Regulatory Elements within the Prodomain of Falcipain-2, a Cysteine Protease of the Malaria Parasite Plasmodium falciparum

Falcipain-2, a papain family cysteine protease of the malaria parasite Plasmodium falciparum, plays a key role in parasite hydrolysis of hemoglobin and is a potential chemotherapeutic target. As with many proteases, falcipain-2 is synthesized as a zymogen, and the prodomain inhibits activity of the mature enzyme. To investigate the mechanism of regulation of falcipain-2 by its prodomain, we expressed constructs encoding different portions of the prodomain and tested their ability to inhibit recombinant mature falcipain-2. We identified a C-terminal segment (Leu155–Asp243) of the prodomain, including two motifs (ERFNIN and GNFD) that are conserved in cathepsin L sub-family papain family proteases, as the mediator of prodomain inhibitory activity. Circular dichroism analysis showed that the prodomain including the C-terminal segment, but not constructs lacking this segment, was rich in secondary structure, suggesting that the segment plays a crucial role in protein folding. The falcipain-2 prodomain also efficiently inhibited other papain family proteases, including cathepsin K, cathepsin L, cathepsin B, and cruzain, but it did not inhibit cathepsin C or tested proteases of other classes. A structural model of pro-falcipain-2 was constructed by homology modeling based on crystallographic structures of mature falcipain-2, procathepsin K, procathepsin L, and procaricain, offering insights into the nature of the interaction between the prodomain and mature domain of falcipain-2 as well as into the broad specificity of inhibitory activity of the falcipain-2 prodomain

Feeding Response of Tree Fodder Bhimal (Grewia Optiva) on Growth Performance of Castrated Male Goats

Bhimal (Grewia optiva) is a fodder tree mostly found in mid hills of mid and far western region of Nepal. Bhimal could constitutes one of the main livestock green fodders, especially for goats when fresh green fodder become limited during the winter dry season. However, the feeding value of Bhimal leaves on growth performance of castrated goats probably has not been evaluated so far. Therefore, an experiment was conducted to evaluate the effect of Bhimal leaves feeding on growth performance of castrated male goats for 90 days. Altogether 16 growing castrated male goats of same breed, age and body weight were selected and equally divided into four treatments T1, T2, T3 and T4 with four replications by using Completely Randomized Design (CRD). Four types of experimental diets were prepared having various levels (0 to 100%) of Bhimal leaves as fodder. Experimental animals of Treatment 1 were fed with seasonal fodder + 100 g concentrate mixture, Treatment 2 with 100% Bhimal fodder + 100 g concentrate mixture, Treatment 3with 75% Bhimal fodder + 25% seasonal fodder + 100 g concentrate mixture, while Treatment 4 with 50% Bhimal fodder + 50% season fodder + 100 g concentrate mixture. All diets were fed ad-lib and experimental animals had free access to drinking water. The diets offered and refusal was measured daily and weight change was observed fortnightly. The result showed that fodder intake (g/d/animal) and total dry matter intake (TDMI g/kg live weight) of goats differed significantly (P<0.01), but concentrate intake was not differed significantly (P<0.01) among treatments. The highest dry matter intake per animal /day was in Treatment 2 (52.75 g/kg live weight) followed by Treatment 4, Treatment 3 and Treatment 1 (51.7, 48.56 and 32.69 g/kg live weight, respectively).The average daily gain in body weight was observed highest in Treatment 2 (66.66 g/d) followed by Treatment 3 (31.66 g/d) and Treatment 4 (30.83 g). The growth rate was significantly (P<0.01) different among diet groups (P<0.05, P<0.01 and P<0.01 for 60, 75 and 90 days, respectively). In case of the feed conversion ratio, Treatment 2 had best ratio (8.79:1) than Treatment 1 (14.21:1), T3 (17.03:1) and Treatment 4 (18.59:1). The present response study showed that body weight in castrated male goats can be increased significantly (P<0.05) implying that in winter season when other green forages are poorly available goat farming can be supported by Bhimal fodder tree.Journal of Nepal Agricultural Research Council Vol.3 2017: 1-1

Awareness and Health Beliefs of Osteoporosis Among Middle Aged Women in Selected Municipality of Kathmandu

Introduction: Osteoporosis is a bone disorder characterized by a reduction in bone density accompanied by increasing porosity and brittleness. It is one of the major public health problem globally and its prevalence is rapidly increasing particularly in women.  Osteoporosis causes more than 8.9 million fractures annually, resulting in an osteoporotic fracture every 3 seconds. Therefore the objectives of the study was to assess the existing awareness and health belief of osteoporosis  among middle aged women. Methods: Descriptive cross-sectional research design was used on a sample of 328 middle aged  women residing  in Nagarjun Municipality, Kathmandu. Non probability purposive sampling technique was used to collect the data. Data was collected after informed consent through face to face interview schedule using  Osteoporosis Knowledge Assessment Tool (OKAT) and Osteoporosis Health Beliefs Scale (OHBS). Descriptive statistics and inferential statistics (Chi-Square test) were used for data analysis at 5% level of significance. Results: The overall osteoporosis awareness and  health beliefs mean scores were  9.39 ± 2.93 and 146.18 ±11.58 respectively.  Majority (60.0%) of the respondents were unaware of osteoporosis. Existing awareness of respondents was significantly  associated with age (p=0.000) and level of education (p= 0.038). Based on the OHBS subscale score, the highest perception was on  health motivation ( 22.73 ± 2.81) and the lowest perception was on barriers to calcium intake (mean score 17.71 ± 4.32). Conclusion: Based on the findings, it is concluded  that the middle aged women of  Nagarjun Municipality-6 are unaware about osteoporosis. Therefore, community based awareness campaigns on osteoporosis should be reinforced.

Piperidinols that show anti-tubercular activity as inhibitors of arylamine N-acetyltransferase: an essential enzyme for mycobacterial survival inside macrophages

Latent M. tuberculosis infection presents one of the major obstacles in the global eradication of tuberculosis (TB). Cholesterol plays a critical role in the persistence of M. tuberculosis within the macrophage during latent infection. Catabolism of cholesterol contributes to the pool of propionyl-CoA, a precursor that is incorporated into cell-wall lipids. Arylamine N-acetyltransferase (NAT) is encoded within a gene cluster that is involved in the cholesterol sterol-ring degradation and is essential for intracellular survival. The ability of the NAT from M. tuberculosis (TBNAT) to utilise propionyl-CoA links it to the cholesterol-catabolism pathway. Deleting the nat gene or inhibiting the NAT enzyme prevents intracellular survival and results in depletion of cell-wall lipids. TBNAT has been investigated as a potential target for TB therapies. From a previous high-throughput screen, 3-benzoyl-4-phenyl-1-methylpiperidinol was identified as a selective inhibitor of prokaryotic NAT that exhibited antimycobacterial activity. The compound resulted in time-dependent irreversible inhibition of the NAT activity when tested against NAT from M. marinum (MMNAT). To further evaluate the antimycobacterial activity and the NAT inhibition of this compound, four piperidinol analogues were tested. All five compounds exert potent antimycobacterial activity against M. tuberculosis with MIC values of 2.3-16.9 µM. Treatment of the MMNAT enzyme with this set of inhibitors resulted in an irreversible time-dependent inhibition of NAT activity. Here we investigate the mechanism of NAT inhibition by studying protein-ligand interactions using mass spectrometry in combination with enzyme analysis and structure determination. We propose a covalent mechanism of NAT inhibition that involves the formation of a reactive intermediate and selective cysteine residue modification. These piperidinols present a unique class of antimycobacterial compounds that have a novel mode of action different from known anti-tubercular drugs

Factors Associated With Small Size at Birth in Nepal: Further Analysis of Nepal Demographic and Health Survey 2011

Background: The global Low Birth Weight (LBW) rate is reported to be 15.5% with more than 95% of these LBW infants being from developing countries. LBW is a major factor associated with neonatal deaths in developing countries. The determinants of low birth weight in Nepal have rarely been studied. This study aimed to identify the factors associated with small size at birth among under-five children. Methods: Data from the 2011 Nepal Demographic and Health Survey (NDHS) were used. The association between small size at birth and explanatory variables were analysed using Chi-square tests (χ2) followed by logistic regression. Complex Sample Analysis was used to adjust for study design and sampling.Results: A total of 5240 mother- singleton under five child pairs were included in the analysis, of which 936 (16.0%) children were reported as small size at birth. Of 1922 infants whose birth weight was recorded, 235 (11.5%) infants had low birth weight (<2500 grams). The mean birth weight was 3030 grams (standard deviation: 648.249 grams). The mothers who had no antenatal visits were more likely (odds ratio (OR) 1.315; 95% confidence interval (CI) (1.042-1.661)) to have small size infants than those who had attended four or more antenatal visits. Mothers who lived in the Far-western development region were more likely to have (OR 1.698; 95% CI (1.228-2.349)) small size infants as compared to mothers from the Eastern development region. Female infants were more likely (OR 1.530; 95% CI (1.245-1.880)) to be at risk of being small than males. Conclusion: One in every six infants was reported to be small at birth. Attendance of antenatal care programs appeared to have a significant impact on birth size. Adequate antenatal care visits combined with counselling and nutritional supplementation should be a focus to reduce adverse birth outcomes such as small size at birth, especially in the geographically and economically disadvantaged areas such as Far-western region of Nepal

An Integrative Multi-Network and Multi-Classifier Approach to Predict Genetic Interactions

Genetic interactions occur when a combination of mutations results in a surprising phenotype. These interactions capture functional redundancy, and thus are important for predicting function, dissecting protein complexes into functional pathways, and exploring the mechanistic underpinnings of common human diseases. Synthetic sickness and lethality are the most studied types of genetic interactions in yeast. However, even in yeast, only a small proportion of gene pairs have been tested for genetic interactions due to the large number of possible combinations of gene pairs. To expand the set of known synthetic lethal (SL) interactions, we have devised an integrative, multi-network approach for predicting these interactions that significantly improves upon the existing approaches. First, we defined a large number of features for characterizing the relationships between pairs of genes from various data sources. In particular, these features are independent of the known SL interactions, in contrast to some previous approaches. Using these features, we developed a non-parametric multi-classifier system for predicting SL interactions that enabled the simultaneous use of multiple classification procedures. Several comprehensive experiments demonstrated that the SL-independent features in conjunction with the advanced classification scheme led to an improved performance when compared to the current state of the art method. Using this approach, we derived the first yeast transcription factor genetic interaction network, part of which was well supported by literature. We also used this approach to predict SL interactions between all non-essential gene pairs in yeast (http://sage.fhcrc.org/downloads/downloads/predicted_yeast_genetic_interactions.zip). This integrative approach is expected to be more effective and robust in uncovering new genetic interactions from the tens of millions of unknown gene pairs in yeast and from the hundreds of millions of gene pairs in higher organisms like mouse and human, in which very few genetic interactions have been identified to date

Mining phenotypes for gene function prediction

<p>Abstract</p> <p>Background</p> <p>Health and disease of organisms are reflected in their phenotypes. Often, a genetic component to a disease is discovered only after clearly defining its phenotype. In the past years, many technologies to systematically generate phenotypes in a high-throughput manner, such as RNA interference or gene knock-out, have been developed and used to decipher functions for genes. However, there have been relatively few efforts to make use of phenotype data beyond the single genotype-phenotype relationships.</p> <p>Results</p> <p>We present results on a study where we use a large set of phenotype data – in textual form – to predict gene annotation. To this end, we use text clustering to group genes based on their phenotype descriptions. We show that these clusters correlate well with several indicators for biological coherence in gene groups, such as functional annotations from the Gene Ontology (GO) and protein-protein interactions. We exploit these clusters for predicting gene function by carrying over annotations from well-annotated genes to other, less-characterized genes in the same cluster. For a subset of groups selected by applying objective criteria, we can predict GO-term annotations from the biological process sub-ontology with up to 72.6% precision and 16.7% recall, as evaluated by cross-validation. We manually verified some of these clusters and found them to exhibit high biological coherence, e.g. a group containing all available antennal Drosophila odorant receptors despite inconsistent GO-annotations.</p> <p>Conclusion</p> <p>The intrinsic nature of phenotypes to visibly reflect genetic activity underlines their usefulness in inferring new gene functions. Thus, systematically analyzing these data on a large scale offers many possibilities for inferring functional annotation of genes. We show that text clustering can play an important role in this process.</p

Structural Basis for Specificity of Propeptide-Enzyme Interaction in Barley C1A Cysteine Peptidases

C1A cysteine peptidases are synthesized as inactive proenzymes. Activation takes place by proteolysis cleaving off the inhibitory propeptide. The inhibitory capacity of propeptides from barley cathepsin L and B-like peptidases towards commercial and barley cathepsins has been characterized. Differences in selectivity have been found for propeptides from L-cathepsins against their cognate and non cognate enzymes. Besides, the propeptide from barley cathepsin B was not able to inhibit bovine cathepsin B. Modelling of their three-dimensional structures suggests that most propeptide inhibitory properties can be explained from the interaction between the propeptide and the mature cathepsin structures. Their potential use as biotechnological tools is discussed