Essays on Fertility and Sex Ratios in India

In recent decades, several countries have experienced a rapid increase in their sex ratios at birth. This dissertation examines the causes and consequences of these imbalances in the Indian context. Lower desired fertility can translate into more male-biased sex ratios if son preference remains strong, especially with greater availability of prenatal sex-selection technology. Chapter 1 investigates whether financial incentives can simultaneously decrease fertility and the sex ratio at birth. I build a model where the effects of incentives on child-bearing and sex-selection are determined by the degree of son preference and the costs of children and sex-selection, relative to the size of incentives. I test the theoretical predictions in the context of Devirupak, a scheme adopted by the Indian state of Haryana. Devirupak incentivizes parents to have either one child or two daughters. Parents of one girl receive a larger benefit than one-boy or two-girl families, who receive the same amount. I construct a woman-year panel dataset from retrospective birth histories and exploit variation in the state and the timing of implementation and the composition of pre-existing children to estimate the causal effect of this scheme. Devirupak lowers the number of children by 0.9 percent, but mainly through a 1.9 percent decrease in the number of daughters. I find no evidence for an increase in the demand for daughters in response to a decrease in their relative price in the overall sample. However, the proportion of one-boy couples and the sex ratio of first and second births increased significantly. Thus, schemes that induce parents to choose either sons or daughters may lower fertility, but have unintended consequences for sex ratios, despite larger incentives for girls, if a minimum number of sons is desired. Chapter 2 examines the impact of tariff decline on fertility, the sex ratio at birth, and infant mortality in rural Indian districts. In relative terms, women more exposed to tariff cuts are more likely to give birth and these births are more likely to be female. These results are primarily driven by low-caste, low-wealth, and uneducated women. Moreover, infant mortality decreases for girls (but not boys) born to these low-status mothers. On the other hand, fertility decreases and female infant mortality increases for high-status women. They also exhibit a weak increase in the sex ratio at birth. Differential effect of the tariff reform on the relative economic opportunities of women across socioeconomic groups is the most likely mechanism for these results. Chapter 3 analyzes the effects of sex ratio imbalances on pre-marital investments and marital outcomes in India. Changes in the availability of pre-natal sex-selection technology differentially altered the mating pool of individuals born in different states, cohorts, and endogamous social groups. I show that increases in the male to female sex ratio at birth are associated with a decrease in educational attainment, age at marriage, and labor force participation rates, and an increase in spouse's age for women relative to men. These findings are consistent with an improvement in the position of women in the marriage market due to their relative scarcity

(Meta)genomic insights into the pathogenome of Cellulosimicrobium cellulans

© The Author(s), 2016. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Scientific Reports 6 (2016): 25527, doi:10.1038/srep25527.Despite having serious clinical manifestations, Cellulosimicrobium cellulans remain under-reported with only three genome sequences available at the time of writing. Genome sequences of C. cellulans LMG16121, C. cellulans J36 and Cellulosimicrobium sp. strain MM were used to determine distribution of pathogenicity islands (PAIs) across C. cellulans, which revealed 49 potential marker genes with known association to human infections, e.g. Fic and VbhA toxin-antitoxin system. Oligonucleotide composition-based analysis of orthologous proteins (n = 791) across three genomes revealed significant negative correlation (P < 0.05) between frequency of optimal codons (Fopt) and gene G+C content, highlighting the G+C-biased gene conversion (gBGC) effect across Cellulosimicrobium strains. Bayesian molecular-clock analysis performed on three virulent PAI proteins (Fic; D-alanyl-D-alanine-carboxypeptidase; transposase) dated the divergence event at 300 million years ago from the most common recent ancestor. Synteny-based annotation of hypothetical proteins highlighted gene transfers from non-pathogenic bacteria as a key factor in the evolution of PAIs. Additonally, deciphering the metagenomic islands using strain MM’s genome with environmental data from the site of isolation (hot-spring biofilm) revealed (an)aerobic respiration as population segregation factor across the in situ cohorts. Using reference genomes and metagenomic data, our results highlight the emergence and evolution of PAIs in the genus Cellulosimicrobium.The authors acknowledge funds from Department of Biotechnology (DBT) and National Bureau of Agriculturally Important Microorganisms (NBAIM). AS gratefully acknowledge National Bureau of Agriculturally Important Microorganisms (NBAIM) for providing research fellowship

Microbiome profile associated with malignant pleural effusion.

INTRODUCTION:There is ongoing research into the development of novel molecular markers that may complement fluid cytology malignant pleural effusion (MPE) diagnosis. In this exploratory pilot study, we hypothesized that there are distinct differences in the pleural fluid microbiome profile of malignant and non-malignant pleural diseases. METHOD:From a prospectively enrolled pleural fluid biorepository, samples of MPE were included. Non-MPE effusion were included as comparators. 16S rRNA gene V4 region amplicon sequencing was performed. Exact Sequence Variants (ESVs) were used for diversity analyses. The Shannon and Richness indices of alpha diversity and UniFrac beta diversity measures were tested for significance using permutational multivariate analysis of variance. Analyses of Composition of Microbiome was used to identify differentially abundant bacterial ESVs between the groups controlled for multiple hypothesis testing. RESULTS:38 patients with MPE and 9 with non-MPE were included. A subgroup of patients with metastatic adenocarcinoma histology were identified among MPE group (adenocarcinoma of lung origin (LA-MPE) = 11, breast origin (BA-MPE) = 11). MPE presented with significantly greater alpha diversity compared to non-MPE group. Within the MPE group, BA-MPE was more diverse compared to LA-MPE group. In multivariable analysis, ESVs belonging to family S24-7 and genera Allobaculum, Stenotrophomonas, and Epulopiscium were significantly enriched in the malignant group compared to the non-malignant group. CONCLUSION:Our results are the first to demonstrate a microbiome signature according to MPE and non-MPE. The role of microbiome in pleural effusion pathogenesis needs further exploration

Gut microbial features can predict host phenotype response to protein deficiency.

Malnutrition remains a major health problem in low- and middle-income countries. During low protein intake, &lt;0.67 g/kg/day, there is a loss of nitrogen (N2 ) balance, due to the unavailability of amino acid for metabolism and unbalanced protein catabolism results. However, there are individuals, who consume the same low protein intake, and preserve N2 balance for unknown reasons. A novel factor, the gut microbiota, may account for these N2 balance differences. To investigate this, we correlated gut microbial profiles with the growth of four murine strains (C57Bl6/J, CD-1, FVB, and NIH-Swiss) on protein deficient (PD) diet. Results show that a PD diet exerts a strain-dependent impact on growth and N2 balance as determined through analysis of urinary urea, ammonia and creatinine excretion. Bacterial alpha diversity was significantly (P &lt; 0.05, FDR) lower across all strains on a PD diet compared to normal chow (NC). Multi-group analyses of the composition of microbiomes (ANCOM) revealed significantly differential microbial signatures between the four strains independent of diet. However, mice on a PD diet demonstrated differential enrichment of bacterial genera including, Allobaculum (C57Bl6/J), Parabacteroides (CD-1), Turicibacter (FVB), and Mucispirillum (NIH-Swiss) relative to NC. For instance, selective comparison of the CD-1 (gained weight) and C57Bl6/J (did not gain weight) strains on PD diet also demonstrated significant pathway enrichment of dihydroorodate dehydrogenase, rRNA methyltransferases, and RNA splicing ligase in the CD-1 strains compared to C57Bl6/J strains; which might account in their ability to retain growth despite a protein deficient diet. Taken together, these results suggest a potential relationship between the specific gut microbiota, N2 balance and animal response to malnutrition

Response and resilience of soil microbial communities inhabiting in edible oil stress/contamination from industrial estates

Metagenomic DNA extracted from polluted as well as control soil sample and electrophoresed on 0.8 % agarosa gel. Lane M is of marker, Lane 1, is for polluted sample (representing pooled metagenomic DNA for P1 + P2 + P3 = P) and Lane 2 is for control soil sample (representing pooled metagenomic DNA for C1 + C2 + C3 = C). Figure S2. Distribution of taxa among bacteria at rank phylum classified according to 16S rDNA using RDP classifier for both polluted as well as control sample. Figure S3. Distribution of taxa among bacteria at rank phylum classified according to lowest common ancestor (LCA) for both polluted as well as control sample. Figure S4. Comparative distribution of taxa among bacteria at rank class classified according to WebCARMA and M5NR datasets for both polluted as well as control sample. Table S1. Enzymes mapped for lipid metabolism pathways in KEEG database. (DOC 300 kb

Bacterial and Archaeal Viruses of Himalayan Hot Springs at Manikaran Modulate Host Genomes

Hot spring-associated viruses, particularly the archaeal viruses, remain under-examined compared to bacteriophages. Previous metagenomic studies of the Manikaran hot springs in India suggested an abundance of viral DNA, which prompted us to examine the virus–host (bacterial and archaeal) interactions in sediment and microbial mat samples collected from the thermal discharges. Here, we characterize the viruses (both bacterial and archaeal) from this Himalayan hot spring using both metagenomics assembly and electron microscopy. We utilized four shotgun samples from sediment (78–98°C) and two from microbial mats (50°C) to reconstruct 65 bacteriophage genomes (24–200 kb). We also identified 59 archaeal viruses that were notably abundant across the sediment samples. Whole-genome analyses of the reconstructed bacteriophage genomes revealed greater genomic conservation in sediments (65%) compared to microbial mats (49%). However, a minimal phage genome was still maintained across both sediment and microbial mats suggesting a common origin. To complement the metagenomic data, scanning-electron and helium-ion microscopy were used to reveal diverse morphotypes of Caudovirales and archaeal viruses. The genome level annotations provide further evidence for gene-level exchange between virus and host in these hot springs, and augments our knowledgebase for bacteriophages, archaeal viruses and Clustered Regularly Interspaced Short Palindromic Repeat cassettes, which provide a critical resource for studying viromes in extreme natural environments

Enhanced Photocatalytic Degradation of the Imidazolinone Herbicide Imazapyr upon UV/Vis Irradiation in the Presence of CaxMnOy-TiO2 Hetero-Nanostructures: Degradation Pathways and Reaction Intermediates

[Abstract] The determination of reaction pathways and identification of products of pollutants degradation is central to photocatalytic environmental remediation. This work focuses on the photocatalytic degradation of the herbicide Imazapyr (2-(4-methyl-5-oxo-4-propan-2-yl-1H-imidazol-2-yl) pyridine-3-carboxylic acid) under UV-Vis and visible-only irradiation of aqueous suspensions of CaᵪMnOᵧ-TiO₂, and on the identification of the corresponding degradation pathways and reaction intermediates. CaᵪMnOᵧ-TiO₂ was formed by mixing CaᵪMnOᵧ and TiO₂ by mechanical grinding followed by annealing at 500 °C. A complete structural characterization of CaᵪMnOᵧ-TiO₂ was carried out. The photocatalytic activity of the hetero-nanostructures was determined using phenol and Imazapyr herbicide as model pollutants in a stirred tank reactor under UV-Vis and visible-only irradiation. Using equivalent loadings, CaᵪMnOᵧ-TiO₂ showed a higher rate (10.6 μM·h⁻¹) as compared to unmodified TiO₂ (7.4 μM·h⁻¹) for Imazapyr degradation under UV-Vis irradiation. The mineralization rate was 4.07 μM·h⁻¹ for CaᵪMnOᵧ-TiO₂ and 1.21 μM·h⁻¹ for TiO₂. In the CaᵪMnOᵧ-TiO₂ system, the concentration of intermediate products reached a maximum at 180 min of irradiation that then decreased to a half in 120 min. For unmodified TiO₂, the intermediates continuously increased with irradiation time with no decrease observed in their concentration. The enhanced efficiency of the CaᵪMnOᵧ-TiO₂ for the complete degradation of the Imazapyr and intermediates is attributed to an increased adsorption of polar species on the surface of CaᵪMnOᵧ. Based on LC-MS, photocatalytic degradation pathways for Imazapyr under UV-Vis irradiation have been proposed. Some photocatalytic degradation was obtained under visible-only irradiation for CaᵪMnOᵧ-TiO₂. Hydroxyl radicals were found to be main reactive oxygen species responsible for the photocatalytic degradation through radical scavenger investigations.This research received external funding from the British Council under the STREAM-MENA Institutional Links Scheme Grant number 278072873. This is a collaboration between Ulster University (UK), Technion Institute (Israel) and Rabat University (Morocco). MC acknowledges support from Ministerio de Economía y Competitividad (Spain) through project CTQ2015-71238-R (MINECO/FEDER). AS would like to acknowledge the financial support received from Ulster University (UK) through the VCRS scholarship. PS would like to acknowledge funding from Invest Northern Ireland for the BioDevices projectBritish Council; 27807287