Prevalence of Hepatitis B and C Viral Markers in Blood Donors Deferred from Donating Blood on the Basis of a History of Jaundice of Unknown Origin

BACKGROUND AND AIMS

The aim of the present study was to know the prevalence of viral hepatitis markers among blood donors deferred on the basis of a history of jaundice of unknown origin and to predict the impact of this deferral on blood safety.

METHODS

Observational study included 200 blood donors deferred on the basis of a history of jaundice of unknown origin and carried out serology and Individual Donation Nucleic Acid Testing (ID-NAT) for hepatitis B and hepatitis C.

RESULTS

Five (2.5%) out of 200 blood donors deferred on the basis of history of jaundice were reactive on ELISA. Three out of five were reactive for HBsAg; whereas two for anti-HCV antibodies. Out of the 12 ID-NAT initial reactive, 10 samples discriminated on further testing; 4 for HBV, 5 for HCV and 1 was co-infection (HBV + HCV). The odds of being picked up as sero reactive on ELISA was 2.53 (95% CI; 1.04-6.19) and being picked up as ID-NAT yield was 13.08 (95% CI; 5.29-32.37) in donors deferred on a history of jaundice of unknown origin as compared to selected donors without a history of jaundice, with the difference in means achieving statistically significance at P = 0.03 and <0.001 respectively.The potential of deferral on a history of jaundice of unknown origin has a capacity to interdict 2-3 HBV and/or HCV reactive blood donors on serology and 5 HBV and/or HCV reactive blood donors on ID-NAT from entering the quarantine blood supply per 100 donors.

CONCLUSION

The findings of the present study support that a deferral for a history of jaundice of unknown origin after attaining the age of 12 years in the present scenario of transfusion transmissible infectious disease screening in India.

Curcumin's antiepileptic effect, and alterations in Nav1.1 and Nav1.6 expression in iron-induced epilepsy

The present study was carried out to evaluate: the antiepileptic effect of dietary curcumin, and the effect of epileptic state and curcumin on the molecular expression of voltage-activated Na⁺ channel subtypes Na_v1.1 and Na_v1.6 in the iron-induced experimental epilepsy in the rat. Rats were divided into four groups; Group I (control rats), Group II (epileptic rats), Group III (curcumin-fed epileptic rats), and Group IV (curcumin-fed rats). Curcumin was fed chronically to rats approximately at the dose of 100 mg/kg body wt. The animals were made epileptic by intracortical injection of FeCl_3. The mRNA and protein expressions of Na_v1.1 and Na_v1.6 were examined by RT-PCR analysis and immuno-histochemistry. Results showed a significant increase (upregulation) in the expression of both Na_v1.1 and Na_v1.6 with seizure activity in the cortex and hippocampus of epileptic rats. Epileptic rats fed with curcumin showed a marked decrease in epileptiform activity, and reduced mRNA and protein levels of Na_v1.1. It appears that the antiepileptic action of curcumin may be associated with the downregulation of Na_v1.1 in the cortex.

Chemical Modification and Performance Evaluation of an Agro-Waste for Column Mode Removal of Textile Dyes

The performance of a newly designed column bed device packed with chemically modified agro-waste (sugarcane bagasse) is evaluated for efficient removal of two textile dyes, Optilan yellow and Lanasyn brown and textile industry dye effluent. The parameters used for performance evaluation are removal efficiency (R%), adsorption capacity (q), and breakthrough (C e/C 0). The column exhibits >90% removal of both the dyes and >80% removal of textile industry dye effluent. The experimental data are fitted to three models, viz., Thomas, Adams-Bohart, and Yoon-Nelson for understanding the kinetic behavior of adsorption. The results reveal that the Yoon-Nelson model is the best-fitted model for both the dyes with R 2 values 0.995 and 0.905 for Optilan yellow and Lanasyn brown, respectively. However, Thomas and Yoon-Nelson fit the best for textile industry effluent. Overall, this investigation provides baseline information about the column mode removal of textile dyes using the agro-waste material as an adsorbent. The Fourier transform infrared spectroscopy spectra show the characteristic vibrational mode of C-H stretching of hydroxyl group around 2800-3000 cm-1. The change in the vibrational pattern is evident after alginic acid treatment, indicating delignification of the bagasse after treatment.

Immunization with Salmonella Abortusequi phage lysate protects guinea pig against the virulent challenge of SAE-742

Salmonella Abortusequi causes important clinical diseases in horses possibly leading to abortion. In the present investigation, the protective efficacy of both plain and aluminum hydroxide gel adjuvanted phage lysate was evaluated in guinea pig model. Broad host range bacteriophage P_IZ-SAE-2, was characterized and used for generation of lysates. Three different lysate batches, produced through separate cycles and characterized, were pooled together for immunization study. Plain and adjuvanted phage lysate preparations elicited both humoral and cellmediated immunity. The adjuvanted lysate at a dose of 50 μl elicited the highest protective efficacy against direct challenge at 28th DPI. Thus, the present study describes a new method of bacterial inactivation for producing a new class of better & safe immunprophylactic agents. This is the first report of producing an inactivated vaccine candidate using a new approach against equine salmonellosis.

Development of a Novel Proteomic Risk-Classifier for Prognostication of Patients With Early-Stage Hormone Receptor-Positive Breast Cancer

Use of proteomic strategies to identify a risk classifier that estimates probability of distant recurrence in early-stage hormone receptor (HR)-positive breast cancer is relevant to physiological cellular function and therefore to intrinsic tumor biology. We used a 298-sample retrospective training set to develop an immunohistochemistry-based novel risk classifier called CanAssist-Breast (CAB) which combines 5 prognostically relevant biomarkers and 3 clinico-pathological parameters to arrive at probability of distant recurrence within 5 years from diagnosis. Five selected biomarkers, namely, CD44, ABCC4, ABCC11, N-cadherin, and pan-cadherin, were chosen based on their role in tumor metastasis. The chosen biomarkers represent the hallmarks of cancer and are distinct from other proliferation and gene expression-based prognostic signatures. The 3 clinico-pathological parameters integrated into the machine learning-based CAB algorithm are tumor size, tumor grade, and node status. These features are used to calculate a "CAB risk score" that classifies patients into low- or high-risk groups and predicts probability of distant recurrence in 5 years. Independent clinical validation of CAB in a retrospective study comprising 196 patients indicated that distant metastasis-free survival (DMFS) was significantly different in the 2 risk groups. The difference in DMFS between the low- and high-risk categories was 19% in the validation cohort (P = .0002). In multivariate analysis, CAB risk score was the most significant independent predictor of distant recurrence with a hazard ratio of 4.3 (P = .0003). CanAssist-Breast is a precise and unique machine learning-based proteomic risk-classifier that can assist in risk stratification of patients with early-stage HR+ breast cancer.

Rapid visual isothermal nucleic acid-based detection assay of Brucella species by polymerase spiral reaction

AIM

The aim of this study was to develop polymerase spiral reaction (PSR) for rapid, sensitive and specific detection of Brucella sp.

METHODS AND RESULTS

Polymerase spiral reaction assay was developed using specifically designed primers targeting the conserved multicopy IS711 gene of Brucella sp. The assay could be performed within 60 min at an isothermal temperature of 64°C. The lower limit of detection of PSR was 11·8 fg and conventional PCR was 1·18 pg of Brucella abortus genomic DNA. Thus, PSR was found to be 100-fold more sensitive than conventional PCR and was comparable to real-time PCR. The specificity of PSR was tested with other non-Brucella bacteria and also with some bacterial and viral pathogens causing abortions. The assay was found to be specific as it did not detect any putative pathogens other than Brucella sp. Fifty-six clinical samples suspected for brucellosis (aborted fetal stomach content) were screened with PSR to validate the applicability of the test to detect Brucella DNA. The same samples were also screened with conventional PCR and real-time PCR. Of 56 samples, 25 samples were found to be positive with both PSR as well as real-time PCR, whereas only 20 samples were found positive with conventional PCR.

CONCLUSIONS

The results of this study indicated that the PSR assay is a simple, rapid, sensitive and specific method for the detection of Brucella sp. that may improve diagnostic potential in clinical laboratories or can be used at diagnostic laboratories with minimal infrastructure.

SIGNIFICANCE AND IMPACT OF THE STUDY

The PSR assay, because of its simplicity and low cost, can be preferred to other molecular methods in the diagnosis of infectious diseases.

Evaluation of multiplex polymerase chain reaction as an alternative to conventional antibiotic sensitivity test

Aim

This study was designed to evaluate the potential of the use of multiplex polymerase chain reaction (PCR) as an alternative to conventional antibiotic sensitivity test.

Materials and Methods

Isolates of Staphylococcus aureus (total = 36) from clinical cases presented to Teaching Veterinary Clinical Complex of College of Veterinary and Animal Sciences (CVAS), Navania, Udaipur, were characterized by morphological, cultural, and biochemical methods. Then, the isolates were further subjected to molecular characterization by PCR targeting S. aureus-specific sequence (107 bp). Phenotypic antibiotic sensitivity pattern was analyzed by Kirby-Bauer disc diffusion method against 11 commonly used antibiotics in veterinary medicine in and around Udaipur region. The genotypic antibiotic sensitivity pattern was studied against methicillin, aminoglycosides, and tetracycline targeting the gene mecA, aacA-aphD, and tetK by multiplex PCR.

Results

There was 100% correlation between the phenotype and genotype of aminoglycoside resistance, more than 90% correlation for methicillin resistance, and 58.3% in the case tetracycline resistance.

Conclusion

As there is a good correlation between phenotype and genotype of antibiotic resistance, multiplex PCR can be used as an alternative to the conventional antibiotic susceptibility testing, as it can give a rapid and true prediction of antibiotic sensitivity pattern.

Abstract P3-08-10: Development and validation of a broad-based second generation multi marker “Morphometric IHC” test for optimal treatment planning of stage 1 and 2 breast cancer patients in low resource settings

Aims:

Assessment of 'risk of recurrence' in ER+ breast cancer patients based on clinical parameters and existing hormone receptor signaling pathway and/or proliferation based biomarkers is insufficient, leading to treatment of majority of patients with chemotherapy. First generation risk identification tests like OncotypeDx and Mammaprint are not impactful in India and SE Asia as are largely prognostic with limited chemotherapy-predictivity and are prohibitively expensive. A cost-effective 'predictive' test which will accurately estimate the 'risk of recurrence' for a 'broader' (node - & +) set of breast cancer patients in low resource settings is urgently required.

Materials and Methods:

Using a retrospective training cohort of 300 node– and node+ patients, we developed 'CanAssist-Breast'- a Morphometric Immunohistochemistry based test comprising 5 biomarkers plus three clinical parameters (Tumor size, grade and node status) to arrive at 'CanAssist-Breast Score'. The risk stratification model was developed using cutting edge support vector based machine learning technology. CanAssist-Breast Score stratifies patients into an all actionable 'low or high' risk for recurrence, with no intermediate zone. CanAssist-Breast biomarkers include cancer stem cell markers, Cadherins, and ATP transporter proteins - all critical players in the various steps of chemotherapy resistance leading to metastasis.

Results:

We validated CanAssist-Breast in accordance with EGAPP recommendations which require that prognostic tests be validated both analytically and clinically prior to being utilized in patients. Analytical validation experiments were performed to assess 'variation' in the outcome prediction due to critical IHC variables. We tested inter-pathologists, sample, operator and laboratory site variation and found high concordance in the outcome predictions across all variables, confirming the robustness and reproducibility of the test.

Extended clinical validation on 1000+ pre and post-menopausal cases shows NPV of 95%. The majority of patients in 'low risk' had Stage 2, Grade 2/3 disease over Stage 1, Grade 1 disease, demonstrating that CanAssist-Breast reclassifies patients who would be considered high risk clinically.

In a head-to-head pilot study of 100 patients with Oncotype Dx, CanAssist-Breast test had about 80% concordance with Oncotype in the 'low risk' category. Importantly, CanAssist-Breast correctly stratified few recurred cases as 'high risk' which were called 'low risk' by Oncotype Dx and thus were not treated with chemotherapy.

Conclusion:

In conclusion, we have developed a robust, accurate and low-cost prognostic test to predict risk of recurrence and enable optimal treatment planning in patients with early stage Breast Cancer.

Citation Format: SP S, Bakre MM, Ramkumar C, Basavaraj C, Attuluri A, Madhav L, Prakash C, Naidu N, Malpani S. Development and validation of a broad-based second generation multi marker “Morphometric IHC” test for optimal treatment planning of stage 1 and 2 breast cancer patients in low resource settings [abstract]. In: Proceedings of the 2017 San Antonio Breast Cancer Symposium; 2017 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2018;78(4 Suppl):Abstract nr P3-08-10.

Whole Genome Characterization of a Few EMS-Induced Mutants of Upland Rice Variety Nagina 22 Reveals a Staggeringly High Frequency of SNPs Which Show High Phenotypic Plasticity Towards the Wild-Type

The Indian initiative, in creating mutant resources for the functional genomics in rice, has been instrumental in the development of 87,000 ethylmethanesulfonate (EMS)-induced mutants, of which 7,000 are in advanced generations. The mutants have been created in the background of Nagina 22, a popular drought- and heat-tolerant upland cultivar. As it is a pregreen revolution cultivar, as many as 573 dwarf mutants identified from this resource could be useful as an alternate source of dwarfing. A total of 541 mutants, including the macromutants and the trait-specific ones, obtained after appropriate screening, are being maintained in the mutant garden. Here, we report on the detailed characterizations of the 541 mutants based on the distinctness, uniformity, and stability (DUS) descriptors at two different locations. About 90% of the mutants were found to be similar to the wild type (WT) with high similarity index (>0.6) at both the locations. All 541 mutants were characterized for chlorophyll and epicuticular wax contents, while a subset of 84 mutants were characterized for their ionomes, namely, phosphorous, silicon, and chloride contents. Genotyping of these mutants with 54 genomewide simple sequence repeat (SSR) markers revealed 93% of the mutants to be either completely identical to WT or nearly identical with just one polymorphic locus. Whole genome resequencing (WGS) of four mutants, which have minimal differences in the SSR fingerprint pattern and DUS characters from the WT, revealed a staggeringly high number of single nucleotide polymorphisms (SNPs) on an average (16,453 per mutant) in the genic sequences. Of these, nearly 50% of the SNPs led to non-synonymous codons, while 30% resulted in synonymous codons. The number of insertions and deletions (InDels) varied from 898 to 2,595, with more than 80% of them being 1-2 bp long. Such a high number of SNPs could pose a serious challenge in identifying gene(s) governing the mutant phenotype by next generation sequencing-based mapping approaches such as Mutmap. From the WGS data of the WT and the mutants, we developed a genic resource of the WT with a novel analysis pipeline. The entire information about this resource along with the panicle architecture of the 493 mutants is made available in a mutant database EMSgardeN22 (http://14.139.229.201/EMSgardeN22).

High Resolution Mapping of QTLs for Heat Tolerance in Rice Using a 5K SNP Array

BACKGROUND

Heat stress is one of the major abiotic threats to rice production, next to drought and salinity stress. Incidence of heat stress at reproductive phase of the crop results in abnormal pollination leading to floret sterility, low seed set and poor grain quality. Identification of QTLs and causal genes for heat stress tolerance at flowering will facilitate breeding for improved heat tolerance in rice. In the present study, we used 272 F₈ recombinant inbred lines derived from a cross between Nagina22, a well-known heat tolerant Aus cultivar and IR64, a heat sensitive popular Indica rice variety to map the QTLs for heat tolerance.

RESULTS

To enable precise phenotyping for heat stress tolerance, we used a controlled phenotyping facility available at ICAR-Indian Institute of Wheat and Barley Research, Karnal, India. Based on 'days to 50% flowering' data of the RILs, we followed staggered sowing to synchronize flowering to impose heat stress at uniform stage. Using the Illumina infinium 5K SNP array for genotyping the parents and the RILs, and stress susceptibility and stress tolerance indices (SSI and STI) of percent spikelet sterility and yield per plant (g), we identified five QTLs on chromosomes 3, 5, 9 and 12. The identified QTLs explained phenotypic variation in the range of 6.27 to 21. 29%. Of these five QTLs, two high effect QTLs, one novel (qSTIPSS9.1) and one known (qSTIY5.1/qSSIY5.2), were mapped in less than 400 Kbp genomic regions, comprising of 65 and 54 genes, respectively.

CONCLUSIONS

The present study identified two major QTLs for heat tolerance in rice in narrow physical intervals, which can be employed for crop improvement by marker assisted selection (MAS) after development of suitable scorable markers for breeding of high yielding heat tolerant rice varieties. This is the first report of a major QTL for heat tolerance on chromosome 9 of rice. Further, a known QTL for heat tolerance on chromosome 5 was narrowed down from 23 Mb to 331 Kbp in this study.

High Resolution Mapping of QTLs for Heat Tolerance in Rice Using a 5K SNP Array

BACKGROUND

Heat stress is one of the major abiotic threats to rice production, next to drought and salinity stress. Incidence of heat stress at reproductive phase of the crop results in abnormal pollination leading to floret sterility, low seed set and poor grain quality. Identification of QTLs and causal genes for heat stress tolerance at flowering will facilitate breeding for improved heat tolerance in rice. In the present study, we used 272 F₈ recombinant inbred lines derived from a cross between Nagina22, a well-known heat tolerant Aus cultivar and IR64, a heat sensitive popular Indica rice variety to map the QTLs for heat tolerance.

RESULTS

To enable precise phenotyping for heat stress tolerance, we used a controlled phenotyping facility available at ICAR-Indian Institute of Wheat and Barley Research, Karnal, India. Based on 'days to 50% flowering' data of the RILs, we followed staggered sowing to synchronize flowering to impose heat stress at uniform stage. Using the Illumina infinium 5K SNP array for genotyping the parents and the RILs, and stress susceptibility and stress tolerance indices (SSI and STI) of percent spikelet sterility and yield per plant (g), we identified five QTLs on chromosomes 3, 5, 9 and 12. The identified QTLs explained phenotypic variation in the range of 6.27 to 21. 29%. Of these five QTLs, two high effect QTLs, one novel (qSTIPSS9.1) and one known (qSTIY5.1/qSSIY5.2), were mapped in less than 400 Kbp genomic regions, comprising of 65 and 54 genes, respectively.

CONCLUSIONS

The present study identified two major QTLs for heat tolerance in rice in narrow physical intervals, which can be employed for crop improvement by marker assisted selection (MAS) after development of suitable scorable markers for breeding of high yielding heat tolerant rice varieties. This is the first report of a major QTL for heat tolerance on chromosome 9 of rice. Further, a known QTL for heat tolerance on chromosome 5 was narrowed down from 23 Mb to 331 Kbp in this study.

RiceMetaSys for salt and drought stress responsive genes in rice: a web interface for crop improvement

Background

Genome-wide microarray has enabled development of robust databases for functional genomics studies in rice. However, such databases do not directly cater to the needs of breeders. Here, we have attempted to develop a web interface which combines the information from functional genomic studies across different genetic backgrounds with DNA markers so that they can be readily deployed in crop improvement. In the current version of the database, we have included drought and salinity stress studies since these two are the major abiotic stresses in rice.

Results

RiceMetaSys, a user-friendly and freely available web interface provides comprehensive information on salt responsive genes (SRGs) and drought responsive genes (DRGs) across genotypes, crop development stages and tissues, identified from multiple microarray datasets. ‘Physical position search’ is an attractive tool for those using QTL based approach for dissecting tolerance to salt and drought stress since it can provide the list of SRGs and DRGs in any physical interval. To identify robust candidate genes for use in crop improvement, the ‘common genes across varieties’ search tool is useful. Graphical visualization of expression profiles across genes and rice genotypes has been enabled to facilitate the user and to make the comparisons more impactful. Simple Sequence Repeat (SSR) search in the SRGs and DRGs is a valuable tool for fine mapping and marker assisted selection since it provides primers for survey of polymorphism. An external link to intron specific markers is also provided for this purpose. Bulk retrieval of data without any limit has been enabled in case of locus and SSR search.

Conclusions

The aim of this database is to facilitate users with a simple and straight-forward search options for identification of robust candidate genes from among thousands of SRGs and DRGs so as to facilitate linking variation in expression profiles to variation in phenotype.

Database URL: http://14.139.229.201

Electronic supplementary material

The online version of this article (10.1186/s12859-017-1846-y) contains supplementary material, which is available to authorized users.

A prototype of novel agro-waste based column bed device for removal of textile dye Optilan Red

The aim of the study was to assess the potentiality of an agro-waste (sugarcane bagasse) for removal of the textile dye (Optilan Red) using novel column based filtration unit with a packed column of chemically treated sugarcane bagasse. The treated and untreated sugarcane bagasse (biosorbent) were characterized by Fourier transform infrared (FT-IR) spectroscopy. Effect of initial dye concentration on percentage removal of dye, equilibrium adsorption of sugarcane bagasse, kinetic studies, breakthrough point equilibrium and desorption of dye from the column material were studied. An inverse dependence of initial dye concentration on percent removal of dye was observed, whereas the equilibrium adsorption (q_e) showed a direct relationship with dye concentration. The time required for reaching breakthrough point was 120 min. Desorption of dye through alkali wash resulted in complete desorption after 1 h washing of the column for its reuse for next cycle. FT-IR analysis shows vibration in valence bands of the hydrogen bond of OH group, and the bands of intra-molecular and intermolecular hydrogen bonds, which results in interaction of treated bagasse with Optilan Red textile dye. The present study showed that more than 93% removal of the dye can be achieved in the concentration range 10-50 ppm (aqueous solution). The removal efficiency of the column remained almost unchanged for the treatment of dye-house wastewater spiked with the dye. The agro-waste based treatment process shows a considerable potential for a low-cost treatment of dye contaminated water.

Protective effect of hydroxytyrosol in arsenic-induced mitochondrial dysfunction in rat brain

The present study was planned to investigate the protective effect of hydroxytyrosol (HT) against arsenic (As)-induced mitochondrial dysfunction in rat brain. Rats exposed to sodium arsenite (25 ppm for 8 weeks) showed decreased mitochondrial complexes (I, II, IV) activities, mitochondrial superoxide dismutase (MnSOD), and catalase activities in brain mitochondria. As-treated rats showed reduced mRNA expression of complex I (ND-1, ND-2), IV (COX-1, COX-4) subunits, and uncoupling protein-2 (UCP-2). In addition to this, As exposure downregulated the protein expression of MnSOD. Administration of HT with As restored the enzymatic activities of mitochondrial complexes, MnSOD and catalase, increased the mRNA levels of complexes subunits and UCP-2 as well as proteins level of MnSOD. These results suggest that HT efficiently restores mitochondrial dysfunction in As neurotoxicity and might be used as potential mitoprotective agent in future.

Cisplatin Induced Renal Insufficiency Measured by Glomerular Filtration Rate with 99mTc-DTPA and by using Serum Creatinine based Formulae: A Prospective Study

INTRODUCTION

Cisplatin also known as Cis-Diammine-Dichloroplatinum (CDDP) is a chemotherapeutic alkylating nephrotoxic agent. Thus, it is necessary to know if renal function is normal before starting chemotherapy. Glomerular Filtration Rate (GFR) can be assessed directly by using a radiopharmaceutical (dGFR). Estimated GFR (eGFR) method use, Serum Creatinine (SCR) levels in mathematical formulae such as Cockroft-Gault (CG) and abbreviated. Modified Diet in Renal Disease (aMDRD). The serum creatinine level is a function of GFR but is relatively insensitive for detecting early renal insufficiency.

AIM

We aimed to correlate the incidence of Renal Insufficiency (RI) before and one month after completion of chemotherapy treatment by various methods.

MATERIALS AND METHODS

In this prospective study, we examined 64 patients with locally advanced head neck and uterine cervix cancers, before and one month after chemotherapy treatment with CDDP. Single agent CDDP was used with dose range between 35mg/m² as concurrent weekly chemotherapy.

RESULTS

Baseline RI was seen in 9.3% of patients by SCR levels, in 21.8% by the dGFR method, in 43.75% by the GFR-CG method and in 25% by the GFR-aMDRD formula. We considered GFR of <60 ml/min and SCR >1.5mg% as RI. After completion of treatment, the median RI was seen in 12.5% by SCR levels, 34.38% by dGFR method, 53.13% by GFR-CG method and 40.63% by GFR-aMDRD formula. None of the methods of GFR estimation showed statistically significant increase in RI one month after CDDP infusion. Only a weak correlation was seen between dGFR and eGFR based on SCR value (p=0.006).

CONCLUSION

Baseline RI was detected in 12% more cases when measured by dGFR as compared with SCR level. However, mathematical formulae overestimated baseline RI as compared to dGFR. One month after completion of treatment with CDDP chemotherapy, RI increased in 10%-15% cases as detected by all the four evaluated methods. There is weak correlation between SCR and dGFR thus implicating the importance of dGFR in assessing RI. Thus, despite normal SCR levels, GFR by radioisotope method should also be done as pre-treatment workup for cisplatin based chemotherapy.

Unraveling the molecular basis of oxidative stress management in a drought tolerant rice genotype Nagina 22

BACKGROUND

Drought stress tolerance for crop improvement is an important goal worldwide. Drought is a complex trait, and it is vital to understand the complex physiological, biochemical, and molecular mechanisms of drought tolerance to tackle it effectively. Osmotic adjustment, oxidative stress management (OSM), and cell membrane stability (CMS) are major components of cellular tolerance under drought stress. In the current study, we explored the molecular basis of OSM in the drought tolerant rice variety, Nagina 22 and compared it with the popular drought sensitive rice variety, IR 64, under drought imposed at the reproductive stage, to understand how the parental polymorphisms correlate with the superiority of Nagina 22 and tolerant bulk populations under drought.

RESULTS

We generated recombinant inbred lines (RIL) from contrasting parents Nagina 22 and IR 64 and focussed on spikelet fertility (SF), in terms of its correlation with OSM, which is an important component of drought tolerance in Nagina 22. Based on SF under drought stress and its correlations with other yield related traits, we used superoxide dismutase (SOD), glutathione reductase (GR), and ascorbate peroxidase (APX) activity assays to establish the relationship between SF and OSM genes in the tolerant and sensitive lines. Among the OSM enzymes studied, GR had a significant and positive correlation with single plant yield (SPY) under drought stress. GR was also positively correlated with APX but negatively so with SOD. Interestingly, none of the enzyme-morphology correlations were significant under irrigated control (IC). Through genome-wide SNP analysis of the 21 genes encoding for OSM enzymes, we identified the functional polymorphisms between the parents and identified superior alleles. By using network analysis of OSM genes in rice, we identified the genes that are central to the OSM network.

CONCLUSIONS

From the biochemical and morphological data and the SNP analysis, the superiority of Nagina 22 in spikelet fertility under drought stress is because of its superior alleles for SOD (SOD2, SODCC1, SODA) and GR (GRCP2) rather than for APX, for which IR 64 had the superior allele (APX8). Nagina 22 can bypass APX8 by directly interacting with SODA. For nine of the 11 genes present in the central network, Nagina 22 had the superior alleles. We propose that Nagina 22 tolerance could mainly be because of SODA which is a reactive oxygen scavenger in mitochondria which is directly associated with spikelet fertility.

Unraveling the molecular basis of oxidative stress management in a drought tolerant rice genotype Nagina 22

BACKGROUND

Drought stress tolerance for crop improvement is an important goal worldwide. Drought is a complex trait, and it is vital to understand the complex physiological, biochemical, and molecular mechanisms of drought tolerance to tackle it effectively. Osmotic adjustment, oxidative stress management (OSM), and cell membrane stability (CMS) are major components of cellular tolerance under drought stress. In the current study, we explored the molecular basis of OSM in the drought tolerant rice variety, Nagina 22 and compared it with the popular drought sensitive rice variety, IR 64, under drought imposed at the reproductive stage, to understand how the parental polymorphisms correlate with the superiority of Nagina 22 and tolerant bulk populations under drought.

RESULTS

We generated recombinant inbred lines (RIL) from contrasting parents Nagina 22 and IR 64 and focussed on spikelet fertility (SF), in terms of its correlation with OSM, which is an important component of drought tolerance in Nagina 22. Based on SF under drought stress and its correlations with other yield related traits, we used superoxide dismutase (SOD), glutathione reductase (GR), and ascorbate peroxidase (APX) activity assays to establish the relationship between SF and OSM genes in the tolerant and sensitive lines. Among the OSM enzymes studied, GR had a significant and positive correlation with single plant yield (SPY) under drought stress. GR was also positively correlated with APX but negatively so with SOD. Interestingly, none of the enzyme-morphology correlations were significant under irrigated control (IC). Through genome-wide SNP analysis of the 21 genes encoding for OSM enzymes, we identified the functional polymorphisms between the parents and identified superior alleles. By using network analysis of OSM genes in rice, we identified the genes that are central to the OSM network.

CONCLUSIONS

From the biochemical and morphological data and the SNP analysis, the superiority of Nagina 22 in spikelet fertility under drought stress is because of its superior alleles for SOD (SOD2, SODCC1, SODA) and GR (GRCP2) rather than for APX, for which IR 64 had the superior allele (APX8). Nagina 22 can bypass APX8 by directly interacting with SODA. For nine of the 11 genes present in the central network, Nagina 22 had the superior alleles. We propose that Nagina 22 tolerance could mainly be because of SODA which is a reactive oxygen scavenger in mitochondria which is directly associated with spikelet fertility.

Unraveling the molecular basis of oxidative stress management in a drought tolerant rice genotype Nagina 22

BACKGROUND

Drought stress tolerance for crop improvement is an important goal worldwide. Drought is a complex trait, and it is vital to understand the complex physiological, biochemical, and molecular mechanisms of drought tolerance to tackle it effectively. Osmotic adjustment, oxidative stress management (OSM), and cell membrane stability (CMS) are major components of cellular tolerance under drought stress. In the current study, we explored the molecular basis of OSM in the drought tolerant rice variety, Nagina 22 and compared it with the popular drought sensitive rice variety, IR 64, under drought imposed at the reproductive stage, to understand how the parental polymorphisms correlate with the superiority of Nagina 22 and tolerant bulk populations under drought.

RESULTS

We generated recombinant inbred lines (RIL) from contrasting parents Nagina 22 and IR 64 and focussed on spikelet fertility (SF), in terms of its correlation with OSM, which is an important component of drought tolerance in Nagina 22. Based on SF under drought stress and its correlations with other yield related traits, we used superoxide dismutase (SOD), glutathione reductase (GR), and ascorbate peroxidase (APX) activity assays to establish the relationship between SF and OSM genes in the tolerant and sensitive lines. Among the OSM enzymes studied, GR had a significant and positive correlation with single plant yield (SPY) under drought stress. GR was also positively correlated with APX but negatively so with SOD. Interestingly, none of the enzyme-morphology correlations were significant under irrigated control (IC). Through genome-wide SNP analysis of the 21 genes encoding for OSM enzymes, we identified the functional polymorphisms between the parents and identified superior alleles. By using network analysis of OSM genes in rice, we identified the genes that are central to the OSM network.

CONCLUSIONS

From the biochemical and morphological data and the SNP analysis, the superiority of Nagina 22 in spikelet fertility under drought stress is because of its superior alleles for SOD (SOD2, SODCC1, SODA) and GR (GRCP2) rather than for APX, for which IR 64 had the superior allele (APX8). Nagina 22 can bypass APX8 by directly interacting with SODA. For nine of the 11 genes present in the central network, Nagina 22 had the superior alleles. We propose that Nagina 22 tolerance could mainly be because of SODA which is a reactive oxygen scavenger in mitochondria which is directly associated with spikelet fertility.

Chronic Arsenic Exposure-Induced Oxidative Stress is Mediated by Decreased Mitochondrial Biogenesis in Rat Liver

The present study was executed to study the effect of chronic arsenic exposure on generation of mitochondrial oxidative stress and biogenesis in rat liver. Chronic sodium arsenite treatment (25 ppm for 12 weeks) decreased mitochondrial complexes activity in rat liver. There was a decrease in mitochondrial superoxide dismutase (MnSOD) activity in arsenic-treated rats that might be responsible for increased protein and lipid oxidation as observed in our study. The messenger RNA (mRNA) expression of mitochondrial and nuclear-encoded subunits of complexes I (ND1 and ND2) and IV (COX I and COX IV) was downregulated in arsenic-treated rats only. The protein and mRNA expression of MnSOD was reduced suggesting increased mitochondrial oxidative damage after arsenic treatment. There was activation of Bax and caspase-3 followed by release of cytochrome c from mitochondria suggesting induction of apoptotic pathway under oxidative stress. The entire phenomenon was associated with decrease in mitochondrial biogenesis as evident by decreased protein and mRNA expression of nuclear respiratory factor 1 (NRF-1), nuclear respiratory factor 2 (NRF-2), peroxisome proliferator activator receptor gamma-coactivator 1α (PGC-1α), and mitochondrial transcription factor A (Tfam) in arsenic-treated rat liver. The results of the present study indicate that arsenic-induced mitochondrial oxidative stress is associated with decreased mitochondrial biogenesis in rat liver that may present one of the mechanisms for arsenic-induced hepatotoxicity.

Skp1, a component of E3 ubiquitin ligase, is necessary for growth, sporulation, development and pathogenicity in rice blast fungus (Magnaporthe oryzae)

Ubiqitination is an important process in eukaryotic cells involving E3 ubiquitin ligase, which co-ordinates with cell cycle proteins and controls various cell functions. Skp1 (S-phase kinase-associated protein 1) is a core component of the SCF (Skp1-Cullin 1-F-box) E3 ubiquitin ligase complex necessary for protein degradation by the 26S proteasomal pathway. The rice blast fungus Magnaporthe oryzae has a single MoSKP1(MGG_04978) required for viability. Skp1 has multiple functions; however, its roles in growth, sporulation and appressorial development are not understood. MoSKP1 complements Skp1 function in the fission yeast temperature-sensitive mutant skp1 A7, restoring the normal length of yeast cells at restrictive temperature. The MoSkp1 protein in M. oryzae is present in spores and germ tubes, and is abundantly expressed in appressoria. Various RNA interference (RNAi) and antisense transformants of MoSKP1 in B157 show reduced sporulation, defective spore morphology, lesser septation and diffuse nuclei. Further, they show elongated germ tubes and are unable to form appressoria. Transformants arrested in G1/S stage during initial spore germination show a similar phenotype to wild-type spores treated with hydroxyurea (HU). Reduced MoSkp1 transcript and protein levels in knockdown transformants result in atypical germ tube development. MoSkp1 interacts with the putative F-box protein (MGG_06351) revealing the ability to form protein complexes. Our investigation of the role of MoSKP1 suggests that a decrease in MoSkp1 manifests in decreased total protein ubiquitination and, consequently, defective cell cycle and appressorial development. Thus, MoSKP1 plays important roles in growth, sporulation, appressorial development and pathogenicity of M. oryzae.

Arsenic-induced mitochondrial oxidative damage is mediated by decreased PGC-1α expression and its downstream targets in rat brain

The present study was carried out to investigate the molecular mechanism of arsenic-induced mitochondrial oxidative damage and its relation to biogenesis in rat brain. Chronic sodium arsenite (25 ppm, orally) administration for 12 weeks decreased mitochondrial complexes activities and mRNA expression of selective complexes subunits. The expression of mitochondrial biogenesis regulator PGC-1α, and its downstream targets NRF-1, NRF-2 and Tfam were decreased significantly both at mRNA and protein levels suggesting impaired biogenesis following chronic arsenic-exposure. In addition to this, protein expression analysis also revealed activation of Bax and caspase-3, leading to translocation of cytochrome c from mitochondria to cytosol suggesting induction of apoptotic pathway under oxidative stress. This was further confirmed by electron microscopy study which depicted morphological changes in mitochondria in terms of altered nuclear and mitochondrial shape and chromatin condensation in arsenic-treated rats. The immunohistochemical studies showed both nuclear and cytosolic localization of NRF-1 and NRF-2 in arsenic-exposed rat brain further suggesting regulatory role of these transcription factors under arsenic neurotoxicity. The results of present study indicate that arsenic-induced mitochondrial oxidative damage is associated with decreased mitochondrial biogenesis in rat brain that may present as important target to reveal the mechanism for arsenic-induced neurotoxicity.

An unusual response with long term survival using erlotinib in NSCLC lung with brain metastases

We present a case of a middle-aged woman with adenocarcinoma of the lung and metastatic brain lesions. In view of her poor general condition and poor compliance to first-line chemotherapy, the patient was kept on tablet erlotinib after whole brain radiotherapy. This novel treatment resulted in a dramatic response with radiological regression in both the primary lung lesion and metastatic intracranial lesions translating in unexpected and ongoing 24-month survival.

A Novel Plated Hepatocyte Relay Assay (PHRA) for In Vitro Evaluation of Hepatic Metabolic Clearance of Slowly Metabolized Compounds

OBJECTIVE

Development and validation of a novel assay, the Plated Hepatocyte Relay Assay (PHRA), for the determination of the metabolic fates of slowly metabolized compounds.

METHOD

Cryopreserved human hepatocytes were cultured for 4 h followed by incubation with slowly metabolized compounds for 24 h (initial incubation). On the next day, the incubated media were collected and added to hepatocytes was similarly prepared on the day of incubation (48 h incubation; 1(st) relay). The procedures were repeated on the next days (72 h (2(nd) relay), 96 h (3rd relay), and 120 h (4(th) relay) incubations).

RESULTS

A proof-of-concept study with two low clearance compounds, diazepam and tolbutamide, and a validation study with 15 ultra-low clearance compounds (CLnon-renal < 1 mL/min/kg) and low clearance compounds (CLnon-renal 1- 5.1 mL/min/kg) were performed. Linear time-dependent disappearance of the parent compounds was observed for all compounds. Application of published free fraction values in combination with a correction factor with in vitro hepatic clearance results obtained with the PHRA accurately predicted in vivo hepatic clearance.

CONCLUSION

PHRA represents a useful experimental system for the evaluation of the metabolic fates of low clearance compounds in drug development.

Biochemical and Molecular Alterations Following Arsenic-Induced Oxidative Stress and Mitochondrial Dysfunction in Rat Brain

Oxidative stress is associated with the generation of reactive oxygen species (ROS), which is supposed to be one of the mechanisms of arsenic-induced neurodegeneration. Mitochondria, being the major source of ROS generation may present an important target of arsenic-mediated neurotoxicity. Hence, we planned the study to elucidate the possible biochemical and molecular alterations induced by arsenic exposure in rat brain mitochondria. Chronic sodium arsenite treatment (25 ppm for 12 weeks) resulted in decreased activity of mitochondrial complexes I, II, and IV followed by increased ROS generation. There was decrease in mitochondrial superoxide dismutase (MnSOD) activity in arsenic-treated rat brain further showing increased superoxide radical generation in mitochondria. The decrease in MnSOD activity might be responsible for the increased protein and lipid oxidation as observed in our study. Protein and messenger RNA (mRNA) levels of MnSOD and mitochondrial uncoupling protein 2 (UCP-2) were downregulated suggesting decreased removal of ROS in rat brain. Fourier transform infrared (FTIR) spectroscopy analysis revealed significant decrease in amide A, amide I, amide II, and Olefinic = CH stretching band area suggesting molecular alteration in proteins and lipids after arsenic treatment. The results of present study indicate that arsenic-induced disturbed mitochondrial metabolism, decreased removal of ROS, decrease in protein synthesis, and altered membrane lipid polarity and fluidity may be responsible for the mitochondrial oxidative damage in rat brain that may further be implicated as contributing factor in arsenic-induced neurodegeneration.

Cross-Species Differences in the Preclinical Pharmacokinetics of CT7758, an α4β1/α4β7 Integrin Antagonist

CT7758, a carboxylate containing α4β1/α4/β7 integrin antagonist, was characterized for its pharmacokinetic profile in various in vitro and in vivo assays in support of clinical development. The oral bioavailability of CT7758 was 4% in mice, 2% in rats, 7-55% in dogs, and 0.2% in cynomolgus monkeys. The low bioavailability in rodents and monkey results from low intestinal absorption as evidenced by a low fraction absorbed in the rat portal vein model (3%), low-to-medium permeability in Caco-2 cells (≤1.3 × 10(-6) cm/s) with evidences of polarized efflux, and high polar surface area (104 Å). In rodents and cynomolgus monkeys, the total plasma clearance was moderate to high (≥50% hepatic blood flow QH) and associated with a short elimination half-life (≤1 hour). This contrast with the dog data which showed a much lower clearance (6% QH) and a longer t1/2 (2.4 hours). The volume of distribution (Vz) also varied significantly across species with value of 5.5, 2.8, 0.24, and 0.93 l/kg in mouse, rat, dog, and cynomolgus monkey, respectively. In vitro assays demonstrated that active hepatic uptake accounted for most of the in vivo clearance and was the source of the large species variability. In vitro uptake assays predicted a total plasma clearance in humans in the low range (33% QH), a finding subsequently confirmed in the clinic. Assays in OAPT1B1-transfected cells demonstrated active uptake transport through this transporter. The prospect of limited absorption in human prompted the synthesis an ethyl ester prodrug, CDP323, which demonstrated higher in vitro permeability, increased oral bioavailability, as well as efficient in vivo release of its active moiety CT7758.

The effect of antidepressants and antipsychotics on weight gain in children and adolescents

Psychiatric illness in the paediatric population is increasing and the weight effect of medications for these problems is often unclear. A comprehensive literature search was undertaken to identify studies reporting weight in relation to antipsychotic and antidepressant use in children and adolescents. From 636 articles, 42 were selected for review. Selective serotonin reuptake inhibitors (SSRIs) and serotonin and norepinephrine reuptake inhibitors (SNRIs) do not cause weight gain and may lead to improvements in weight status over the short, but not, long term. Antipsychotics were generally associated with weight gain. In drug comparison studies, risperidone had a larger weight gain effect than lithium, divalproex sodium and pimozide. Studies assessing the weight-protective effects of augmentation therapy with metformin or topiramate show less weight gain with addition of these agents. In conclusion, prescribing of SSRIs and SNRIs may be associated with improvements in weight status in children and adolescents but trials assessing their use in obesity, outside of established psychiatric illness, are limited and still experimental. Youth prescribed antipsychotic medication should be monitored for exaggerated weight gain and in those where obesity is a pre-existing concern agents other than olanzapine, clozapine and risperidone may be advantageous.

Nuclear Receptors in Drug Metabolism, Drug Response and Drug Interactions

Orally delivered small-molecule therapeutics are metabolized in the liver and intestine by phase I and phase II drug-metabolizing enzymes (DMEs), and transport proteins coordinate drug influx (phase 0) and drug/drug-metabolite efflux (phase III). Genes involved in drug metabolism and disposition are induced by xenobiotic-activated nuclear receptors (NRs), i.e. PXR (pregnane X receptor) and CAR (constitutive androstane receptor), and by the 1α, 25-dihydroxy vitamin D3-activated vitamin D receptor (VDR), due to transactivation of xenobiotic-response elements (XREs) present in phase 0-III genes. Additional NRs, like HNF4-α, FXR, LXR-α play important roles in drug metabolism in certain settings, such as in relation to cholesterol and bile acid metabolism. The phase I enzymes CYP3A4/A5, CYP2D6, CYP2B6, CYP2C9, CYP2C19, CYP1A2, CYP2C8, CYP2A6, CYP2J2, and CYP2E1 metabolize >90% of all prescription drugs, and phase II conjugation of hydrophilic functional groups (with/without phase I modification) facilitates drug clearance. The conjugation step is mediated by broad-specificity transferases like UGTs, SULTs, GSTs. This review delves into our current understanding of PXR/CAR/VDR-mediated regulation of DME and transporter expression, as well as effects of single nucleotide polymorphism (SNP) and epigenome (specified by promoter methylation, histone modification, microRNAs, long non coding RNAs) on the expression of PXR/CAR/VDR and phase 0-III mediators, and their impacts on variable drug response. Therapeutic agents that target epigenetic regulation and the molecular basis and consequences (overdosing, underdosing, or beneficial outcome) of drug-drug/drug-food/drug-herb interactions are also discussed. Precision medicine requires understanding of a drug's impact on DME and transporter activity and their NR-regulated expression in order to achieve optimal drug efficacy without adverse drug reactions. In future drug screening, new tools such as humanized mouse models and microfluidic organs-on-chips, which mimic the physiology of a multicellular environment, will likely replace the current cell-based workflow.

A new quaternary ammonium cysteine analogue as a trapping reagent for reactive metabolites screening

The novel cysteine-cholamine (Cys-chol) trapping reagent was synthesized by coupling N-(tertbutoxycarbonyl)- S-trityl-L-cysteine with cholamine in the presence of HBTU (O-(benzotriazol-1-yl)- N,N,N',N'-tetramethyluronium hexafluorophosphate), and then deprotecting by trifluoroacetic acid. Cys-chol reagent enhanced the sensitivity of reactive metabolite screening 4 to 20 times without introducing additional sample preparation or derivatization steps. Retention of Cys-chol conjugates on reversed-phase column is higher than for respective GSH conjugates which helps in reduction of background interference. The use of Cys-chol trapping reagent can potentially improve sensitivity and specificity of routine reactive metabolite screening assay in drug discovery.

The pharmacokinetics, metabolism, and clearance mechanisms of tofacitinib, a janus kinase inhibitor, in humans

Tofacitinib is a novel, oral Janus kinase inhibitor. The objectives of this study were to summarize the pharmacokinetics and metabolism of tofacitinib in humans, including clearance mechanisms. Following administration of a single 50-mg (14)C-labeled tofacitinib dose to healthy male subjects, the mean (standard deviation) total percentage of administered radioactive dose recovered was 93.9% (±3.6), with 80.1% (±3.6) in the urine (28.8% parent), and 13.8% (±1.9) in feces (0.9% parent). Tofacitinib was rapidly absorbed, with plasma concentrations and total radioactivity peaking at around 1 hour after oral administration. The mean terminal phase half-life was approximately 3.2 hours for both parent drug and total radioactivity. Most (69.4%) circulating radioactivity in plasma was parent drug, with all metabolites representing less than 10% each of total circulating radioactivity. Hepatic clearance made up around 70% of total clearance, while renal clearance made up the remaining 30%. The predominant metabolic pathways of tofacitinib included oxidation of the pyrrolopyrimidine and piperidine rings, oxidation of the piperidine ring side-chain, N-demethylation and glucuronidation. Cytochrome P450 (P450) profiling indicated that tofacitinib was mainly metabolized by CYP3A4, with a smaller contribution from CYP2C19. This pharmacokinetic characterization of tofacitinib has been consistent with its clinical experience in drug-drug interaction studies.