An insight into MDR Acinetobacter baumannii infection and its pathogenesis: Potential therapeutic targets and challenges.

Acinetobacter baumannii is observed as a common species of Gram-negative bacteria that exist in soil and water. Despite being accepted as a typical component of human skin flora, it has become an important opportunistic pathogen, especially in healthcare settings. The pathogenicity of A. baumannii is attributed to its virulence factors, which include adhesins, pili, lipopolysaccharides, outer membrane proteins, iron uptake systems, autotransporter, secretion systems, phospholipases etc. These elements provide the bacterium the ability to cling to and penetrate host cells, get past the host immune system, and destroy tissue. Its infection is a major contributor to human pathophysiological conditions including pneumonia, bloodstream infections, urinary tract infections, and surgical site infections. It is challenging to treat infections brought on by this pathogen since this bacterium has evolved to withstand numerous drugs and further emergence of drug-resistant A. baumannii results in higher rates of morbidity and mortality. The long-term survival of this bacterium on surfaces of medical supplies and hospital furniture facilitates its frequent spread in humans from one habitat to another. There is a need for urgent investigations to find effective drug targets for A. baumannii as well as designing novel drugs to reduce the survival and spread of infection. In the current review, we represent the specific features, pathogenesis, and molecular intricacies of crucial drug targets of A. baumannii. This would also assist in proposing strategies and alternative therapies for the prevention and treatment of A. baumannii infections and their spread.

AMMI and GGE biplot analysis of genotype by environment interaction for yield and yield contributing traits in confectionery groundnut.

The global market has a high demand for premium edible grade groundnut, particularly for table use. India, in particular, exhibits significant potential for exporting confectionary grade large seeded groundnut. The environment plays a significant impact in influencing the expression of seed traits, which subsequently affects the confectionary quality of groundnut genotypes. The states of Gujarat and Rajasthan in India are prominent producers of high-quality groundnuts specifically used for confectionary purposes. The current study was conducted with 43 confectionery groundnut genotypes at Junagadh, Gujarat, and Bikaner, Rajasthan, with the goals of understanding genotype-by-environment interaction (GEI) effects and identifying stable, high yielding confectionery quality groundnut genotypes using AMMI and GGE biplot models. Pod yield per plant (PYP), number of pods per plant (NPP), hundred kernel weight (HKW), and shelling percent (SP) were estimated. The interplay between the environment and genotype has had a notable impact on the manifestation of confectionary grade characteristics in peanuts. The results from the Interaction Principal Component Analysis (IPCA) indicate that HKW contributed 76.68% and 18.95% towards the Global Environmental Index (GEI) through IPCA1 and IPCA2, respectively. Similarly, NPP contributed 87.52% and 8.65%, PYP contributed 95.87% and 2.1%, and SP contributed 77.4% and 16.22% towards GEI through IPCA1 and IPCA2, respectively. Based on the ranking of genotypes, the ideal genotypes were PBS 29079B for HKW, PBS 29230 for NPP. The genotypes PBS 29233 and PBS 29230 exhibited superior performance and stability in terms of pod yield, hundred kernel weight, number of pods per plant, and shelling percentage across various sites. These breeding lines have the potential to be developed for the purpose of producing confectionary grade groundnut with larger seeds, in order to fulfil the growing demand for export.

Barriers in utilization and provisioning of obstetric care services (OCS) in India: a mixed-methods systematic review.

BACKGROUND: Despite the reduction in the maternal mortality ratio, barriers in obstetric care services (OCS) remain a significant risk factor for adverse maternal and perinatal outcomes in India. This review covers the 'continuum of care' (ANC, child delivery, and PNC services) and identifies multiple barriers in provisioning as well as utilization of OCS in India. We conducted a systematic review to understand the barriers using a mixed-methods approach. METHODS: PubMed, Scopus, Web of Science, Google Scholar, and Science Direct databases were searched from 1 January 2000 to 30 June 2022. The methodological quality of the included studies was assessed using appropriate tools. After a full-text review of 164 studies, total of 56 studies (33 quantitative, 18 qualitative, and 5 mixed-methods studies) were finally included in the review. All the barriers were classified into five major themes: (i) individual and interpersonal barriers, (ii) social and cultural barriers, (iii) structural barriers, (iv) logistical barriers, and (v) organizational barriers. A thematic synthesis approach was used to present the findings of the included studies. RESULTS: Lack of knowledge and awareness and less family support in availing the required OCS were key individual and interpersonal barriers. Negative social and cultural practices, such as belief in traditional herbs/healers, dietary restrictions, and discarding colostrum were frequently reported barriers, especially in rural settings. Poor economic status and high health service costs were the most often cited barriers to low institutional delivery and delayed ANC services. Long distances to health facilities and poor road conditions were the most frequently reported logistical barriers. On the provisioning side, poor quality of treatment, shortage of drugs and equipment, and non-cooperative attitude of health professionals were the most significant barriers. CONCLUSION: This review identified several important barriers ranging from individual and cultural to structural, logistical, and organizational, which are prevalent in India. To mitigate the barriers, the governments need to develop strategies at the individual and organizational levels. Innovative interventions and program implementation at the community and village levels could also be contributory steps towards improving OCS utilization in India.

Ethrel-induced release of fresh seed dormancy causes remodelling of amylase activity, proteomics, phytohormone and fatty acid profile of groundnut (Arachis hypogaea L.).

It is important to have a short period of fresh seed dormancy in some of the groundnut species to counter pre-harvest sprouting (PHS). One of the main causes of PHS is the activation of ethylene-mediated pathways. To determine the effect of ethylene, the study was conducted and alterations in amylase, proteins and fatty acids were observed at the 0, 6, 12, and 24 h stages after ethrel administration. The result showed an increase in amylase activity, and the fatty acids profile showed a unique alteration pattern at different germination stages. Two-dimensional gel electrophoresis (2DGE) revealed differential expression of proteins at each stage. The trypsin digestion following spectral development through UPLC-MS/MS enabled identification of number of differentially expressed proteins. A total of 49 proteins were identified from 2DGE excised spots. The majority were belonged to seed storage-related proteins like Arah1, Arah2, AAI- domain containing protein, conglutin, Arah3/4, arachin, glycinin. Expression of lipoxygenase1, lipoxygenase9 and Arah2 genes were further confirmed by qRT-PCR which showed its involvement at transcript level. Up-regulation of lipoxygenase9 is correlated with decreased content of fatty acids during germination. Phytohormone detection revealed decrease in ABA, SA and JA content which are generally inhibitor of seed germination while GA, IAA and kinetin concentration increased revealing positive regulation of seed germination. We present an integrated view of proteomics, phytohormone profile, carbohydrate and lipid metabolism to unravel mechanism of fresh seed dormancy. Supplementary Information: The online version contains supplementary material available at 10.1007/s12298-023-01332-6.

Accumulation of resveratrol, ferulic acid and iron in seeds confer iron deficiency chlorosis tolerance to a novel genetic stock of peanut (Arachis hypogaea L.) grown in calcareous soils.

Peanut is mostly grown in calcareous soils with high pH which are deficient in available iron (Fe2+) for plant uptake causing iron deficiency chlorosis (IDC). The most pertinent solution is to identify efficient genotypes showing tolerance to limited Fe availability in the soil. A field screening of 40 advanced breeding lines of peanut using NRCG 7472 and ICGV 86031 as IDC susceptible and tolerant checks, respectively, was envisaged for four years. PBS 22040 and 29,192 exhibited maximum tolerance while PBS 12215 and 12,185 were most susceptible. PBS 22040 accumulated maximum seed resveratrol (5.8 ± 0.08 ppm), ferulic acid (378.6 ± 0.31 ppm) and Fe (45.59 ± 0.41 ppm) content. Enhanced chlorophyll retention (8.72-9.50 µg ml-1), carotenoid accumulation (1.96-2.08 µg ml-1), and antioxidant enzyme activity (APX: 35.9-103.9%; POX: 51- 145%) reduced the MDA accumulation (5.61-9.11 µM cm-1) in tolerant lines. The overexpression of Fe transporters IRT1, ZIP5, YSL3 was recorded to the tune of 2.3-9.54; 1.45-3.7; 2.20-2.32- folds respectively in PBS 22040 and 29,192, over NRCG 7472. PBS 22040 recorded the maximum pod yield (282 ± 4.6 g/row), hundred kernel weight (55 ± 0.7 g) and number of pods per three plants (54 ± 1.7). The study thus reports new insights into the roles of resveratrol, ferulic acid and differential antioxidant enzyme activities in imparting IDC tolerance. PBS 22040, being the best performing line, can be the potent source of IDC tolerance for introgression in high yielding but susceptible genotypes under similar edaphic conditions. Supplementary Information: The online version contains supplementary material available at 10.1007/s12298-023-01321-9.

NOD1 activation in 3T3-L1 adipocytes confers lipid accumulation in HepG2 cells.

AIMS: Activation of specific innate immune receptors has been characterized to modulate nutrient metabolism in individual metabolic tissue directly or indirectly via secretory molecules. Activation of the nucleotide-binding oligomerization domain-containing protein 1 (NOD1) in adipocytes has been reported to induce lipolysis linked with insulin resistance and inflammatory response. These cues are positioned to modulate metabolic action in distal organs through paracrine/endocrine signaling. Here, we assessed the role of NOD1-mediated lipolysis and inflammatory response in adipocytes to affect lipid metabolism in hepatocytes. MAIN METHODS: Human hepatoma cells (HepG2) were exposed to conditioned medium obtained from 3 T3-L1 adipocytes pretreated with NOD1 ligand (iE-DAP) and the effects on lipid accumulation, inflammation and insulin response were assessed. Activation of mechanisms leading to hepatic lipid accumulation was investigated by gene expression analysis. KEY FINDINGS: The conditioned medium from NOD1-activated 3 T3-L1 adipocytes (CM-DAP) induced lipid accumulation in HepG2 cells, driven by both lipolysis and inflammatory responses. The CM-DAP-induced lipid accumulation was independent to de novo lipogenesis and resulted from the enhanced transport of fatty acids inside and consequent increase in rate of triglycerides synthesis in hepatocytes. Moreover, CM-DAP-induced lipid accumulation instigated the expression of the markers of fatty acid oxidation and VLDL assembly for the export of triglycerides from hepatocyte. Furthermore, CM-DAP-induced lipid accumulation was associated with induction of inflammatory response and impairment of insulin signaling in HepG2 cells. SIGNIFICANCE: Beyond showing liver-specific mechanisms to adipocytes-derived factors, our findings support the involvement of adipose tissue as a mediator in NOD1-mediated biological responses to modulate hepatic metabolism.

Moringa oleifera impedes protein glycation and exerts reno-protective effects in streptozotocin-induced diabetic rats.

ETHNOPHARMACOLOGICAL RELEVANCE: Moringa oleifera is a valued plant with wide distribution in tropical and subtropical regions of the world. It is traditionally used for the treatment of fever, infections, rheumatism, cancer, improving cardiac, renal and hepatic functions, and regulating blood glucose level. The plant has been scientifically reported for the anti-inflammatory, antioxidant, renoprotective, and anti-diabetic properties. Diabetic patients are prone to develop end-stage renal diseases due to incidence of diabetes-induced renal dysfunctions. Given that, increased production and accumulation of advanced glycation end-products (AGEs) play a conspicuous role in the development of diabetes-linked renal dysfunctions, nature-based interventions with AGEs inhibitory activity can prevent renal dysfunctions leading to renoprotection. AIM OF THE STUDY: The study aimed to demonstrate the preventive effects of the ethanolic extract of the leaves of Moringa oleifera (EEMO) on protein glycation and its further assessment for the renoprotective effect in diabetic rats. MATERIALS AND METHODS: Antiglycation activity of EEMO was assessed in vitro using bovine serum albumin. For reno-protective activity assessment, streptozotocin (STZ)-induced diabetic rats were orally treated with EEMO (100 mg/kg) or standard antiglycation agent aminoguanidine (100 mg/kg) for consecutive 8 weeks. The effects on glucose homeostasis, renal functions, and renal morphology were assessed by clinical biochemistry, molecular and histological examination. RESULTS: Presence of EEMO efficiently prevented glucose-, fructose- or methylglyoxal-mediated glycation of protein. Under in vivo set-up, compared to diabetic control rats, EEMO treatment effectively improved the glucose tolerance and body weight, and reduced the serum levels of triglycerides and total cholesterol. Additionally, EEMO administration significantly ameliorated renal dysfunctions in diabetic rats characterized by improved levels of creatinine, urea nitrogen, and uric acid in serum, and total protein level in urine, accompanied by improved kidney morphology. The diabetes-associated pro-inflammatory response characterized by upregulated expression of the inducible nitric oxide synthase (iNos), activation of nuclear factor kappa B (NF-κB) and the raised levels of inflammatory factors, interleukin-1 beta (IL-1ß) and interleukin-6 (IL-6) in renal tissue was significantly attenuated in EEMO-treated rats. Moreover, EEMO treatment diminished renal reactive oxygen species (ROS) levels in diabetic animals. CONCLUSIONS: Our study demonstrated that EEMO prevented AGEs formation and ameliorated renal dysfunctions in diabetic rats by blocking inflammatory/oxidative pathways. Our observations justify M. oleifera as a potential source of therapeutic interventions for diabetic nephropathy management.

Convergence of Fructose-Induced NLRP3 Activation with Oxidative Stress and ER Stress Leading to Hepatic Steatosis.

High fructose flux enhances hepatocellular triglyceride accumulation (hepatic steatosis), which is a prime trigger in the emergence of hepatic ailments. Nevertheless, the pathophysiology underlying the process is not completely understood. Emerging evidences have revealed the inputs from multiple cues including inflammation, oxidative stress, and endoplasmic reticulum (ER) stress in the development of hepatic steatosis. Here, we substantiated the role of NLRP3 inflammasome and its convergence with oxidative and ER stress leading to hepatic steatosis under high fructose diet feeding. Male SD rats were fed on 60% high fructose diet (HFrD) for 10 weeks and treated with antioxidant quercetin or NLRP3 inflammasome inhibitor glyburide during the last 6 weeks, followed by metabolic characterization and analysis of hepatic parameters. HFrD-induced hepatic steatosis was associated with the activation of NLRP3 inflammasome, pro-inflammatory response, oxidative, and ER stress in liver. Treatment with quercetin abrogated HFrD-induced oxidative stress, along with attenuation of NLRP3 activation in the liver. On the other hand, inhibition of NLRP3 signaling by glyburide suppressed HFrD-induced oxidative and ER stress. Both glyburide or quercetin treatment significantly attenuated hepatic steatosis, associated with mitigated expression of the lipogenic markers in liver. Our findings verified the association of NLRP3 inflammasome with oxidative and ER stress in fructose-induced lipogenic response and indicate that in addition to be a target of oxidative/ER stress, NLRP3 can act as a trigger for oxidative/ER stress to activate a vicious cycle where these cues act in a complex manner to propagate inflammatory response, leading to hepatic steatosis.

An expedient ion chromatography based method for high-throughput analysis of phytic acid in groundnut kernels.

A study was made to expedite ion chromatography method using IonPac analytical column and self-regenerating anion suppressor for phytic acid determination in groundnut seeds and compared with a widely adopted spectrophotometric method based on enzymatic hydrolysis. The Ion Chromatography method equipped with AG11 guard and AS11 analytical columns in isocratic mode using 65 mM NaOH mobile phase at 1 mL min-1 flow rate showed a sharp peak for phytic acid with a retention time of 2.42 ± 0.2 min. The peak area was plotted v/s concentration showed linearity with an R2 value of 0.997, detection limit of 0.028 mg L-1 and recovery of 98% as against R2 value of 0.988 and detection limit of 0.065 mg L-1 in the spectrophotometric method. The study demonstrates that Ion Chromatography method was more accurate with a better detection limit than spectrophotometry. Also, this method provides robust handling with lesser reagent requirements due to combined eluent generation and self-regenerating suppression. Supplementary Information: The online version contains supplementary material available at 10.1007/s13197-022-05527-9.

Fructose-mediated NLRP3 activation induces inflammation and lipogenesis in adipose tissue.

Adipose tissue plays a crucial role in energy intake and regulation of metabolic homeostasis. Fructose consumption implicates in development and progression of metabolic dysfunctions. Fructose is a lipogenic sugar known to induce inflammatory response. However, the role of specific inflammatory signal such as nucleotide-binding and oligomerization domain-like receptor, leucine-rich repeat and pyrin domain containing protein 3 (NLRP3) in fructose-induced inflammatory response and its relevance to lipogenesis in adipose tissue are elusive. We assessed NLRP3 activation and its significance in inflammatory response and lipogenesis in epididymal adipose tissue of 60% fructose diet (HFrD)-fed rats. The long-term consumption of HFrD led to impairment of glucose metabolism, development of visceral adiposity, insulin resistance, and elevation of serum triglycerides level, accompanied by activation of NLRP3 in adipose tissue. NLRP3 inflammasome activation in adipose tissue was associated with up-regulated expression of Nlrp3, Asc, and Caspase-1, and raised caspase-1 activity, which resulted in increased expression of IL-1ß and IL-18 and secretion of IL-1ß. Moreover, lipid accumulation and expression of transcription factors exacerbating accumulation of lipids were augmented in adipose tissue of HFrD-fed rats. Treatment with glyburide, quercetin or allopurinol corrected HFrD-induced dyslipidemia or hyperuricemia, and blocked NLRP3 activation, leading to mitigated inflammatory signaling and lipid accumulation in adipose tissue, improved glucose tolerance and insulin sensitivity in HFrD-fed rats. These data suggest the role of NLRP3 inflammasome to establish linkage among inflammation, lipid accumulation and insulin resistance in adipose tissue, and targeting NLRP3 inflammasome may be a plausible approach for prevention and management for fructose-induced metabolic impairments.

Insulin resistance corresponds with a progressive increase in NOD1 in high fat diet-fed mice.

PURPOSE: Innate immune components participate in obesity-induced inflammation, which can contribute to endocrine dysfunction during metabolic diseases. However, the chronological activation of specific immune proteins such as Nucleotide-binding oligomerization domain-containing protein 1 (NOD1) and relevance to cellular crosstalk during the progression of obesity-associated insulin resistance (IR) is not known. METHODS: The NOD1 signaling in various insulin-sensitive metabolic tissues during the progression of diet-insulin resistance was assessed in C57BL/6J mice fed with 60% high-fat diet (HFD) for 4, 8, 12, and 16 weeks. Intestinal permeability was measured using FITC-dextran. NOD1 activating potential was analyzed using HEK-Blue mNOD1 cells. RESULTS: HFD-fed mice showed progressive induction of glucose intolerance and impairment of insulin signaling in key metabolic tissues. We found a time-dependent increase in intestinal permeability coupled with transport and accumulation of NOD1 activating ligand in the serum of HFD-fed mice. We also observed a progressive accumulation of γ-D-glutamyl-meso-diaminopimelic acid (DAP), a microbial peptidoglycan ligand known to activate NOD1, in serum samples of the HFD-fed mice. There was also a progressive increase in transcripts levels of NOD1 in bone marrow-derived macrophages during HFD-feeding. In addition, skeletal muscle, adipose and liver, the key insulin sensitive metabolic tissues also had a time-dependent increase in transcripts of NOD1 and Rip2 and a corresponding activation of pro-inflammatory responses in these tissues. CONCLUSION: These data highlight the correlation of inflammation and insulin resistance to NOD1 activation in the bone marrow derived macrophages and insulin responsive metabolic tissues during high fat diet feeding in mice.

Antiglycation activity of ß-glucogallin from Asparagus racemosus.

The increased formation and accumulation of advanced glycation end products (AGEs) has been implicated in pathogenesis of various chronic ailments, including diabetes-associated secondary complications, atherosclerosis, aging, inflammatory and neurodegenerative diseases. Therefore, inhibition of AGEs formation is an imperative strategy for alleviating diverse pathologies. Here, we have demonstrated the AGEs inhibitory activity of ß-glucogallin, isolated for the first time from the roots of Asparagus racemosus. ß-glucogallin significantly mitigated fructose-, glucose- and methylglyoxal-induced glycation of bovine serum albumin (BSA). Also, the presence of ß-glucogallin decreased fructosamine and protein carbonyls content, and increased thiol group content in the fructose-BSA system. These activities of ß-glucogallin from Asparagus racemosus underscore its likely pharmacological potential for impeding AGEs-related metabolic disorders.

NOD1 activation induces oxidative stress via NOX1/4 in adipocytes.

Activation of innate immune components promotes cell autonomous inflammation in adipocytes. Oxidative stress links pattern recognition receptor-mediated detection of inflammatory ligands and the immune response. Reactive oxygen species (ROS) may mediate the effect of nucleotide-binding oligomerization domain protein-1 (NOD1) activation on inflammation in adipocytes. Here, we define the potential role of NADPH oxidase (NOX)-derived ROS in NOD1-mediated inflammatory response in adipocytes. Differentiated 3T3-L1 adipocytes were treated with NOD1 activating ligand D-gamma-Glu-meso-diaminopimelic acid (iE-DAP) to evaluate the oxidative stress and contribution of NOX as source of intracellular ROS. NOD1 activation potently induced ROS generation in 3T3-L1 adipocytes. Of the NOX family members, expression of NOX1 and NOX4 was increased upon NOD1 activation, in a PKCδ-dependent manner. siRNA-mediated down-regulation of NOX1 or NOX4 inhibited NOD1-mediated ROS production and increased the expression of antioxidant defense enzyme catalase and superoxide dismutase (SOD). siRNA-mediated lowering of NOX1 or NOX4 also suppressed NOD1-mediated activation of JNK1/2 and NF-κB, and consequent activation of inflammatory response in 3T3-L1 adipocytes. In summary, our findings demonstrate that NOD1 activation provokes oxidative stress in adipocytes via NOX1/4 and that oxidative stress, at least in part, contributes to induction of inflammatory response. Defining the source of ROS after immune response engagement may lead to new therapeutic strategies for adipose tissue inflammation.

Nod1-mediated lipolysis promotes diacylglycerol accumulation and successive inflammation via PKCδ-IRAK axis in adipocytes.

Chronic inflammation contributes to obesity mediated metabolic disturbances, including insulin resistance. Obesity is associated with altered microbial load in metabolic tissues that can contribute to metabolic inflammation. Different bacterial components such as, LPS, peptidoglycans have been shown to underpin metabolic disturbances through interaction with host innate immune receptors. Activation of Nucleotide-binding oligomerization domain-containing protein 1 (Nod1) with specific peptidoglycan moieties promotes insulin resistance, inflammation and lipolysis in adipocytes. However, it was not clear how Nod1-mediated lipolysis and inflammation is linked. Here, we tested if Nod1-mediated lipolysis caused accumulation of lipid intermediates and promoted cell autonomous inflammation in adipocytes. We showed that Nod1-mediated lipolysis caused accumulation of diacylglycerol (DAG) and activation of PKCδ in 3T3-L1 adipocytes, which was prevented with a Nod1 inhibitor. Nod1-activated PKCδ caused downstream stimulation of IRAK1/4 and was associated with increased expression of proinflammatory cytokines such as, IL-1ß, IL-18, IL-6, TNFα and MCP-1. Pharmacological inhibition or siRNA mediated knockdown of IRAK1/4 attenuated Nod1-mediated activation of NF-κB, JNK, and the expression of proinflammatory cytokines. These results reveal that Nod1-mediated lipolysis promoted accumulation of DAG, which engaged PKCδ and IRAK1/4 to augment inflammation in 3T3-L1 adipocytes.

Sequencing of the Dutch elm disease fungus genome using the Roche/454 GS-FLX Titanium System in a comparison of multiple genomics core facilities.

As part of the DNA Sequencing Research Group of the Association of Biomolecular Resource Facilities, we have tested the reproducibility of the Roche/454 GS-FLX Titanium System at five core facilities. Experience with the Roche/454 system ranged from <10 to >340 sequencing runs performed. All participating sites were supplied with an aliquot of a common DNA preparation and were requested to conduct sequencing at a common loading condition. The evaluation of sequencing yield and accuracy metrics was assessed at a single site. The study was conducted using a laboratory strain of the Dutch elm disease fungus Ophiostoma novo-ulmi strain H327, an ascomycete, vegetatively haploid fungus with an estimated genome size of 30-50 Mb. We show that the Titanium System is reproducible, with some variation detected in loading conditions, sequencing yield, and homopolymer length accuracy. We demonstrate that reads shorter than the theoretical minimum length are of lower overall quality and not simply truncated reads. The O. novo-ulmi H327 genome assembly is 31.8 Mb and is comprised of eight chromosome-length linear scaffolds, a circular mitochondrial conti of 66.4 kb, and a putative 4.2-kb linear plasmid. We estimate that the nuclear genome encodes 8613 protein coding genes, and the mitochondrion encodes 15 genes and 26 tRNAs.

Chemopreventive properties of indole-3-carbinol, diindolylmethane and other constituents of cardamom against carcinogenesis.

Oxidative stress results from an imbalance in the production of reactive oxygen species (ROS) and cell's own antioxidant defenses that in part lead to numerous carcinogenesis. Several phytochemicals, derived from vegetables, fruits, herbs and spices, have demonstrated excellent chemopreventive properties against carcinogenesis by regulating the redox status of the cells during oxidative stress. I3C (indole-3-carbinol) and DIM (diindolylmethane) are the phytochemicals that are found in all types of cruciferous vegetables and demonstrated exceptional anti-cancer effects against hormone responsive cancers like breast, prostate and ovarian cancers. Novel analogs of I3C were designed to enhance the overall efficacy, particularly with respect to the therapeutic activity and oral bioavailability and that results in several patent applications on symptoms associated with endometriosis, vaginal neoplasia, cervical dysplasia and mastalgia. Likewise, DIM and its derivatives are patented for treatment and prevention of leiomyomas, HPV infection, respiratory syncytial virus, angiogenesis, atherosclerosis and anti-proliferative actions. On the other hand, phytochemicals in cardamom have not been explored in great details but limonene and cineole demonstrate promising effects against carcinogenesis. Thus studies with selected phytochemicals of cardamom and bioavailability research might lead to many patent applications. This review is focused on the patents generated on the effects of I3C, DIM and selected phytochemicals of cardamom on carcinogenesis.

The feasibility of using high resolution genome sequencing of influenza A viruses to detect mixed infections and quasispecies.

BACKGROUND: The rapidly expanding availability of de novo sequencing technologies can greatly facilitate efforts to monitor the relatively high mutation rates of influenza A viruses and the detection of quasispecies. Both the mutation rates and the lineages of influenza A viruses are likely to play an important role in the natural history of these viruses and the emergence of phenotypically and antigenically distinct strains. METHODOLOGY AND PRINCIPAL FINDINGS: We evaluated quasispecies and mixed infections by de novo sequencing the whole genomes of 10 virus isolates, including eight avian influenza viruses grown in embryonated chicken eggs (six waterfowl isolates - five H3N2 and one H4N6; an H7N3 turkey isolate; and a bald eagle isolate with H1N1/H2N1 mixed infection), and two tissue cultured H3N2 swine influenza viruses. Two waterfowl cloacal swabs were included in the analysis. Full-length sequences of all segments were obtained with 20 to 787-X coverage for the ten viruses and one cloacal swab. The second cloacal swab yielded 15 influenza reads of approximately 230 bases, sufficient for bioinformatic inference of mixed infections or quasispecies. Genomic subpopulations or quasispecies of viruses were identified in four egg grown avian influenza isolates and one cell cultured swine virus. A bald eagle isolate and the second cloacal swab showed evidence of mixed infections with two (H1 and H2) and three (H1, H3, and H4) HA subtypes, respectively. Multiple sequence differences were identified between cloacal swab and the virus recovered using embryonated chicken eggs. CONCLUSIONS: We describe a new approach to comprehensively identify mixed infections and quasispecies in low passage influenza A isolates and cloacal swabs and add to the understanding of the ecology of influenza A virus populations.

Identification of optimal protocols for sequencing difficult templates: results of the 2008 ABRF DNA Sequencing Research Group difficult template study 2008.

The 2008 ABRF DNA Sequencing Research Group (DSRG) difficult template sequencing study was designed to identify a general set of guidelines that would constitute the best approaches for sequencing difficult templates. This was a continuation of previous DSRG difficult template studies performed in 1996, 1997, and 2003. The distinguishing factors in the present study were the number of DNA templates used, the number of different types of difficult regions tested, and the inclusion of a follow-up phase of the study to identify optimal protocols for each type of difficult template. DNA templates with associated sequencing primers were distributed to participating laboratories and each laboratory returned their sequencing results along with descriptions of the experimental conditions used. The data were analyzed and the best protocols were identified for each difficult template. This information was subsequently distributed to the participating laboratories for a second round of sequencing to evaluate the general applicability of the optimized protocols. The average improvements in sequencing results were 11% overall, with a range of -25% to +43% using the optimized protocols. The full results from this study are presented here and they demonstrate that general experimental protocols and common additives can be used to improve the sequencing success for many difficult templates.

Chronic olanzapine treatment causes differential expression of genes in frontal cortex of rats as revealed by DNA microarray technique.

Recent emerging biochemical data indicate that several important neuroregulatory genes and proteins may be involved in the etiology of schizophrenia and bipolar disorder. Additionally, the same genes appear to be targets of several psychotropic medications that are used to treat these disorders. Recent DNA microarray studies show that genes involved in synaptic neurotransmission, signal transduction, and glutamate/GABA regulation may be differentially regulated in brains of subjects with schizophrenia. We hypothesized that chronic administration of olanzapine to rats would alter expression of various genes that may be involved in the etiology of schizophrenia and mood disorders. Rats were administered olanzapine (N=20, 2 mg/kg/day) or sterile saline intraperitoneally (N=20) daily for 21 days. Control and olanzapine-treated frontal cortices were analyzed using cDNA microarray technology. The results showed significant downregulation of 31 genes and upregulation of 38 genes by greater than two-fold in the drug-treated brains vs controls. Our results provide evidence for altered regulation of genes involved with signal transduction and cell communication, metabolism and energy pathways, transport, immune response, nucleic acid metabolism, and neuronal growth factors. Real-time quantitative RT-PCR analysis verified the direction and magnitude of change in six genes of interest: calbindin 3, homer 1, regulator of G-protein signaling (RGS) 2, pyruvate kinase, Reelin and insulin 2. Western blotting showed significant upregulation in protein products for Reelin 410 and Reelin 180 kDa and downregulation for NMDA3B and RGS2. Our results show for the first time that olanzapine causes changes in levels of several important genes that may be involved in the etiology and treatment of schizophrenia and other psychiatric disorders.

Suppression subtractive hybridization coupled with microarray analysis to examine differential expression of genes in virus infected cells.

High throughput detection of differential expression of genes is an efficient means of identifying genes and pathways that may play a role in biological systems under certain experimental conditions. There exist a variety of approaches that could be used to identify groups of genes that change in expression in response to a particular stimulus or environment. We here describe the application of suppression subtractive hybridization (SSH) coupled with cDNA microarray analysis for isolation and identification of chicken transcripts that change in expression on infection of host cells with a paramyxovirus. SSH was used for initial isolation of differentially expressed transcripts, a large-scale validation of which was accomplished by microarray analysis. The data reveals a large group of regulated genes constituting many biochemical pathways that could serve as targets for future investigations to explore their role in paramyxovirus pathogenesis. The detailed methods described herein could be useful and adaptable to any biological system for studying changes in gene expression.