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1.  Detecting hepatic steatosis using ultrasound-induced thermal strain imaging: an ex vivo animal study 
Physics in medicine and biology  2014;59(4):881-895.
Hepatic steatosis or fatty liver disease occurs when lipids accumulate within the liver and can lead to steatohepatitis, cirrhosis, liver cancer, and eventual liver failure requiring liver transplant. Conventional brightness mode (B-mode) ultrasound (US) is the most common noninvasive diagnostic imaging modality used to diagnose hepatic steatosis in clinics. However, it is mostly subjective or requires a reference organ such as the kidney or spleen with which to compare. This comparison can be problematic when the reference organ is diseased or absent. The current work presents an alternative approach to noninvasively detecting liver fat content using ultrasound-induced thermal strain imaging (US-TSI). This technique is based on the difference in the change in the speed of sound as a function of temperature between water- and lipid-based tissues. US-TSI was conducted using two system configurations including a mid-frequency scanner with a single linear array transducer (5-14 MHz) for both imaging and heating and a high-frequency (13-24 MHz) small animal imaging system combined with a separate custom-designed US heating transducer array. Fatty livers (n=10) with high fat content (45.6 ± 11.7%) from an obese mouse model and control livers (n=10) with low fat content (4.8± 2.9%) from wild-type mice were embedded in gelatin. Then, US imaging was performed before and after US induced heating. Heating time periods of ~3 s and ~9.2 s were used for the mid-frequency imaging and high-frequency imaging systems, respectively to induce temperature changes of approximately 1.5 °C. The apparent echo shifts that were induced as a result of sound speed change were estimated using 2D phase-sensitive speckle tracking. Following US-TSI, histology was performed to stain lipids and measure percentage fat in the mouse livers. Thermal strain measurements in fatty livers (−0.065±0.079%) were significantly (p<0.05) higher than those measured in control livers (−0.124±0.037%). Using histology as a gold standard to classify mouse livers, US-TSI had a sensitivity and specificity of 70% and 90%, respectively. The area under the receiver operating characteristic (ROC) curve (AUC) was 0.775. This ex vivo study demonstrates the feasibility of using US-TSI to detect fatty livers and warrants further investigation of US-TSI as a diagnostic tool for hepatic steatosis.
PMCID: PMC3971123  PMID: 24487698
Fatty liver disease; Obese mouse; Ultrasound thermal strain
2.  Identification and Characterization of a Novel Phosphodiesterase from the Metagenome of an Indian Coalbed 
PLoS ONE  2015;10(2):e0118075.
Phosphoesterases are involved in the degradation of organophosphorus compounds. Although phosphomonoesterases and phosphotriesterases have been studied in detail, studies on phosphodiesterases are rather limited. In our search to find novel phosphodiesterases using metagenomic approach, we cloned a gene encoding a putative phosphodiesterase (PdeM) from the metagenome of the formation water collected from an Indian coal bed. Bioinformatic analysis showed that PdeM sequence possessed the characteristic signature motifs of the class III phosphodiesterases and phylogenetic study of PdeM enabled us to identify three distinct subclasses (A, B, and C) within class III phosphodiesterases, PdeM clustering in new subclass IIIB. Bioinformatic, biochemical and biophysical characterization of PdeM further revealed some of the characteristic features of the phosphodiesterases belonging to newly described subclass IIIB. PdeM is a monomer of 29.3 kDa, which exhibits optimum activity at 25°C and pH 8.5, but low affinity for bis(pNPP) as well as pNPPP. The recombinant PdeM possessed phosphodiesterase, phosphonate-ester hydrolase and nuclease activity. It lacked phosphomonoesterase, phosphotriesterase, and RNAse activities. Overexpression of PdeM in E.coli neither affected catabolite respression nor did the recombinant protein hydrolyzed cAMP in vitro, indicating its inability to hydrolyze cAMP. Although Mn2+ was required for the activity of PdeM, but addition of metals (Mn2+ or Fe3+) did not induce oligomerization. Further increase in concentration of Mn2+ upto 3 mM, increased α-helical content as well as the phosphodiesterase activity. Structural comparison of PdeM with its homologs showed that it lacked critical residues required for dimerization, cAMP hydrolysis, and for the high affinity binding of bis(pNPP). PdeM, thus, is a novel representative of new subclass of class III phosphodiesterases.
PMCID: PMC4320098  PMID: 25658120
3.  Influence of Malnutrition on Adverse Outcome in Children with Confirmed or Probable Viral Encephalitis: A Prospective Observational Study 
BioMed Research International  2015;2015:407473.
A prospective observational study was conducted in a tertiary care teaching hospital from August 2008 to August 2009 to explore the independent predictors of adverse outcome in the patients with confirmed/probable viral encephalitis. The primary outcome variable was the incidence of adverse outcomes defined as death or severe neurological deficit such as loss of speech, motor deficits, behavioural problems, blindness, and cognitive impairment. Patients with confirmed or probable viral encephalitis were classified into two groups based on their Z-score of weight-for-age as per WHO growth charts. Group I. Patients with confirmed or probable viral encephalitis with weight-for-age (W/A) Z-scores below −2SD were classified as undernourished. Group II. Patients with confirmed or probable viral encephalitis were classified as having normal nutritional status (weight-for-age Z-score >−2SD). A total of 114 patients were classified as confirmed or probable viral encephalitis based on detailed investigations. On multivariate logistic regression, undernutrition (adjusted OR: 5.05; 95% CI: 1.92 to 13.44) and requirement of ventilation (adjusted OR: 6.75; 95% CI: 3.63 to 77.34) were independent predictors of adverse outcomes in these patients. Thus, the results from our study highlight that the association between undernutrition and adverse outcome could be extended to the patients with confirmed/probable viral encephalitis.
PMCID: PMC4324747
4.  Metabolic pathway for degradation of 2-chloro-4-aminophenol by Arthrobacter sp. SPG 
Microbial Cell Factories  2014;13(1):164.
A degradation pathway of 2-chloro-4-aminophenol (2C4AP) was studied in an Arthrobacter sp. SPG that utilized 2C4AP as its sole source of carbon and energy. The 2C4AP degradation was initiated by a 2C4AP-deaminase that catalyzed the conversion of 2C4AP into chlorohydroquinone (CHQ) with removal of ammonium ion. In the next step, a CHQ-dehalogenase dehalogenated CHQ to hydroquinone (HQ) that cleaved into γ-hydroxymuconic semialdehyde by a HQ-dioxygenase. The 2C4AP degradation was also investigated in sterile and non-sterile soil microcosms using strain SPG. The results show that the SPG cells degraded 2C4AP more rapidly in sterile soil than non-sterile soil. Our studies showed that strain SPG may be used for bioremediation of 2C4AP-contaminated sites. This is the first report of the 2C4AP degradation by any bacteria.
PMCID: PMC4251673  PMID: 25427856
5.  Progenitors Mobilized by Gamma-Tocotrienol as an Effective Radiation Countermeasure 
PLoS ONE  2014;9(11):e114078.
The purpose of this study was to elucidate the role of gamma-tocotrienol (GT3)-mobilized progenitors in mitigating damage to mice exposed to a supralethal dose of cobalt-60 gamma-radiation. CD2F1 mice were transfused 24 h post-irradiation with whole blood or isolated peripheral blood mononuclear cells (PBMC) from donors that had received GT3 72 h prior to blood collection and recipient mice were monitored for 30 days. To understand the role of GT3-induced granulocyte colony-stimulating factor (G-CSF) in mobilizing progenitors, donor mice were administered a neutralizing antibody specific to G-CSF or its isotype before blood collection. Bacterial translocation from gut to heart, spleen and liver of irradiated recipient mice was evaluated by bacterial culture on enriched and selective agar media. Endotoxin in serum samples also was measured. We also analyzed the colony-forming units in the spleens of irradiated mice. Our results demonstrate that whole blood or PBMC from GT3-administered mice mitigated radiation injury when administered 24 h post-irradiation. Furthermore, administration of a G-CSF antibody to GT3-injected mice abrogated the efficacy of blood or PBMC obtained from such donors. Additionally, GT3-mobilized PBMC inhibited the translocation of intestinal bacteria to the heart, spleen, and liver, and increased colony forming unit-spleen (CFU-S) numbers in irradiated mice. Our data suggests that GT3 induces G-CSF, which mobilizes progenitors and these progenitors mitigate radiation injury in recipient mice. This approach using mobilized progenitor cells from GT3-injected donors could be a potential treatment for humans exposed to high doses of radiation.
PMCID: PMC4244184  PMID: 25423021
6.  Meiotic Studies in Some Species of Tribe Cichorieae (Asteraceae) from Western Himalayas 
The Scientific World Journal  2014;2014:673456.
The present paper deals with meiotic studies in 15 species belonging to 6 genera of the tribe Cichorieae from various localities of Western Himalayas. The chromosome number has been reported for the first time in Hieracium crocatum (2n = 10) and Lactuca lessertiana (2n = 2x = 16). Further, intraspecific variability has been reported for the first time in H. umbellatum (2n = 2x = 10 and 2n = 6x = 54), Tragopogon dubius (2n = 2x = 14 and 2n = 4x = 28), and T. gracilis (2n = 2x = 14). The chromosome report of 2n = 2x = 10 in Youngia tenuifolia is made for the first time in India. Maximum numbers of the populations show laggards, chromosome stickiness, and cytomixis from early prophase to telophase-II, leading to the formation of aneuploid cells or meiocytes with double chromosome number. Such meiotic abnormalities produce unreduced pollen grains and the reduced pollen viability.
PMCID: PMC4247967  PMID: 25489603
7.  Surface Levels of CD20 Determine Anti-CD20 Antibodies Mediated Cell Death In Vitro 
PLoS ONE  2014;9(11):e111113.
The sensitivity of human Burkitt's lymphoma cells to rituximab (Rtx) and tositumomab (Tst) was assessed on cells expressing different levels of CD20 on surface. Cells that harbor low CD20 levels may resists against therapeutics response to CD20-specific antibodies. We postulated that, radiation-induced modulation of CD20 surface levels may play a crucial and central role in determining the relative efficacy of rituximab and tositumomab in treating Burkitt's lymphoma disease. Here, we examined the γ-radiation-induced CD20 expression in the Burkitt lymphoma cell line ‘Daudi’ and the relation of differential levels of CD20 with anti-CD20 mAbs mediated cell death.
In this study we examined kinetics of CD20 expression following sub lethal doses ofγ-radiation to Daudi cells and thereafter anti-CD20 mAbs (rituximab and tositumomab) were added in cell suspensions. The correlation of kinetics of CD20 expression and cells treated with anti-CD20 mAbs/or corresponding isotype Abs with special reference to changes in mitochondrial membrane potential and reactive oxygen species generation was also examined. Further, we also investigated the efficacy of anti-CD20 mAbs and possible induction of cell death in relation to levels of CD20 cell surface expression.
This report provides evidence that CD20 expression can be induced by exposure of cells to γ-radiation. In addition, these findings demonstrated that the efficacy of anti-CD20 mAbs is dependent on the surface levels of CD20. Based on these findings, we hypothesized (i) irradiation just prior to immunotherapy may provide new treatment options even in aggressive B cell tumors, which are resistant to current therapies in vivo (ii) The efficacy of induction of apoptosis varies with type of monoclonal antibodies in vitro.
PMCID: PMC4217761  PMID: 25364827
8.  Vitamin E: tocopherols and tocotrienols as potential radiation countermeasures 
Journal of Radiation Research  2013;54(6):973-988.
Despite the potential devastating health consequences of intense total-body irradiation, and the decades of research, there still remains a dearth of safe and effective radiation countermeasures for emergency, radiological/nuclear contingencies that have been fully approved and sanctioned for use by the US FDA. Vitamin E is a well-known antioxidant, effective in scavenging free radicals generated by radiation exposure. Vitamin E analogs, collectively known as tocols, have been subject to active investigation for a long time as radioprotectors in patients undergoing radiotherapy and in the context of possible radiation accidents or terrorism scenarios. Eight major isoforms comprise the tocol group: four tocopherols and four tocotrienols. A number of these agents and their derivatives are being investigated actively as radiation countermeasures using animal models, and several appear promising. Although the tocols are well recognized as potent antioxidants and are generally thought to mediate radioprotection through ‘free radical quenching’, recent studies have suggested several alternative mechanisms: most notably, an ‘indirect effect’ of tocols in eliciting specific species of radioprotective growth factors/cytokines such as granulocyte colony-stimulating factor (G-CSF). The radioprotective efficacy of at least two tocols has been abrogated using a neutralizing antibody of G-CSF. Based on encouraging results of radioprotective efficacy, laboratory testing of γ-tocotrienol has moved from a small rodent model to a large nonhuman primate model for preclinical evaluation. In this brief review we identify and discuss selected tocols and their derivatives currently under development as radiation countermeasures, and attempt to describe in some detail their in vivo efficacy.
PMCID: PMC3823775  PMID: 23658414
Countermeasures; mice; radiation; tocopherols; tocotrienols; vitamin E
9.  Director Field Model of the Primary Visual Cortex for Contour Detection 
PLoS ONE  2014;9(10):e108991.
We aim to build the simplest possible model capable of detecting long, noisy contours in a cluttered visual scene. For this, we model the neural dynamics in the primate primary visual cortex in terms of a continuous director field that describes the average rate and the average orientational preference of active neurons at a particular point in the cortex. We then use a linear-nonlinear dynamical model with long range connectivity patterns to enforce long-range statistical context present in the analyzed images. The resulting model has substantially fewer degrees of freedom than traditional models, and yet it can distinguish large contiguous objects from the background clutter by suppressing the clutter and by filling-in occluded elements of object contours. This results in high-precision, high-recall detection of large objects in cluttered scenes. Parenthetically, our model has a direct correspondence with the Landau - de Gennes theory of nematic liquid crystal in two dimensions.
PMCID: PMC4201468  PMID: 25329158
10.  Future Climate Data from RCP 4.5 and Occurrence of Malaria in Korea 
Since its reappearance at the Military Demarcation Line in 1993, malaria has been occurring annually in Korea. Malaria is regarded as a third grade nationally notifiable disease susceptible to climate change. The objective of this study is to quantify the effect of climatic factors on the occurrence of malaria in Korea and construct a malaria occurrence model for predicting the future trend of malaria under the influence of climate change. Using data from 2001–2011, the effect of time lag between malaria occurrence and mean temperature, relative humidity and total precipitation was investigated using spectral analysis. Also, a principal component regression model was constructed, considering multicollinearity. Future climate data, generated from RCP 4.5 climate change scenario and CNCM3 climate model, was applied to the constructed regression model to simulate future malaria occurrence and analyze the trend of occurrence. Results show an increase in the occurrence of malaria and the shortening of annual time of occurrence in the future.
PMCID: PMC4210996  PMID: 25321875
malaria; climate change; PCA-regression analysis; climate variable
11.  Fibrosis Reduces Severity of Acute-on-Chronic Pancreatitis in Humans 
Gastroenterology  2013;145(2):466-475.
Acute pancreatitis (AP) and chronic pancreatitis (CP) share etiologies, but AP can be more severe and has higher mortality. We investigated features of CP that protect against severity. The amount of intra-pancreatic fat (IPF) is increased in obesity and fibrosis is increased in CP; so we studied whether fibrosis or fat regulate severity of AP attacks in patients with CP.
We reviewed records from the University of Pittsburg Medical Center Autopsy database (1998–2008) for patients with diagnosed AP (n=23), CP (n=35), or both (AP-on-CP; n=15). Pancreatic histology samples from these patients and 50 randomly selected Controls (no pancreatic disease) were analyzed, and IPF data were correlated with computed tomography data. An adipocyte and acinar cell transwell co-culture system, with or without collagen Type-I (collagen-I), was used to study the effects of fibrosis on acinar-adipocyte interactions. We studied the effects of non-esterified fatty acids (NEFA) and adipokines on acinar cells in culture.
Levels of IPF were significantly higher among non-obese patients with CP than non-obese Controls. In CP or AP-on-CP, areas of IPF were surrounded by significantly more fibrosis than in Controls or patients with AP. Fat necrosis (FN)-associated peri-fat acinar necrosis (PFAN, indicated by NEFA spillage) contributed to most of the necrosis observed in AP samples; however, PFAN and total necrosis were significantly lower in samples from patients with CP and AP-on-CP. Fibrosis appeared to wall off the FN and limit PFAN, reducing acinar necrosis. In vitro, collagen-I limited the lipolytic flux between acinar cells and adipocytes and prevented increases in adipokines in the acinar compartment. This was associated with reduced acinar cell necrosis. However, NEFA, but not adipokines, caused acinar-cell necrosis.
Based on analysis of pancreatic samples from patients with CP, AP and AP-on-CP, and in vitro studies, fibrosis reduces the severity of acute exacerbations of CP by reducing lipolytic flux between adipocytes and acinar cells.
PMCID: PMC3964816  PMID: 23684709
pancreas; inflammation; necrosis; mechanism
12.  Crystal structure of 4-bromo-N-(2-bromo-3-nitro­benz­yl)-2-nitro­naphthalen-1-amine 
In the title compound, C17H11Br2N3O4, the dihedral angle between the planes of the naphthalene system and the benzene ring is 52.86 (8)°. The nitro substituent and the attached naphthalene system are almost coplanar [dihedral angle = 5.6 (4)°], probably as a consequence of an intra­molecular N—H⋯O hydrogen bond with the amine group. The nitro substituent attached to the benzene ring is disordered over two sets of sites with occupancies of 0.694 (3) and 0.306 (3). The major component deviates significantly from the ring plane [dihedral angle = 53.6 (2)°]. In the crystal, the mol­ecules are linked into a three-dimensional array by extensive π–π inter­actions involving both the naphthalene and benzene rings [range of centroid–centroid distances = 3.5295 (16)–3.9629 (18) Å] and C—H⋯O inter­actions involving the methyl­ene H atoms and the phenyl-attached nitro group.
PMCID: PMC4186169  PMID: 25309280
crystal structure; naphthalen-1-amine; π–π inter­actions; hydrogen bonding; aryl­selenium compounds; photoluminescent seleno­spiro­cyclic compounds
13.  A Novel Gene SbSI-2 Encoding Nuclear Protein from a Halophyte Confers Abiotic Stress Tolerance in E. coli and Tobacco 
PLoS ONE  2014;9(7):e101926.
Salicornia brachiata is an extreme halophyte that grows luxuriantly in coastal marshes. Previously, we have reported isolation and characterization of ESTs from Salicornia with large number of novel/unknown salt-responsive gene sequences. In this study, we have selected a novel salt-inducible gene SbSI-2 (Salicornia brachiata salt-inducible-2) for functional characterization. Bioinformatics analysis revealed that SbSI-2 protein has predicted nuclear localization signals and a strong protein-protein interaction domain. Transient expression of the RFP:SbSI2 fusion protein confirmed that SbSI-2 is a nuclear-localized protein. Genomic organization study showed that SbSI-2 is intronless and has a single copy in Salicornia genome. Quantitative RT-PCR analysis revealed higher SbSI-2 expression under salt stress and desiccation conditions. The SbSI-2 gene was transformed in E. coli and tobacco for functional characterization. pET28a-SbSI-2 recombinant E. coli cells showed higher tolerance to desiccation and salinity compared to vector alone. Transgenic tobacco plants overexpressing SbSI-2 have improved salt- and osmotic tolerance, accompanied by better growth parameters, higher relative water content, elevated accumulation of compatible osmolytes, lower Na+ and ROS accumulation and lesser electrolyte leakage than the wild-type. Overexpression of the SbSI-2 also enhanced transcript levels of ROS-scavenging genes and some stress-related transcription factors under salt and osmotic stresses. Taken together, these results demonstrate that SbSI-2 might play an important positive modulation role in abiotic stress tolerance. This identifies SbSI-2 as a novel determinant of salt/osmotic tolerance and suggests that it could be a potential bioresource for engineering abiotic stress tolerance in crop plants.
PMCID: PMC4084957  PMID: 24999628
14.  Contamination of water resources by pathogenic bacteria 
AMB Express  2014;4:51.
Water-borne pathogen contamination in water resources and related diseases are a major water quality concern throughout the world. Increasing interest in controlling water-borne pathogens in water resources evidenced by a large number of recent publications clearly attests to the need for studies that synthesize knowledge from multiple fields covering comparative aspects of pathogen contamination, and unify them in a single place in order to present and address the problem as a whole. Providing a broader perceptive of pathogen contamination in freshwater (rivers, lakes, reservoirs, groundwater) and saline water (estuaries and coastal waters) resources, this review paper attempts to develop the first comprehensive single source of existing information on pathogen contamination in multiple types of water resources. In addition, a comprehensive discussion describes the challenges associated with using indicator organisms. Potential impacts of water resources development on pathogen contamination as well as challenges that lie ahead for addressing pathogen contamination are also discussed.
PMCID: PMC4077002  PMID: 25006540
Pathogens; Contamination; Water resources; Watershed; Pathogens transport
15.  Rosa26-GFP Direct Repeat (RaDR-GFP) Mice Reveal Tissue- and Age-Dependence of Homologous Recombination in Mammals In Vivo 
PLoS Genetics  2014;10(6):e1004299.
Homologous recombination (HR) is critical for the repair of double strand breaks and broken replication forks. Although HR is mostly error free, inherent or environmental conditions that either suppress or induce HR cause genomic instability. Despite its importance in carcinogenesis, due to limitations in our ability to detect HR in vivo, little is known about HR in mammalian tissues. Here, we describe a mouse model in which a direct repeat HR substrate is targeted to the ubiquitously expressed Rosa26 locus. In the Rosa26 Direct Repeat-GFP (RaDR-GFP) mice, HR between two truncated EGFP expression cassettes can yield a fluorescent signal. In-house image analysis software provides a rapid method for quantifying recombination events within intact tissues, and the frequency of recombinant cells can be evaluated by flow cytometry. A comparison among 11 tissues shows that the frequency of recombinant cells varies by more than two orders of magnitude among tissues, wherein HR in the brain is the lowest. Additionally, de novo recombination events accumulate with age in the colon, showing that this mouse model can be used to study the impact of chronic exposures on genomic stability. Exposure to N-methyl-N-nitrosourea, an alkylating agent similar to the cancer chemotherapeutic temozolomide, shows that the colon, liver and pancreas are susceptible to DNA damage-induced HR. Finally, histological analysis of the underlying cell types reveals that pancreatic acinar cells and liver hepatocytes undergo HR and also that HR can be specifically detected in colonic somatic stem cells. Taken together, the RaDR-GFP mouse model provides new understanding of how tissue and age impact susceptibility to HR, and enables future studies of genetic, environmental and physiological factors that modulate HR in mammals.
Author Summary
Cancer is a disease of the genome, caused by accumulated genetic changes, such as point mutations and large-scale sequence rearrangements. Homologous recombination (HR) is a critical DNA repair pathway. While generally accurate, HR between misaligned sequences or between homologous chromosomes can lead to insertions, deletions, and loss of heterozygosity, all of which are known to promote cancer. Indeed, most cancers harbor sequence changes caused by HR, and genetic and environmental conditions that induce or suppress HR are often carcinogenic. To enable studies of HR in vivo, we created the Rosa26 Direct Repeat-Green Fluorescent Protein (RaDR-GFP) mice that carry an integrated transgenic recombination reporter targeted to the ubiquitously expressed Rosa26 locus. Being able to detect recombinant cells by fluorescence reveals that the frequency of recombination is highly variable among tissues. Furthermore, new recombination events accumulate over time, which contributes to our understanding of why our risk for cancer increases with age. This mouse model provides new understanding of this important DNA repair pathway in vivo, and also enables future studies of genetic, environmental and physiological factors that impact the risk of HR-induced sequence rearrangements in vivo.
PMCID: PMC4046920  PMID: 24901438
16.  Reassignment of Scattered Emission Photons in Multifocal Multiphoton Microscopy 
Scientific Reports  2014;4:5153.
Multifocal multiphoton microscopy (MMM) achieves fast imaging by simultaneously scanning multiple foci across different regions of specimen. The use of imaging detectors in MMM, such as CCD or CMOS, results in degradation of image signal-to-noise-ratio (SNR) due to the scattering of emitted photons. SNR can be partly recovered using multianode photomultiplier tubes (MAPMT). In this design, however, emission photons scattered to neighbor anodes are encoded by the foci scan location resulting in ghost images. The crosstalk between different anodes is currently measured a priori, which is cumbersome as it depends specimen properties. Here, we present the photon reassignment method for MMM, established based on the maximum likelihood (ML) estimation, for quantification of crosstalk between the anodes of MAPMT without a priori measurement. The method provides the reassignment of the photons generated by the ghost images to the original spatial location thus increases the SNR of the final reconstructed image.
PMCID: PMC4046171  PMID: 24898470
17.  Determinants of Prelacteal Feeding in Rural Northern India 
Prelacteal feeding is an underestimated problem in a developing country like India, where infant mortality rate is quite high. The present study tried to find out the factors determining prelacteal feeding in rural areas of north India.
A crosssectional study was conducted among recently delivered women of rural Uttar Pradesh, India. Multistage random sampling was used for selecting villages. From them, 352 recently delivered women were selected as the subjects, following systematic random sampling. Chi-square test and logistic regression were used to find out the predictors for prelacteal feeding.
Overall, 40.1% of mothers gave prelacteal feeding to their newborn. Factors significantly associated with such practice, after simple logistic regression, were age, caste, socioeconomic status, and place of delivery. At multivariate level, age (odds ratio (OR) = 1.76, 95% confidence interval (CI) = 1.13-2.74), caste and place of delivery (OR = 2.23, 95% CI = 1.21-4.10) were found to determine prelacteal feeding significantly, indicating that young age, high caste, and home deliveries could affect the practice positively.
The problem of prelacteal feeding is still prevalent in rural India. Age, caste, and place of delivery were associated with the problem. For ensuring neonatal health, the problem should be addressed with due gravity, with emphasis on exclusive breast feeding.
PMCID: PMC4050689  PMID: 24932400
Breast feeding; colostrum; infant feeding; prelacteal feeding; rural India
18.  Genetically Encoded Multispectral Labeling of Proteins with Polyfluorophores on a DNA Backbone 
Genetically-encoded methods for protein conjugation are of high importance as biological tools. Here we describe the development of a new class of dyes for genetically encoded tagging that add new capabilities for protein reporting and detection via HaloTag methodology. Oligodeoxyfluoroside (ODFs) are short DNA-like oligomers in which the natural nucleic acid bases are replaced by interacting fluorescent chromophores, yielding a broad range of emission colors using a single excitation wavelength. We describe the development of an alkyl halide dehalogenase-compatible chloroalkane linker phosphoramidite derivative that enables the rapid automated synthesis of many possible dyes for protein conjugation. Experiments in vitro test enzymatic self-conjugation of nine different DNA-like dyes to proteins with HaloTag domains, and the data confirm rapid and efficient covalent labeling of proteins. Notably, a number of the ODF dyes are found to increase in brightness or change color upon protein conjugation. Tests in mammalian cellular settings reveal that the dyes are functional in multiple cellular contexts, both on the cell surface and within the cytoplasm, allowing protein localization to be imaged in live cells by epifluorescence and laser confocal microscopy.
PMCID: PMC3646636  PMID: 23590213
19.  Degradation of 4-chloro-3-nitrophenol via a novel intermediate, 4-chlororesorcinol by Pseudomonas sp. JHN 
Scientific Reports  2014;4:4475.
A 4-chloro-3-nitrophenol (4C3NP)-mineralizing bacterium, Pseudomonas sp. JHN was isolated from a waste water sample collected from a chemically-contaminated area, India by an enrichment method. Pseudomonas sp. JHN utilized 4C3NP as a sole carbon and energy source and degraded it with the release of stoichiometric amounts of chloride and nitrite ions. Gas chromatography and gas chromatography-mass spectrometry detected 4-chlororesorcinol as a major metabolite of the 4C3NP degradation pathway. Inhibition studies using 2,2′-dipyridyl showed that 4-chlororesorcinol is a terminal aromatic compound in the degradation pathway of 4C3NP. The activity for 4C3NP-monooxygenase was detected in the crude extracts of the 4C3NP-induced JHN cells that confirmed the formation of 4-chlororesorcinol from 4C3NP. The capillary assay showed that Pseudomonas sp. JHN exhibited chemotaxis toward 4C3NP. The bioremediation capability of Pseudomonas sp. JHN was monitored to carry out the microcosm experiments using sterile and non-sterile soils spiked with 4C3NP. Strain JHN degraded 4C3NP in sterile and non-sterile soil with same degradation rates. This is the first report of (i) bacterial degradation and bioremediation of 4C3NP, (ii) formation of 4-chlororesorcinol in the degradation pathway of 4C3NP, (iii) bacterial chemotaxis toward 4C3NP.
PMCID: PMC3966030  PMID: 24667329
20.  Posterior Interosseous Nerve Syndrome from Thermal Injury 
Case Reports in Surgery  2014;2014:891393.
Background. Due to anatomical proximity to bone, the radial nerve is the most frequently injured major nerve of the upper extremity, frequently secondary to fractures (Li et al. (2013)). We describe an incidence when a branch of the radial nerve is injured as a result of a thermal injury. Observation. Radial nerve injury can occur anywhere along the anatomical course with varied etiologies, but commonly related to trauma. The most frequent site is in the proximal forearm involving the posterior interosseous branch. However, problems can occur at the junction of the middle and proximal thirds of the humerus and wrist radially. When the radial nerve is injured by a burn, a new rehabilitation dynamic arises. Not only does one agonize about the return of nerve function but also fret about the skin grafts that replaced the devitalized tissue housing that compartment. Discussion. Although posterior interosseous nerve syndrome has been described in the context of many different etiologies, it has not previously been discussed in relation to burn injuries. In this case, not only did the patient's rehabilitation involve aggressive therapy for return of sensation and function of the arm, but also prevention of contracture normally seen in replacement of full thickness burns.
PMCID: PMC3965921  PMID: 24707432
21.  New Approaches to Radiation Protection 
Frontiers in Oncology  2015;4:381.
Radioprotectors are compounds that protect against radiation injury when given prior to radiation exposure. Mitigators can protect against radiation injury when given after exposure but before symptoms appear. Radioprotectors and mitigators can potentially improve the outcomes of radiotherapy for cancer treatment by allowing higher doses of radiation and/or reduced damage to normal tissues. Such compounds can also potentially counteract the effects of accidental exposure to radiation or deliberate exposure (e.g., nuclear reactor meltdown, dirty bomb, or nuclear bomb explosion); hence they are called radiation countermeasures. Here, we will review the general principles of radiation injury and protection and describe selected examples of radioprotectors/mitigators ranging from small-molecules to proteins to cell-based treatments. We will emphasize agents that are in more advanced stages of development.
PMCID: PMC4299410  PMID: 25653923
radiation protection; radioprotectors; mitigators; cancer treatment; irradiation
22.  Three dimensional HiLo-based structured illumination for a digital scanned laser sheet microscopy (DSLM) in thick tissue imaging 
Optics Express  2012;20(25):27337-27347.
Laser sheet based microscopy has become widely accepted as an effective active illumination method for real time three-dimensional (3D) imaging of biological tissue samples. The light sheet geometry, where the camera is oriented perpendicular to the sheet itself, provides an effective method of eliminating some of the scattered light and minimizing the sample exposure to radiation. However, residual background noise still remains, limiting the contrast and visibility of potentially interesting features in the samples. In this article, we investigate additional structuring of the illumination for improved background rejection, and propose a new technique, “3D HiLo” where we combine two HiLo images processed from orthogonal directions to improve the condition of the 3D reconstruction. We present a comparative study of conventional structured illumination based demodulation methods, namely 3Phase and HiLo with a newly implemented 3D HiLo approach and demonstrate that the latter yields superior signal-to-background ratio in both lateral and axial dimensions, while simultaneously suppressing image processing artifacts.
PMCID: PMC3601593  PMID: 23262684
(180.6900) Three-dimensional microscopy; (180.2520) Fluorescence microscopy; (110.6880) Three-dimensional image acquisition; (100.3020) Image reconstruction-restoration
23.  5-AED enhances survival of irradiated mice in a G-CSF-dependent manner, stimulates innate immune cell function, reduces radiation-induced DNA damage and induces genes that modulate cell cycle progression and apoptosis 
Journal of Radiation Research  2012;53(6):840-853.
The steroid androst-5-ene-3ß,17ß-diol (5-androstenediol, 5-AED) elevates circulating granulocytes and platelets in animals and humans, and enhances survival during the acute radiation syndrome (ARS) in mice and non-human primates. 5-AED promotes survival of irradiated human hematopoietic progenitors in vitro through induction of Nuclear Factor-κB (NFκB)-dependent Granulocyte Colony-Stimulating Factor (G-CSF) expression, and causes elevations of circulating G-CSF and interleukin-6 (IL-6). However, the in vivo cellular and molecular effects of 5-AED are not well understood. The aim of this study was to investigate the mechanisms of action of 5-AED administered subcutaneously (s.c.) to mice 24 h before total body γ- or X-irradiation (TBI). We used neutralizing antibodies, flow cytometric functional assays of circulating innate immune cells, analysis of expression of genes related to cell cycle progression, DNA repair and apoptosis, and assessment of DNA strand breaks with halo-comet assays. Neutralization experiments indicated endogenous G-CSF but not IL-6 was involved in survival enhancement by 5-AED. In keeping with known effects of G-CSF on the innate immune system, s.c. 5-AED stimulated phagocytosis in circulating granulocytes and oxidative burst in monocytes. 5-AED induced expression of both bax and bcl-2 in irradiated animals. Cdkn1a and ddb1, but not gadd45a expression, were upregulated by 5-AED in irradiated mice. S.c. 5-AED administration caused decreased DNA strand breaks in splenocytes from irradiated mice. Our results suggest 5-AED survival enhancement is G-CSF-dependent, and that it stimulates innate immune cell function and reduces radiation-induced DNA damage via induction of genes that modulate cell cycle progression and apoptosis.
PMCID: PMC3483857  PMID: 22843381
24.  Ultrastructural Changes of Airway in Murine Models of Allergy and Diet-Induced Metabolic Syndrome 
ISRN Allergy  2013;2013:261297.
Studying ultrastructural changes could reveal novel pathophysiology of obese-asthmatic condition as existing concepts in asthma pathogenesis are based on the histological changes of the diseased airway. While asthma is defined in functional terms, the potential of electron microscopy (EM) in providing cellular and subcellular detail is underutilized. With this view, we have performed transmission EM in the lungs from allergic mice that show key features of asthma and high-fat- or high-fructose-fed mice that mimicked metabolic syndrome to illustrate the ultrastructural changes. The primary focus was epithelial injury and metaplasia, which are cardinal features of asthma and initiate airway remodeling. EM findings of the allergically inflamed mouse lungs correlate with known features of human asthma such as increased mitochondria in airway smooth muscle, platelet activation and subepithelial myofibroblasts. Interestingly, we found a clear and unambiguous evidence to suggest that ciliated cells can become goblet cells using immunoelectron microscopy. Additionally, we show for the first time the stressed mitochondria in the bronchial epithelia of high-fat- or high-fructose-fed mice even without allergen exposure. These results may stimulate interest in using EM in understanding novel pathological mechanisms for different subtypes of asthma including obese asthma.
PMCID: PMC3782840  PMID: 24106613
25.  Identification of two regions in the p140Cap adaptor protein that retain the ability to suppress tumor cell properties 
p140Cap is an adaptor protein that negatively controls tumor cell properties, by inhibiting in vivo tumor growth and metastasis formation. Our previous data demonstrated that p140Cap interferes with tumor growth and impairs invasive properties of cancer cells inactivating signaling pathways, such as the tyrosine kinase Src or E-cadherin/EGFR cross-talk. In breast cancer p140Cap expression inversely correlates with tumor malignancy. p140Cap is composed of several conserved domains that mediate association with specific partners. Here we focus our attention on two domains of p140Cap, the TER (Tyrosine Enriched Region) which includes several tyrosine residues, and the CT (Carboxy Terminal) which contains a proline rich sequence, involved in binding to SH2 and SH3 domains, respectively. By generating stable cell lines expressing these two proteins, we demonstrate that both TER and CT domains maintain the ability to associate the C-terminal Src kinase (Csk) and Src, to inhibit Src activation and Focal adhesion kinase (Fak) phosphorylation, and to impair in vitro and in vivo tumor cell features. In particular expression of TER and CT proteins in cancer cells inhibits in vitro and in vivo growth and directional migration at a similar extent of the full length p140Cap protein. Moreover, by selective point mutations and deletion we show that the ability of the modules to act as negative regulators of cell migration and proliferation mainly resides on the two tyrosines (Y) inserted in the EPLYA and EGLYA sequences in the TER module and in the second proline-rich stretch contained in the CT protein. Gene signature of cells expressing p140Cap, TER or CT lead to the identification of a common pattern of 105 down-regulated and 128 up-regulated genes, suggesting that the three proteins can act through shared pathways. Overall, this work highlights that the TER and CT regions of p140Cap can efficiently suppress tumor cell properties, opening the perspective that short, defined p140Cap regions can have therapeutic effects.
PMCID: PMC3696535  PMID: 23841028
p140Cap; breast cancer; lung cancer; colon cancer; cell signaling; Csk; Src

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