Increased heterogeneity in expression of genes associated with cancer progression and drug resistance

Fluctuations in the number of regulatory molecules and differences in timings of molecular events can generate variation in gene expression among genetically identical cells in the same environmental condition. This variation, termed as expression noise, can create differences in metabolic state and cellular functions, leading to phenotypic heterogeneity. Expression noise and phenotypic heterogeneity have been recognized as important contributors to intra-tumor heterogeneity, and have been associated with cancer growth, progression, and therapy resistance. However, how expression noise changes with cancer progression in actual cancer patients has remained poorly explored. Such an analysis, through identification of genes with increasing expression noise, can provide valuable insights into generation of intra-tumor heterogeneity, and could have important implications for understanding immune-suppression, drug tolerance and therapy resistance. In this work, we performed a genome-wide identification of changes in gene expression noise with cancer progression using single-cell RNA-seq data of lung adenocarcinoma patients at different stages of cancer. We identified 37 genes in epithelial cells that showed an increasing noise trend with cancer progression, many of which were also associated with cancer growth, EMT and therapy resistance. We found that expression of several of these genes was positively associated with expression of mitochondrial genes, suggesting an important role of mitochondria in generation of heterogeneity. In addition, we uncovered substantial differences in sample-specific noise profiles which could have implications for personalized prognosis and treatment.

Transcription factor binding process is the primary driver of noise in gene expression

Noise in expression of individual genes gives rise to variations in activity of cellular pathways and generates heterogeneity in cellular phenotypes. Phenotypic heterogeneity has important implications for antibiotic persistence, mutation penetrance, cancer growth and therapy resistance. Specific molecular features such as the presence of the TATA box sequence and the promoter nucleosome occupancy have been associated with noise. However, the relative importance of these features in noise regulation is unclear and how well these features can predict noise has not yet been assessed. Here through an integrated statistical model of gene expression noise in yeast we found that the number of regulating transcription factors (TFs) of a gene was a key predictor of noise, whereas presence of the TATA box and the promoter nucleosome occupancy had poor predictive power. With an increase in the number of regulatory TFs, there was a rise in the number of cooperatively binding TFs. In addition, an increased number of regulatory TFs meant more overlaps in TF binding sites, resulting in competition between TFs for binding to the same region of the promoter. Through modeling of TF binding to promoter and application of stochastic simulations, we demonstrated that competition and cooperation among TFs could increase noise. Thus, our work uncovers a process of noise regulation that arises out of the dynamics of gene regulation and is not dependent on any specific transcription factor or specific promoter sequence.

Designer bacterial cell factories for improved production of commercially valuable non-ribosomal peptides

Non-ribosomal peptides have gained significant attention as secondary metabolites of high commercial importance. This group houses a diverse range of bioactive compounds, ranging from biosurfactants to antimicrobial and cytotoxic agents. However, low yield of synthesis by bacteria and excessive losses during purification hinders the industrial-scale production of non-ribosomal peptides, and subsequently limits their widespread applicability. While isolation of efficient producer strains and optimization of bioprocesses have been extensively used to enhance yield, further improvement can be made by optimization of the microbial strain using the tools and techniques of metabolic engineering, synthetic biology, systems biology, and adaptive laboratory evolution. These techniques, which directly target the genome of producer strains, aim to redirect carbon and nitrogen fluxes of the metabolic network towards the desired product, bypass the feedback inhibition and repression mechanisms that limit the maximum productivity of the strain, and even extend the substrate range of the cell for synthesis of the target product. The present review takes a comprehensive look into the biosynthesis of bacterial NRPs, how the same is regulated by the cell, and dives deep into the strategies that have been undertaken for enhancing the yield of NRPs, while also providing a perspective on other potential strategies that can allow for further yield improvement. Furthermore, this review provides the reader with a holistic perspective on the design of cellular factories of NRP production, starting from general techniques performed in the laboratory to the computational techniques that help a biochemical engineer model and subsequently strategize the architectural plan.

Assessment of asthma control in users of oral anti-asthma medications

BACKGROUND: Despite guidelines recommending inhalation therapy as the preferred choice, oral therapy is still widely used in the treatment of asthma in India. However, data about the level of asthma control and healthcare use in patients on oral anti-asthma medications are scarce.METHODS: A retrospective study was conducted to assess the level of asthma control and healthcare use in patients taking oral anti-asthma medications.RESULTS: The study population consisted of 381 adults randomly selected from health screening programmes. All subjects were already receiving oral anti-asthma medications; however, up to 72% had not been diagnosed with asthma by their treating doctors prior to the screening programmes. The cohort had a mean age of 48.26 ± 13.83 years (70% males) and mean peak expiratory flow of 245 ± 78.93 mL/sec. The mean Asthma Control Questionnaire 5 (ACQ-5) score was 2.53 ± 1.15, with respectively 33%, 49.3% and 32.6% reporting at least one episode of breathlessness, one emergency doctor visit and one hospitalisation due to asthma or its symptoms in the past year.CONCLUSION: Underdiagnosis and inappropriate management, as indicated by the poor asthma control and increased hospitalisations seen in this study, is probably a key contributor to the increased burden of the disease in India.

A large-scale computational screen identifies strong potential inhibitors for disrupting SARS-CoV-2 S-protein and human ACE2 interaction

SARS-CoV-2 has infected millions of individuals across the globe and has killed over 2.7 million people. Even though vaccines against this virus have recently been introduced, the antibody generated in the process has been reported to decline quickly. This can reduce the efficacy of vaccines over time and can result in re-infections. Thus, drugs that are effective against COVID-19 can provide a second line of defence and can prevent occurrence of the severe form of the disease. The interaction between SARS-CoV2 S-protein and human ACE2 (hACE2) is essential for the infection of the virus. Thus, drugs that block this interaction could potentially inhibit SARS-CoV-2 infection into the host cells. To identify such drugs, we first analyzed the recently published crystal structure of S-protein-hACE2 complex and identified essential residues of both S-protein and hACE2 for this interaction. We used this knowledge to virtually dock a drug library containing 4115 drug molecules against S-protein for repurposing drugs that could inhibit binding of S-protein to hACE2. We identified several potential inhibitors based on their docking scores, pharmacological effects and ability to block residues of S protein required for interaction with hACE2. The top inhibitors included drugs used for the treatment of hepatitis C (velpatasvir, pibrentasvir) as well as several vitamin D derivatives. Several molecules obtained from our screen already have good experimental support in published literature. Thus, we believe that our results will facilitate the discovery of an effective drug against COVID-19. Communicated by Ramaswamy H. Sarma.

A two-step PCR assembly for construction of gene variants across large mutational distances

Construction of empirical fitness landscapes has transformed our understanding of genotype–phenotype relationships across genes. However, most empirical fitness landscapes have been constrained to the local genotype neighbourhood of a gene primarily due to our limited ability to systematically construct genotypes that differ by a large number of mutations. Although a few methods have been proposed in the literature, these techniques are complex owing to several steps of construction or contain a large number of amplification cycles that increase chances of non-specific mutations. A few other described methods require amplification of the whole vector, thereby increasing the chances of vector backbone mutations that can have unintended consequences for study of fitness landscapes. Thus, this has substantially constrained us from traversing large mutational distances in the genotype network, thereby limiting our understanding of the interactions between multiple mutations and the role these interactions play in evolution of novel phenotypes. In the current work, we present a simple but powerful approach that allows us to systematically and accurately construct gene variants at large mutational distances. Our approach relies on building-up small fragments containing targeted mutations in the first step followed by assembly of these fragments into the complete gene fragment by polymerase chain reaction (PCR). We demonstrate the utility of our approach by constructing variants that differ by up to 11 mutations in a model gene. Our work thus provides an accurate method for construction of multi-mutant variants of genes and therefore will transform the studies of empirical fitness landscapes by enabling exploration of genotypes that are far away from a starting genotype.

COPD exacerbation rates are higher in non-smoker patients in India

BACKGROUND: Chronic obstructive pulmonary disease (COPD) is common among non-smokers exposed to solid fuel combustion at home. Different clinical characteristics in these patients may have significant therapeutic and prognostic implications.METHODS: We used medical record review and a questionnaire among COPD patients at 15 centres across India to capture data on demographic details, different types of exposures and clinical characteristics. Chest radiography and pulmonary function testing were performed in all 1984 cases; C-reactive protein and exhaled breath nitric oxide were measured wherever available.RESULTS: There were 1388 current or ex-smokers and 596 (30.0%) non-smokers who included 259 (43.5%) male and 337 (56.5%) female patients. Sputum production was significantly more common in smokers with COPD (P < 0.05). The frequency of acute symptomatic worsening, emergency visits and hospitalisation were significantly higher (P < 0.05) in non-smokers with COPD; however, intensive care unit admissions were similar in the two groups. There was no significant difference with respect to the use of bronchodilators, inhalational steroids or home nebulisation among smoker and non-smoker patients. The mean predicted forced expiratory volume in 1 sec in smokers (43.1%) was significantly lower than in non-smokers (46.5%).CONCLUSION: Non-smoker COPD, more commonly observed in women exposed to biomass fuels, was characterised by higher rate of exacerbations and higher healthcare resource utilisation.

Abstract 3127: To investigate the role of BRAF V600E co-occurring mutations in Langerhans cell histiocytosis (LCH)

a. Introduction :

Langerhans cell histiocytosis (LCH) is an inflammatory myeloid neoplasia caused by alterations of several genes in the MAPKinase pathway. The cell of origin is a white blood cell known as a dendritic cell priviously called as histiocyte characterized by a unique cytoplasmic organelle, the Birbeck granule, and the expression of CD1a and class II major histocompatibility complex molecules . The mutations cause these dendritic cells to attract other white blood cells and cause a “lesion” in any organ of the body. LCH has multi-orgnan involvement affecting skin bones, lymph nodes, brain etc. Systemic symptoms may include fever, bone pain, weight loss, jaundice, diabetes insipidus.

b. Description:

LCH is a rare sporadic, non-hereditary and non-malignant disease with unknown etiology characterized with a clonal proliferation of pathologic cells.Recent discovery of recurrent somatic mutations, BRAFV600E in MAPK pathway genes at critical stages of myeloid hematopoietic differentiation in LCH patients supports redefinition of the disease as a myeloproliferative disorder and provides opportunities to develop novel approaches to diagnosis and therapy. In the present proposal, we intend to analyze the BRAFV600E status along with other co-occurring mutations in a cohort of pediatric LCH patients by DNA sequencing in bone marrow samples or Peripheral Blood. Additionally we approach the above unanswered questions by applying an improved machine learning approach for classification and defining an algorithm for disease into different clusters for immediate clinical implication and to address its clinical heterogeneity.

c. Results :

We screened about 5 LCH patients and performed tageted exome seq to asertain the mutational profile of these patients. Sequencing detected BRAF V600E mutation in 3 of 5 samples for a mutation frequency of 60%. IHC based immunofloroscence shows that the intensity of phospho-MEK and phospho-ERK staining shows no significant alterations samples with mutation in BRAF. We are currently investigating mutations in other members of MAK pathways

d. Conclusion :

BRAF-V600E mutations were detected in few of our LCH patients. Neverless seeing the disease heterogeneity, we expect additionall mutations. More studies are needed to investigate mutations in the MAPK pathways that could efffect the course of disease management.We further plan to integrate the clinical and genomic findings to design a predictive model for the disease outcome.

Citation Format: Subhradip Karmakar, R Dhar, K Purkayastha, R Seth, S Karmakar. To investigate the role of BRAF V600E co-occurring mutations in Langerhans cell histiocytosis (LCH) [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 3127.

Outcomes and risk factors of cholecystectomy in high risk patients: A case series

Introduction

Many studies looked at outcomes and risk factors in laparoscopic cholecystectomies in general, including a few studies on risk factors and scoring systems in predicting conversion to open surgery. Little data has been produced on high-risk patients undergoing cholecystectomy. Identifying risk factors in this group could help stratify decision making regarding best management strategies.

The aim of this study was to investigate outcomes of laparoscopic cholecystectomies in patients with ASA 3 and 4.

Methods

Data was collected and collated from a prospectively maintained database of all laparoscopic cholecystectomies performed by 13 general surgeons in a single unit. Case notes were reviewed for all patients with ASA 3 and 4 between 2013 and 2017. Data analysis was performed using R studio v 3.4.

Results

244 cases were reviewed. Common bile duct was dilated in 52 cases (21.31%). Gall bladder wall was thick in 102 (41.8%) of the patients. Surgery was elective in 203 (83.2%) of the patients. ERCP was performed in 41 (16.9%) of the patients prior to surgery. 150 patients (62.2%) stayed for 1 day while 36 (14.9%) stayed for 2 days and the remaining 55 (22.9%) stayed for 3 days or more. Complications occurred in 37 (15.16%) of the patients while 23 (9.43%) of the patients were readmitted. 7 patients (2.87%) returned to theatre and 8 (3.28%) stayed in ITU post-op. Two patients died (0.82%).

Conclusion

Laparoscopic cholecystectomies in higher risk populations are safe. Alternative methods such as cholecystostomy and ERCP may be of benefit in these patients.

•

Gallstone disease represents a significant volume of elective and emergency work in the United Kingdom.

•

The primary aim of the study was to explore the factors that lead to complications in high risk patients (ASA 3-4).

•

Histological gallbladder thickness and emergency surgery were the factors most strongly associated with negative outcomes.

•

Age greater than 65 as an independent variable does not lead to an increase in negative outcomes.

•

Cholecystectomy is a relatively safe procedure in what is typically considered higher risk patients.

Elucidation of the de Vries behavior in terms of the orientational order parameter, apparent tilt angle, and field-induced tilt angle for smectic liquid crystals by polarized infrared spectroscopy

We report experimental results of the orientational order parameter, the apparent tilt angle, and the field-induced tilt angle for three chiral smectic liquid crystalline materials investigated using infrared (IR) polarized spectroscopy. The common feature in these materials is use of the core 5-methyl-2- pyrimidine benzoate as the central part of the mesogen. This core is terminated by siloxane or carbosilane chains on one of the ends and by the chiral alkoxy chains on the opposite. These compounds exhibit low concomitant layer shrinkage at the smectic A^{*} (SmA^{*}) to smectic C^{*} (SmC^{*}) transition temperature and within the SmC^{*} phase itself. The maximum layer shrinkage in SmC^{*} is observed as ∼1.5%. We calculate the apparent orientational order parameter, S_{app} in the laboratory reference frame from the observed IR absorbance for homeotropic aligned samples, and the true order parameter, S, is calculated using the measured tilt angle and is also interpolated from Iso-SmA^{*} transition temperature closer to SmC^{*} phase. The apparent tilt angle in the SmA^{*} phase calculated from a comparison of order parameters S and S_{app} is found to be significantly large. A low magnitude of S_{app} found for homeotropic aligned samples in the SmA^{*} phase indicates that the order parameter plays a vital role in determining the de Vries characteristics, especially of exhibiting larger apparent tilt angles. Furthermore there is a significant increase in the true order parameter at temperatures close to SmA^{*} to SmC^{*} transition temperature in all three compounds. The planar-aligned samples are used to study the dependence of induced tilt angle on the applied electric field. The generalized Langevin-Debye model given by Shen et al. reasonably fits the experimental data on the field-induced tilt angle. The results show that the dipole moment of the tilt correlated domain in SmA^{*} diverges as temperature is lowered to the SmA^{*}-SmC^{*} transition temperature. The generalized Langevin-Debye model is also found to be extremely effective in confirming some of the conclusions of the de Vries behavior.

Changes in gene expression predictably shift and switch genetic interactions

Non-additive interactions between mutations occur extensively and also change across conditions, making genetic prediction a difficult challenge. To better understand the plasticity of genetic interactions (epistasis), we combine mutations in a single protein performing a single function (a transcriptional repressor inhibiting a target gene). Even in this minimal system, genetic interactions switch from positive (suppressive) to negative (enhancing) as the expression of the gene changes. These seemingly complicated changes can be predicted using a mathematical model that propagates the effects of mutations on protein folding to the cellular phenotype. More generally, changes in gene expression should be expected to alter the effects of mutations and how they interact whenever the relationship between expression and a phenotype is nonlinear, which is the case for most genes. These results have important implications for understanding genotype-phenotype maps and illustrate how changes in genetic interactions can often—but not always—be predicted by hierarchical mechanistic models.

Non-additive genetic interactions are plastic and can complicate genetic prediction. Here, using deep mutagenesis of the lambda repressor, Li et al. reveal that changes in gene expression can alter the strength and direction of genetic interactions between mutations in many genes and develop mathematical models for predicting them.

Single cell functional genomics reveals the importance of mitochondria in cell-to-cell phenotypic variation

Mutations frequently have outcomes that differ across individuals, even when these individuals are genetically identical and share a common environment. Moreover, individual microbial and mammalian cells can vary substantially in their proliferation rates, stress tolerance, and drug resistance, with important implications for the treatment of infections and cancer. To investigate the causes of cell-to-cell variation in proliferation, we used a high-throughput automated microscopy assay to quantify the impact of deleting >1500 genes in yeast. Mutations affecting mitochondria were particularly variable in their outcome. In both mutant and wild-type cells mitochondrial membrane potential - but not amount - varied substantially across individual cells and predicted cell-to-cell variation in proliferation, mutation outcome, stress tolerance, and resistance to a clinically used anti-fungal drug. These results suggest an important role for cell-to-cell variation in the state of an organelle in single cell phenotypic variation.

Chiral smectic-A and smectic-C phases with de Vries characteristics

Infrared and dielectric spectroscopic techniques are used to investigate the characteristics of two chiral smectics, namely, 1,1,3,3,5,5,5-heptamethyltrisiloxane 1-[4^{'}-(undecyl-1-oxy)-4-biphenyl(S,S)-2-chloro-3-methylpentanoate] (MSi_{3}MR_{11}) and tricarbosilane-hexyloxy-benzoic acid (S)-4'-(1-methyl-hexyloxy)-3'-nitro-biphenyl-4-yl ester (W599). The orientational features and the field dependencies of the apparent tilt angle and the dichroic ratio for homogeneous planar-aligned samples were calculated from the absorbance profiles obtained at different temperatures especially in the smectic-A* phase of these liquid crystals. The dichroic ratios of the C-C phenyl ring stretching vibrations were considered for the determination of the tilt angle at different temperatures and different voltages. The low values of the order parameter obtained with and without an electric field applied across the cell in the Sm-A^{*} phase for both smectics are consistent with the de Vries concept. The generalized Langevin-Debye model introduced in the literature for explaining the electro-optical response has been applied to the results from infrared spectroscopy. The results show that the dipole moment of the tilt-correlated domain diverges as the transition temperature from Sm-A^{*} to Sm-C^{*} is approached. The Debye-Langevin model is found to be extremely effective in confirming some of the conclusions of the de Vries chiral smectics and gives additional results on the order parameter and the dichroic ratio as a function of the field across the cell. Dielectric spectroscopy finds large dipolar fluctuations in the Sm-A^{*} phase for both compounds and again these confirm their de Vries behavior.

Neurologic complications of transplantation

Major neurologic morbidity, such as seizures and encephalopathy, complicates 20-30% of organ and stem cell transplantation procedures. The majority of these disorders occur in the early posttransplant period, but recipients remain at risk for opportunistic infections and other nervous system disorders for many years. These long-term risks may be increasing as acute survival increases, and a greater number of "sicker" patients are exposed to long-term immunosuppression. Drug neurotoxicity accounts for a significant proportion of complications, with posterior reversible leukoencephalopathy syndrome, primarily associated with calcineurin inhibitors (i.e., cyclosporine and tacrolimus), being prominent as a cause of seizures and neurologic deficits. A thorough evaluation of any patient who develops neurologic symptoms after transplantation is mandatory, since reversible and treatable conditions could be found, and important prognostic information can be obtained.

A Concentration-Dependent Liquid Phase Separation Can Cause Toxicity upon Increased Protein Expression

Multiple human diseases are associated with a liquid-to-solid phase transition resulting in the formation of amyloid fibers or protein aggregates. Here, we present an alternative mechanism for cellular toxicity based on a concentration-dependent liquid-liquid demixing. Analyzing proteins that are toxic when their concentration is increased in yeast reveals that they share physicochemical properties with proteins that participate in physiological liquid-liquid demixing in the cell. Increasing the concentration of one of these proteins indeed results in the formation of cytoplasmic foci with liquid properties. Demixing occurs at the onset of toxicity and titrates proteins and mRNAs from the cytoplasm. Focus formation is reversible, and resumption of growth occurs as the foci dissolve as protein concentration falls. Preventing demixing abolishes the dosage sensitivity of the protein. We propose that triggering inappropriate liquid phase separation may be an important cause of dosage sensitivity and a determinant of human disease.

•

Dosage-sensitive proteins in yeast have a high propensity for liquid-liquid demixing

•

Increased protein concentration can force a liquid phase separation, titrating proteins and RNAs from the cytoplasm

•

Preventing liquid-liquid demixing averts dosage sensitivity

•

Inappropriate liquid phase separation may be a determinant of human genetic disease

Species spectrum and antifungal susceptibility profile of vaginal isolates of Candida in Kuwait

OBJECTIVE

The study was undertaken to determine the prevalence of vulvovaginal candidiasis (VVC) among patients with vaginitis, frequency of different Candida species, and their susceptibility profile.

PATIENTS AND METHODS

Over six months period, high vaginal swabs were cultured on Sabouraud's dextrose agar and isolates were identified by culture on CHROMagar Candida and Vitek2 yeast identification system or/and API 20C (BioMerieux, France). Antifungal susceptibility of the Candida isolates was determined by E-test against amphotericin B, flucytosine, fluconazole, voriconazole, posaconazole and caspofungin.

RESULTS

One thousand seven hundred and fifty-two women with vaginitis were screened for the prevalence of Candida spp. Vaginal swab cultures of 231 (13.2%) women yielded Candida spp. The isolation rates of different species were as follows: Candida albicans (73.9%), Candida glabrata (19.8%), Candida kefir (1.94%), Candida tropicalis (0.96%), Candida parapsilosis (0.96%), Candida krusei (0.96%), Candida guilliermondii (0.96%), and Saccharomyces cerevisiae (0.52%). All strains of C. albicans and non-C. albicans were susceptible to most of the antifungal agents tested.

CONCLUSION

The high frequency with which C. albicans was recovered and its azole susceptibility support the continued use of azole agents for empirical therapy of uncomplicated VVC. However, a larger controlled study is required to determine the role of non-C. albicans in recurrent VVC.

Adaptation of Saccharomyces cerevisiae to saline stress through laboratory evolution

Most laboratory evolution studies that characterize evolutionary adaptation genomically focus on genetically simple traits that can be altered by one or few mutations. Such traits are important, but they are few compared with complex, polygenic traits influenced by many genes. We know much less about complex traits, and about the changes that occur in the genome and in gene expression during their evolutionary adaptation. Salt stress tolerance is such a trait. It is especially attractive for evolutionary studies, because the physiological response to salt stress is well-characterized on the molecular and transcriptome level. This provides a unique opportunity to compare evolutionary adaptation and physiological adaptation to salt stress. The yeast Saccharomyces cerevisiae is a good model system to study salt stress tolerance, because it contains several highly conserved pathways that mediate the salt stress response. We evolved three replicate lines of yeast under continuous salt (NaCl) stress for 300 generations. All three lines evolved faster growth rate in high salt conditions than their ancestor. In these lines, we studied gene expression changes through microarray analysis and genetic changes through next generation population sequencing. We found two principal kinds of gene expression changes, changes in basal expression (82 genes) and changes in regulation (62 genes). The genes that change their expression involve several well-known physiological stress-response genes, including CTT1, MSN4 and HLR1. Next generation sequencing revealed only one high-frequency single-nucleotide change, in the gene MOT2, that caused increased fitness when introduced into the ancestral strain. Analysis of DNA content per cell revealed ploidy increases in all the three lines. Our observations suggest that evolutionary adaptation of yeast to salt stress is associated with genome size increase and modest expression changes in several genes.

Clinical presentation of adult coeliac disease

The mode of presentation of coeliac disease has been changing to more atypical or silent disease. Few studies described the clinical presentation of adult coeliac disease in Ireland in recent years. We retrospectively collected the clinical data for all patients who had a diagnosis of coeliac disease made in our centre between January 07 and December 08. Forty seven adults, predominantly females (n = 30), had a confirmed diagnosis of coeliac disease made during the study period. In our patient cohort, the presenting symptom was diarrhoea in 19 (40%) patients, while 16 patients (34%) did not have any G.I. symptoms, 10 (21%) presented with anaemia. Females presented at a significantly younger age compared to males, with median ages at diagnosis of 44.5 and 57 years, respectively (p = 0.04). Females also presented more commonly with non G.I. symptoms (p = 0.07). The reasons behind this gender difference need further study.

Analyzing the catalytic mechanism of protein tyrosine phosphatase PtpB from Staphylococcus aureus through site-directed mutagenesis

Protein tyrosine phosphatase B (PtpB) from Staphylococcus aureus, MRSA 252, is a low molecular weight protein tyrosine phosphatase involved in its pathogenicity. PtpB has been modeled in silico and site-directed mutagenesis performed to ascertain the importance of active site residues Cys8, Arg14, Ser15 and Asp120 in its catalytic mechanism. Kinetic characterization of wild-type and the mutant PtpBs, C8S, R14A, S15T, S15A, D120A, D120E, D120N revealed the reaction mechanism followed by this LMWPTPase. The mutations caused major changes in the local environment resulting in significant decrease of its catalytic activity. Inhibition kinetics for the wild-type enzyme was performed with maleimide and maleimidobutyric acid.

Interface of apoptotic protein complexes has distinct properties

Apoptosis is a programmed mechanism of cell death that is a normal component of development and health of multi-cellular organisms. In this study, we ask if interface properties of apoptotic protein complexes are different from protein complexes in general. We find that although in apoptotic protein complexes the overall distribution of interface size, surface complementarity, hydrogen bonding, hydrophobicity are similar to general interface properties, apoptotic complexes tend to have more fragmented interfaces and different secondary structural preferences. The statistics on the number of interfaces where specific amino acid(s) occur with significantly enhanced frequency suggest that Arg, Met and Asp are most important functional residues. The role of Met is believed to be unique, as evidenced from the existing data on hot spot potential of residues. These findings together provide insight into the possible role of various physico-chemical attributes at the protein interface in regulation of the apoptosis process.

Characteristics of the collective dielectric relaxation mode of the incommensurate SmC(α)(*) phase

Employing the dielectric relaxation spectroscopy technique, we have observed two different characteristics of the collective relaxation mode of an incommensurate SmC(α)(*) phase. Recent theoretical advances predict two different natures for the dielectric relaxation mode in the SmC(α)(*) phase. Our experimental results confirm two different behaviours of the relaxation mode in different temperature ranges for this phase for one unique compound having an exceptionally wide temperature range (∼9 °C) for the SmC(α)(*) phase.

Surveillance of antibacterial resistance in Staphylococcus aureus isolated in Kuwaiti hospitals

OBJECTIVE

To investigate the prevalence of antibiotic resistance among Staphylococcus aureus isolated in Kuwaiti hospitals.

MATERIALS AND METHODS

S. aureus were isolated and identified following standard microbiological methods. Antibacterial susceptibility test was performed by disk diffusion and the measurement of minimum inhibitory concentration with E-test strips.

RESULTS

A total of 1,846 S. aureus isolates were analyzed from 13 hospitals between 1 March and 30 October 2005. They were isolated from 1,765 (95.6%) inpatients and 81 (4.4%) outpatients. Methicillin resistance was detected in 588 (32.0%) of the isolates. The methicillin-resistant S. aureus (MRSA) consisted of 461 (78%) multiresistant and 127 (22%) nonmultiresistant isolates. The nonmultiresistant MRSA consisted of epidemic MRSA-15 and community-associated MRSA. The community-associated MRSA was detected in all hospitals with MRSA, indicating its establishment in Kuwaiti hospitals. The proportion of isolates resistant to gentamicin, kanamycin, erythromycin, tetracycline, ciprofloxacin, fusidic acid and trimethoprim was higher among MRSA than methicillin-susceptible S. aureus (MSSA) isolates. Twenty-four and 22% of MRSA and MSSA isolates, respectively, expressed reduced susceptibility to vancomycin (minimum inhibitory concentration = 3-4 mg/l).

CONCLUSION

The study revealed the presence of methicillin resistance in 32% of S. aureus isolated in Kuwaiti hospitals and revealed an increase in the number of MRSA and MSSA with reduced susceptibility to vancomycin.

High prevalence and level of resistance to metronidazole, but lack of resistance to other antimicrobials in Helicobacter pylori, isolated from a multiracial population in Kuwait

BACKGROUND

The primary treatment regimen for Helicobacter pylori infection for Kuwaitis does not contain metronidazole, but that for expatriates does. There is also increasing failure of antimicrobial therapy.

AIM

To determine the susceptibility of H. pylori from upper gastrointestinal biopsies of Kuwaitis and non-Kuwaitis to find out if differences existed in the susceptibilities of the isolates from the two different populations.

METHODS

The susceptibilities of 96 H. pylori isolates were tested against metronidazole, amoxicillin, clarithromycin and tetracycline by the E test. The rdxA gene was analysed from selected metronidazole-susceptible and metronidazole-resistant strains to find out polymorphism and the basis of metronidazole resistance.

RESULTS

Approximately, 70% of isolates from both populations were metronidazole resistant with 65% isolates showing high minimum inhibitory concentration values of >256 mug/mL. No resistance to the other three antimicrobials was found. There were novel nonsense and missense mutations with no deletion in the rdxA gene by insertion of mini-IS605.

CONCLUSIONS

The prevalence and level of metronidazole resistance in H. pylori in the two populations was high with no difference, in spite of different treatment regimens. Metronidazole resistance in this transitional country appeared to be independent of prior metronidazole use for treatment of H. pylori infection.

Are rheumatologists' treatment decisions influenced by patients' age?

OBJECTIVES

The objective of this study was to determine whether physicians' treatment preferences are influenced by patients' age.

METHODS

We mailed a survey to a random sample of rheumatologists practicing in the US. The survey included a scenario describing a hypothetical patient with rheumatoid arthritis (RA) on hydroxychloroquine, sulfasalazine and low-dose prednisolone, who presents with active disease during a follow-up appointment. The scenario was formulated in two versions that were identical except for the age of the patient. After reading the scenario, respondents were asked to rate (on a 10 cm numerical rating scale) their recommendations for each of the three options: (i) increasing the dose of prednisolone, (ii) adding a new disease-modifying anti-rheumatic drug (DMARD) and (iii) switching DMARDs. Rheumatologists who rated either adding a new DMARD or switching DMARDs higher than increasing the dose of prednisolone were classified as 'preferring aggressive treatment with DMARDs', while the others were classified as 'NOT preferring aggressive treatment with DMARDs'.

RESULTS

A total of 480 rheumatologists were mailed a questionnaire; 204 responded, giving a response rate of 42.5%. Overall 163 (80%) respondents were classified as preferring aggressive treatment with DMARDs. Rheumatologists responding to this survey were more likely to prefer aggressive DMARD treatment for the young RA patient vs the older RA patient (87 vs 71%, P= 0.007).

CONCLUSIONS

Our findings suggest that rheumatologists' treatment recommendations may be influenced by age. Future educational efforts should increase physician awareness of this possible bias in order to ensure equal service delivery across ages.

Dielectric spectroscopy of a binary mixture of liquid crystals showing wide temperature range twisted grain boundary phase with re-entrant cholesteric phase

There are only few materials, which have shown long temperature range twisted grain boundary (TGB) phases. One such material is the chiral binary mixture of 7OCB and 5* CBB (mole ratio 0.8 and 0.2) which shows unique phase sequence of cholesteric ( N*) , a wide temperature range TGBA (approximately 31 degrees C) and reentrant cholesteric (N*re) phases. In the present work we are reporting the dielectric spectroscopy of the above mixture with a chiral analog of earlier reported nematic (N) , smectic- A (SmA) , and reentrant nematic (Nre) phase sequences [Phys. Rev. A 46, 7733 (1992)] for different conditions of molecular orientations. Two modes of dielectric relaxations have been detected in a homeotropically aligned sample with unusually low relaxation frequencies for one of them. Planar oriented molecules in the TGBA phase show a soft mode of relaxation and support the recently proposed theory for the soft mode relaxation of the TGBA phase [Phys. Rev. E 65, 11701 (2001)]. By applying the dc electric field on planar oriented molecules in the TGBA phase, it has been possible to obtain a helix free homeotropically aligned TGBA phase.

Significance of atypical pathogens among community-acquired pneumonia adult patients admitted to hospital in Kuwait

OBJECTIVES

The aim of this study is to determine the microbial etiology and severity of community-acquired pneumonia (CAP) in Kuwait.

SUBJECTS AND METHODS

The severity of consecutive adult CAP cases admitted to 3 hospitals over a 1-year period was classified according to the Pneumonia Outcome Research Team (PORT) severity index. The microbial etiology was determined using standard methods for bacteria and serological tests for atypical and viral pathogens.

RESULTS

The study population was 124 of the 135 admissions; 63 female, 61 male; mean age 41.3+/-18 years. The severity class distribution was: class I 31%, class II 37%, class III 17%, class IV 13%, and class V 2%. Etiological agents were identified from 44 patients (35%), with one pathogen in 31 (25%), two in 9 (7%), and three or more in 4 (3%). The most common pathogens identified were: Mycoplasma pneumoniae in 14 patients (11%), Legionella pneumophila in 10 (8%), Chlamydia pneumoniae in 8 (6%), influenza B virus in 8 (6%), influenza A virus in 5 (4%), Haemophilus influenzae in 4 (3%), Streptococcus pneumoniae in 3 (2%), Staphylococcus aureus in 3 (2%), gram-negative enterobacteria in 5 (4%), Moraxellacatarrhalis in 2 (2%), and viruses in 4 (3%). The yields from laboratory tests were 48% for paired serology, 20% from adequate sputum sample, and 3% from blood culture.

CONCLUSION

Our study shows that a large percentage of mild CAP cases are admitted to hospitals in Kuwait. Atypical pathogens have a significant role in the etiology of CAP. There is overtreatment of CAP with a combination treatment consisting mainly of third-generation chephalosporins and macrolides.

Consumer research: in search of identity

Although the consumer research field has made great progress over the past 30 years with respect to the scope, quality, and quantity of research, there are still significant disagreements about what consumer research is, what its objectives are, and how it should differ from related disciplines. As a result, the field appears to be rather fragmented and even divided on some fundamental issues. In this review we first examine the original vision for the field and its limitations. In the second section we explore the consequences of the ambiguity about the domain and identity of consumer research and the multidisciplinary influences on the field. In particular, we review key trends and "camps" in consumer research, which represent complementary and, in some cases, conflicting views regarding the main topics of investigation and how research is conducted. This review is based in part on systematic analyses of articles that have been published in the leading consumer research journals over the past 30 years. Finally, in the third section we revisit the question of what might differentiate the field from related disciplines, as well as the role of theory testing, studies of substantive phenomena, and relevance in consumer research.

Increasing mortality due to end-stage liver disease in patients with human immunodeficiency virus infection

Highly active antiretroviral therapy has decreased human immunodeficiency virus (HIV)-associated mortality; other comorbidities, such as chronic liver disease, are assuming greater importance. We retrospectively examined the causes of death of HIV-seropositive patients at our institution in 1991, 1996, and 1998-1999. In 1998-1999, 11 (50%) of 22 deaths were due to end-stage liver disease, compared with 3 (11.5%) of 26 in 1991 and 5 (13.9%) of 36 in 1996 (P=.003). In 1998-1999, 55% of patients had nondetectable plasma HIV RNA levels and/or CD4 cell counts of >200 cells/mm(3) within the year before death. Most of the patients that were tested had detectable antibodies to hepatitis C virus (75% of patients who died in 1991, 57.7% who died in 1996, and 93.8% who died in 1998-1999; P=NS). In 1998-1999, 7 patients (31.8%) discontinued antiretroviral therapy because of hepatotoxicity, compared with 0 in 1991 and 2 (5.6%) in 1996. End-stage liver disease is now the leading cause of death in our hospitalized HIV-seropositive population.

Anopheles gambiae salivary gland proteins as putative targets for blocking transmission of malaria parasites

Anopheles gambiae is the primary vector of human malaria in sub-Saharan Africa. Invasion of Anopheles salivary glands by Plasmodium sporozoites is a necessary step in the transmission of malaria and is likely to be mediated by specific receptor-ligand interactions. We are interested in identifying putative an A. gambiae salivary gland receptor or receptors for sporozoite invasion as a possible target for blocking malaria transmission. By using monoclonal antibodies against female-specific A. gambiae salivary gland proteins, two molecules, one of 29 kDa and one of 100 kDa, were identified and characterized with respect to the age and blood-feeding process of mosquitoes. In an in vivo bioassay, the monoclonal antibody against the 100-kDa protein inhibited Plasmodium yoelii sporozoite invasion of salivary glands >/=75%. These results show that A. gambiae salivary gland proteins are accessible to monoclonal antibodies that inhibit sporozoite invasion of the salivary glands and suggest alternate targets for blocking the transmission of malaria by this most competent of malaria vectors.

Mex67p of Schizosaccharomyces pombe interacts with Rae1p in mediating mRNA export

We identified the Schizosaccharomyces pombe mex67 gene (spmex67) as a multicopy suppressor of rae1-167 nup184-1 synthetic lethality and the rae1-167 ts mutation. spMex67p, a 596-amino-acid-long protein, has considerable sequence similarity to the Saccharomyces cerevisiae Mex67p (scMex67p) and human Tap. In contrast to scMEX67, spmex67 is essential for neither growth nor nuclear export of mRNA. However, an spmex67 null mutation (Deltamex67) is synthetically lethal with the rae1-167 mutation and accumulates poly(A)(+) RNA in the nucleus. We identified a central region (149 to 505 amino acids) within spMex67p that associates with a complex containing Rae1p that complements growth and mRNA export defects of the rae1-167 Deltamex67 synthetic lethality. This region is devoid of RNA-binding, N-terminal nuclear localization, and the C-terminal nuclear pore complex-targeting regions. The (149-505)-green fluorescent protein (GFP) fusion is found diffused throughout the cell. Overexpression of spMex67p inhibits growth and mRNA export and results in the redistribution of the diffused localization of the (149-505)-GFP fusion to the nucleus and the nuclear periphery. These results suggest that spMex67p competes for essential mRNA export factor(s). Finally, we propose that the 149-505 region of spMex67p could act as an accessory factor in Rae1p-dependent transport and that spMex67p participates at various common steps with Rae1p export complexes in promoting the export of mRNA.