Predicting genome-wide redundancy using machine learning

Background  

Gene duplication can lead to genetic redundancy, which masks the function of mutated genes in genetic analyses. Methods to increase sensitivity in identifying genetic redundancy can improve the efficiency of reverse genetics and lend insights into the evolutionary outcomes of gene duplication. Machine learning techniques are well suited to classifying gene family members into redundant and non-redundant gene pairs in model species where sufficient genetic and genomic data is available, such as Arabidopsis thaliana, the test case used here.     

Development and Characterization of Mucoadhesive <Emphasis Type="Italic">In Situ</Emphasis> Nasal Gel of Midazolam Prepared with <Emphasis Type="Italic">Ficus carica</Emphasis> Mucilage

The objective of the present study was to prepare mucoadhesive in situ nasal gels with mucilage isolated from fig fruits (Ficus carica, family: Moraceae) containing midazolam hydrochloride. Nasal gels of midazolam were prepared using three different concentrations (0.5%, 1.0% and 1.5% w/v) of F. carica mucilage (FCM) and synthetic polymers (hydroxypropylmethyl cellulose and Carbopol 934). Evaluation of FCM showed that it was as safe as the synthetic polymers for nasal administration. In situ gels were prepared with mixture Pluronic F127 and mucoadhesive agents. Evaluation of the prepared gels was carried out, including determination of viscosity, texture profile analysis and mucoadhesive strength. In vitro drug permeation study was conducted with the gels prepared with and without permeation enhancer (0.5% w/v sodium taurocholate) using excised goat nasal mucosa. In vitro permeation profiles were evaluated, and histological study of nasal mucosae before and after permeation study was also conducted to determine histological change, if any. In vivo experiments conducted in rabbits further confirmed that in situ nasal gels provided better bioavailability of midazolam than the gels prepared from synthetic mucoadhesive polymers. It was observed that the nasal gel containing 0.5% FCM and 0.5% sodium taurocholate exhibited appropriate rheological, mechanical and mucoadhesive properties and showed better drug release profiles. Moreover, this formulation produced no damage to the nasal mucosa that was used for the permeation study, and absolute bioavailability was also higher compared to gels prepared from synthetic polymers.     

Age and sex variation of body mass index and waist circumference among the Santal children of Jharkhand, India

Central body fat (CBF) as measured by waist circumference (WC) etc. has now been considered as risk factor for chronic disease, disability, and death. It has been assumed that one's characteristic level of body fat, as measured by body mass index (BMI), and CBF unfolds during the normal course of growth and development. However, studies of the development of CBF show relatively weak consistency in comparison to body fat. But to the best of our knowledge, no study in this aspect has been undertaken on any Indian population to study the effect of age and sex on body fat and CBF during development. In view of the above consideration, the present work has been undertaken among 179 Santal (a tribal population) children (Boys = 107, Girls = 72) of the Galudih area in East Singbhum, Jharkhand, India. Anthropometric measurements of height, weight, and circumference of waist were taken from each subject using standard procedure. The mean ages of boys and girls were 10.94 years and 9.48 years, respectively. The mean BMI for boys and girls were 14.48 kg/m2 and 13.78 kg/m2 Percent of variance explained by age was much greater for BMI (> 50%) as compared to WC (7-10%) in both sexes. Two way ANOVA showed that BMI had a significant (p < 0.05) effect of age and not of sex, whereas age-sex interaction had a significant impact on WC. The results of the present cross-sectional study indicated that during growth and development unfolding of CBF and BMI is independent of one another. Different set(s) of gene(s), onset of growth hormones during the normal development or their interaction could have been considered for this differentiation.     

Income, birth order, siblings, and anthropometry

The purpose of the present cross-sectional study was to examine the relationship and effect of monthly household income, birth order, and number of siblings on adult body dimensions, adiposity index, and body composition among adult Bengali females. One hundred seventy-one adult Bengali females, age 20.35 +/- 1.51 years (mean +/- SD; range: 18-21 years) from Kolkata (formerly Calcutta) were studied. Anthropometric measures (weight, height, waist circumference, hip circumference, and triceps, biceps, subscapular, suprailiac, and medial calf skinfold thicknesses) were taken from all participants using standard protocols. BMI and log10 of the sum of the five skinfold thicknesses were computed subsequently. Percentage of body fat was estimated from the triceps skinfold thickness following the equation of Durnin and Womersley (1974), and fat mass was then calculated. Results of the correlation analysis revealed that monthly household income had significant (p < 0.05) positive association with all anthropometric variables. Birth order and number of siblings showed significant (p < 0.05) inverse association. The correlation of monthly household income with anthropometric variables was much stronger for number of siblings and birth order. The results of the analysis of variance showed that monthly household income, birth order, and number of siblings (tertiles used to categorize all variables) had significant effects (p < 0.05) on anthropometric variables, indicating differences in adult body dimensions, the adiposity index, and body composition in relation to income, birth order, and number of siblings.     

Molecular characterization and localization of Plasmodium falciparum choline kinase

Generation of phosphocholine by choline kinase is important for phosphatidylcholine biosynthesis via Kennedy pathway and phosphatidylcholine biosynthesis is essential for intraerythrocytic growth of malaria parasite. A putative gene (Gene ID PF14_0020) in chromosome 14, having highest sequence homology with choline kinase, has been identified by BLAST searches from P. falciparum genome sequence database. This gene has been PCR amplified, cloned, over-expressed and characterized. Choline kinase activity of the recombinant protein (PfCK) was validated as it catalyzed the formation of phosphocholine from choline in presence of ATP. The K(m) values for choline and ATP are found to be 145+/-20 microM and 2.5+/-0.3 mM, respectively. PfCK can phosphorylate choline efficiently but not ethanolamine. Southern blotting indicates that PfCK is a single copy gene and it is a cytosolic protein as evidenced by Western immunoblotting and confocal microscopy. A model structure of PfCK was constructed based on the crystal structure of choline kinase of C. elegans to search the structural homology. Consistent with the homology modeling predictions, CD analysis indicates that the alpha and beta content of PfCK are 33% and 14%, respectively. Since choline kinase plays a vital role for growth and multiplication of P. falciparum during intraerythrocytic stages, we can suggest that this well characterized PfCK may be exploited in the screening of new choline kinase inhibitors to evaluate their antimalarial activity.     

Genetic analysis of the roles of BMP2, BMP4, and BMP7 in limb patterning and skeletogenesis

Bone morphogenetic protein (BMP) family members, including BMP2, BMP4, and BMP7, are expressed throughout limb development. BMPs have been implicated in early limb patterning as well as in the process of skeletogenesis. However, due to complications associated with early embryonic lethality, particularly for Bmp2 and Bmp4, and with functional redundancy among BMP molecules, it has been difficult to decipher the specific roles of these BMP molecules during different stages of limb development. To circumvent these issues, we have constructed a series of mouse strains lacking one or more of these BMPs, using conditional alleles in the case of Bmp2 and Bmp4 to remove them specifically from the limb bud mesenchyme. Contrary to earlier suggestions, our results indicate that BMPs neither act as secondary signals downstream of Sonic Hedghog (SHH) in patterning the anteroposterior axis nor as signals from the interdigital mesenchyme in specifying digit identity. We do find that a threshold level of BMP signaling is required for the onset of chondrogenesis, and hence some chondrogenic condensations fail to form in limbs deficient in both BMP2 and BMP4. However, in the condensations that do form, subsequent chondrogenic differentiation proceeds normally even in the absence of BMP2 and BMP7 or BMP2 and BMP4. In contrast, we find that the loss of both BMP2 and BMP4 results in a severe impairment of osteogenesis.     

Inhibition of TNF-α, and NF-κB and JNK pathways accounts for the prophylactic action of the natural phenolic,allylpyrocatechol against indomethacin gastropathy

Background

The gastro-intestinal disorders, induced by the NSAIDs including indomethacin (IND) remain unresolved medical problems. Herein, we disclose allylpyrocatechol (APC) as a potential agent against IND-gastropathy and rationalize its action mechanistically.

Methods

Mice were pre-treated with APC for 1 h followed by IND (18 mg kg^− 1) administration, and the ulcer-prevention capacity of APC was evaluated on the 3rd day by histology. Its effect on the inflammatory (MPO, cytokines, adhesion molecules), ulcer-healing (COX, prostaglandins, growth factors and their receptors) and signaling parameters (NF-κB and MAPKs) were assessed by immunoblots/mRNA, and ELISA at the time points of their maximal changes due to IND administration.

Results

IND induced oxidative stress, triggering mucosal TNF-α that activated NF-κB and JNK MAPK signaling in mice. These increased the pro-inflammatory biochemical parameters, but reduced the healing factors. APC reversed all the adverse effects to prevent gastric ulceration. APC (5 mg kg^− 1), trolox (50 mg kg^− 1) and NAC (250 mg kg^− 1) showed similar protection that was better than that by misoprostol (5 μg kg^− 1) and omeprazole (3 mg kg^− 1).

Conclusions

The anti-ulcer effect of APC can be primarily attributed to its antioxidant action that helped in controlling various inflammatory parameters and augmenting angiogenesis.

General significance

Given that APC is an effective, non-toxic antioxidant with appreciable natural abundance, further evaluation of its pharmacokinetics and dynamics would help in promoting it as a new anti-inflammatory agent.