Critical evaluation of the reliability of DNA methylation probes on the Illumina MethylationEPIC v1.0 BeadChip microarrays

DNA methylation (DNAm) plays a crucial role in a number of complex diseases. However, the reliability of DNAm levels measured using Illumina arrays varies across different probes. Previous research primarily assessed probe reliability by comparing duplicate samples between the 450k-450k or 450k-EPIC platforms, with limited investigations on Illumina EPIC v1.0 arrays. We conducted a comprehensive assessment of the EPIC v1.0 array probe reliability using 69 blood DNA samples, each measured twice, generated by the Alzheimer's Disease Neuroimaging Initiative study. We observed higher reliability in probes with average methylation beta values of 0.2 to 0.8, and lower reliability in type I probes or those within the promoter and CpG island regions. Importantly, we found that probe reliability has significant implications in the analyses of Epigenome-wide Association Studies (EWAS). Higher reliability is associated with more consistent effect sizes in different studies, the identification of differentially methylated regions (DMRs) and methylation quantitative trait locus (mQTLs), and significant correlations with downstream gene expression. Moreover, blood DNAm measurements obtained from probes with higher reliability are more likely to show concordance with brain DNAm measurements. Our findings, which provide crucial reliability information for probes on the EPIC v1.0 array, will serve as a valuable resource for future DNAm studies.

Single incision laparoscopy versus conventional multiport laparoscopy for colorectal surgery: a systematic review and meta-analysis

INTRODUCTION

There has been an increase in colorectal cancer resections worldwide and in the UK. Initially conducted as an open procedure, this was replaced with the conventional multiport technique. Laparoscopic colectomy became the standard surgical technique in 1991. With innovation in surgical technology, single incision laparoscopy (SIL) has attracted more attention as the possible next step in colorectal resection. The aim of this review was to compare outcomes between SIL and conventional laparoscopy (CL).

METHODS

A literature search was carried out in accordance with the PRISMA (Preferred Reporting Items for Systematic reviews and Meta-Analyses) guidelines. The PubMed®, MEDLINE®, Embase®, Google Scholar™ and Cochrane Library databases were used to extract randomised controlled trials (RCTs) published between January 2000 and May 2021. Statistical analysis was performed with RevMan software.

RESULTS

A total of 11 RCTs were extracted with 1,370 patients (686 SIL, 684 CL). There was no significant difference between SIL and CL for operative time (standardised mean difference [SMD]: 0.01, 95% confidence interval [CI]: -0.19 to 0.22, z=0.11, p=0.91), length of hospital stay (SMD: -0.10, 95% CI: 0.22 to 0.02, z=1.61, p=0.11) or overall complications (odds ratio [OR]: 0.99, 95% CI: 0.75 to 1.30, z=0.09, p=0.93). SIL had a shorter mean incision (SMD: -0.99, 95% CI: -1.35 to -0.62, z=5.25, p<0.00001). Patients undergoing SIL had a higher conversion rate to CL or an open approach (OR: 3.10, 95% CI: 0.95 to 10.14, z=1.87, p=0.06) but this just missed statistical significance.

CONCLUSIONS

SIL can be considered a safe alternative to CL if performed by experienced surgeons.

Critical evaluation of the reliability of DNA methylation probes on the Illumina MethylationEPIC BeadChip microarrays

DNA methylation (DNAm) plays a crucial role in a number of complex diseases. However, the reliability of DNAm levels measured using Illumina arrays varies across different probes. Previous research primarily assessed probe reliability by comparing duplicate samples between the 450k-450k or 450k-EPIC platforms, with limited investigations on Illumina EPIC arrays. We conducted a comprehensive assessment of the EPIC array probe reliability using 138 duplicated blood DNAm samples generated by the Alzheimer's Disease Neuroimaging Initiative study. We introduced a novel statistical measure, the modified intraclass correlation, to better account for the disagreement in duplicate measurements. We observed higher reliability in probes with average methylation beta values of 0.2 to 0.8, and lower reliability in type I probes or those within the promoter and CpG island regions. Importantly, we found that probe reliability has significant implications in the analyses of Epigenome-wide Association Studies (EWAS). Higher reliability is associated with more consistent effect sizes in different studies, the identification of differentially methylated regions (DMRs) and methylation quantitative trait locus (mQTLs), and significant correlations with downstream gene expression. Moreover, blood DNAm measurements obtained from probes with higher reliability are more likely to show concordance with brain DNAm measurements. Our findings, which provide crucial reliable information for probes on the EPIC array, will serve as a valuable resource for future DNAm studies.

Critical evaluation of the reliability of DNA methylation probes on the Illumina MethylationEPIC BeadChip microarrays

DNA methylation (DNAm) plays a crucial role in a number of complex diseases. However, the reliability of DNAm levels measured using Illumina arrays varies across different probes. Previous research primarily assessed probe reliability by comparing duplicate samples between the 450k-450k or 450k-EPIC platforms, with limited investigations on Illumina EPIC arrays. We conducted a comprehensive assessment of the EPIC array probe reliability using 138 duplicated blood DNAm samples generated by the Alzheimer's Disease Neuroimaging Initiative study. We introduced a novel statistical measure, the modified intraclass correlation, to better account for the disagreement in duplicate measurements. We observed higher reliability in probes with average methylation beta values of 0.2 to 0.8, and lower reliability in type I probes or those within the promoter and CpG island regions. Importantly, we found that probe reliability has significant implications in the analyses of Epigenome-wide Association Studies (EWAS). Higher reliability is associated with more consistent effect sizes in different studies, the identification of differentially methylated regions (DMRs) and methylation quantitative trait locus (mQTLs), and significant correlations with downstream gene expression. Moreover, blood DNAm measurements obtained from probes with higher reliability are more likely to show concordance with brain DNAm measurements. Our findings, which provide crucial reliable information for probes on the EPIC array, will serve as a valuable resource for future DNAm studies.

Distinct CSF biomarker-associated DNA methylation in Alzheimer's disease and cognitively normal subjects

BACKGROUND

Growing evidence has demonstrated that DNA methylation (DNAm) plays an important role in Alzheimer's disease (AD) and that DNAm differences can be detected in the blood of AD subjects. Most studies have correlated blood DNAm with the clinical diagnosis of AD in living individuals. However, as the pathophysiological process of AD can begin many years before the onset of clinical symptoms, there is often disagreement between neuropathology in the brain and clinical phenotypes. Therefore, blood DNAm associated with AD neuropathology, rather than with clinical data, would provide more relevant information on AD pathogenesis.

METHODS

We performed a comprehensive analysis to identify blood DNAm associated with cerebrospinal fluid (CSF) pathological biomarkers for AD. Our study included matched samples of whole blood DNA methylation, CSF Aβ₄₂, phosphorylated tau₁₈₁ (pTau₁₈₁), and total tau (tTau) biomarkers data, measured on the same subjects and at the same clinical visits from a total of 202 subjects (123 CN or cognitively normal, 79 AD) in the Alzheimer's Disease Neuroimaging Initiative (ADNI) cohort. To validate our findings, we also examined the association between premortem blood DNAm and postmortem brain neuropathology measured on a group of 69 subjects in the London dataset.

RESULTS

We identified a number of novel associations between blood DNAm and CSF biomarkers, demonstrating that changes in pathological processes in the CSF are reflected in the blood epigenome. Overall, the CSF biomarker-associated DNAm is relatively distinct in CN and AD subjects, highlighting the importance of analyzing omics data measured on cognitively normal subjects (which includes preclinical AD subjects) to identify diagnostic biomarkers, and considering disease stages in the development and testing of AD treatment strategies. Moreover, our analysis revealed biological processes associated with early brain impairment relevant to AD are marked by DNAm in the blood, and blood DNAm at several CpGs in the DMR on HOXA5 gene are associated with pTau₁₈₁ in the CSF, as well as tau-pathology and DNAm in the brain, nominating DNAm at this locus as a promising candidate AD biomarker.

CONCLUSIONS

Our study provides a valuable resource for future mechanistic and biomarker studies of DNAm in AD.

Distinct CSF biomarker-associated DNA methylation in Alzheimer's disease and cognitively normal subjects

Background Growing evidence has demonstrated that DNA methylation (DNAm) plays an important role in Alzheimer's disease (AD) and that DNAm differences can be detected in the blood of AD subjects. Most studies have correlated blood DNAm with the clinical diagnosis of AD in living individuals. However, as the pathophysiological process of AD can begin many years before the onset of clinical symptoms, there is often disagreement between neuropathology in the brain and clinical phenotypes. Therefore, blood DNAm associated with AD neuropathology, rather than with clinical data, would provide more relevant information on AD pathogenesis. Methods We performed a comprehensive analysis to identify blood DNAm associated with cerebrospinal fluid (CSF) pathological biomarkers for AD. Our study included matched samples of whole blood DNA methylation, CSF Aβ ₄₂ , phosphorylated tau ₁₈₁ (pTau ₁₈₁ ), and total tau (tTau) biomarkers data, measured on the same subjects and at the same clinical visits from a total of 202 subjects (123 CN or cognitively normal, 79 AD) in the Alzheimer's Disease Neuroimaging Initiative (ADNI) cohort. To validate our findings, we also examined the association between premortem blood DNAm and postmortem brain neuropathology measured on a group of 69 subjects in the London dataset. Results We identified a number of novel associations between blood DNAm and CSF biomarkers, demonstrating that changes in pathological processes in the CSF are reflected in the blood epigenome. Overall, the CSF biomarker-associated DNAm is relatively distinct in CN and AD subjects, highlighting the importance of analyzing omics data measured on cognitively normal subjects (which includes preclinical AD subjects) to identify diagnostic biomarkers, and considering disease stages in the development and testing of AD treatment strategies. Moreover, our analysis revealed biological processes associated with early brain impairment relevant to AD are marked by DNAm in the blood, and blood DNAm at several CpGs in the DMR on HOXA5 gene are associated with pTau ₁₈₁ in the CSF, as well as tau-pathology and DNAm in the brain, nominating DNAm at this locus as a promising candidate AD biomarker. Conclusions Our study provides a valuable resource for future mechanistic and biomarker studies of DNAm in AD.

Enhancement of Xanthan Biosynthesis Using Medicinal Herbs - A Novel Approach

This study aimed to evaluate the potential of five medicinal herbs in the enhancement of xanthan gum production when used against indigenously isolated (from molasses, an agricultural waste) phytopathogen Xanthomonas campestris MW741556. Antibiotic susceptibility of five medicinal herbs (Moringa oleifera, Bacopa monnieri, Glycyrrhiza glabra, Withania somnifera, and Arthrospira platensis) against X. campestris culture was first checked. All five herbs exhibited a clear zone of inhibition against X. campestris during the investigation. Thereafter their effect on enhancing the xanthan gum production was studied using molasses enriched medium. The results of this experiment showed that all five herbs were capable of enhancing xanthan gum production significantly. Xanthan gum produced differed in viscosity and dried biomass. Among all, A. platensis and M. oleifera were found to be the most promising for xanthan gum production with higher viscosity. These results were further confirmed by the characterization of xanthan gum produced by five herbs using Fourier Transform Infrared Spectroscopy. Further, a multivariate approach using principal component analysis confirmed the variability among the herbs used. This versatility of these medicinal herbs opens the possibility of their utilization and application in various fields.

Distinct sex-specific DNA methylation differences in Alzheimer's disease

BACKGROUND

Sex is increasingly recognized as a significant factor contributing to the biological and clinical heterogeneity in AD. There is also growing evidence for the prominent role of DNA methylation (DNAm) in Alzheimer's disease (AD).

METHODS

We studied sex-specific DNA methylation differences in the blood samples of AD subjects compared to cognitively normal subjects, by performing sex-specific meta-analyses of two large blood-based epigenome-wide association studies (ADNI and AIBL), which included DNA methylation data for a total of 1284 whole blood samples (632 females and 652 males). Within each dataset, we used two complementary analytical strategies, a sex-stratified analysis that examined methylation to AD associations in male and female samples separately, and a methylation-by-sex interaction analysis that compared the magnitude of these associations between different sexes. After adjusting for age, estimated immune cell type proportions, batch effects, and correcting for inflation, the inverse-variance fixed-effects meta-analysis model was used to identify the most consistent DNAm differences across datasets. In addition, we also evaluated the performance of the sex-specific methylation-based risk prediction models for AD diagnosis using an independent external dataset.

RESULTS

In the sex-stratified analysis, we identified 2 CpGs, mapped to the PRRC2A and RPS8 genes, significantly associated with AD in females at a 5% false discovery rate, and an additional 25 significant CpGs (21 in females, 4 in males) at P-value < 1×10^-5. In methylation-by-sex interaction analysis, we identified 5 significant CpGs at P-value < 10^-5. Out-of-sample validations using the AddNeuroMed dataset showed in females, the best logistic prediction model included age, estimated immune cell-type proportions, and methylation risk scores (MRS) computed from 9 of the 23 CpGs identified in AD vs. CN analysis that are also available in AddNeuroMed dataset (AUC = 0.74, 95% CI: 0.65-0.83). In males, the best logistic prediction model included only age and MRS computed from 2 of the 5 CpGs identified in methylation-by-sex interaction analysis that are also available in the AddNeuroMed dataset (AUC = 0.70, 95% CI: 0.56-0.82).

CONCLUSIONS

Overall, our results show that the DNA methylation differences in AD are largely distinct between males and females. Our best-performing sex-specific methylation-based prediction model in females performed better than that for males and additionally included estimated cell-type proportions. The significant discriminatory classification of AD samples with our methylation-based prediction models demonstrates that sex-specific DNA methylation could be a predictive biomarker for AD. As sex is a strong factor underlying phenotypic variability in AD, the results of our study are particularly relevant for a better understanding of the epigenetic architecture that underlie AD and for promoting precision medicine in AD.

Cross-tissue analysis of blood and brain epigenome-wide association studies in Alzheimer's disease

To better understand DNA methylation in Alzheimer's disease (AD) from both mechanistic and biomarker perspectives, we performed an epigenome-wide meta-analysis of blood DNA methylation in two large independent blood-based studies in AD, the ADNI and AIBL studies, and identified 5 CpGs, mapped to the SPIDR, CDH6 genes, and intergenic regions, that are significantly associated with AD diagnosis. A cross-tissue analysis that combined these blood DNA methylation datasets with four brain methylation datasets prioritized 97 CpGs and 10 genomic regions that are significantly associated with both AD neuropathology and AD diagnosis. An out-of-sample validation using the AddNeuroMed dataset showed the best performing logistic regression model includes age, sex, immune cell type proportions, and methylation risk score based on prioritized CpGs in cross-tissue analysis (AUC = 0.696, 95% CI: 0.616 - 0.770, P-value = 2.78 × 10^-5). Our study offers new insights into epigenetics in AD and provides a valuable resource for future AD biomarker discovery.

Bilateral ganglion cysts at L4/5 causing central canal stenosis and producing sciatica and neurogenic claudication: a case report

Symptomatic bilateral juxtafacet ganglion cysts are relatively uncommon in the degenerated spine. The literature describes 16 cases of bilateral ganglion or synovial cysts, none reported sciatica and neurogenic claudication simultaneously. We present a case of a 60-year-old woman who presented with symptoms of bilateral sciatica and neurogenic claudication. Magnetic resonance imaging of the lumbar spine revealed bilateral lesions related to the facet joints at the L4/5 level, causing bilateral lateral recess stenosis and narrowing of the central canal due to encroachment of these bilateral lesions at the same level. She underwent an elective central canal decompression of the L4/5 level and excision of the facet cysts bilaterally with lateral recess decompression, which resulted in good relief of both the radicular and claudication symptoms.

Bilateral ganglion cysts at L4/5 causing central canal stenosis and producing sciatica and neurogenic claudication: a case report

Symptomatic bilateral juxtafacet ganglion cysts are relatively uncommon in the degenerated spine. The literature describes 16 cases of bilateral ganglion or synovial cysts, none reported sciatica and neurogenic claudication simultaneously. We present a case of a 60-year-old woman who presented with symptoms of bilateral sciatica and neurogenic claudication. Magnetic resonance imaging of the lumbar spine revealed bilateral lesions related to the facet joints at the L4/5 level, causing bilateral lateral recess stenosis and narrowing of the central canal due to encroachment of these bilateral lesions at the same level. She underwent an elective central canal decompression of the L4/5 level and excision of the facet cysts bilaterally with lateral recess decompression, which resulted in good relief of both the radicular and claudication symptoms.

Treatment tolerability and outcomes in elderly patients with head and neck cancer

PURPOSE

The number of elderly patients with head and neck squamous cell carcinoma (HNSCC) continues to grow. Management of this cohort remains poorly defined. We investigated treatment tolerability and clinical outcomes in this underrepresented population.

METHODS

We identified patients aged ≥70 with nonrecurrent, nonmetastatic HNSCC treated curatively from 2007-2018 and analyzed clinical covariates.

RESULTS

Two hundred and twenty patients with a median age of 75 (interquartile range:72-80) were identified. Age and comorbidities were not correlated with toxicity (P ≥ .05). Patients who experienced a treatment interruption had significantly greater weight loss (P = .042) and worse overall survival (OS) (P < .001), but not worse disease-specific survival (P = .45), or locoregional control (P = .21).

CONCLUSIONS

Treatment interruptions were associated with weight loss and worse OS, but not disease related outcomes, suggesting an interruption in the elderly may be a surrogate for another issue. In sum, our data should guide clinical trial design to benefit this growing, neglected cohort.

Research protocol of two concurrent cluster-randomized trials: Real-life Effect of a CAMPaign with Measles Vaccination (RECAMP-MV) and Real-life Effect of a CAMPaign with Oral Polio Vaccination (RECAMP-OPV) on mortality and morbidity among children in rural Guinea-Bissau

BACKGROUND

Measles and oral polio vaccinations may reduce child mortality to an extent that cannot be explained by prevention of measles and polio infections; these vaccines seem to have beneficial non-specific effects. In the last decades, billions of children worldwide have received measles vaccine (MV) and oral polio vaccine (OPV) through campaigns. Meanwhile the under-five child mortality has declined. Past MV and OPV campaigns may have contributed to this decline, even in the absence of measles and polio infections. However, cessation of these campaigns, once their targeted infections are eradicated, may reverse the decline in the under-five child mortality. No randomized trial has assessed the real-life effect of either campaign on child mortality and morbidity. We present the research protocol of two concurrent trials: RECAMP-MV and RECAMP-OPV.

METHODS

Both trials are cluster-randomized trials among children registered in Bandim Health Project's rural health and demographic surveillance system throughout Guinea-Bissau. RECAMP-MV is conducted among children aged 9-59 months and RECAMP-OPV is conducted among children aged 0-8 months. We randomized 222 geographical clusters to intervention or control clusters. In intervention clusters, children are offered MV or OPV (according to age at enrolment) and a health check-up. In control clusters, children are offered only a health check-up. Enrolments began in November 2016 (RECAMP-MV) and March 2017 (RECAMP-OPV). We plan 18,000 enrolments for RECAMP-MV with an average follow-up period of 18 months and 10,000 enrolments for RECAMP-OPV with an average follow-up period of 10 months. Data collection is ongoing. The primary outcome in both trials is non-accidental death or non-accidental first non-fatal hospitalization with overnight stay (composite outcome). Secondary outcomes are: non-accidental death, repeated non-fatal hospitalizations with overnight stay, cause-specific primary outcome, outpatient visit, and illness. We obtained ethical approval from Guinea-Bissau and consultative approval from Denmark.

DISCUSSION

Cluster randomization and minimum risk of loss to follow-up are strengths, and no placebo a limitation. Our trials challenge the understanding that MV and OPV only prevent measles and polio, and that once both infections are eradicated, campaigns with MV and OPV can be phased out without negative implications on child health and survival.

TRIAL REGISTRATION

NCT03460002.

Erratum to: 36th International Symposium on Intensive Care and Emergency Medicine: Brussels, Belgium. 15-18 March 2016

[This corrects the article DOI: 10.1186/s13054-016-1208-6.].

Putative bacterial volatile-mediated growth in soybean (Glycine max L. Merrill) and expression of induced proteins under salt stress

AIMS

Plant root-associated rhizobacteria elicit plant immunity referred to as induced systemic tolerance (IST) against multiple abiotic stresses. Among multibacterial determinants involved in IST, the induction of IST and promotion of growth by putative bacterial volatile compounds (VOCs) is reported in the present study.

METHODS AND RESULTS

To characterize plant proteins induced by putative bacterial VOCs, proteomic analysis was performed by MALDI-MS/MS after exposure of soybean seedlings to a new strain of plant growth promoting rhizobacteria (PGPR) Pseudomonas simiae strain AU. Furthermore, expression analysis by Western blotting confirmed that the vegetative storage protein (VSP), gamma-glutamyl hydrolase (GGH) and RuBisCo large chain proteins were significantly up-regulated by the exposure to AU strain and played a major role in IST. VSP has preponderant roles in N accumulation and mobilization, acid phosphatase activity and Na(+) homeostasis to sustain plant growth under stress condition. More interestingly, plant exposure to the bacterial strain significantly reduced Na(+) and enhanced K(+) and P content in root of soybean seedlings under salt stress. In addition, high accumulation of proline and chlorophyll content also provided evidence of protection against osmotic stress during the elicitation of IST by bacterial exposure.

CONCLUSIONS

The present study reported for the first time that Ps. simiae produces a putative volatile blend that can enhance soybean seedling growth and elicit IST against 100 mmol l(-1) NaCl stress condition.

SIGNIFICANCE AND IMPACT OF THE STUDY

The identification of such differentially expressed proteins provide new targets for future studies that will allow assessment of their physiological roles and significance in the response of glycophytes to stresses. Further work should uncover more about the chemical side of VOC compounds and a detailed study about their molecular mechanism responsible for plant growth.

Clinical assessment of the sensory ataxias; diagnostic algorithm with illustrative cases

Ataxia is a common neurological syndrome resulting from cerebellar, vestibular or sensory disorders. The recognition and characterisation of sensory ataxia remains a challenge. Cerebellar ataxia is the more common and easier to identify; sensory ataxia is often mistaken for cerebellar ataxia, leading to diagnostic errors and delays. A coherent aetiological work-up is only possible if clinicians initially recognise sensory ataxia. We discuss ways to separate sensory from cerebellar ataxia, the causes of sensory ataxia and the clinico-neurophysiological syndromes causing the sensory ataxia syndromes. We summarise a logical tiered approach as a diagnostic algorithm.

Parametric sensitivity of stoichiometric flux balance models applied to wild-type Escherichia coli metabolism

Stoichiometrically based flux balance models provide a method to quantify the metabolic pathway fluxes within a living cell. Predictions of flux balance models are expected to have applications in pathway engineering as well as in bioprocess design and control. These models utilize optimality principles applied to metabolic pathway stoichiometry along with the metabolic requirements for growth to determine the flux distribution in a metabolic network. A flux balance model has been developed for Escherichia coli W3110 using five experimentally determined strain-specific parameters. In this report, we determine the sensitivity of the predictions of the flux balance model to these five strain-specific parameters. Model predictions are shown to be sensitive to the two parameters describing metabolic capacity, while they are relatively insensitive to the three parameters that describe the metabolic requirements for growth. Thus, when stoichiometrically based models are formulated for additional strains one needs to measure the metabolic capacity (maximum rates of nutrient and oxygen utilization) accurately. Determination of metabolic capacity from batch experiments is relatively easy to perform. On the other hand, the harder to determine maintenance parameters need not be as accurately determined. (c) 1995 John Wiley & Sons, Inc.

Determinants of in-hospital death after acute spinal cord injury: a population-based study

OBJECTIVES

First, to evaluate the influence of comorbid diseases and concomitant injuries on the risk of in-hospital death after traumatic spinal cord injury (TSCI). Second, to identify the risk characteristics of TSCI patients with likelihood of death.

STUDY DESIGN

Population-based retrospective cohort study.

SETTING

Sixty-two acute care hospitals in South Carolina, USA.

METHODS

Records of 3389 TSCI patients hospitalized with acute TSCI were evaluated. Days elapsing from the date of injury to date of death established the survival time (T). Cox regression examined risk of in-hospital death as a function of counts of comorbid conditions and injuries along with their joint effects controlling for other covariates.

RESULTS

Counts of comorbid conditions and injuries showed dose-dependent risk of death while in-hospital independent of demographical and clinical covariates. Hazard ratios (HR) for counts 3+, 2 and 1 comorbid conditions were 2.19 (P<0.001), 1.73 (P=0.005) and 1.20 (P=0.322), respectively. For counts of 4+, 3 and 2 other injuries were 1.85 (P<0.001), 1.81 (P<0.001) and 1.46 (P=0.022), respectively. The joint effect of the two was transadditive with statistically significant HR ranging from 1.72-3.14.

CONCLUSION

Counts of comorbid conditions and injured body regions strongly indicate risk of in-hospital death after TSCI and their joint effects elicited dose-dependent gradient independent of demographical and clinical covariates. Assessing risk of in-hospital death based on joint use of counts of comorbid diseases and injuries is highly informative to target TSCI patients at high risk of dying.

Evidence of the Association of Radish leaf curl virus with Tobacco Yellow Leaf Curl Disease in Bihar, India

A new disease of tobacco with characteristic mild leaf curl and yellowing symptoms was observed in 2007 in commercial plantings in Pusa, Bihar, India. A begomovirus and a betasatellite were found associated with the disease. The associated begomovirus was identified as a strain of Radish leaf curl virus (RaLCV) based on nucleotide sequence of the viral genome (2,761 nucleotides; EU194914). The betasatellite (HQ180397) associated with TbYLCD was identified as a variant of Chilli leaf curl betasatellite (ChLCB). Recombination events were detected both in the RaLCV and ChLCB sequences. This is the first report of yellow leaf curl disease of tobacco, and the association of RaLCV with a disease of tobacco.

Autoimmune encephalitis: a case series and comprehensive review of the literature

Encephalitic syndromes are a common medical emergency. The importance of early diagnosis and appropriate treatment is paramount. If initial investigations for infectious agents prove negative, other diagnoses must be considered promptly. Autoimmune encephalitides are being increasingly recognized as important (and potentially reversible) non-infectious causes of an encephalitic syndrome. We describe four patients with autoimmune encephalitis--3 auto-antibody positive, 1 auto-antibody negative--treated during the last 18 months. A comprehensive review of the literature in this expanding area will be of interest to the infectious diseases, general medical and neurology community.

Molecular characterization of Tobacco leaf curl Pusa virus, a new monopartite Begomovirus associated with tobacco leaf curl disease in India

Leaf curl disease of tobacco (TbLCD) is endemic in India. A monopartite Begomovirus, a betasatellite and an alphasatellite were found associated with the disease in Pusa, Bihar. The DNA-A of the Begomovirus associated with TbLCD in Pusa, Bihar was found to comprise of 2707 nt with a typical Old World begomovirus-like genome organization. The full-length sequence of DNA-A [HQ180391] showed that the Pusa isolate is a newly described member of the genus Begomovirus, as it had <89% sequence homology with DNA-A of all the known begomoviruses. The isolate is tentatively named as Tobacco leaf curl Pusa virus [India:Pusa:2010]. The betasatellite (HQ180395) associated with TbLCD in Pusa was identified as a variant of Tomato leaf curl Bangladesh betasatellite [IN:Raj:03], with which it shared 90.4% sequence identity. The alphasatellite (HQ180392) associated with the disease had highest 87% nucleotide sequence identity with Tomato leaf curl alphasatellite. The Begomovirus, betasatellite, and alphasatellite associated with TbLCD in Pusa, Bihar, India were found to be recombinants of extant begomoviruses, betasatellites and alphasatellites spreading in the Indian sub-continent and South-East Asia.

Diversity of Apple mosaic virus Isolates in India Based on Coat Protein and Movement Protein Genes

Apple mosaic virus (ApMV), an Ilarvirus is one of the most common pathogens of apple worldwide. During field surveys in commercial plantations of Himachal Pradesh and Jammu & Kashmir, observations of bright chlorotic mosaic like symptoms on apple trees indicated probable infection by the virus, which was later detected by double antibody sandwich-enzyme linked immunosorbent assay (DAS-ELISA). An incidence of 24 and 28% (based on ELISA) was obtained as 6/25 and 15/53 samples from HP and J&K were positive, respectively. An amplification of approximately 700 and 850 bp was obtained for coat and movement protein genes (CP and MP), respectively. The CP was 223 amino acids in length and showed 87-99% identity when compared to 21 ApMV isolates. Whereas, MP (286 amino acids) showed 91-95% identity with other isolates. However, the gene sequences were quite conserved among Indian isolates and grouped together phylogenetically. CP of the Indian isolates showed maximum identity of 95% with Korean isolate (AY 125977) in apple and in other host these showed a maximum identity of 98% to Czech Republic pear isolate. MP showed maximum identity with Chinese isolate i.e., 95%. The diversity study will also help in analyzing variability among the isolates and also to formulate diagnostic and resistance strategies.

Metabolic capabilities of Escherichia coli: I. synthesis of biosynthetic precursors and cofactors

Metabolism of living cells converts substrates into metabolic energy, redox potential and metabolic end products that are essential to maintain cellular function. The flux distribution among the various biochemical pathways is determined by the kinetic properties of enzymes which are subject to strict regulatory control. Simulation of metabolic behavior therefore requires the complete knowledge of biochemical pathways, enzyme kinetics as well as their regulation. Unfortunately, complete kinetic and regulatory information is not available for microbial cells, thus preventing accurate dynamic simulation of their metabolic behavior. However, it is possible to define wider limits on metabolic behavior based solely on flux balances of biochemical pathways. We present here comprehensive information about the catabolic pathways of the bacterium Escherichia coli. Using this biochemical database, we formulate a stoichiometric model of the bacterial network of fueling reactions. After logical structural reduction, the network consists of 53 metabolic fluxes and 30 metabolites. The solution space of this under-determined system of equations presents the bounds of metabolic flux distribution that the bacterial cell can achieve. We use specific objective functions and linear optimization to investigate the capability of E. coli catabolism to maximally produce the 12 biosynthetic precursors and three key cofactors within this solution space. For the three cofactors, the maximum yields are calculated to be 18.67 ATP, 11.6 NADH and 11 NADPH per glucose molecule, respectively. The yields of NADH and NADPH are less than 12 owing to the energy costs of importing glucose. These constraints are made explicit by the interpretation of shadow prices. The optimal yields of the 12 biosynthetic precursors are computed. Four of the 12 precursors (3-phosphoglycerate, phosphoenolpyruvate, pyruvate and oxaloacetate) can be made by E. coli with complete carbon conversion. Conversely, none of the sugar monophosphates can be made with 100% carbon conversion and analysis of the shadow prices reveals that this conversion is constrained by the energy cost of importing glucose. Three of the 12 precursors (acetyl-coA, α-ketoglutarate, and succinyl-coA) cannot be made with full carbon conversion owing to stoichiometric constraints; there is no route to these compounds without carrying out a decarboxylation reaction. Metabolite flux balances and linear optimization have thus been used to determine the catabolic capabilities of E. coli .

Photoluminescent nano-sized ternary and quaternary complexes of thorium(IV)

Some ternary and quaternary complexes of thorium(IV) with the general formula [Th(OOCCH3)2−n (SB) n (OOCC15H31)2] (HSB=Schiff bases and n=1 or 2) have been synthesized by the stepwise substitutions of acetate ions from thorium(IV) acetate, first with straight chain carboxylic acid and then with Schiff bases. The complexes are characterized by elemental analyses, spectral (electronic, infrared, 1H NMR, FAB mass, photoluminescence and powder XRD) and TEM studies. Conductance measurements indicated non-conducting behaviour of the complexes. Structural parameters from powder XRD data for complexes 5 and 6 which indicate poorly crystalline nano-sized triclinic particles. Electronic absorption spectra of the complexes showed π→π * and n→π * charge transfer transitions. All complexes displayed fluorescence and a correlation was sought between luminescence spectra of complexes in solution at room temperature. On the basis of physico-chemical studies, coordination number 8 was assigned for thorium(IV) in the complexes. The morphology and microstructure of the complexes were examined with transmission electron microscopy (TEM) and the selected area electron diffraction (SAED).

Biochemical production capabilities of Escherichia coli

Microbial metabolism provides at mechanism for the conversion of substrates into useful biochemicals. Utilization of microbes in industrial processes requires a modification of their natural metabolism in order to increase the efficiency of the desired conversion. Redirection of metabolic fluxes forms the basis of the newly defined field of metabolic engineering. In this study we use a flux balance based approach to study the biosynthesis of the 20 amino acids and 4 nucleotides as biochemical products. These amino acids and nucleotides are primary products of biosynthesis as well as important industrial products and precursors for the production of other biochemicals. The biosynthetic reactions of the bacterium Escherichia coli have been formulated into a metabolic network, and growth has been defined as a balanced drain on the metabolite pools corresponding to the cellular composition. Theoretical limits on the conversion of glucose, glycerol, and acetate substrates to biomass as well as the biochemical products have been computed. The substrate that results in the maximal carbon conversion to a particular product is identified. Criteria have been developed to identify metabolic constraints in the optimal solutions. The constraints of stoichiometry, energy, and redox have been determined in the conversions of glucose, glycerol, and acetate substrates into the biochemicals. Flux distributions corresponding to the maximal production of the biochemicals are presented. The goals of metabolic engineering are the optimal redirection of fluxes from generating biomass toward producing the desired biochemical. Optimal biomass generation is shown to decrease in a piecewise linear manner with increasing product formation. In some cases, synergy is observed between biochemical production and growth, leading to an increased overall carbon conversion. Balanced growth and product formation are important in a bioprocess, particularly for nonsecreted products.