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1.  Divergent Temporal Expression of Hyaluronan Metabolizing Enzymes and Receptors with Craniotomy vs. Controlled-Cortical Impact Injury in Rat Brain: A Pilot Study 
Traumatic brain injury (TBI) triggers many secondary changes in tissue biology, which ultimately determine the extent of injury and clinical outcome. Hyaluronan [hyaluronic acid (HA)] is a protective cementing gel present in the intercellular spaces whose degradation has been reported as a causative factor in tissue damage. Yet little is known about the expression and activities of genes involved in HA catabolism after TBI. Young adult male Sprague-Dawley rats were assigned to three groups: naïve control, craniotomy, and controlled-cortical impact-induced TBI (CCI-TBI). Four animals per group were sacrificed at 4 h, 1, 3, and 7 days post-CCI. The mRNA expression of hyaluronan synthases (HAS1-3), hyaluronidases (enzymes for HA degradation, HYAL 1–4, and PH20), and CD44 and RHAMM (membrane receptors for HA signaling and removal) were determined using real-time PCR. Compared to the naïve controls, expression of HAS1 and HAS2 mRNA, but not HAS3 mRNA increased significantly following craniotomy alone and following CCI with differential kinetics. Expression of HAS2 mRNA increased significantly in the ipsilateral brain at 1 and 3 days post-CCI. HYAL1 mRNA expression also increased significantly in the craniotomy group and in the contralateral CCI at 1 and 3 days post-CCI. CD44 mRNA expression increased significantly in the ipsilateral CCI at 4 h, 1, 3, and 7 days post-CCI (up to 25-fold increase). These data suggest a dynamic regulation and role for HA metabolism in secondary responses to TBI.
PMCID: PMC4161003  PMID: 25309501
TBI; secondary injury factors; hyaluronic acid; receptor; synthesis; degradation; hyaluronidase; rat brain
2.  Analysis of bile in various hepatobiliary disease states: A pilot study 
Our study aims to find various enzymatic and biochemical components of bile and their clinical or prognostic correlation with regard to progression and severity of hepatobiliary diseases.
Materials and Methods:
It was a cross-sectional study where all the patients suffering from choledochal cyst (CDC), extrahepatic portal venous obstruction (EHPVO), and infantile obstructive cholangiopathy undergoing diagnostic preoperative cholangiogram; and patients with history of total parenteral nutrition (TPN) undergoing surgery for some other condition were included in the study. Intraoperatively, bile was collected from the gallbladder and sent for estimation of amylase, lipase, sodium, potassium, calcium, chloride, bicarbonate, total bilirubin, pH, cholesterol, triglycerides, and total bile acid.
A total of 80 patients were included in the study (20 in each of the four disease-based groups). Amylase, lipase, and pH were significantly different among the patients of CDC when compared with the presence or absence of dilated intrahepatic biliary radicals. Similarly, amylase, lipase, and pH were also significantly different among the patients of EHPVO when compared with presence or absence of biliopathy. Levels of cholesterol and bile acid were significantly higher in patients who were evaluated after 1 year following TPN than those who were evaluated before 1 year. The patients of infantile cholangiopathy, who had history of fever, had significantly higher level of calcium.
The components of bile show close correlation with various clinical and prognostic markers, there is a very close correlation between these parameters and the clinical severity, disease progression, and final outcome.
PMCID: PMC4155632  PMID: 25197193
Bile; choledochal cyst; extrahepatic portal venous obstruction; neonatal cholangitis; total parenteral nutrition
3.  Weaning of mechanically ventilated chronic obstructive pulmonary disease patients by using non-invasive positive pressure ventilation: A prospective study 
Chronic obstructive pulmonary disease (COPD) patients frequently pose difficulty in weaning from invasive mechanical ventilation (MV). Prolonged invasive ventilation brings along various complications. Non-invasive positive pressure ventilation (NIPPV) is proposed to be a useful weaning modality in such cases.
To evaluate the usefulness of NIPPV in weaning COPD patients from invasive MV, and compare it with weaning by conventional pressure support ventilation (PSV).
Materials and Methods:
For this prospective randomized controlled study, we included 50 COPD patients with type II respiratory failure requiring initial invasive MV. Upon satisfying weaning criteria and failing a t-piece weaning trial, they were randomized into two groups: Group I (25 patients) weaned by NIPPV, and group II (25 patients) weaned by conventional PSV. The groups were similar in terms of disease severity, demographic, clinical and biochemical parameters. They were compared in terms of duration of MV, weaning duration, length of intensive care unit (ICU) stay, occurrence of nosocomial pneumonia and outcome.
Statistically significant difference was found between the two groups in terms of duration of MV, weaning duration, length of ICU stay, occurrence of nosocomial pneumonia and outcome.
NIPPV appears to be a promising weaning modality for mechanically ventilated COPD patients and should be tried in resource-limited settings especially in developing countries.
PMCID: PMC3999671  PMID: 24778474
Chronic obstructive pulmonary disease; invasive mechanical ventilation; non-invasive positive pressure ventilation; weaning
4.  Buccal Injection of 2% Lidocaine With Epinephrine for the Removal of Maxillary Third Molars 
Anesthesia Progress  2013;60(3):95-98.
The aim of the study was to demonstrate if 2% lidocaine hydrochloride with 1 : 200,000 epinephrine could provide palatal anesthesia in maxillary tooth removal with a single buccal injection. The subjects included in the clinical study were those requiring extraction of the maxillary third molar of either side. For the purpose of comparison, the sample was randomly divided into 2 main groups: group 1 (study group) included 100 subjects who were to receive a single injection before extraction, and group 2 (control group) included 100 subjects who were to receive a single buccal injection and a single palatal injection before extraction. After 5 minutes the extraction was performed. All patients were observed for Faces Pain Scale during extraction and asked for the same on a 100-mm visual analog scale after extraction. According to visual analog scale and Faces Pain Scale scores, when maxillary third molar removal without palatal injection (study group) and with palatal injection (control group) were compared the difference was not statistically significant (P > .05). Removal of maxillary third molars without palatal injection is possible by depositing 2 mL of 2% lidocaine hydrochloride with 1 : 200,000 epinephrine to the buccal vestibule of the tooth.
PMCID: PMC3771203  PMID: 24010986
Maxillary third molar; Lidocaine hydrochloride with 1 : 200,000 epinephrine single buccal injection; Local anesthesia
5.  Ortho-surgical management of condylar hyperplasia: Rare case reports 
Condylar hyperplasia of the mandible is a clinical condition of over-development and growth because of excessive cellular growth of one condylar part of the mandible leading to facial asymmetry, mandibular deviation and enlargement of condyle. The elongation of the condylar neck in turn leads to malocclusion and articular dysfunction. In the past the interceptive and corrective procedures of growth and deformity in condylar hyperplasia were either condylectomy or high condylotomy. However, the deformity ceases after growth is completed. Therefore, other surgical procedures have to be undertaken to correct the manifested deformity of condylar hyperplasia. Further it has to be stressed that no single procedure can completely correct the deformity. So in addition to condylectomy, other orthognathic surgical procedures both on body and ramus and also on maxilla can be undertaken to correct the canting of occlusion. Two rare cases of unilateral hyperplasia encountered in our hospital are presented which required different lines of treatment.
PMCID: PMC4178358  PMID: 25298720
Condyle; condylar hyperplasia; facial asymmetry
6.  Noninvasive mechanical ventilation: An 18-month experience of two tertiary care hospitals in north India 
Noninvasive mechanical ventilation (NIMV) is the delivery of positive pressure ventilation through an interface to upper airways without using the invasive airway. Use of NIMV is becoming common with the increasing recognition of its benefits.
This study was done to evaluate the feasibility and outcome of NIMV in tertiary care centres.
Materials and Methods:
An observational, retrospective study conducted over a period of 18 months in two tertiary level hospitals of north India on 184 consecutive patients who were treated by NIMV, regardless of the indication. NIMV was given in accordance with the arterial blood gas (ABG) parameters defining respiratory failure (Type 1/Type 2).
The most common indication of NIMV in our hospitals was acute exacerbation of chronic obstructive pulmonary disease (AE-COPD 80.43%), and 90.54% AE-COPD patients were improved by NIMV. Application of NIMV resulted in significant improvement of pH and blood gases in COPD patients, while non-COPD patients showed significant improvement in partial pressure of oxygen (PaO2) alone. The mean duration of NIMV was 8.35 ± 5.98 days, and patients of interstitial lung disease (ILD) were on NIMV for the maximum duration (17 ± 8.48 days). None of the patients of acute respiratory distress syndrome were cured by NIMV; 13.04% patients on NIMV required intubation and mechanical ventilation.
This study demonstrates and encourages the use of NIMV as the first-line ventilatory treatment in AE-COPD patients with respiratory failure. It also supports NIMV usage in other causes of respiratory failure as a promising step toward prevention of mechanical ventilation.
PMCID: PMC3841687  PMID: 24339488
Acute exacerbation; chronic obstructive pulmonary disease; noninvasive mechanical ventilation; respiratory failure
7.  Endoscopic treatment of vesico-ureteral reflux: Experience of 99 ureteric moieties 
To study the outcome of endoscopic hyaluronic acid/dextranomer injection in patients with vesico-ureteric reflux (VUR).
Materials and Methods:
Sixty-three children were evaluated with a median follow up of 18 months (12-55 months) before injecting hyaluronic acid/dextranomer in a total of 99 ureteric moieties. Median age at presentation was 24 months (6-72 months). Primary VUR was the main presenting diagnosis in 60%. Patients were monitored for urinary tract infection (UTI), glomerular filtration rate (GFR), renal scarring, persistence, or appearance of contra-lateral reflux.
Grade III VUR was the most common (38%) followed by Grade IV (24%), Grade V (17%), Grade II (14%), and Grade I (7%). Most common cause for VUR was Primary (60%), followed by posterior urethral valve (PUV) (19%), bladder exstrophy (5%), anorectal malformation (ARM), epispadias, and duplex system. Analysis of patients characteristics at presentation revealed renal scarring (40%), split renal functions <35% (35%), recurrent UTI (15%), GFR <50 ml/min/1.73 m2 (15%), serum creatinine >1.4 mg/dL (10%). Complete resolution (100%) of Grade I and Grade II VUR was achieved after single injection. For Grade III VUR, single injection resolved reflux in 85.5% ureters, 100% resolution was seen after 2nd injection. In Grade IV VUR, 1st injection resolved VUR in 83.3% ureters, 95.8% ureters were reflux free after 2nd injection, and 100% resolution was seen after 3rd injection. In Grade V VUR, 94% ureters showed absent reflux after three injections.
Hyaluronic acid/dextranomer injection holds promise even in higher grades of VUR.
PMCID: PMC3853853  PMID: 24347865
Deflux; hyaluronic acid/dextranomer injection; outcome; vesico-ureteric reflux
8.  Necrosis of maxilla, nasal, and frontal bone secondary to extensive rhino-cerebral mucormycosis 
Mucormycosis is an opportunistic fulminant fungal infection caused by zygomycetes. This fungus can cause a variety of infections in human beings, particularly in the uncontrolled diabetes mellitus. Zygomycetes impinge into the vascular network, resulting in thrombosis and necrosis of the surrounding hard and soft tissues. The infection begins in the nose and paranasal sinuses due to inhalation of fungal spores and spread to orbital and intracranial structures either by direct invasion or through the blood vessels. Sinus mucormycosis is often accompanied by a poor prognosis and a high mortality rate. Hence, aggressive surgical intervention with antifungal therapy is usually necessary. Early diagnosis and prompt treatment can reduce the mortality and morbidity of this lethal fungal infection. We report a case of aggressive rhino-cerebral mucormycosis in a 58-year-old female patient with uncontrolled diabetes mellitus.
PMCID: PMC3961907  PMID: 24665188
Fungal infection; mucormycosis; rhino-cerebral; uncontrolled diabetes
9.  Pseudomonas fluorescens-like bacteria from the stomach: A microbiological and molecular study 
AIM: To characterize oxidase- and urease-producing bacterial isolates, grown aerobically, that originated from antral biopsies of patients suffering from acid peptic diseases.
METHODS: A total of 258 antral biopsy specimens were subjected to isolation of bacteria followed by tests for oxidase and urease production, acid tolerance and aerobic growth. The selected isolates were further characterized by molecular techniques viz. amplifications for 16S rRNA using universal eubacterial and HSP60 gene specific primers. The amplicons were subjected to restriction analysis and partial sequencing. A phylogenetic tree was generated using unweighted pair group method with arithmetic mean (UPGMA) from evolutionary distance computed with bootstrap test of phylogeny. Assessment of acidity tolerance of bacteria isolated from antrum was performed using hydrochloric acid from 10-7 mol/L to 10-1 mol/L.
RESULTS: Of the 258 antral biopsy specimens collected from patients, 179 (69.4%) were positive for urease production by rapid urease test and 31% (80/258) yielded typical Helicobacter pylori (H. pylori) after 5-7 d of incubation under a microaerophilic environment. A total of 240 (93%) antral biopsies yielded homogeneous semi-translucent and small colonies after overnight incubation. The partial 16S rRNA sequences revealed that the isolates had 99% similarity with Pseudomonas species. A phylogenetic tree on the basis of 16S rRNA sequences denoted that JQ927226 and JQ927227 were likely to be related to Pseudomonas fluorescens (P. fluorescens). On the basis of HSP60 sequences applied to the UPGMA phylogenetic tree, it was observed that isolated strains in an aerobic environment were likely to be P. fluorescens, and HSP60 sequences had more discriminatory potential rather than 16S rRNA sequences. Interestingly, this bacterium was acid tolerant for hours at low pH. Further, a total of 250 (96.9%) genomic DNA samples of 258 biopsy specimens and DNA from 240 bacterial isolates were positive for the 613 bp amplicons by targeting P. fluorescens-specific conserved putative outer membrane protein gene sequences.
CONCLUSION: This study indicates that bacterial isolates from antral biopsies grown aerobically were P. fluorescens, and thus acid-tolerant bacteria other than H. pylori can also colonize the stomach and may be implicated in pathogenesis/protection.
PMCID: PMC3581993  PMID: 23466902
Antral biopsy; Helicobacter pylori; Pseudomonas fluorescens; HSP60; Nested polymerase chain reaction; Acid-tolerant bacteria
10.  Impaired cortical mitochondrial function following TBI precedes behavioral changes 
Traumatic brain injury (TBI) pathophysiology can be attributed to either the immediate, primary physical injury, or the delayed, secondary injury which begins minutes to hours after the initial injury and can persist for several months or longer. Because these secondary cascades are delayed and last for a significant time period post-TBI, they are primary research targets for new therapeutics. To investigate changes in mitochondrial function after a brain injury, both the cortical impact site and ipsilateral hippocampus of adult male rats 7 and 17 days after a controlled cortical impact (CCI) injury were examined. State 3, state 4, and uncoupler-stimulated rates of oxygen consumption, respiratory control ratios (RCRs) were measured and membrane potential quantified, and all were significantly decreased in 7 day post-TBI cortical mitochondria. By contrast, hippocampal mitochondria at 7 days showed only non-significant decreases in rates of oxygen consumption and membrane potential. NADH oxidase activities measured in disrupted mitochondria were normal in both injured cortex and hippocampus at 7 days post-CCI. Respiratory and phosphorylation capacities at 17 days post-CCI were comparable to naïve animals for both cortical and hippocampus mitochondria. However, unlike oxidative phosphorylation, membrane potential of mitochondria in the cortical lining of the impact site did not recover at 17 days, suggesting that while diminished cortical membrane potential at 17 days does not adversely affect mitochondrial capacity to synthesize ATP, it may negatively impact other membrane potential-sensitive mitochondrial functions. Memory status, as assessed by a passive avoidance paradigm, was not significantly impaired until 17 days after injury. These results indicate pronounced disturbances in cortical mitochondrial function 7 days after CCI which precede the behavioral impairment observed at 17 days.
PMCID: PMC3912469  PMID: 24550822
traumatic brain injury; energy metabolism; mitochondria; oxidative phosphorylation; animal behavior
11.  Kartagener's syndrome: A case series 
Kartagener's syndrome is a rare, autosomal recessive genetic ciliary disorder comprising the triad of situs inversus, chronic sinusitis, and bronchiectasis. The basic problem lies in the defective movement of cilia, leading to recurrent chest infections, ear/nose/throat symptoms, and infertility. We hereby report three unusual cases of this rare entity – an infertile male with azoospermia in whom Bochdalek's diaphragmatic hernia coexisted, another case of an infertile female, and a third of an infertile male with oligospermia. The need for a high index of suspicion to make an early diagnosis cannot be overemphasized in such patients so that wherever possible, options for timely treatment of infertility may be offered and unnecessary evaluation of symptoms is avoided.
PMCID: PMC3519024  PMID: 23243352
Bronchiectasis; Kartagener's syndrome; sinusitis; situs inversus
12.  Locally invasive pulmonary inflammatory myofibroblastic tumors in children 
Two uncommon cases of locally invasive pulmonary inflammatory myofibroblastic tumor are reported. Diagnosis was established by a prior thoracotomy and incisional biopsy. Complete excision was curative and both children remain asymptomatic at last follow up.
PMCID: PMC3409906  PMID: 22869984
Inflammatory myofibroblastic tumors; inflammatory pseudotumors; pulmonary tumors
13.  A microplate technique to simultaneously assay calcium accumulation in endoplasmic reticulum and SERCA release of inorganic phosphate 
Traditional analyses of calcium homeostasis have separately quantified either calcium accumulation or release mechanisms. To define the system as a whole, however, requires multiple experimental techniques to examine both accumulation and release. Here we describe a technique that couples the simultaneous quantification of radio-labeled calcium accumulation in endoplasmic reticulum (ER) microsomes with the release of inorganic phosphate (Pi) by the hydrolytic activity of sarco-endoplasmic reticulum calcium ATPase (SERCA) all in the convenience of a 96-well format.
PMCID: PMC3388579  PMID: 22472432
Calcium; SERCA activity; Microsomes; Inorganic phosphate; Malachite green
14.  Glucose-6-phosphate reduces calcium accumulation in rat brain endoplasmic reticulum 
Brain cells expend large amounts of energy sequestering calcium (Ca2+), while loss of Ca2+ compartmentalization leads to cell damage or death. Upon cell entry, glucose is converted to glucose-6-phosphate (G6P), a parent substrate to several metabolic major pathways, including glycolysis. In several tissues, G6P alters the ability of the endoplasmic reticulum (ER) to sequester Ca2+. This led to the hypothesis that G6P regulates Ca2+ accumulation by acting as an endogenous ligand for sarco-endoplasmic reticulum calcium ATPase (SERCA). Whole brain ER microsomes were pooled from adult male Sprague-Dawley rats. Using radio-isotopic assays, 45Ca2+ accumulation was quantified following incubation with increasing amounts of G6P, in the presence or absence of thapsigargin, a potent SERCA inhibitor. To qualitatively assess SERCA activity, the simultaneous release of inorganic phosphate (Pi) coupled with Ca2+ accumulation was quantified. Addition of G6P significantly and decreased Ca2+ accumulation in a dose-dependent fashion (1–10 mM). The reduction in Ca2+ accumulation was not significantly different that seen with addition of thapsigargin. Addition of glucose-1-phosphate or fructose-6-phosphate, or other glucose metabolic pathway intermediates, had no effect on Ca2+ accumulation. Further, the release of Pi was markedly decreased, indicating G6P-mediated SERCA inhibition as the responsible mechanism for reduced Ca2+ uptake. Simultaneous addition of thapsigargin and G6P did decrease inorganic phosphate in comparison to either treatment alone, which suggests that the two treatments have different mechanisms of action. Therefore, G6P may be a novel, endogenous regulator of SERCA activity. Additionally, pathological conditions observed during disease states that disrupt glucose homeostasis, may be attributable to Ca2+ dystasis caused by altered G6P regulation of SERCA activity.
PMCID: PMC3330244  PMID: 22529775
glucose-6-phosphate; G6P; calcium; SERCA; microsome; endoplasmic reticulum; thapsigargin; brain
Synapse (New York, N.Y.)  2010;64(8):649-653.
In vitro experiments have shown that protoporphyrin IX (PPIX) binds to the translocator protein 18 kD (TSPO), which transports cholesterol across the outer mitochondrial membrane. The purpose of this study was to examine whether binding of PPIX to TSPO can also be detected in vivo using positron emission tomography (PET) and [11C]PBR28, a radioligand that binds with high affinity and selectivity to TSPO. Rats were injected with a high dose of 5-aminolevulinic acid (ALA, 200 mg/kg i.v.), which is a precursor for PPIX. ALA-pretreatment significantly decreased the uptake of [11C]PBR28 in TSPO-rich organs such as heart, kidneys, lungs, parotid glands, and spleen by 57% to 80%. As a control experiment, injection of a receptor-saturating does of PK 11195, which is selective for TSPO, produced a pattern of displacement similar to that after ALA but with greater magnitude (88% to 97%). This study provides the first evidence that PPIX binds in vivo to TSPO. Although PPIX at physiological concentrations would likely occupy an insignificant percentage of TSPOs, it does reach high enough concentrations in porphyria to occupy and have pharmacological effects via this target.
PMCID: PMC2889214  PMID: 20336621
Peripheral benzodiazepine receptor; 5-Aminolevulinic acid; porphyria
16.  Phosphorylation Status of Pyruvate Dehydrogenase Distinguishes Metabolic Phenotypes of Cultured Rat Brain Astrocytes and Neurons 
Glia  2010;58(10):1168-1176.
Glucose metabolism in nervous tissue has been proposed to occur in a compartmentalized manner with astrocytes contributing largely to glycolysis and neurons being the primary site of glucose oxidation. However, mammalian astrocytes and neurons both contain mitochondria and it remains unclear why in culture neurons oxidize glucose, lactate, and pyruvate to a much larger extent than astrocytes. The objective of this study was to determine whether pyruvate metabolism is differentially regulated in cultured neurons vs. astrocytes. Expression of all components of the pyruvate dehydrogenase complex (PDC), the rate-limiting step for pyruvate entry into the Krebs cycle, was determined in cultured astrocytes and neurons. In addition, regulation of PDC enzymatic activity in the two cell types via protein phosphorylation was examined. We show that all components of the PDC are expressed in both cell types in culture but that PDC activity is kept strongly inhibited in astrocytes through phosphorylation of the pyruvate dehydrogenase alpha subunit (PDHα). In contrast, neuronal PDC operates close to maximal levels with much lower levels of phosphorlyated PDHα. Dephosphorylation of astrocytic PDHα restores PDC activity and lowers lactate production. Our findings suggest that the glucose metabolism of astrocytes and neurons may be far more flexible than previously believed.
PMCID: PMC2915787  PMID: 20544852
Glycolysis; oxidation; lactate; dichloroacetate
17.  Overgrowth of costochondral graft in temporomandibular joint ankylosis: An unusual case 
Costochondral graft (CCG) replacement of the mandibular condyle was first described by Gilles in 1920. Since then CCGs have gained increasing popularity in reconstruction of the TMJ and condyle in children. The influence of CCGs on mandibular growth and function is not known in detail. Adaptation of the graft has been observed to be better in children, but CCGs have also been shown to grow in adult patients. One of the major disadvantages of the CCGs is its growth pattern, which is extremely unpredictable and may manifest as excessive growth or no growth at all. A mandibular overgrowth on the grafted site can actually be more troublesome than lack of growth. Furthermore, maxillary growth is proportionality influenced by vertical mandibular growth of the graft. This is a report of such a case in which a bizarre overgrowth of the graft was seen following a reconstruction of TMJ by CCG and the devastating outcomes of the treatment. He required one further resection because the grafted tissue had overgrown five years later.
PMCID: PMC3343407  PMID: 22639507
Costochondral graft; overgrowth; TMJ ankylosis
18.  Intestinal parasitic infestation among children in a semi-urban Indian population 
Tropical Parasitology  2011;1(2):104-107.
Survey on the prevalence of various intestinal parasitic infestations in different geographic regions is a prerequisite to obtain an accurate understanding of the burden and cause of intestinal parasitic infestations in a particular area. The aim of the present study was to determine the intestinal parasitic infestation among children in a semi-urban area.
Materials and Methods:
A total of 335 stool samples were collected, processed, and microscopically examined for intestinal parasites.
One hundred twenty-eight (38%) stool samples showed presence of ova/cysts. Multiple parasites were seen in 42 (32.8%) samples. Among the protozoans, Entamoeba histolytica (55.3%) was the most common followed by Giardia lamblia (40.4%). Ascaris lumbricoides and Hymenolepis nana (24.2%) were the most common helminths detected.
In most of the cases, intestinal parasitic infestation spreads due to low standards of personal hygiene, poor sanitation, non-usage of toilets and an illiterate population, thus suggesting regular surveys to help in devising optimum methods of control.
PMCID: PMC3593484  PMID: 23508675
Diarrhea; intestinal parasites; semi-urban population
20.  The population genomics of begomoviruses: global scale population structure and gene flow 
Virology Journal  2010;7:220.
The rapidly growing availability of diverse full genome sequences from across the world is increasing the feasibility of studying the large-scale population processes that underly observable pattern of virus diversity. In particular, characterizing the genetic structure of virus populations could potentially reveal much about how factors such as geographical distributions, host ranges and gene flow between populations combine to produce the discontinuous patterns of genetic diversity that we perceive as distinct virus species. Among the richest and most diverse full genome datasets that are available is that for the dicotyledonous plant infecting genus, Begomovirus, in the Family Geminiviridae. The begomoviruses all share the same whitefly vector, are highly recombinogenic and are distributed throughout tropical and subtropical regions where they seriously threaten the food security of the world's poorest people.
We focus here on using a model-based population genetic approach to identify the genetically distinct sub-populations within the global begomovirus meta-population. We demonstrate the existence of at least seven major sub-populations that can further be sub-divided into as many as thirty four significantly differentiated and genetically cohesive minor sub-populations. Using the population structure framework revealed in the present study, we further explored the extent of gene flow and recombination between genetic populations.
Although geographical barriers are apparently the most significant underlying cause of the seven major population sub-divisions, within the framework of these sub-divisions, we explore patterns of gene flow to reveal that both host range differences and genetic barriers to recombination have probably been major contributors to the minor population sub-divisions that we have identified. We believe that the global Begomovirus population structure revealed here could facilitate population genetics studies into how central parameters of population genetics namely selection, recombination, mutation, gene flow, and genetic drift shape the global begomovirus diversity.
PMCID: PMC2945956  PMID: 20828421
21.  Rifampicin-induced thrombocytopenia 
Indian Journal of Pharmacology  2010;42(4):240-242.
In the treatment of tuberculosis there are special therapeutic problems related to adverse effects of drugs, compliance to treatment, and microbial resistance. Thrombocytopenia is an uncommon but potentially fatal adverse effect of certain anti-tubercular drugs when the incriminating drug is taken by a susceptible individual. We report a case of rifampicin-induced thrombocytopenia, which although rare, needs attention.
PMCID: PMC2941616  PMID: 20927251
Rifampicin; thrombocytopenia; tuberculosis
22.  Mitochondrial mutations contribute to HIF1α accumulation via increased reactive oxygen species and upregulated PDK2 in head and neck squamous cell carcinoma 
Mitochondrial mutations have been identified in head and neck squamous cell carcinoma (HNSCC), but the pathways by which phenotypic effects of these mutations are exerted remain unclear. Previously, we found that mitochondrial ND2 mutations in primary HNSCC increased reactive oxygen species (ROS) and conferred an aerobic, glycolytic phenotype with HIF1α accumulation and increased cell growth. The purpose of present study was to examine the pathways relating these alterations.
Experimental Design
Mitochondrial mutant and wild-type ND2 constructs were transfected into oral keratinocyte immortal cell line OKF6 and head and neck cancer cell line JHU-O19 and established transfectants. The protein levels of HIF1α, pyruvate dehydrogenease (PDH), phospho-PDH, and pyruvate dehydrogenease kinase (PDK) 2, together with ROS generation, were compared between the mutant and wild type. Meanwhile, the effects of small molecule inhibitors targeting PDK2, and mitochondrial targeted catalase, were evaluated on the ND2 mutant transfectants.
We determined that ND2 mutant downregulated PDH expression via upregulated PDK2, with an increase in phospho-PDH. Inhibition of PDK2 with dichloroacetate decreased HIF1α accumulation and reduced cell growth. Extracellular treatment with hydrogen peroxide, a ROS mimic, increased PDK2 expression and HIF1α expression, and introduction of mitochondrial targeted catalase decreased mitochondrial mutation mediated PDK2 and HIF1α expression and suppressed cell growth.
Our findings suggest that mitochondrial ND2 mutation contributes to HIF1α accumulation via increased ROS production, upregulation of PDK2, attenuating PDH activity, thereby increasing pyruvate, resulting in HIF1α stabilization. This may provide insight into a potential mechanism by which mitochondrial mutations contribute to HNSCC development.
PMCID: PMC2729126  PMID: 19147752
Mitochondrial mutation; Head and neck cancer; HIF1α; Glycolysis; Pyruvate; Reactive oxygen species; PDK2
23.  Increased Lactate Levels and Reduced pH in Postmortem Brains of Schizophrenics: Medication Confounds 
Journal of neuroscience methods  2007;169(1):208-213.
A number of postmortem studies have found decreased pH in brains of patients with schizophrenia. Insofar as lower pH has been associated with decreased mRNA expression in postmortem human brain, decreased pH in schizophrenia may represent an important potential confound in comparisons between patients and controls. We hypothesized that decreased pH may be related to increased concentration of lactic acid. However, in contrast to the previous notion that an increase in lactic acid represents evidence for primary metabolic abnormalities in schizophrenia, we hypothesized that this increase is secondary to prior antipsychotic treatment. We have tested this by first demonstrating that lactate levels in the cerebellum of patients with schizophrenia (n=35) are increased relative to control subjects (n=42) by 28%, p=0.001. Second, we have shown that there is an excellent correlation between lactate levels in the cerebellum and pH, and that this correlation is particularly strong in patients (r=− 0.78, p=3e-6). Third, we have shown in rats that chronic haloperidol (0.8 mg/kg/day) and clozapine (5 mg/kg/day) increase lactic acid concentration in the frontal cortex relative to vehicle (by 31% and 22% respectively, p<0.01). These data suggest that lactate increases in postmortem human brain of patients with schizophrenia are associated with decreased pH and that these changes are possibly related to antipsychotic treatment rather than a primary metabolic abnormality in the prefrontal cortex of patients with schizophrenia.
PMCID: PMC2288700  PMID: 18177946
24.  Abnormal energy regulation in early life: childhood gene expression may predict subsequent chronic mountain sickness 
BMC Pediatrics  2008;8:47.
Life at altitude depends on adaptation to ambient hypoxia. In the Andes, susceptibility to chronic mountain sickness (CMS), a clinical condition that occurs to native highlanders or to sea level natives with prolonged residence at high altitude, remains poorly understood. We hypothesized that hypoxia-associated gene expression in children of men with CMS might identify markers that predict the development of CMS in adults. We assessed distinct patterns of gene expression of hypoxia-responsive genes in children of highland Andean men, with and without CMS.
We compared molecular signatures in children of highland (HA) men with CMS (n = 10), without CMS (n = 10) and in sea level (SL) children (n = 20). Haemoglobin, haematocrit, and oxygen saturation were measured. Gene expression in white cells was assessed at HA and then, in the same subjects, within one hour of arrival at sea level.
HA children showed higher expression levels of genes regulated by HIF (hypoxia inducible factor) and lower levels of those involved in glycolysis and in the tricarboxilic acid (TCA) cycle. Pyruvate dehydrogenase kinase 1(PDK1) and HIF prolyl hydroxylase 3 (HPH3) mRNA expressions were lowest in children of CMS fathers at altitude. At sea level the pattern of gene expression in the 3 children's groups was indistinguishable.
The molecular signatures of children of CMS patients show impaired adaptation to hypoxia. At altitude children of CMS fathers had defective coupling between glycolysis and mitochondria TCA cycle, which may be a key mechanism/biomarker for adult CMS. Early biologic markers of disease susceptibility in Andeans might impact health services and social planning.
PMCID: PMC2582028  PMID: 18954447

Results 1-25 (28)