Comparative expression analysis of water buffalo (Bubalus bubalis) to identify genes associated with economically important traits

The milk, meat, skins, and draft power of domestic water buffalo (Bubalus bubalis) provide substantial contributions to the global agricultural economy. The world's water buffalo population is primarily found in Asia, and the buffalo supports more people per capita than any other livestock species. For evaluating the workflow, output rate, and completeness of transcriptome assemblies within and between reference-free (RF) de novo transcriptome and reference-based (RB) datasets, abundant bioinformatics studies have been carried out to date. However, comprehensive documentation of the degree of consistency and variability of the data produced by comparing gene expression levels using these two separate techniques is lacking. In the present study, we assessed the variations in the number of differentially expressed genes (DEGs) attained with RF and RB approaches. In light of this, we conducted a study to identify, annotate, and analyze the genes associated with four economically important traits of buffalo, viz., milk volume, age at first calving, post-partum cyclicity, and feed conversion efficiency. A total of 14,201 and 279 DEGs were identified in RF and RB assemblies. Gene ontology (GO) terms associated with the identified genes were allocated to traits under study. Identified genes improve the knowledge of the underlying mechanism of trait expression in water buffalo which may support improved breeding plans for higher productivity. The empirical findings of this study using RNA-seq data-based assembly may improve the understanding of genetic diversity in relation to buffalo productivity and provide important contributions to answer biological issues regarding the transcriptome of non-model organisms.

Validation of an obstetric quality of recovery scoring tool (ObsQoR-11) after elective caesarean delivery in a developing country: a prospective observational study

BACKGROUND

The obstetric quality of recovery scoring tool (ObsQoR-11) was developed and validated in the United Kingdom for use after elective and emergency caesarean delivery. Quality of recovery scoring tools validated in one country may not be valid in other countries with significant cultural, socio-economic and linguistic variations. The aim of the current study was to validate a Hindi version of the ObsQoR-11.

METHODS

In this prospective observational study, 100 parturients who underwent elective caesarean delivery in a tertiary care obstetric referral university hospital in North India were asked to complete a Hindi version of the ObsQoR-11 scoring tool 24 h after surgery. The performance of the Hindi version of ObsQoR-11 was assessed using measures of validity, reliability, and feasibility.

RESULTS

The Hindi version of ObsQoR-11 correlated moderately with the global health visual analogue scale (r=0.45, 95% CI 0.27 to 0.59; P <0.0001) and discriminated well between good and poor recovery (mean (SD) score 84.6 (9.4) vs 75.0 (11.2); P <0.0001). The reliability and internal consistency were moderate (Cronbach's alpha=0.66; Spearman-Brown Prophesy Reliability estimate=0.57) with good repeatability (intraclass correlation coefficient 0.85, 95% CI 0.69 to 0.93; P <0.0001) and no floor or ceiling effects. All parturients completed the questionnaire (median (IQR) time of completion of 3 (1.5 - 5.5) min).

CONCLUSION

The Hindi version of the ObsQoR-11 questionnaire is a promising scoring tool to evaluate quality of recovery after elective caesarean delivery. Further research is needed to evaluate the Hindi tool in other institutions in India, as well as in other languages.

Inferring Relationship of Blood Metabolic Changes and Average Daily Gain With Feed Conversion Efficiency in Murrah Heifers: Machine Learning Approach

Machine learning algorithms were employed for predicting the feed conversion efficiency (FCE), using the blood parameters and average daily gain (ADG) as predictor variables in buffalo heifers. It was observed that isotonic regression outperformed other machine learning algorithms used in study. Further, we also achieved the best performance evaluation metrics model with additive regression as the meta learner and isotonic regression as the base learner on 10-fold cross-validation and leaving-one-out cross-validation tests. Further, we created three separate partial least square regression (PLSR) models using all 14 parameters of blood and ADG as independent (explanatory) variables and FCE as the dependent variable, to understand the interactions of blood parameters, ADG with FCE each by inclusion of all FCE values (i), only higher FCE values (negative RFI) (ii), and inclusion of only lower FCE (positive RFI) values (iii). The PLSR model including only the higher FCE values was concluded the best, based on performance evaluation metrics as compared to PLSR models developed by inclusion of the lower FCE values and all types of FCE values. IGF1 and its interactions with the other blood parameters were found highly influential for higher FCE measures. The strength of the estimated interaction effects of the blood parameter in relation to FCE may facilitate understanding of intricate dynamics of blood parameters for growth.

Gold nanoparticles modulate the steroidogenic and apoptotic pathway in a buffalo granulosa cell model

OBJECTIVES

Granulosa cells are associated with steroidogenesis and ovarian function in females. Aims of the study are to understand the effects of gold nanoparticles (AuNP) on steroidogenesis and apoptotic pathway associated genes in buffalo granulosa cells.

RESULTS

The AuNP were prepared chemically and thereby characterized by transmission electron microscope (TEM) imaging, absorbance and dynamic light scattering (DLS) measurements for hydrodynamic diameter and zeta potential. The cultured buffalo granulosa cells (BGC) were co-incubated with AuNP in two concentrations (2 × 10⁹ and 2 × 10¹⁰ AuNP/ml) for 24 h. Treatment of BGC with AuNP significantly modulated the steroidogenesis associated genes (3β-Hsd and Cyp19A1) expression and progesterone accumulation in the culture fluid. AuNP affected the apoptotic pathway in BGC by affecting the gene expression of Caspase-3, Bad and Bax. The AuNP did not exert oxidative stress through anti-oxidant induction & lipid peroxidation in the buffalo GC.

CONCLUSIONS

AuNP may modulate the endocrine system by having impact on the steroidogenesis pathway and also have the potential to affect apoptotic pathway in a buffalo granulosa cell model.

Identification and characterization of trait-specific SNPs using ddRAD sequencing in water buffalo

Single Nucleotide Polymorphism (SNP) is one of the important molecular markers widely used in animal breeding program for improvement of any desirable genetic traits. Considering this, the present study was carried out to identify, annotate and analyze the SNPs related to four important traits of buffalo viz. milk volume, age at first calving, post-partum cyclicity and feed conversion efficiency. We identified 246,495, 168,202, 74,136 and 194,747 genome-wide SNPs related to mentioned traits, respectively using ddRAD sequencing technique based on 85 samples of Murrah Buffaloes. Distribution of these SNPs were highest (61.69%) and lowest (1.78%) in intron and exon regions, respectively. Under coding regions, the SNPs for the four traits were further classified as synonymous (4697) and non-synonymous (3827). Moreover, Gene Ontology (GO) terms of identified genes assigned to various traits. These characterized SNPs will enhance the knowledge of cellular mechanism for enhancing productivity of water buffalo through molecular breeding.

Publication of research article: an art or science?

The publication process is a shared responsibility. Besides the writing, reviewing, publishing, and editorial teams, readers are one of the most important pillars of this process. Readers and authors cannot be dealt with separately, because most of the readers are authors. The varieties of articles and improvement in presentations reflect the rising interest and enthusiasm of writers and readers. Increasing number in critical comments and author's reply can be considered as a post-publication peer review process. Impact Factor, which was used as a proxy for the relative importance of a journal, is now being considered a misleading tool in assessing the quality of a paper or the researcher. Here, we are trying to discuss in brief the points which should be kept in mind before manuscript preparation and submission, so that our research should reach to maximum readers in an unbiased form.

Outcome of older patients with severe pneumonia predicted by recursive partitioning

OBJECTIVES

To develop a prognostic model to predict outcome of older patients with severe pneumonia requiring mechanical ventilation.

DESIGN

A nonconcurrent prospective study.

SETTING

A 24-bed intensive care unit (ICU) within two university-affiliated tertiary care hospitals.

PARTICIPANTS

All patients age 75 and older with severe pneumonia between June 1996 and September 1999 were included. Demographic data including activities of daily living (ADL) index score before admission, and clinical and laboratory data were collected in the first 24 hours of admission to the ICU. One hundred four patients (mean age +/- standard deviation (SD) 82.3 +/- 5.5 years) met the inclusion criteria.

MEASUREMENTS

A classification tree was developed using binary recursive partitioning to predict hospital discharge. The model was compared with a logistic regression model using variables selected by the tree analysis and with the Acute Physiologic and Chronic Health Evaluation (APACHE) II.

RESULTS

Outcome predictors for the classification tree were use of vasopressors, presence of multilobar pneumonia on chest radiograph, ratio of blood urea nitrogen to creatinine, Glasgow Coma Scale, urine output, and ADL score before admission. The tree achieved a sensitivity of 83.8% (95% confidence interval (CI) 69.2-92.4) and a specificity of 93.3% (95% CI 83-98.1). The predictive accuracy as assessed by the area under the curve (c-index +/- standard error) was significantly higher with the classification tree (0.932 +/- 0.03) than with logistic regression and APACHE II, (0.801 +/- 0.028 and 0.711 +/- 0.049, respectively (P < .05).

CONCLUSIONS

The classification tree model demonstrated a superior predictive accuracy to that of logistic regression and APACHE II. If validated prospectively, the classification tree can be used as a tool to assess the outcome of older patients with severe pneumonia requiring mechanical ventilation on admission to the ICU. In addition, the classification tree can be used to assist healthcare workers in providing a concise summary of local outcome experience and prognostic information to patients and their surrogates.

Morbid obesity in the medical ICU

STUDY OBJECTIVE

To describe the clinical course, complications, and prognostic factors of morbidly obese patients admitted to the ICU compared to a control group of nonobese patients.

DESIGN

A retrospective study.

SETTING

Two university-affiliated hospitals.

METHODS

We reviewed the medical records of 117 morbidly obese patients (body mass index >/= 40 kg/m(2)) admitted to the medical ICU between January 1994 and June 2000. Data collected included demographic information, comorbid condition, APACHE (acute physiology and chronic health evaluation) II score, invasive procedures, organ failure, and in-hospital mortality.

RESULTS

Obstructive airway disease, pneumonia, and sepsis were the main reasons for admission to the ICU in the morbidly obese group. Sixty-one percent of the morbidly obese patients and 46% of the nonobese group required mechanical ventilation (p = 0.02). The mean lengths of mechanical ventilation and ICU stay were significantly longer for the morbidly obese group (7.7 +/- 9.6 days and 9.3 +/- 10.5 days vs 4.6 +/- 7.1 days and 5.8 +/- 8.2 days, respectively; p < 0.001). APACHE II scores were not significantly different in the two groups (19.1 +/- 7.6 and 20.6 +/- 12.2; p = 0.6). Overall mortality was 30% for the morbidly obese patients and 17% for the nonobese group (p = 0.019). By multivariate analysis, multiorgan failure (odds ratio [OR], 4.6; 95% confidence interval [CI], 2.1 to 16.6), PaO(2)/fraction of inspired oxygen < 200 for > 48 h (OR, 2.3; 95% CI, 1.2 to 7.8), and depressed left ventricular ejection fraction < 40% (OR, 1.4; 95% CI, 1.03 to 13.8) were independently associated with ICU mortality in the morbidly obese group.

CONCLUSION

We conclude that critically ill morbidly obese patients are at increased risk of morbidity and mortality compared to the nonobese patients.

Co-existing granular cell tumor and adenocarcinoma of the lung: a case report and review of the literature

Granular cell tumor (GCT) of the lung is a rare tumor, constituting less than 10% of all GCTs. It is a multicentric tumor and infiltrates into adjoining tissue, but malignant GCT of the lung has not been reported. Diagnosis is usually obtained with bronchoscopic biopsy. Treatment options include bronchoscopic extirpation, laser therapy, and sleeve resection. We present a case of GCT co-existing with adenocarcinoma of the lung and review the literature.

Etiology of severe pneumonia in the very elderly

The etiology of severe pneumonia requiring mechanical ventilation in the very elderly has been imprecise because of lack of comprehensive studies and low yield of diagnostic approach. Overall, 104 patients 75 yr of age and older with severe pneumonia were studied prospectively at two university-affiliated hospitals. Microbial investigation included blood culture, serology, pleural fluid, and bronchoalveolar secretions. Streptococcus pneumoniae (14%), gram-negative enteric bacilli (14%), Legionella sp. (9%), Hemophilus influenzae (7%), and Staphylococcus aureus (7%) were the predominant pathogens in community-acquired pneumonia (CAP). Staphylococcus aureus (29%), gram-negative enteric bacilli (15%), Streptococcus pneumoniae (9%), and Pseudomonas aeruginosa (4%) accounted for most isolates of nursing home-acquired pneumonia (NHAP). The case fatality rate was 55% (53% for CAP and 57% for NHAP; p > 0.5). Activity of Daily Living (ADL) Index, pulmonary, endocrine and central nervous system (CNS) comorbidities were associated with distinct microbial etiology. By multivariate analysis, hospital mortality was associated independently with 24-h urine output (odds ratio [OR], 5.6; 95% confidence interval [CI], 2.5 to 7.9; p < 0.001), septic shock (OR, 4.3; 95% CI, 1.9 to 8.9; p = 0.0059), radiographic multilobar involvement (OR, 3.7; 95% CI, 1.8 to 15.6; p = 0.02), and inadequate antimicrobial therapy (OR, 2.6; 95% CI, 1.4 to 23.9; p = 0.034). Further studies should focus on identifying effective antimicrobial regimens in randomized trials.

Composite interval mapping reveals a major locus influencing embryonic development rate in rainbow trout (Oncorhynchus mykiss)

Little is known about the genetics controlling the rate of embryonic development in salmonids, despite the fact that this trait plays an important role in the life history of wild and cultured stocks. We investigated the genetics of embryonic development rate by performing an analysis of quantitative trait loci (QTL) on two families of androgenetically derived doubled haploid rainbow trout produced from a hybrid of two clonal lines with divergent embryonic development rates. A total of 170 doubled haploid individuals were genotyped at 222 marker loci [219 amplified fragment length polymorphism (AFLP) markers, 2 microsatellites, and p53]. A genetic linkage analysis resulted in a map consisting of 27 linkage groups with 21 of the markers remaining unlinked at a minimum LOD of 3.0 and maximum theta of 0.40. Eight of these linkage groups were matched to published rainbow trout linkage groups. Composite interval mapping (CIM) revealed evidence for two QTL influencing time to hatch, and suggestive evidence for a third. These QTL accounted for a total of 24.6% of the variation in time to hatch. One of these QTL had a large effect on development rate, especially in one family of doubled haploids, in which it explained 25.6% of the variance in time to hatch. QTL influencing embryonic length and weight at the commencement of exogenous feeding were also identified. The QTL with the strongest effect on embryonic length (lenR13) mapped to the same position as the QTL with the strongest effect on time to hatch (tthR13), suggesting a single QTL may have a pleiotropic effect on both these traits. These results suggest that the use of clonal lines with a doubled haploid crossing design is an effective way of analyzing the genetic basis of complex traits in salmonids.

A comparison of severity of illness scoring systems for elderly patients with severe pneumonia

OBJECTIVE

To evaluate the predictive ability of three severity of illness scoring systems in elderly patients with severe pneumonia requiring mechanical ventilation compared to a younger age group.

DESIGN

Prospective cohort study.

SETTING

Two university-affiliated tertiary care hospitals.

PATIENTS AND PARTICIPANTS

One hundred four patients 75 years of age and older and 253 patients younger than 75 years of age enrolled from medical intensive care units.

MEASUREMENTS AND RESULTS

Probabilities of hospital death for patients were estimated by the Acute Physiology and Chronic Health Evaluation (APACHE) II, the Mortality Probability Model (MPM) II and the Simplified Acute Physiology Score (SAPS) II. Predicted risks of hospital death were compared with observed outcomes using three methods of assessing the overall goodness of fit. The actual mortality of the elderly group was 54.87 % (95 % confidence interval [CI]: 45.2-64.4 %) compared to 28.9 % (95 % CI, 23.3-34.4 %) in the younger age group. There was a significant difference in the predictive accuracy of the scoring systems as assessed by the c-index, which is equivalent to the area under the receiver operator characteristics (ROC) curve, between the two groups, but not within individual groups. Calibration was insufficient for APACHE II and SAPS II in the elderly cohort as in-hospital mortality was lower than the predicted mortality for both models.

CONCLUSIONS

Although the three severity of illness scoring systems (APACHE II, MPM II and SAPS II) demonstrated average discrimination when applied to estimate hospital mortality in the elderly patients with severe pneumonia, MPM II had the closest fit to our database. Alternative modeling approaches might be needed to customize the model coefficients to the elderly population for more accurate probabilities or to develop specialized models targeted to the designed population.