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1.  Both the Charged Linker Region and ATPase Domain of Hsp90 Are Essential for Rad51-Dependent DNA Repair 
Eukaryotic Cell  2014;14(1):64-77.
The inhibition of Hsp90 in cancerous cells has been correlated with the reduction in double-strand break (DSB repair) activity. However, the precise effect of Hsp90 on the DSB repair pathway in normal cells has remained enigmatic. Our results show that the Hsp82 chaperone, the ortholog of mammalian Hsp90, is indispensable for homologous-recombination (HR)-mediated DNA repair in the budding yeast Saccharomyces cerevisiae. A considerable reduction in cell viability is observed in an Hsp82-inactivated mutant upon methyl methanesulfonate (MMS) treatment as well as upon UV treatment. The loss of Hsp82 function results in a dramatic decrease in gene-targeting efficiency and a marked decrease in the endogenous levels of the key recombination proteins Rad51 and Rad52 without any notable change in the levels of RAD51 or RAD52 transcripts. Our results establish Rad51 as a client of Hsp82, since they interact physically in vivo, and also show that when Hsp82 is inhibited by 17-AAG, Rad51 undergoes proteasomal degradation. By analyzing a number of point mutants with mutations in different domains of Hsp82, we observe a strong association between the sensitivity of an ATPase mutant of Hsp82 to DNA damage and the decreases in the amounts of Rad51 and Rad52 proteins. The most significant observations include the dramatic abrogation of HR activity and the marked decrease in Rad51 focus formation in the charged linker deletion mutant of Hsp82 upon MMS treatment. The charged linker region of Hsp82 is evolutionarily conserved in all eukaryotes, but until now, no biological significance has been assigned to it. Our findings elucidate the importance of this region in DNA repair for the first time.
doi:10.1128/EC.00159-14
PMCID: PMC4279015  PMID: 25380755
2.  Heat Stress-Induced Cup9-Dependent Transcriptional Regulation of SIR2 
Molecular and Cellular Biology  2014;35(2):437-450.
The epigenetic writer Sir2 maintains the heterochromatin state of chromosome in three chromosomal regions, namely, the silent mating type loci, telomeres, and the ribosomal DNA (rDNA). In this study, we demonstrated the mechanism by which Sir2 is regulated under heat stress. Our study reveals that a transient heat shock causes a drastic reduction in the SIR2 transcript which results in sustained failure to initiate silencing for as long as 90 generations. Hsp82 overexpression, which is the usual outcome of heat shock treatment, leads to a similar downregulation of SIR2 transcription. Using a series of genetic experiments, we have established that heat shock or Hsp82 overexpression causes upregulation of CUP9 that, in turn, represses SIR2 transcription by binding to its upstream activator sequence. We have mapped the cis regulatory element of SIR2. Our study shows that the deletion of cup9 causes reversal of the Hsp82 overexpression phenotype and upregulation of SIR2 expression in heat-induced Hsp82-overexpressing cells. On the other hand, we found that Cup9 overexpression represses SIR2 transcription and leads to a failure in the establishment of heterochromatin. The results of our study highlight the mechanism by which environmental factors amend the epigenetic configuration of chromatin.
doi:10.1128/MCB.01046-14
PMCID: PMC4272432  PMID: 25384977
3.  Identification of Plasmodium falciparum DNA Repair Protein Mre11 with an Evolutionarily Conserved Nuclease Function 
PLoS ONE  2015;10(5):e0125358.
The eukaryotic Meiotic Recombination protein 11 (Mre11) plays pivotal roles in the DNA damage response (DDR). Specifically, Mre11 senses and signals DNA double strand breaks (DSB) and facilitates their repair through effector proteins belonging to either homologous recombination (HR) or non-homologous end joining (NHEJ) repair mechanisms. In the human malaria parasite Plasmodium falciparum, HR and alternative-NHEJ have been identified; however, little is known about the upstream factors involved in the DDR of this organism. In this report, we identify a putative ortholog of Mre11 in P. falciparum (PfalMre11) that shares 22% sequence similarity to human Mre11. Homology modeling reveals striking structural resemblance of the predicted PfalMre11 nuclease domain to the nuclease domain of Saccharomyces cerevisiae Mre11 (ScMre11). Complementation analyses reveal functional conservation of PfalMre11 nuclease activity as demonstrated by the ability of the PfalMre11 nuclease domain, in conjunction with the C-terminal domain of ScMre11, to functionally complement an mre11 deficient yeast strain. Functional complementation was virtually abrogated by an amino acid substitution in the PfalMre11 nuclease domain (D398N). PfalMre11 is abundant in the mitotically active trophozoite and schizont stages of P. falciparum and is up-regulated in response to DNA damage, suggesting a role in the DDR. PfalMre11 exhibits physical interaction with PfalRad50. In addition, yeast 2-hybrid studies show that PfalMre11 interacts with ScRad50 and ScXrs2, two important components of the well characterized Mre11-Rad50-Xrs2 complex which is involved in DDR signaling and repair in S. cerevisiae, further supporting a role for PfalMre11 in the DDR. Taken together, these findings provide evidence that PfalMre11 is an evolutionarily conserved component of the DDR in Plasmodium.
doi:10.1371/journal.pone.0125358
PMCID: PMC4418825  PMID: 25938776
4.  Inhibition of nucleoporin member Nup214 expression by miR-133b perturbs mitotic timing and leads to cell death 
Molecular Cancer  2015;14:42.
Background
Nucleoporins mediate nucleocytoplasmic exchange of macromolecules and several have been assigned active mitotic functions. Nucleoporins can participate in various mitotic functions like spindle assembly, kinetochore organisation and chromosome segregation- important for genome integrity. Pathways to genome integrity are frequently deregulated in cancer and many are regulated in part by microRNAs. Indeed, altered levels of numerous microRNAs have frequently been associated with tumorigenesis. Here, we unveil a microRNA-mediated regulation of the nucleoporin Nup214 and its downstream effect on genome integrity.
Methods
Databases/bioinformatic tools such as miRBase, Oncomine and RNAhybrid predicted Nup214 as a miR-133b target. To validate this, we used luciferase reporter assays, Real-Time PCR and immuno-blotting. Flow cytometry and immuno-blots of mitotic markers were used to analyse cell cycle pattern upon thymidine synchronization and miR-133b treatment. Mitotic indices and chromosomal abnormalities were assessed by immuno-fluorescence for FITC-tagged phospho-H3 as well as video-microscopy for GFP-tagged histone H4. Annexin V/propidium iodide staining, caspase3/PARP cleavage and colony formation assays were done to investigate cell death upon either miR-133b transfection or NUP214 knockdown by siRNA. UPCI:SCC084, HCT116, HeLa-H4-pEGFP and HEK293 (human oral squamous cell carcinoma, colorectal, cervical carcinomas and embryonic kidney cell lines, respectively) were used. miR-133b and NUP214 expressions were validated in cancer cell lines and tissues by Real-Time PCR.
Results
Examination of head and neck tumour tissues and cancer cell lines revealed that Nup214 and miR-133b expressions are negatively correlated. In vitro, Nup214 was significantly downregulated by ectopic miR-133b. This downregulation elevated mitotic indices and delayed degradation of mitotic marker proteins cyclinB1 and cyclinA and dephosphorylation of H3. Moreover, this mitotic delay enhanced chromosomal abnormalities and apoptosis.
Conclusions
We have identified NUP214, a member of the massive nuclear pore complex, as a novel miR-133b target. Thus, we have shown a hitherto unknown microRNA regulation of mitosis mediated by a member of the nucleoporin family. Based on observations, we also raise some hypotheses regarding transport-dependent/independent functions of Nup214 in this study. Our results hence attempt to explain why miR-133b is generally downregulated in tumours and lay out the potential for Nup214 as a therapeutic target in the treatment of cancer.
Electronic supplementary material
The online version of this article (doi:10.1186/s12943-015-0299-z) contains supplementary material, which is available to authorized users.
doi:10.1186/s12943-015-0299-z
PMCID: PMC4335456  PMID: 25743594
Nucleoporin; Nup214; miR-133b; Mitosis; Apoptosis; Cell cycle; MicroRNA; Cancer; Head and neck cancer; Chromosomal abnormality
5.  Radicicol Confers Mid-Schizont Arrest by Inhibiting Mitochondrial Replication in Plasmodium falciparum 
Radicicol, an antifungal antibiotic, was previously identified as a compound having antimalarial activity. However, its mechanism of action in Plasmodium falciparum was not elucidated. While characterizing its antimalarial function, we observed that radicicol manifested two distinct developmental defects in cultured P. falciparum in a concentration-dependent manner. At a low concentration of radicicol, a significant percentage of drug-treated parasites were arrested at the schizont stage, while at a higher concentration, the parasites were unable to multiply from schizont to ring. Also, the newly formed rings and trophozoites were extremely delayed in development, eventually leading to cell death. We intended to characterize the potential molecular target of radicicol at its sublethal doses. Our results demonstrated that radicicol specifically impaired mitochondrial replication. This decrement was associated with a severalfold increment of the topoisomerase VIB transcript as well as protein in treated cells over that of untreated parasites. Topoisomerase VIB was found to be localized in the organelle fraction. Our docking study revealed that radicicol fits into the Bergerat fold of Pf topoisomerase VIB present in its ATPase domain. Altogether, these data allow us to conclude that P. falciparum topoisomerase VIB might be one of the targets of radicicol causing inhibition of mitochondrial replication. Hence, radicicol can be suitably employed to explore the mitochondrial physiology of malaria parasites.
doi:10.1128/AAC.02519-13
PMCID: PMC4136038  PMID: 24841259
6.  Myeloproliferative neoplasms working group consensus recommendations for diagnosis and management of primary myelofibrosis, polycythemia vera, and essential thrombocythemia 
According to the 2008 revision of the World Health Organization (WHO) classification of myeloid malignancies, philadelphia chromosome (Ph)-negative myeloproliferative neoplasms (MPNs) include clonal, hematologic disorders such as polycythemia vera, primary myelofibrosis, and essential thrombocythemia.Recent years have witnessed major advances in the understanding of the molecular pathophysiology of these rare subgroups of chronic, myeloproliferative disorders. Identification of somatic mutations in genes associated with pathogenesis and evolution of these myeloproliferative conditions (Janus Kinase 2; myeloproliferative leukemia virus gene; calreticulin) led to substantial changes in the international guidelines for diagnosis and treatment of Ph-negative MPN during the last few years.The MPN-Working Group (MPN-WG), a panel of hematologists with expertise in MPN diagnosis and treatment from various parts of India, examined applicability of this latest clinical and scientific evidence in the context of hematology practice in India.This manuscript summarizes the consensus recommendations formulated by the MPN-WG that can be followed as a guideline for management of patients with Ph-negative MPN in the context of clinical practice in India.
doi:10.4103/0971-5851.151770
PMCID: PMC4363847  PMID: 25810569
Essential thrombocythemia; myeloproliferative neoplasms; polycythemia vera; primary myelofibrosis
7.  Understanding the patterns of antibiotic susceptibility of bacteria causing urinary tract infection in West Bengal, India 
Urinary tract infection (UTI) is one of the most common infectious diseases at the community level. In order to assess the adequacy of empirical therapy, the susceptibility of antibiotics and resistance pattern of bacteria responsible for UTI in West Bengal, India, were evaluated throughout the period of 2008–2013. The infection reports belonging to all age groups and both sexes were considered. Escherichia coli was the most abundant uropathogen with a prevalence rate of 67.1%, followed by Klebsiella spp. (22%) and Pseudomonas spp. (6%). Penicillin was least effective against UTI-causing E. coli and maximum susceptibility was recorded for the drugs belonging to fourth generation cephalosporins. Other abundant uropathogens, Klebsiella spp., were maximally resistant to broad-spectrum penicillin, followed by aminoglycosides and third generation cephalosporin. The antibiotic resistance pattern of two principal UTI pathogens, E. coli and Klebsiella spp. in West Bengal, appears in general to be similar to that found in other parts of the Globe. Higher than 50% resistance were observed for broad-spectrum penicillin. Fourth generation cephalosporin and macrolides seems to be the choice of drug in treating UTIs in Eastern India. Furthermore, improved maintenance of infection incident logs is needed in Eastern Indian hospitals in order to facilitate regular surveillance of the occurrence of antibiotic resistance patterns, since such levels continue to change.
doi:10.3389/fmicb.2014.00463
PMCID: PMC4166956  PMID: 25278932
antibiotic susceptibility; uropathogens; West Bengal; India; pathogenic bacteria
8.  A study to correlate histopathology, biochemical marker and immunohistochemical expression of sex-steroid receptors in prostatic growth 
Prostate gland is a fibromusculoglandular structure situated at the neck of urinary bladder. So, enlargement or growth of prostate due to nodular hyperplasia (NHP) or prostatic intraepithelial neoplasia (PIN) or adenocarcinoma may give rise to bladder outlet obstruction. Malignant growth i.e., PIN or adenocarcinoma cases are associated with increased blood level of prostate-specific antigen (PSA) and increased expression of different sex-steroid receptors because the growth is dependent on the interactions of androgen, progesterone and estrogen. The aim of our study is to correlate the histopathology, PSA levels and expression of different sex-steroid receptors by immunohistochemistry in different prostatic growth lesions. Among the total 50 cases received, inclusive of transurethral resection of prostate (TURP), transrectal ultrasound-guided biopsy and radical prostatectomy, 34 cases were diagnosed as NHP, 4 cases as PIN and 12 cases as adenocarcinoma histopathologically. Serum PSA values above 10 ng/ml were seen in 2 cases of PIN and 11 cases of adenocarcinoma and none of NHP. Estrogen receptor (ER) () expressions were negative in all cases. Progesterone receptor (PR) expressions were strongly positive in 35% cases of both NHP and adenocarcinoma, whereas androgen receptor (AR) expressions were strong among all cases of adenocarcinoma and only in four cases of NHP. By observing these findings it can be suggested that antiandrogen and antiprogesterone therapy simultaneously will do better than antiandrogen alone in treating prostatic growth lesions.
doi:10.4103/0971-5851.133719
PMCID: PMC4080662  PMID: 25006283
Androgen receptor; immunohistochemistry; progesterone receptor; prostatic growth; prostate-specific antigen
9.  Thyroid disorders in pregnancy 
Thyroid disorders are common in pregnancy and the most common disorder is subclinical hypothyroidism. Due to the complex hormonal changes during pregnancy, it is important to remember that thyroxine requirements are higher in pregnancy. According to recent American Thyroid Association (ATA) guidelines, the recommended reference ranges for TSH are 0.1 to 2.5 mIU/L in the first trimester, 0.2 to 3.0 mIU/L in the second trimester, and 0.3 to 3.0 mIU/L in the third trimester. Maternal hypothyroidism is an easily treatable condition that has been associated with increased risk of low birth weight, fetal distress, and impaired neuropsychological development. Hyperthyroidism in pregnancy is less common as conception is a problem. Majority of them are due to Graves’ disease, though gestational hyperthyroidism is to be excluded. Preferred drug is propylthiouracil (PTU) with the target to maintain free T4 in upper normal range. Doses can be reduced in third trimester due to the immune-suppressant effects of pregnancy. Early and effective treatment of thyroid disorder ensures a safe pregnancy with minimal maternal and neonatal complications.
doi:10.4103/2230-8210.104031
PMCID: PMC3603018  PMID: 23565370
Thyroid disorders; pregnancy; hypothyroidism
10.  Physicochemical and biological factors controlling water column metabolism in Sundarbans estuary, India 
Aquatic Biosystems  2012;8:26.
Background
Sundarbans is the single largest deltaic mangrove forest in the world, formed at estuarine phase of the Ganges - Brahmaputra river system. Primary productivity of marine and coastal phytoplankton contributes to 15% of global oceanic production. But unfortunately estuarine dynamics of tropical and subtropical estuaries have not yet received proper attention in spite of the fact that they experience considerable anthropogenic interventions and a baseline data is required for any future comparison. This study is an endeavor to this end to estimate the primary productivity (gross and net), community respiration and nitrification rates in different rivers and tidal creeks around Jharkhali island, a part of Sundarbans estuary surrounded by the mangrove forest during a period of three years starting from November’08 to October’11.
Results
Various physical and chemical parameters of water column like pH, temperature, conductivity, dissolved oxygen, turbidity, suspended particulate matter, secchi disc index, tidal fluctuation and tidal current velocity, standing crop and nutrients were measured along with water column productivity. Relationship of net water column productivity with algal biomass (standing crop), nutrient loading and turbidity were determined experimentally. Correlations of bacterial abundance with community respiration and nitrification rates were also explored. Annual integrated phytoplankton production rate of this tidal estuary was estimated to be 151.07 gC m-2 y-1. Gross primary productivity showed marked inter annual variation being lowest in monsoon and highest in postmonsoon period.
Conclusion
Average primary production was a function of nutrient loading and light penetration in the water column. High aquatic turbidity, conductivity and suspended particulate matter were the limiting factors to attenuate light penetration with negative influence on primary production. Community respiration and nitrification rates of the estuary were influenced by the bacterial abundance. The estuary was phosphorus limited in postmonsoon whereas nitrogen-limited in premonsoon and monsoon period. High algal biomass and primary productivity indicated the estuary to be in eutrophic state in most of the time throughout the year. Our study also indicated a seasonal shifting between autotrophic and heterotrophic conditions in Sundarban estuarine ecosystem and it is a tropical, well mixed (high tidal influx) and marine dominated (no fresh water connection) system.
doi:10.1186/2046-9063-8-26
PMCID: PMC3543332  PMID: 23083531
Net ecosystem metabolism; Gross primary productivity; Community respiration; Nitrification; Nutrient load; Sundarban estuary
11.  Characterization of Rad51 from Apicomplexan Parasite Toxoplasma gondii: An Implication for Inefficient Gene Targeting 
PLoS ONE  2012;7(7):e41925.
Repairing double strand breaks (DSBs) is absolutely essential for the survival of obligate intracellular parasite Toxoplasma gondii. Thus, DSB repair mechanisms could be excellent targets for chemotherapeutic interventions. Recent genetic and bioinformatics analyses confirm the presence of both homologous recombination (HR) as well as non homologous end joining (NHEJ) proteins in this lower eukaryote. In order to get mechanistic insights into the HR mediated DSB repair pathway in this parasite, we have characterized the key protein involved in homologous recombination, namely TgRad51, at the biochemical and genetic levels. We have purified recombinant TgRad51 protein to 99% homogeneity and have characterized it biochemically. The ATP hydrolysis activity of TgRad51 shows a higher KM and much lower kcat compared to bacterial RecA or Rad51 from other related protozoan parasites. Taking yeast as a surrogate model system we have shown that TgRad51 is less efficient in gene conversion mechanism. Further, we have found that TgRad51 mediated gene integration is more prone towards random genetic loci rather than targeted locus. We hypothesize that compromised ATPase activity of TgRad51 is responsible for inefficient gene targeting and poor gene conversion efficiency in this protozoan parasite. With increase in homologous flanking regions almost three fold increments in targeted gene integration is observed, which is similar to the trend found with ScRad51. Our findings not only help us in understanding the reason behind inefficient gene targeting in T. gondii but also could be exploited to facilitate high throughput knockout as well as epitope tagging of Toxoplasma genes.
doi:10.1371/journal.pone.0041925
PMCID: PMC3408395  PMID: 22860032
12.  HSP90 Controls SIR2 Mediated Gene Silencing 
PLoS ONE  2011;6(8):e23406.
In recent years, Hsp90 is found to interact with several telomeric proteins at various phases of cell cycle. The Hsp90 chaperone system controls assembly and disassembly of telomere structures and thus maintains the dynamic state of telomere. Here, for the first time we report that the activity of another telomeric protein Sir2p is modulated by Hsp82, the ortholog of Hsp90 from budding yeast (Saccharomyces cerevisiae). In a temperature sensitive Hsp90 deficient yeast strain (iG170Dhsp82), less abundant Sir2p is observed, resulting in de-repression of telomere silencing and a complete loss of mating type silencing. Intriguingly, over expression of Hsp90, either by exposing cells to heat shock or by introducing HSP82 overexpression plasmid also yields reduced level of Sir2p, with a consequential loss of telomere silencing. Thus, Hsp90 homeostasis maintains the cellular pool of Sir2p and thereby controls the reversible nature of telomere silencing. Interestingly, such regulation is independent of one of its major co-chaperones Sba1 (human ortholog of p23).
doi:10.1371/journal.pone.0023406
PMCID: PMC3150437  PMID: 21829731
13.  Dynamics of Sundarban estuarine ecosystem: eutrophication induced threat to mangroves 
Saline Systems  2010;6:8.
Background
Sundarbans is the largest chunk of mangrove forest and only tiger mangrove land in the world. Compared to the rich species diversity and uniqueness, very few studies have so far been conducted here, mainly due to its inaccessibility. This study explores water quality, density of biomass, species diversity, phytoplankton abundance and bacterial population of a tidal creek in Sunderban estuary during the post and pre monsoon period of 2008-09.
Results
Phytoplankton community was observed to be dominated by diatoms (Biacillariophyceae) followed by Pyrrophyceae (Dinoflagellates) and Chlorophyceae. A total of 46 taxa belonging to 6 groups were recorded. Other algal groups were Cyanophyceae, Euglenophyceae and Chrysophyceae. Species diversity was highest in summer (March) and lowest in winter season (November) in all the sample stations indicating its close correlation with ambient temperature. Species evenness was fairly high in all five stations throughout the study period. Present study indicated that dissolved oxygen, nutrients and turbidity are the limiting factors for the phytoplankton biomass. The estuary was in eutrophic condition (Chlorophyll-a ≥10 μg/L) in winter. During the month of May phytoplankton biomass declined and at high salinity level (21.2PSU) new phytoplankton species take over, which are definitely better resilient to the high saline environment. Bio-indicator species like Polykrikos schwartzil, Dinophysis norvegica and Prorocentrum concavum points to moderately polluted water quality of the estuary.
Conclusion
Eutrophication as well as presence of toxic Dinoflagellates and Cyanophyceae in the tidal creek of Sundarban estuary definitely revealed the deteriorated status of the water quality. The structure and function of the mangrove food web is unique, driven by both marine and terrestrial components. But little attention has been paid so far to the adaptive responses of mangrove biota to the various disturbances, and now our work unfolds the fact that marine status of Sundarban estuary is highly threatened which in turn will affect the ecology of the mangrove. This study indicates that ecosystem dynamics of the world heritage site Sundarban may facilitate bioinvasion putting a question mark on the sustainability of mangroves.
doi:10.1186/1746-1448-6-8
PMCID: PMC2928246  PMID: 20699005
15.  Correlation between physical anomaly and behavioral abnormalities in Down syndrome 
Objective:
The minor physical anomaly (MPA) is believed to reflect abnormal development of the CNS. The aim is to find incidence of MPA and its behavioral correlates in Down syndrome and to compare these findings with the other causes of intellectual disability and normal population.
Materials and Methods:
One-hundred and forty intellectually disabled people attending a tertiary care set-up and from various NGOs are included in the study. The age-matched group from normal population was also studied for comparison. MPA are assessed by using Modified Waldrop scale and behavioral abnormality by Diagnostic assessment scale for severely handicapped (DASH II scale).
Results:
The Down syndrome group had significantly more MPA than other two groups and most of the MPA is situated in the global head region. There is strong correlation (P < 0.001) between the various grouped items of Modified Waldrop scale. Depression subscale is correlated with anomalies in the hands (P < 0.001), feet and Waldrop total items (P < 0.005). Mania item of DASH II scale is related with anomalies around the eyes (P < 0.001). Self-injurious behavior and total Waldrop score is negatively correlated with global head.
Conclusion:
Down syndrome group has significantly more MPA and a pattern of correlation between MPA and behavioral abnormalities exists which necessitates a large-scale study.
doi:10.4103/1817-1745.76096
PMCID: PMC3087984  PMID: 21559153
Behavioral abnormalities; correlation; Down syndrome; minor physical anomaly
16.  A Case of Corpus Callosum Agenesis Presenting with Recurrent Brief Depression 
Agenesis of corpus callosum can have various neuropsychiatric manifestations. Following case report highlights the case of a young man presenting with features of recurrent brief depressive disorder, each lasting for about 3 to 7 days, for over a year. He had history of occasional headache and episodes of swooning attack in between, usually precipitated by emotional events. His neuroimaging revealed agenesis of corpus callosum. He was experiencing swooning attacks as he became aware that some ‘unusual’ findings were present in his reports. Recurrent brief depression can be a manifestation of this congenital anomaly, and conversion disorder can be present as comorbid diagnosis perhaps due to ignorance and fear of this apparently innocuous congenital malformation.
doi:10.4103/0253-7176.63580
PMCID: PMC3168092  PMID: 21938102
Conversion disorder; corpus callosum agenesis; recurrent depression
17.  Regulation of Impaired Protein Kinase C Signaling by Chemokines in Murine Macrophages during Visceral Leishmaniasis  
Infection and Immunity  2005;73(12):8334-8344.
The protein kinase C (PKC) family regulates macrophage function involved in host defense against infection. In the case of Leishmania donovani infection, the impairment of PKC-mediated signaling is one of the crucial events for the establishment of parasite into the macrophages. Earlier reports established that C-C chemokines mediated protection against leishmaniasis via the generation of nitric oxide after 48 h. In this study, we investigated the role of MIP-1α and MCP-1 in the regulation of impaired PKC activity in the early hours (6 h) of infection. These chemokines restored Ca2+-dependent PKC activity and inhibited Ca2+-independent atypical PKC activity in L. donovani-infected macrophages under both in vivo and in vitro conditions. Pretreatment of macrophages with chemokines induced superoxide anion generation by activating NADPH oxidase components in infected cells. Chemokine administration in vitro induced the migration of infected macrophages and triggered the production of reactive oxygen species. In vivo treatment with chemokines significantly restricted the parasitic burden in livers as well as in spleens. Collectively, these results indicate a novel regulatory role of C-C chemokines in controlling the intracellular growth and multiplication of L. donovani, thereby demonstrating the antileishmanial properties of C-C chemokines in the disease process.
doi:10.1128/IAI.73.12.8334-8344.2005
PMCID: PMC1307035  PMID: 16299331
18.  Hyperthyroidism in an elderly patient 
Postgraduate Medical Journal  2000;76(899):597-598.
doi:10.1136/pmj.76.899.597a
PMCID: PMC1741720  PMID: 11032535
19.  iPSC-Derived Forebrain Neurons from FXS Individuals Show Defects in Initial Neurite Outgrowth 
Stem Cells and Development  2014;23(15):1777-1787.
Fragile X syndrome (FXS) is the most common form of inherited intellectual disability and is closely linked with autism. The genetic basis of FXS is an expansion of CGG repeats in the 5′-untranslated region of the FMR1 gene on the X chromosome leading to the loss of expression of the fragile X mental retardation protein (FMRP). The cause of FXS has been known for over 20 years, yet the full molecular and cellular consequences of this mutation remain unclear. Although mouse and fly models have provided significant understanding of this disorder and its effects on the central nervous system, insight from human studies is limited. We have created human induced pluripotent stem cell (iPSC) lines from fibroblasts obtained from individuals with FXS to enable in vitro modeling of the human disease. Three young boys with FXS who came from a well-characterized cohort representative of the range of affectedness typical for the syndrome were recruited to aid in linking cellular and behavioral phenotypes. The FMR1 mutation is preserved during the reprogramming of patient fibroblasts to iPSCs. Mosaicism of the CGG repeat length in one of the patient's fibroblasts allowed for the generation of isogenic lines with differing CGG repeat lengths from the same patient. FXS forebrain neurons were differentiated from these iPSCs and display defective neurite initiation and extension. These cells provide a well-characterized resource to examine potential neuronal deficits caused by FXS as well as the function of FMRP in human neurons.
doi:10.1089/scd.2014.0030
PMCID: PMC4103262  PMID: 24654675
20.  Molecular characterization of systemic sclerosis esophageal pathology identifies inflammatory and proliferative signatures 
Introduction
Esophageal involvement in patients with systemic sclerosis (SSc) is common, but tissue-specific pathological mechanisms are poorly understood. There are no animal scleroderma esophagus models and esophageal smooth muscle cells dedifferentiate in culture prohibiting in vitro studies. Esophageal fibrosis is thought to disrupt smooth muscle function and lead to esophageal dilatation, but autopsy studies demonstrate esophageal smooth muscle atrophy and the absence of fibrosis in the majority of SSc cases. Herein, we perform a detailed characterization of SSc esophageal histopathology and molecular signatures at the level of gene expression.
Methods
Esophageal biopsies were prospectively obtained during esophagogastroduodenoscopy in 16 consecutive SSc patients and 7 subjects without SSc. Upper and lower esophageal biopsies were evaluated for histopathology and gene expression.
Results
Individual patient’s upper and lower esophageal biopsies showed nearly identical patterns of gene expression. Similar to skin, inflammatory and proliferative gene expression signatures were identified suggesting that molecular subsets are a universal feature of SSc end-target organ pathology. The inflammatory signature was present in biopsies without high numbers of infiltrating lymphocytes. Molecular classification of esophageal biopsies was independent of SSc skin subtype, serum autoantibodies and esophagitis.
Conclusions
Proliferative and inflammatory molecular gene expression subsets in tissues from patients with SSc may be a conserved, reproducible component of SSc pathogenesis. The inflammatory signature is observed in biopsies that lack large inflammatory infiltrates suggesting that immune activation is a major driver of SSc esophageal pathogenesis.
Electronic supplementary material
The online version of this article (doi:10.1186/s13075-015-0695-1) contains supplementary material, which is available to authorized users.
doi:10.1186/s13075-015-0695-1
PMCID: PMC4518531  PMID: 26220546
21.  TET1-Mediated Hydroxymethylation Facilitates Hypoxic Gene Induction in Neuroblastoma 
Cell reports  2014;7(5):1343-1352.
SUMMARY
The ten-eleven-translocation 5-methylcytosine dioxygenase (TET) family of enzymes catalyzes the conversion of 5-methylcytosine (5-mC) to 5-hydroxyme-thylcytosine (5-hmC), a modified cytosine base that facilitates gene expression. Cells respond to hypoxia by inducing a transcriptional program regulated in part by oxygen-dependent dioxygenases that require Fe(II) and α-ketoglutarate. Given that the TET enzymes also require these cofactors, we hypothesized that the TETs regulate the hypoxia-induced transcriptional program. Here, we demonstrate that hypoxia increases global 5-hmC levels, with accumulation of 5-hmC density at canonical hypoxia response genes. A subset of 5-hmC gains colocalize with hypoxia response elements facilitating DNA demethylation and HIF binding. Hypoxia results in transcriptional activation of TET1, and full induction of hypoxia-responsive genes and global 5-hmC increases require TET1. Finally, we show that 5-hmC increases and TET1 upregulation in hypoxia are HIF-1 dependent. These findings establish TET1-mediated 5-hmC changes as an important epigenetic component of the hypoxic response.
doi:10.1016/j.celrep.2014.04.040
PMCID: PMC4516227  PMID: 24835990
22.  Comparison of Bile Acids and Acetaminophen Protein Adducts in Children and Adolescents with Acetaminophen Toxicity 
PLoS ONE  2015;10(7):e0131010.
Metabolomics approaches have enabled the study of new mechanisms of liver injury in experimental models of drug toxicity. Disruption of bile acid homeostasis is a known mechanism of drug induced liver injury. The relationship of individual bile acids to indicators of oxidative drug metabolism (acetaminophen protein adducts) and liver injury was examined in children with acetaminophen overdose, hospitalized children with low dose exposure to acetaminophen, and children with no recent exposure to acetaminophen. Nine bile acids were quantified through targeted metabolomic analysis in the serum samples of the three groups. Bile acids were compared to serum levels of acetaminophen protein adducts and alanine aminotransferase. Glycodeoxycholic acid, taurodeoxycholic acid, and glycochenodeoxycholic acid were significantly increased in children with acetaminophen overdose compared to healthy controls. Among patients with acetaminophen overdose, bile acids were higher in subjects with acetaminophen protein adduct values > 1.0 nmol/mL and modest correlations were noted for three bile acids and acetaminophen protein adducts as follows: taurodeoxycholic acid (R=0.604; p<0.001), glycodeoxycholic acid (R=0.581; p<0.001), and glycochenodeoxycholic acid (R=0.571; p<0.001). Variability in bile acids was greater among hospitalized children receiving low doses of acetaminophen than in healthy children with no recent acetaminophen exposure. Compared to bile acids, acetaminophen protein adducts more accurately discriminated among children with acetaminophen overdose, children with low dose exposure to acetaminophen, and healthy control subjects. In children with acetaminophen overdose, elevations of conjugated bile acids were associated with specific indicators of acetaminophen metabolism and non-specific indicators of liver injury.
doi:10.1371/journal.pone.0131010
PMCID: PMC4514842  PMID: 26208104
23.  Sulfonoquinovosyl diacylglyceride selectively targets acute lymphoblastic leukemia cells and exerts potent anti-leukemic effects in vivo 
Scientific Reports  2015;5:12082.
DNA topoisomerase II inhibitors e.g. doxorubicin and etoposide are currently used in the chemotherapy for acute lymphoblastic leukemia (ALL). These inhibitors have serious side effects during the chemotherapy e.g. cardiotoxicity and secondary malignancies. In this study we show that sulfonoquinovosyl diacylglyceride (SQDG) isolated from Azadirachta indica exerts potent anti-ALL activity both in vitro and in vivo in nude mice and it synergizes with doxorubicin and etoposide. SQDG selectively targets ALL MOLT-4 cells by inhibiting catalytic activity of topoisomerase I enzyme and inducing p53 dependent apoptotic pathway. SQDG treatment induces recruitment of ATR at chromatin and arrests the cells in S-phase. Down-regulation of topoisomerase I or p53 renders the cells less sensitive for SQDG, while ectopic expression of wild type p53 protein in p53 deficient K562 cells results in chemosensitization of the cells for SQDG. We also show that constant ratio combinations of SQDG and etoposide or SDQG and doxorubicin exert synergistic effects on MOLT-4 cell killing. This study suggests that doses of etoposide/doxorubicin can be substantially reduced by combining SQDG with these agents during ALL chemotherapy and side effects caused can be minimized. Thus dual targeting of topoisomerase I and II enzymes is a promising strategy for improving ALL chemotherapy.
doi:10.1038/srep12082
PMCID: PMC4507174  PMID: 26189912
24.  Recent progress in the development of polysaccharide conjugates of docetaxel and paclitaxel 
Taxanes are one of the most potent and broadest spectrum chemotherapeutics used clinically, but also induce significant side effects. Different strategies have been developed to produce a safer taxane formulation. Development of polysaccharide drug conjugates has increased in the recent years due to the demonstrated biocompatibility, biodegradability, safety and low cost of the biopolymers. This review focuses on polysaccharide taxane conjugates and provides an overview on various conjugation strategies and their effect on the efficacy. Detailed analyses on the designing factors of an effective polysaccharide drug conjugate are provided with a discussion on the future direction of this field.
doi:10.1002/wnan.1264
PMCID: PMC4057951  PMID: 24652678
25.  Deregulation of Rb-E2F1 Axis Causes Chromosomal Instability by Engaging the Transactivation Function of Cdc20–Anaphase-Promoting Complex/Cyclosome 
Molecular and Cellular Biology  2014;35(2):356-369.
The E2F family of transcription factors regulates genes involved in various aspects of the cell cycle. Beyond the well-documented role in G1/S transition, mitotic regulation by E2F has also been reported. Proper mitotic progression is monitored by the spindle assembly checkpoint (SAC). The SAC ensures bipolar separation of chromosomes and thus prevents aneuploidy. There are limited reports on the regulation of the SAC by E2F. Our previous work identified the SAC protein Cdc20 as a novel transcriptional regulator of the mitotic ubiquitin carrier protein UbcH10. However, none of the Cdc20 transcription complex proteins have any known DNA binding domain. Here we show that an E2F1-DP1 heterodimer is involved in recruitment of the Cdc20 transcription complex to the UBCH10 promoter and in transactivation of the gene. We further show that inactivation of Rb can facilitate this transactivation process. Moreover, this E2F1-mediated regulation of UbcH10 influences mitotic progression. Deregulation of this pathway results in premature anaphase, chromosomal abnormalities, and aneuploidy. We conclude that excess E2F1 due to Rb inactivation recruits the complex of Cdc20 and the anaphase-promoting complex/cyclosome (Cdc20-APC/C) to deregulate the expression of UBCH10, leading to chromosomal instability in cancer cells.
doi:10.1128/MCB.00868-14
PMCID: PMC4272426  PMID: 25368385

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