α) and GnRH at the time of artificial insemination (AI) on the pregnancy per artificial insemination (P/AI) and the pregnancy survival rate of dairy cows. A number of 830 lactating Holstein cows were randomly divided into four groups. Cows in group 1 (n=200) treated with 150 µg d-cloprostenol. In group 2 (n=212), cows received 10 µg buserelin acetate, and group 3 (n=205) was treated with both 150 µg d-cloprostenol and 10 µg buserelin acetate. In addition, 213 cows were assigned as control group which received normal saline as placebo (group 4). To measure progesterone, milk samples were collected at the insemination day and five days later. Pregnancy diagnosis was performed 28 and 60 days after the insemination, and the size and number of corpus luteum (CL) and twin pregnancies were recorded. Hormone therapies had no effect on the P/AI, pregnancy survival rate, and the size and number of CL. The P/AI ratio in groups 1, 2, 3 and 4 were 38.50%, 42.92%, 41.46% and 40.84%, and the pregnancy survival rates in groups 1, 2, 3 and 4 were 84.42%, 86.81%, 88.23% and 83.91%, respectively. The probability of a twin pregnancy was significantly higher in group 1 (15.58%) than other groups. There was no significant difference between groups in terms of the offspring gender. In conclusion, the administration of d-cloprostenol or buserelin acetate at the time of AI had no effect on P/AI and pregnancy survival rate in dairy cattle under no heat stress condition, while the administration of d-cloprostenol increased the probability of twin pregnancies.

A high prevalence of tylosin resistance among Staphylococcus aureus strains isolated from bovine mastitis

The macrolides appear to have considerable effects for treatment of bovine mastitis because of excellent diffusion into the mammary gland, long half-life, low protein binding, high intracellular concentration and lipid solubility. Acquired resistance to macrolides in Staphylococcus aureus is primarily related to target-site modification through acquisition of an erm gene. In the present study the prevalence of both phenotypic and genotypic tylosin resistance in S. aureus isolates (n = 103) from subclinical mastitis in nine dairy farms belonging to three different province of Iran were investigated. Overall, ermA, ermB and ermC was found in 7.80%, 32.00%, and 20.40% of S.aureus isolates, respectively. A very high percent of isolates (56.90%) were resistant to tylosin. MIC₉₀ and MIC₅₀ values were 64 and 32 µg mL^-1, respectively. Most of tylosin resistant isolates did not harbour any erm gene but ermB was dominant gene among 58 tylosin resistant isolates of S. aureus. In overall, tylosin resistance was prevalent in S. aureus isolates obtained from bovine mastitis in Iran.

Synthesis of Ag-ZnO with multiple rods (multipods) morphology and its application in the simultaneous photo-catalytic degradation of methyl orange and methylene blue

In this study, the photo-decolorization of a mixture of methylene blue (MB) and methyl orange (MO) was investigated using Ag-ZnO multipods. The photo-catalyst used, ZnO multipods, was successfully synthesized. The surface of ZnO microstructure was modified by deposition of different amounts of Ag nanoparticles (Ag NPs) using the photo-reduction method. The as-prepared samples were characterized by X-ray diffraction (XRD), scanning electron microscopy (SEM), UV-Vis and atomic absorption spectroscopy. The photo-catalytic efficiency of Ag-ZnO is mainly controlled by the amount of Ag NPs deposited on the ZnO surface. The results obtained suggest that Ag-ZnO containing 6.5% Ag NPs, has the highest photo-catalytic performance in the simultaneous photo-degradation of dyes at a shorter time.

Landscape genomics of Populus trichocarpa: the role of hybridization, limited gene flow, and natural selection in shaping patterns of population structure

Populus trichocarpa is an ecologically important tree across western North America. We used a large population sample of 498 accessions over a wide geographical area genotyped with a 34K Populus SNP array to quantify geographical patterns of genetic variation in this species (landscape genomics). We present evidence that three processes contribute to the observed patterns: (1) introgression from the sister species P. balsamifera, (2) isolation by distance (IBD), and (3) natural selection. Introgression was detected only at the margins of the species' distribution. IBD was significant across the sampled area as a whole, but no evidence of restricted gene flow was detected in a core of drainages from southern British Columbia (BC). We identified a large number of FST outliers. Gene Ontology analyses revealed that FST outliers are overrepresented in genes involved in circadian rhythm and response to red/far-red light when the entire dataset is considered, whereas in southern BC heat response genes are overrepresented. We also identified strong correlations between geoclimate variables and allele frequencies at FST outlier loci that provide clues regarding the selective pressures acting at these loci.

Effects of demographic factors, body mass index, alcohol drinking and smoking habits on irritable bowel syndrome: a case control study

BACKGROUND

Irritable Bowel Syndrome (IBS) is a common functional gastrointestinal disorder.

AIMS

To identify demographic factors in patients with IBS.

SUBJECTS AND METHODS

One-hundred and fifty three IBS patients seen at Taleghani Hospital Gastroenterology Clinic and met the Rome III criteria and 163 peoples who did not meet IBS criteria were consecutively enrolled. Both groups were asked to complete a self-rating questionnaire containing information, which included questions about age, sex, monthly income, education level, marital status, height, weight, alcohol drinking and smoking habits. Student's t-test, Pearson's Chi-square and logistic regression were used to statistical analysis.

RESULTS

The mean (SD) age for IBS patients 36.3 (13.5) years and 33.1 (9.9) years in non-IBS group (P < 0.001). Frequency of IBS defined by Rome III criteria was higher in females and younger individuals. Univariate analysis showed that IBS in males was associated with a lower monthly income and educational level and in females younger age, single, lower monthly income and educational level, body mass index (BMI), and unemployment status. Multivariate logistic regression identified a low level of education in males (Odds ratio [OR] = 3.6, 95% Confidence interval [CI]: 1.4-9.6) and in females, lower education level (OR = 2.4, 95% CI: 1.1-5.2), lower BMI (OR = 0.94, 95% CI: 0.89-0.99), unemployed (OR = 0.31, 95% CI: 0.11-0.85) and smoking (OR = 6.2, 95% CI: 1.03-37.2).

CONCLUSION

We identified demographic factors in IBS patients. Being single and having a lower educational level, income, lower BMI and being unemployed were the most important factors associated with IBS, particularly in females.

A 34K SNP genotyping array for Populus trichocarpa: design, application to the study of natural populations and transferability to other Populus species

Genetic mapping of quantitative traits requires genotypic data for large numbers of markers in many individuals. For such studies, the use of large single nucleotide polymorphism (SNP) genotyping arrays still offers the most cost-effective solution. Herein we report on the design and performance of a SNP genotyping array for Populus trichocarpa (black cottonwood). This genotyping array was designed with SNPs pre-ascertained in 34 wild accessions covering most of the species latitudinal range. We adopted a candidate gene approach to the array design that resulted in the selection of 34 131 SNPs, the majority of which are located in, or within 2 kb of, 3543 candidate genes. A subset of the SNPs on the array (539) was selected based on patterns of variation among the SNP discovery accessions. We show that more than 95% of the loci produce high quality genotypes and that the genotyping error rate for these is likely below 2%. We demonstrate that even among small numbers of samples (n = 10) from local populations over 84% of loci are polymorphic. We also tested the applicability of the array to other species in the genus and found that the number of polymorphic loci decreases rapidly with genetic distance, with the largest numbers detected in other species in section Tacamahaca. Finally, we provide evidence for the utility of the array to address evolutionary questions such as intraspecific studies of genetic differentiation, species assignment and the detection of natural hybrids.

Effects of monensin on metabolism and production in dairy saanen goats in periparturient period

This trial evaluated the effects of dietary supplementation with monensin sodium on dry matter intake, metabolic parameters and milk yield and milk composition of dairy Saanen goats in the periparturient period. Twelve Saanen pregnant dairy goats were assigned to a treatment and a control group. Saanen goats were fed monensin as its 10% sodium salt in the amount of 33 mg/kg of total dry matter intake during 30 d before parturition till d 42 in milk. Blood samples were collected from each goat at d 30, 15 and 7 before expected kidding time and also in d 1, 7, 13, 19, 21, 28, 35 and 42 postpartum. The serum concentrations of β-Hydroxybutyrate (BHBA), non-esterifed fatty acid (NEFA), calcium, magnesium, inorganic phosphorus, cholesterol, triglyceride, urea, total protein, albumin and glucose and aspartate aminotransferase (AST) activity were determined. The BHBA concentration significantly decreased in goats, which received monensin in comparison to controls in the postpartum period (p = 0.049). The concentration of sodium (Na) was significantly influenced by monensin treatment in the postpartum period (p = 0.048). In addition, the difference in dry matter intake was highly significant between the two groups during the pre-partum period. Controls had more dry matter intake (DMI) than treatment goats (p = 0.0001). Mean 3.5% fat corrected milk production was not influenced by monensin treatment. However, milk fat percentage was significantly decreased in monensin treated goats (p = 0.0017).

Reproductive performance in out-of-breeding season of fatty ewes using implant norgestomet with or without PMSG

Pregnancy in out-of-breeding season in ewes increases the economical goals. Synchronization of estrus and ovulation is essential for above program. The aims of this study using implant norgestomet with or without Pregnant Mare Serum Gonadotropin (PMSG) were to evaluate the serum progesterone (P4) concentration changes: the conception rate and estimation of the lambing rate and litter size. In total, 80 non-cycling multiparous Iranian Kurdish breed fat-tailed ewes with <0/5 ng/ml P4 were used in April and May 2008 in the suburb of Mashhad, Iran. The animals were randomly divided into three groups: a control group (n = 30) without hormonal treatment, another group (n = 25) received 3 mg of norgestomet implant placed subcutaneously in the convex surface of the ear for 9 days, and the third group (n = 25) treated with 3 mg of norgestomet implant for 9 days with an IM injection of 500 IU PMSG at implant removal. The progesterone of treatment and control groups were measured on days 4, 9, and 13 after removal of the norgestomet using radioimmunoassay. Every five ewes were exposed to one ram after 24 h of norgestomet removal in treatment and control groups, simultaneously. The pregnancy was examined after 25 days of ram removal using ultrasonography. Progesterone concentration was significantly higher in treatment groups on 9 and 13 days after norgestomet removal (P < 0.05). The pregnancy rate in the control, non-PMSG, and PMSG treatments groups were 17%, 52%, and 72%, respectively. The rates of single and twin pregnancy in the non-PMSG treatment group were 69% and 31%, respectively. These rates in norgestomet and PMSG treatment group were 50% and 39%, respectively. Triplet pregnancy (11%) was observed only in the PMSG treatment group. It was concluded that using implant norgestomet especially accompanied with PMSG can increase and improve the fertilization rate of ewe in the out-of-breeding season program.

Metabolic Changes in Cows with or without Retained Fetal Membranes in Transition Period

The purpose of the study was to evaluate the effect of retained fetal membranes (RFM) on serum minerals and energy- and protein-related metabolites in dairy cows at a herd with a recent history of fatty liver syndrome. Forty-seven multiparous Holstein cows were selected during transition period. Nine cows had RFM longer than 24 h after calving. Blood samples were obtained on prepartum days 21 and 7 and postpartum days 7 and 21. We used repeated measure procedure of anova to evaluate the effect of RFM on serum metabolites. Cows with RFM had significantly higher concentrations of beta-hydroxybutyrate, non-esterified fatty acids and triglycerides after calving, but had lower concentrations of cholesterol during transition period. The concentrations of serum albumin and blood urea nitrogen were also significantly lower in RFM-affected cows than non-affected ones after parturition. Our results suggested that negative energy balance (NEB) postpartum was associated with RFM in dairy cattle. However, our findings did not reveal a cause and effect relationship with respect to the role of NEB as a possible risk factor for RFM.

First report of Neospora caninum-associated bovine abortion in Mashhad area, Iran

Neospora caninum is an apicomplexan protozoan which causes abortion in cattle worldwide. The present study was designed to assess the importance of bovine neosporosis for causing abortion in Iranian cattle. Infection was primarily diagnosed by polymerase chain reaction (PCR), complemented with histopathology and immunohistochemistry (IHC). One hundred brains of aborted bovine fetuses were collected from Iranian dairy herd between 2003 and 2005 in Mashhad area. N. caninum was detected by PCR in the brains of 13 aborted fetuses. Lesions consistent with N. caninum infection were observed in 12 of fetal brains. Immunohistochemical examination of brain detected N. caninum organisms in three aborted fetuses, and a thick-walled (2 mum) cyst with 50 mum diameter was identified in one of the IHC-positive brain. The results indicated that neosporosis is an important cause of abortion in dairy cattle of Iran.

Seroepidemiology of Neospora caninum infection in dairy cattle herds in Mashhad area, Iran

A seroepidemiology study of Neospora caninum was conducted in Mashhad area, Khorasan province, Iran on 337 cattle from 30 dairy using ELISA. All herds had seropositive cattle and antibodies were formed in 46% of the cattle. Abortion was significantly associated with seropositivity of cattle. The highest risk of abortion was observed in the 1-2-year-old cows. Our results indicate that Neospora infection is widespread in Iran.