Arindam RoyChoudhury

Comparative and demographic analysis of orang-utan genomes

‘Orang-utan’ is derived from a Malay term meaning ‘man of the forest’ and aptly describes the southeast Asian great apes native to Sumatra and Borneo. The orang-utan species, Pongo abelii (Sumatran) and Pongo pygmaeus (Bornean), are the most phylogenetically distant great apes from humans, thereby providing an informative perspective on hominid evolution. Here we present a Sumatran orang-utan draft genome assembly and short read sequence data from five Sumatran and five Bornean orang-utan genomes. Our analyses reveal that, compared to other primates, the orang-utan genome has many unique features. Structural evolution of the orang-utan genome has proceeded much more slowly than other great apes, evidenced by fewer rearrangements, less segmental duplication, a lower rate of gene family turnover and surprisingly quiescent Alu repeats, which have played a major role in restructuring other primate genomes. We also describe a primate polymorphic neocentromere, found in both Pongo species, emphasizing the gradual evolution of orang-utan genome structure. Orang-utans have extremely low energy usage for a eutherian mammal, far lower than their hominid relatives. Adding their genome to the repertoire of sequenced primates illuminates new signals of positive selection in several pathways including glycolipid metabolism. From the population perspective, both Pongo species are deeply diverse; however, Sumatran individuals possess greater diversity than their Bornean counterparts, and more species-specific variation. Our estimate of Bornean/Sumatran speciation time, 400,000 years ago, is more recent than most previous studies and underscores the complexity of the orang-utan speciation process. Despite a smaller modern census population size, the Sumatran effective population size (Ne) expanded exponentially relative to the ancestral Ne after the split, while Bornean Ne declined over the same period. Overall, the resources and analyses presented here offer new opportunities in evolutionary genomics, insights into hominid biology, and an extensive database of variation for conservation efforts.

Inferring Species Trees Directly from Biallelic Genetic Markers: Bypassing Gene Trees in a Full Coalescent Analysis

The multispecies coalescent provides an elegant theoretical framework for estimating species trees and species demographics from genetic markers. However, practical applications of the multispecies coalescent model are limited by the need to integrate or sample over all gene trees possible for each genetic marker. Here we describe a polynomial-time algorithm that computes the likelihood of a species tree directly from the markers under a finite-sites model of mutation effectively integrating over all possible gene trees. The method applies to independent (unlinked) biallelic markers such as well-spaced single nucleotide polymorphisms, and we have implemented it in SNAPP, a Markov chain Monte Carlo sampler for inferring species trees, divergence dates, and population sizes. We report results from simulation experiments and from an analysis of 1997 amplified fragment length polymorphism loci in 69 individuals sampled from six species of Ourisia (New Zealand native foxglove).

Short sleep duration increases energy intakes but does not change energy expenditure in normal-weight individuals

BACKGROUND Evidence suggests a relation between short sleep duration and obesity. OBJECTIVE We assessed energy balance during periods of short and habitual sleep in normal-weight men and women. DESIGN Fifteen men and 15 women aged 30-49 y with a body mass index (in kg/m(2)) of 22-26, who regularly slept 7-9 h/night, were recruited to participate in this crossover inpatient study. All participants were studied under short (4 h/night) and habitual (9 h/night) sleep conditions, in random order, for 5 nights each. Food intake was measured on day 5, and energy expenditure was measured with the doubly labeled water method over each period. RESULTS Participants consumed more energy on day 5 during short sleep (2813.6 ± 593.0 kcal) than during habitual sleep (2517.7 ± 593.0 kcal; P = 0.023). This effect was mostly due to increased consumption of fat (20.7 ± 37.4 g; P = 0.01), notably saturated fat (8.7 ± 20.4 g; P = 0.038), during short sleep. Resting metabolic rate (short sleep: 1455.4 ± 129.0 kcal/d; habitual sleep: 1486.5 ± 129.5 kcal/d; P = 0.136) and total energy expenditure (short sleep: 2589.2 ± 526.5 kcal/d; habitual sleep: 2611.1 ± 529.0 kcal/d; P = 0.832) did not differ significantly between sleep phases. CONCLUSIONS Our data show that a reduction in sleep increases energy and fat intakes, which may explain the associations observed between sleep and obesity. If sustained, as observed, and not compensated by increased energy expenditure, the dietary intakes of individuals undergoing short sleep predispose to obesity. This trial is registered at clinicaltrials.gov as NCT00935402.

Short sleep duration, glucose dysregulation and hormonal regulation of appetite in men and women.

STUDY OBJECTIVE To determine the hormonal effects of reducing sleep duration under controlled feeding conditions. DESIGN Randomized, crossover study. SETTING Inpatient. PARTICIPANTS Twenty-seven normal weight, 30- to 45-yr-old men and women habitually sleeping 7-9 hr/night. INTERVENTION PARTICIPANTS WERE STUDIED UNDER TWO SLEEP CONDITIONS: short (4 hr in bed) or habitual (9 hr in bed) sleep. A controlled diet was provided for each 4-day study period. MEASUREMENTS AND RESULTS Fasting blood samples were obtained daily and frequent blood samples were obtained throughout day 4. The main outcomes measures included glucose, insulin, leptin, ghrelin, adiponectin, total glucagon-like peptide 1 (GLP-1) and peptide YY(3-36) (PYY(3-36)) concentrations. Body weights were reduced by 2.2 ± 0.4 lb and 1.7 ± 0.4 lb during the habitual and short sleep phases, respectively (both P < 0.0001). There was no effect of sleep duration on glucose, insulin, and leptin profiles (all P > 0.05). Ghrelin and GLP-1 responses differed by sex. Short sleep increased fasting (P = 0.054) and morning (08:00-12:00) (P = 0.042) total ghrelin in men but not women. The reverse was observed for GLP-1: afternoon levels (12:30-19:00) were lower (P = 0.016) after short sleep compared with habitual sleep in women but not men. CONCLUSIONS These data suggest that, in the context of negative energy balance, short sleep does not lead to a state of increased insulin resistance, but may predispose to overeating via separate mechanisms in men and women. CLINICAL TRIAL INFORMATION Trial registration on http://www.clinicaltrials.gov. #NCT00935402.

Alterations in sleep architecture in response to experimental sleep curtailment are associated with signs of positive energy balance.

Sleep reduction is associated with increased energy intake and weight gain, though few studies have explored the relationship between sleep architecture and energy balance measures in the context of experimental sleep restriction. Fourteen males and 13 females (body mass index: 22-26 kg/m(2)) participated in a crossover sleep curtailment study. Participants were studied under two sleep conditions: short (4 h/night; 0100-0500 h) and habitual (9 h/night; 2200-0700 h), for 5 nights each. Sleep was polysomnographically recorded nightly. Outcome measures included resting metabolic rate (RMR), feelings of appetite-satiety, and ad libitum food intake. Short sleep resulted in reductions in stage 2 sleep and rapid eye movement (REM) sleep duration (P < 0.001), as well as decreased percentage of stage 2 sleep and REM sleep and increased slow wave sleep (SWS) percentage (P < 0.05). Linear mixed model analysis demonstrated a positive association between stage 2 sleep duration and RMR (P = 0.051). Inverse associations were observed between REM sleep duration and hunger (P = 0.031) and between stage 2 sleep duration and appetite for sweet (P = 0.015) and salty (P = 0.046) foods. Stage 2 sleep percentage was inversely related to energy consumed (P = 0.024). Stage 2 sleep (P = 0.005), SWS (P = 0.008), and REM sleep (P = 0.048) percentages were inversely related to fat intake, and SWS (P = 0.040) and REM sleep (P = 0.050) were inversely related to carbohydrate intake. This study demonstrates that changes in sleep architecture are associated with markers of positive energy balance and indicate a means by which exposure to short sleep duration and/or an altered sleep architecture profile may lead to excess weight gain over time.

Relative efficacy of perioperative gemcitabine and cisplatin versus methotrexate, vinblastine, adriamycin, and cisplatin in the management of locally advanced urothelial carcinoma of the bladder.

OBJECTIVE To compare the outcomes of patients treated in the perioperative setting with methotrexate, vinblastine, adriamycin, and cisplatin (MVAC) versus gemcitabine and cisplatin (GC). Systemic cisplatin-based chemotherapy regimens are the mainstay of treatment for patients with advanced bladder cancer. GC has often been used interchangeably with MVAC in neoadjuvant or adjuvant settings for patients with locally advanced (cT2N0M0-cT4N2M0) bladder cancer without adequate evidence. METHODS A total of 114 patients treated with systemic chemotherapy for Stage T2-T4N0-N2M0 urothelial cell carcinoma of the bladder were included in the present study. The survival times were estimated and compared using the Kaplan-Meier method and log-rank test, respectively. Univariate and multivariate Cox proportional hazards models were used to determine the statistical significance. RESULTS Of the 114 patients included in the present study, 37 (32%) were treated with GC and 77 (68%) with MVAC. In the neoadjuvant group, no difference was found between the 2 chemotherapeutic regimens in terms of the pathologic complete response rate at either cystectomy or during cystoscopy (14 [31%] of 45 MVAC patients vs 4 [25%] of 16 GC patients; P=.645). On multivariate analysis, the choice of regimen was not an independent predictor of cancer-specific death (hazard ratio 1.3, 95% confidence interval 0.67-2.57; P=.421) or overall survival (hazard ratio 1.3, 95% confidence interval 0.76-2.24; P=.330). CONCLUSION Despite the lack of data on the relative efficacy of GC versus MVAC in the neoadjuvant and adjuvant settings, these regimens have been used interchangeably. The present investigation did not find the choice of cisplatin-based regimen to be an independent predictor of survival. A trend was seen toward improved survival and a greater complete response rate in the MVAC group.

A Two-Stage Pruning Algorithm for Likelihood Computation for a Population Tree

We have developed a pruning algorithm for likelihood estimation of a tree of populations. This algorithm enables us to compute the likelihood for large trees. Thus, it gives an efficient way of obtaining the maximum-likelihood estimate (MLE) for a given tree topology. Our method utilizes the differences accumulated by random genetic drift in allele count data from single-nucleotide polymorphisms (SNPs), ignoring the effect of mutation after divergence from the common ancestral population. The computation of the maximum-likelihood tree involves both maximizing likelihood over branch lengths of a given topology and comparing the maximum-likelihood across topologies. Here our focus is the maximization of likelihood over branch lengths of a given topology. The pruning algorithm computes arrays of probabilities at the root of the tree from the data at the tips of the tree; at the root, the arrays determine the likelihood. The arrays consist of probabilities related to the number of coalescences and allele counts for the partially coalesced lineages. Computing these probabilities requires an unusual two-stage algorithm. Our computation is exact and avoids time-consuming Monte Carlo methods. We can also correct for ascertainment bias.

Quantitating Contrast Medium–induced Nephropathy: Controlling the Controls

Davenport et al and McDonald et al find no evidence of nephropathy in patients with mild renal failure, even if other common risks to kidney function exist; for patients with more severe renal failure, if we assume that the real chances of contrast medium-induced nephropathy lie somewhere between the estimates of the two articles, the risk is still relatively low-certainly lower than that suggested by publications lacking control groups, lower than those found in articles reporting experience with angiocardiography, and lower yet if prophylactic hydration is used.

Validation of a frailty index in patients undergoing curative surgery for urologic malignancy and comparison with other risk stratification tools.

OBJECTIVE To retrospectively validate and compare a modified frailty index predicting adverse outcomes and other risk stratification tools among patients undergoing urologic oncological surgeries. MATERIALS AND METHODS The American College of Surgeons National Surgical Quality Improvement Program was queried from 2005 to 2013 to identify patients undergoing cystectomy, prostatectomy, nephrectomy, and nephroureterectomy. Using the Canadian Study of Health and Aging Frailty Index, 11 variables were matched to the database; 4 were also added because of their relevance in oncology patients. The incidence of mortality, Clavien-Dindo IV complications, and adverse events were assessed with patients grouped according to their modified frailty index score. RESULTS We identified 41,681 patients who were undergoing surgery for presumed urologic malignancy. Patients with a high frailty index score of >0.20 had a 3.70 odds of a Clavien-Dindo IV event (CI: 2.865-4.788, P<0.0005) and a 5.95 odds of 30-day mortality (CI: 3.72-9.51, P<0.0005) in comparison with nonfrail patients after adjusting for race, sex, age, smoking history, and procedure. Using C-statistics to compare the sensitivity and specificity of the predictive ability of different models per risk stratification tool and the Akaike information criteria to assess for the fit of the models with the data, the modified frailty index was comparable or superior to the Charlson comorbidity index but inferior to the American Society of Anesthesiologists Risk Class in predicting 30-day mortality or Clavien-Dindo IV events. When the modified frailty index was augmented with the American Society of Anesthesiologists Risk Class, the new index was superior in all aspects in comparison to other risk stratification tools. CONCLUSION Existing risk stratification tools may be improved by incorporating variables in our 15-point modified frailty index as well as other factors such as walking speed, exhaustion, and sarcopenia to fully assess frailty. This is relevant in diseases such as kidney and prostate cancer, where surveillance and other nonsurgical interventions exist as alternatives to a potentially complicated surgery. In these scenarios, our modified frailty index augmented by the American Society of Anesthesiologists Risk Class may help inform which patients have increased surgical complications that may outweigh the benefit of surgery although this index needs prospective validation.

New HBV subgenotype D9, a novel D/C recombinant, identified in patients with chronic HBeAg‐negative infection in Eastern India

Genome diversity is a hallmark of hepatitis B virus (HBV), which allowed its classification into 10 genotypes (A–J) and numerous subgenotypes. Among them, Genotype D is currently segregated into eight subgenotypes (D1–D8). Here, we report the identification and characterization of a novel subgenotype within genotype D of HBV from chronic hepatitis B e antigen (HBeAg)‐negative patients of Eastern India. Phylogenetic tree analysis based on complete genome sequences revealed that six of 39 HBV/D isolates formed a distinct cluster supported by high bootstrap value and had nucleotide divergence >4% relative to the known D subgenotypes (D1–D8), justifying their assignment into a new subgenotype (D9). By comparing the amino acid sequences of the four ORFs of HBV/D9 with D1–D8, 36 specific residues, including a unique one (E112 in the core region), were identified that could be considered as a signature of D9. Further analysis by Simplot, BootScan and jpHMM demonstrated that D9 resulted from a discrete recombination with genotype C over the precore–core region. This type of recombination has not been described previously as all C/D recombinants reported so far possessed genotype C backbones with mosaic fragments derived from HBV/D. Interestingly, compared to other subgenotypes of HBV/D, D9 isolates had a higher frequency of mutations (A1762T and G1764A) in the basal core promoter region that had been implicated in the development of hepatocellular carcinoma. Further investigations are needed to determine the overall prevalence and clinical significance of these newly characterized D9 strains and to assess the impact of inter‐genotypic recombination on viral properties.