Molecular mechanisms in response to phosphate starvation in rice

Phosphorus is one of the most important elements that significantly affect plant growth and metabolism. Among the macro-nutrients, phosphorus is the least available to the plants as major phosphorus content of the fertiliser is sorbed by soil particles. An increased knowledge of the regulatory mechanisms controlling plant's phosphorus status is vital for improving phosphorus uptake and P-use efficiency and for reducing excessive input of fertilisers, while maintaining an acceptable yield. Phosphorus use efficiency has been studied using forward and reverse genetic analyses of mutants, quantitative genomic approaches and whole plant physiology but all these studies need to be integrated for a clearer understanding. We provide a critical overview on the molecular mechanisms and the components involved in the plant during phosphorus starvation. Then we summarize the information available on the genes and QTLs involved in phosphorus signalling and also the methods to estimate total phosphate in plant tissue. Also, an effort is made to build a comprehensive picture of phosphorus uptake, homeostasis, assimilation, remobilization, its deposition in the grain and its interaction with other micro- and macro-nutrients as well as phytohormones.     

StressDB: a locally installable web-based relational microarray database designed for small user communities

We have built a microarray database, StressDB, for management of microarray data from our studies on stress-modulated genes in Arabidopsis. StressDB provides small user groups with a locally installable web-based relational microarray database. It has a simple and intuitive architecture and has been designed for cDNA microarray technology users. StressDB uses Windows(trade mark) 2000 as the centralized database server with Oracle(trade mark) 8i as the relational database management system. It allows users to manage microarray data and data-related biological information over the Internet using a web browser. The source-code is currently available on request from the authors and will soon be made freely available for downloading from our website athttp://arastressdb.cac.psu.edu.     

Taxonomic description and draft genome of <Emphasis Type="Italic">Pseudomonas sediminis</Emphasis> sp. nov., isolated from the rhizospheric sediment of <Emphasis Type="Italic">Phragmites karka</Emphasis>

The taxonomic position of a Gram-stain-negative, rod-shaped bacterial strain, designated PI11^T, isolated from the rhizospheric sediment of Phragmites karka was characterized using a polyphasic approach. Strain PI11^T could grow optimally at 1.0% NaCl concentration with pH 7.0 at 30°C and was positive for oxidase and catalase but negative for hydrolysis of starch, casein, and esculin ferric citrate. Phylogenetic analysis of 16S rRNA gene sequences indicated that the strain PI11^T belonged to the genus Pseudomonas sharing the highest sequence similarities with Pseudomonas indoloxydans JCM 14246^T (99.72%), followed by, Pseudomonas oleovorans subsp. oleovorans DSM 1045^T (99.29%), Pseudomonas toyotomiensis JCM 15604^T (99.15%), Pseudomonas chengduensis DSM 26382^T (99.08%), Pseudomonas oleovorans subsp. lubricantis DSM 21016^T (99.08%), and Pseudomonas alcaliphila JCM 10630^T (99.01%). Experimental DNA-DNA relatedness between strain PI11^T and P. indoloxydans JCM 14246^T was 49.4%. The draft genome of strain PI11^T consisted of 4,884,839 bp. Average nucleotide identity between the genome of strain PI11^T and other closely related type strains ranged between 77.25–90.74%. The polar lipid pattern comprised of phosphatidylglycerol, diphosphatidylglycerol, and phosphatidylcholine. The major (> 10%) cellular fatty acids were C_18:1ω6c/ω7c, C_16:1ω6c/ω7c, and C_16:0. The DNA G + C content of strain PI11^T was 62.4 mol%. Based on the results of polyphasic analysis, strain PI11^T was delineated from other closely related type strains. It is proposed that strain PI11^T represents represents a novel species of the genus Pseudomonas, for which the name Pseudomonas sediminis sp. nov. is proposed. The type strain is PI11^T (= KCTC 42576^T = DSMZ 100245^T).     

Incorporation of transition to transversion ratio and nonsense mutations,improves the estimation of the number of synonymous and non-synonymous sites in codons

A common approach to estimate the strength and direction of selection acting on protein coding sequences is to calculate the dN/dS ratio. The method to calculate dN/dS has been widely used by many researchers and many critical reviews have been made on its application after the proposition by Nei and Gojobori in 1986. However, the method is still evolving considering the non-uniform substitution rates and pretermination codons. In our study of SNPs in 586 genes across 156 Escherichia coli strains, synonymous polymorphism in 2-fold degenerate codons were higher in comparison to that in 4-fold degenerate codons, which could be attributed to the difference between transition (Ti) and transversion (Tv) substitution rates where the average rate of a transition is four times more than that of a transversion in general. We considered both the Ti/Tv ratio, and nonsense mutation in pretermination codons, to improve estimates of synonymous (S) and non-synonymous (NS) sites. The accuracy of estimating dN/dS has been improved by considering the Ti/Tv ratio and nonsense substitutions in pretermination codons. We showed that applying the modified approach based on Ti/Tv ratio and pretermination codons results in higher values of dN/dS in 29 common genes of equal reading-frames between E. coli and Salmonella enterica. This study emphasizes the robustness of amino acid composition with varying codon degeneracy, as well as the pretermination codons when calculating dN/dS values.     

Effect of Chronic Athletic Activity on Brown Fat in Young Women

BackgroundThe effect of chronic exercise activity on brown adipose tissue (BAT) is not clear, with some studies showing positive and others showing negative associations. Chronic exercise is associated with increased resting energy expenditure (REE) secondary to increased lean mass and a probable increase in BAT. Many athletes are in a state of relative energy deficit suggested by lower fat mass and hypothalamic amenorrhea. States of severe energy deficit such as anorexia nervosa are associated with reduced BAT. There are no data regarding the impact of chronic exercise activity on BAT volume or activity in young women and it is unclear whether relative energy deficiency modifies the effects of exercise on BAT.PurposeWe assessed cold induced BAT volume and activity in young female athletes compared with non-athletes, and further evaluated associations of BAT with measures of REE, body composition and menstrual status.MethodsThe protocol was approved by our Institutional Review Board. Written informed consent was obtained from all participants prior to study initiation. This was a cross-sectional study of 24 women (16 athletes and8 non-athletes) between 18–25 years of age. Athletes were either oligo-amenorrheic (n = 8) or eumenorrheic (n = 8).We used PET/CT scans to determine cold induced BAT activity, VMAX Encore 29 metabolic cart to obtain measures of REE, and DXA for body composition.ResultsAthletes and non-athletes did not differ for age or BMI. Compared with non-athletes, athletes had lower percent body fat (p = 0.002), higher percent lean mass (p = 0.01) and trended higher in REE (p = 0.09). BAT volume and activity in athletes trended lower than in non-athletes (p = 0.06; p = 0.07, respectively). We found negative associations of BAT activity with duration of amenorrhea (r = -0.46, p = 0.02).BAT volume correlated inversely with lean mass (r = -0.46, p = 0.02), and positively with percent body fat, irisin and thyroid hormones.ConclusionsOur study shows a trend for lower BAT in young female athletes compared with non-athletes, and shows associations of brown fat with menstrual status and body composition. Brown fat may undergo adaptive reductions with increasing energy deficit.     

Maternal Infection Is a Risk Factor for Early Childhood Infection in Filariasis

Background

Global Program to Eliminate Lymphatic Filariasis (GPELF) launched by WHO aims to eliminate the disease by 2020. To achieve the goal annual mass drug administration (MDA) with diethylcarbamazine (DEC) plus albendazole (ABZ) has been introduced in all endemic countries. The current policy however excludes pregnant mothers and children below two years of age from MDA. Since pregnancy and early childhood are critical periods in determining the disease outcome in older age, the present study was undertaken to find out the influence of maternal filarial infection at the time of pregnancy on the susceptibility outcome of children born in a community after implementation of MDA for the first time.

Methodology and Principal Findings

The participants in this cohort consists of pregnant mothers and their subsequently born children living in eight adjacent villages endemic for filarial infections, in Khurda District, Odisha, India, where MDA has reduced microfilariae (Mf) rate from 12% to 0.34%. Infection status of mother and their children were assessed by detection of Mf as well as circulating filarial antigen (CFA) assay. The present study reveals a high rate of acquiring filarial infection by the children born to infected mother than uninfected mothers even though Mf rate has come down to < 1% after implementation of ten rounds of MDA.

Significance

To attain the target of eliminating lymphatic filariasis the current MDA programme should give emphasis on covering the women of child bearing age. Our study recommends incorporating supervised MDA to Adolescent Reproductive and Sexual Health Programme (ARSH) to make the adolescent girls free from infection by the time of pregnancy so as to achieve the goal.     

Statistical learning methods as a preprocessing step for survival analysis: evaluation of concept using lung cancer data

Background

Despite its superb lateral resolution, flat-panel-detector (FPD) based tomosynthesis suffers from low contrast and inter-plane artifacts caused by incomplete cancellation of the projection components stemming from outside the focal plane. The incomplete cancellation of the projection components, mostly due to the limited scan angle in the conventional tomosynthesis scan geometry, often makes the image contrast too low to differentiate the malignant tissues from the background tissues with confidence.

Methods

In this paper, we propose a new method to suppress the inter-plane artifacts in FPD-based tomosynthesis. If 3D whole volume CT images are available before the tomosynthesis scan, the CT image data can be incorporated into the tomosynthesis image reconstruction to suppress the inter-plane artifacts, hence, improving the image contrast. In the proposed technique, the projection components stemming from outside the region-of-interest (ROI) are subtracted from the measured tomosynthesis projection data to suppress the inter-plane artifacts. The projection components stemming from outside the ROI are calculated from the 3D whole volume CT images which usually have lower lateral resolution than the tomosynthesis images. The tomosynthesis images are reconstructed from the subtracted projection data which account for the x-ray attenuation through the ROI. After verifying the proposed method by simulation, we have performed both CT scan and tomosynthesis scan on a phantom and a sacrificed rat using a FPD-based micro-CT.

Results

We have measured contrast-to-noise ratio (CNR) from the tomosynthesis images which is an indicator of the residual inter-plane artifacts on the focal-plane image. In both cases of the simulation and experimental imaging studies of the contrast evaluating phantom, CNRs have been significantly improved by the proposed method. In the rat imaging also, we have observed better visual contrast from the tomosynthesis images reconstructed by the proposed method.

Conclusions

The proposed tomosynthesis technique can improve image contrast with aids of 3D whole volume CT images. Even though local tomosynthesis needs extra 3D CT scanning, it may find clinical applications in special situations in which extra 3D CT scan is already available or allowed.     

Comparison of DXA and CT in the Assessment of Body Composition in Premenopausal Women With Obesity and Anorexia Nervosa

Accurate methods for assessing body composition in subjects with obesity and anorexia nervosa (AN) are important for determination of metabolic and cardiovascular risk factors and to monitor therapeutic interventions. The purpose of our study was to assess the accuracy of dual‐energy X‐ray absorptiometry (DXA) for measuring abdominal and thigh fat, and thigh muscle mass in premenopausal women with obesity, AN, and normal weight compared to computed tomography (CT). In addition, we wanted to assess the impact of hydration on DXA‐derived measures of body composition by using bioelectrical impedance analysis (BIA). We studied a total of 91 premenopausal women (34 obese, 39 with AN, and 18 lean controls). Our results demonstrate strong correlations between DXA‐ and CT‐derived body composition measurements in AN, obese, and lean controls (r = 0.77–0.95, P < 0.0001). After controlling for total body water (TBW), the correlation coefficients were comparable. DXA trunk fat correlated with CT visceral fat (r = 0.51–0.70, P < 0.0001). DXA underestimated trunk and thigh fat and overestimated thigh muscle mass and this error increased with increasing weight. Our study showed that DXA is a useful method for assessing body composition in premenopausal women within the phenotypic spectrum ranging from obesity to AN. However, it is important to recognize that DXA may not accurately assess body composition in markedly obese women. The level of hydration does not significantly affect most DXA body composition measurements, with the exceptions of thigh fat.     

Ethnicity influences gut metabolites and microbiota of the tribes of Assam,India

Introduction

The human gut microbes and their metabolites are involved in multiple host metabolic pathways. Dysbiosis in the gut microbiota and altered metabolite profiles were reported in diseased state. In a region like Assam, where 12.4% of the populations are tribal population, evaluating the influence of ethnicity on gut microbiota and metabolites has become important to further differentiate it from the diseased state.

Objective

To study the influence of ethnicity on fecal metabolite profile and their association with the gut microbiota composition.

Methods

In this study, we determined the untargeted fecal metabolites from five ethnic groups of Assam (Tai-Aiton, Bodo, Karbi, Tea-tribe and Tai-Phake) using GC–MS and compared them among the tribes for common and unique metabolites. Metabolites of microbial origin were related with the available metagenomic data on gut bacterial profiles of the same ethnic groups and functional analysis were carried out based on HMDB.

Results

The core fecal metabolite profile of the Tea-tribe contained aniline, benzoate and acetaldehyde. PLS-DA based on the metabolites suggested that the individuals grouped based on their ethnicity. PCA plot of the data on bacterial abundance at the level of genus indicated clustering of individuals based on ethnicity. Positive correlations were observed between propionic acid and the genus Clostridium (R?=?0.43 and p?=?0.03), butyric acid and the genus Lactobacillus (R?=?0.45 and p?=?0.024), acetic acid and the genus Bacteroides (R?=?0.63 and p?=?0.001) and methane and the genus Escherichia (R?=?0.58 and p?=?0.002).

Conclusion

Results of this study indicated that ethnicity influences both gut bacterial profile and their metabolites.