Immunological depiction of synthetic B-cell epitopes of Mycobacterium tuberculosis

Background

To combat the tuberculosis (TB) epidemic, the development of a better and faster diagnosis or more effective vaccine is essential. Pulmonary TB (PTB) is one of the major causes of morbidity and mortality. Early diagnosis of TB is difficult. Serological assays have been performed with several antigens of laboratory strains such as Mycobacterium tuberculosis H37Rv which have not been found to be highly sensitive. In the present study, various peptides were synthesized which were predicted on the basis of immunoreactivity and differential expression in clinical isolates of M. tuberculosis compared to their expression in a laboratory strain of M. tuberculosis. Therefore, the aim of this study was to compare the antibody levels in PTB and healthy controls against these peptides.

Methods

An effort was made to evaluate antibody response to peptides derived from proteins Rv2588c, Rv0512, Rv0148, Rv0896, and Rv0635 of M. tuberculosis in PTB patients and healthy individuals through enzyme-linked immunosorbent assay. Five milliliters of venous blood samples was collected from each participant, and serum was separated and stored until use.

Results

Antibody levels against these peptides, Rv2588c, Rv0512, Rv0148, Rv0896. and Rv0635 in 139 PTB patients and 52 healthy controls were evaluated. Higher immune response was observed in PTB patients when compared with healthy individuals. Strong immunoglobulin G responses with high percentage, considerable difference among patients and healthy controls was observed with P < 0.0001.

Conclusion

In our study, we found significant statistical differences in antibody levels in PTB patients and healthy individuals against these peptides. These peptides are suggestive of being a potential new candidate (s) for early diagnosis of TB.

Burden of Stroke in Nepal: Findings from Global Burden of Disease Dataset 2017

Background Stroke is the second leading cause of death and disability worldwide including Asian countries, surpassing ischemic heart disease. Stroke accounts for 10% of global death, of which more than three fourth occur in low- and middle-income countries. An exact estimate of the burden of stroke in Nepal is not available. Objective To assess the burden of stroke including disability and death over time in Nepal and compare it with other South Asian countries. Method We retrieved data from the Institute of Health Metrics and Evaluation's Global Burden of Diseases database of 2017 on stroke deaths, disability-adjusted life years, incidence, and prevalence rates, for both genders from Nepal, Bangladesh, Pakistan, Bhutan, and India by year. We assessed the trend of deaths and Disability-Adjusted Life Years (DALYs) due to stroke from 1990 to 2017; and the contribution of major risk factors to stroke burden in 2017. Result Stroke contributed 7.6% of total deaths and 3.5% of total DALYs in Nepal, with a higher burden among the male and old age population. Intracerebral hemorrhage was the dominant type of stroke in Nepal with the highest proportion of deaths and DALYs. Among the South Asian countries, incidence, prevalence, and burden of stroke were highest in Bangladesh. Intracerebral hemorrhage contributed the highest DALYs in South Asian countries. High systolic blood pressure was contributing the maximum DALYs due to stroke in Nepal. Conclusion Hemorrhagic stroke causes high mortality and DALYs in Nepal. Most of the burden of stroke is attributed to high blood pressure in Nepal.

Knowledge, attitudes and practices on childhood TB among healthcare workers

BACKGROUND: Increasing childhood TB case detection requires the deployment of diagnostic services at peripheral healthcare level. Capacity and readiness of healthcare workers (HCWs) are key to the delivery of innovative approaches.METHODS: In 2019, HCWs from five district hospitals (DHs) and 20 primary healthcare centres (PHCs) in Cambodia, Cameroon, Cote d´Ivoire, Sierra Leone and Uganda completed a self-administered knowledge-attitudes-practices (KAP) questionnaire on childhood TB. We computed knowledge and attitudes as scores and identified HCW characteristics associated with knowledge scores using linear regression.RESULT: Of 636 eligible HCWs, 497 (78%) participated. Median knowledge scores per country ranged between 7.4 and 12.1 (/18). Median attitude scores ranged between 2.8 and 3.3 (/4). Between 13.3% and 34.4% of HCWs reported diagnosing childhood with (presumptive) TB few times a week. Practising at PHC level, being female, being involved in indirect TB care, having a non-permanent position, having no previous research experience and working in Cambodia, Cameroon, Cote d´Ivoire and Sierra Leone as compared to Uganda were associated with a lower knowledge score.CONCLUSION: HCWs had overall limited knowledge, favourable attitudes and little practice of childhood TB diagnosis. Increasing HCW awareness, capacity and skills, and improving access to effective diagnosis are urgently needed.

Rapid Prescreening for Antiviral Agents against HIV-1 Based on Their Inhibitory Activity in Site-Directed Immunoassays. I. The V3 Loop of gp 120 as Target

The anionic triphenylmethane derivative aurintricarboxylic acid (ATA) was reported to inhibit the replication and cytopathogenicity of human immunodeficiency virus type 1 (HIV-1). This antiviral effect, ascribed to the inhibitory activity of ATA on the virus reverse transcriptase, was subsequently also explained by binding of ATA to the HIV-1 envelope glycoprotein gp120 and/or to the CD4 receptor for the virus. Results presented here show: (1) the effectiveness of ATA as a potential antiviral drug by demonstrating that HIV-1 replication in vitro can be completely aborted in the presence of ATA as measured by the polymerase chain reaction; (2) that ATA inhibited the reaction between gp120 and antibodies specific for the V3 hypervariable loop of gp120; (3) that additional compounds with anti-HIV-1 activity can be rapidly identified based on their inhibitory effects measured by radioimmunoassays and/or enzyme-linked immunoadsorbent assays; and (4) that ATA also bound to synthetic peptides representing V3 loops of several HIV-1 isolates, suggesting the possibility that selected chemicals would interfere with the biological function of V3 loops of most HIV-1 isolates and would be effective for chemotherapy, and possibly for prophylaxis, of HIV-1 infections.

Model-based stability assessment of ventilatory control in overweight adolescents with obstructive sleep apnea during NREM sleep

Obstructive sleep apnea (OSA) involves the interplay of several different factors such as an unfavorable upper airway anatomy, deficiencies in pharyngeal muscle responsiveness, a low arousal threshold, and ventilatory control instability. Although the stability of ventilatory control has been extensively studied in adults, little is known about its characteristics in the pediatric population. In this study, we developed a novel experimental setup that allowed us to perturb the respiratory system during natural non-rapid eye movement (NREM) sleep conditions by manipulating the inspiratory pressure, provided by a bilevel pressure ventilator, to induce sighs after upper airway stabilization. Furthermore, we present a modeling framework that utilizes the noninvasively measured ventilatory responses to the induced sighs and spontaneous breathing data to obtain representations of the processes involved in the chemical regulation of respiration and extract their stability characteristics. After validation with simulated data, the modeling technique was applied to data collected experimentally from 11 OSA and 15 non-OSA overweight adolescents. Statistical analysis of the model-derived stability parameters revealed a significantly higher plant gain and lower controller gain in the OSA group (P = 0.046 and P = 0.007, respectively); however, no differences were found in loop gain (LG) and circulatory time delay between the groups. OSA severity and LG, within the 0.03-0.04-Hz frequency band, were significantly negatively associated (r = -0.434, P = 0.026). Contrary to what has been found in adults, our results suggest that in overweight adolescents, OSA is unlikely to be initiated through ventilatory instability resulting from elevated chemical loop gain.

Impact of intensified case-finding strategies on childhood TB case registration in Nepal

SETTING

Seven intervention districts with intensified childhood tuberculosis (TB) case-finding strategies implemented by a non-governmental organisation and seven control districts under the National Tuberculosis Programme, Nepal.

OBJECTIVES

To assess the differences in childhood TB case registrations and case registration rates per 100 000 population between two time periods (Year 1 = March 2012-March 2013 and Year 2 = March 2013-March 2014) in intervention and control districts.

DESIGN

Retrospective record review using routinely collected data.

RESULTS

Childhood TB cases increased from 271 to 360 between Years 1 and 2 in the intervention districts (case registration rate from 18.2 to 24.2/100 000) and from 97 to 113 in the control districts (13.4 to 15.6/100 000): the increases were significantly higher in the intervention districts compared with the control districts. The increases were also significantly higher in children aged 0-4 years and in those with smear-negative pulmonary TB and extra-pulmonary TB. Of the various case-finding strategies, household contact screening, private-public mix services and mobile health chest camps produced the highest yield of TB.

CONCLUSION

A package of intensified case-finding strategies in children was associated with an increase in childhood TB case registrations in Nepal. Additional diagnostic approaches to increase case registrations also need to be considered.

Fetal Transcerebellar Diameter/ Abdominal Circumference Ratio as a Gestational Age Independent Parameter for Fetal Growth

Aims: The purpose of this study was to evaluate accuracy of trans-cerebellar diameter / abdominal circumference (TCD/AC) ratio to assess fetal growth. The ratio of TCD with head circumference (HC) and biparietal diameter (BPD) was also determined. Methods: This was a prospective cross-sectional study involving 442 women with uncomplicated singleton gestation between 15-40 weeks. Protocol included obtaining the BPD, HC, TCD and AC in conventional planes  and obtaining ratio of TCD with other biometric parameters.Results: We were able to visualize the cerebellum in about 93% of scans. The TCD/ AC ratio remained nearly constant throughout gestational age and was 0.138. The mean TCD/HC ratio was 0.124 and mean TCD/BPD ratio was 0.476.Conclusions: TCD/HC and TCD/BPD ratio showed a small increase towards the completion of gestation while TCD/AC ratio remained nearly constant throughout gestational age. TCD/AC ratio is reliable as a gestational age independent parameter of fetal growth.DOI: http://dx.doi.org/10.3126/njog.v9i2.11770   

Occurrence of amino acid mutation (Ala98Val) of HNF1α in association with type II diabetes

BACKGROUND

Maturity onset diabetes of the young type 3 is a monogenic form of diabetes. Gene defects in the Hepatocyte Nuclear Factor -1 alpha (HNF1a) causes MODY3. HNF1a gene located in the chromosome (12q24.2) codes for a transcription factor which helps in signalling of insulin exocytosis in pancreatic Beta cells. A prevalent amino acid polymorphism at codon 98-Ala98Val (exon 1) of the HNF1a was shown to be associated with diabetes in the South Indian population. Since Nepal shares the ancestral origin with India and people have been sharing similar lifestyles for a long period of life it was relevant to check the occurrence of same mutation in diabetic population of Nepal as well. The study was carried out to identify the occurrence of amino acid mutation (Ala98Val) of HNF 1 alpha in association with type 2 diabetes in diabetic population of Kathmandu.

METHODS

DNA samples were randomly collected from 12 non-diabetic and 56 diabetic patients. The DNA samples were amplified using Polymerase Chain Reaction (PCR). Restriction Fragment Length Polymorphism (RFLP) was carried out to identify the occurrence of the mutation.

RESULTS

During the study, out of 12 non-diabetic samples, nine were normal while three samples showed heterozygous Ala98Val mutation. Whereas, eight diabetic patients were found to have Ala98Val mutation and rest 48 had normal genotype. The study thus showed 16.17% occurence of Ala98Val mutation among 68 samples.

CONCLUSIONS

The study showed the occurrence of Ala98Val amino acid mutation in diabetic samples that were taken under study.

Risks for impaired cerebral autoregulation during cardiopulmonary bypass and postoperative stroke

BACKGROUND

Impaired cerebral autoregulation may predispose patients to cerebral hypoperfusion during cardiopulmonary bypass (CPB). The purpose of this study was to identify risk factors for impaired autoregulation during coronary artery bypass graft, valve surgery with CPB, or both and to evaluate whether near-infrared spectroscopy (NIRS) autoregulation monitoring could be used to identify this condition.

METHODS

Two hundred and thirty-four patients were monitored with transcranial Doppler and NIRS. A continuous, moving Pearson's correlation coefficient was calculated between mean arterial pressure (MAP) and cerebral blood flow (CBF) velocity, and between MAP and NIRS data, to generate the mean velocity index (Mx) and cerebral oximetry index (COx), respectively. Functional autoregulation is indicated by an Mx and COx that approach zero (no correlation between CBF and MAP); impaired autoregulation is indicated by an Mx and COx approaching 1. Impaired autoregulation was defined as an Mx ≥0.40 at all MAPs during CPB.

RESULTS

Twenty per cent of patients demonstrated impaired autoregulation during CPB. Based on multivariate logistic regression analysis, time-averaged COx during CPB, male gender, Pa(CO(2)), CBF velocity, and preoperative aspirin use were independently associated with impaired CBF autoregulation. Perioperative stroke occurred in six of 47 (12.8%) patients with impaired autoregulation compared with five of 187 (2.7%) patients with preserved autoregulation (P=0.011).

CONCLUSIONS

Impaired CBF autoregulation occurs in 20% of patients during CPB. Patients with impaired autoregulation are more likely than those with functional autoregulation to have perioperative stroke. Non-invasive monitoring autoregulation may provide an accurate means to predict impaired autoregulation. Clinical trials registration. www.clinicaltrials.gov (NCT00769691).

Serological diagnosis of tuberculosis

OBJECTIVE

To evaluate the efficacy of ELISA for the detection of IgG antibodies against antigen 85 complex (Ag 85 complex) of Mycobacterium tuberculosis.

METHODS

Children of either sex, 0-18 years of age, attending the outpatient department and admitted in the casualty and wards of the Department of Pediatrics, S.N. Medical College, Agra, were included in present study. The study was carried out on children with pulmonary and CNS tuberculosis along with matching controls (83 cases and 32 controls). Informed consents of their parents or guardians were taken. They were subjected to clinical examination, relevant laboratory investigations, tuberculin test and chest radiograph. Relevant body fluids were subjected to bacteriological tests; ELISA was applied to serum samples for detection of IgG antibodies against antigen 85 complex (Ag85). The result of ELISA was compared with bacteriological tests [Ziehl Neelson (ZN) staining for acid-fast bacilli, culture on Lowenstein Jensen (LJ) medium and culture on BacT/Alert 3D system].

RESULTS

ELISA tests showed a significantly higher sensitivity (59.1%) as compared with LJ medium culture method (19.3%), BacT/Alert 3D system (24.1%) and ZN staining (16.9%) in all patients (p<0.001). Specificity of ELISA test was 71.9%.

CONCLUSION

In view of the convenience, low cost and good sensitivity, ELISA tests have a promising future in the diagnosis of childhood tuberculosis.

Which obese children should have a sleep study?

BACKGROUND

The UK government has recommended the development of obesity services for children. As obesity is common, studying every obese child for obstructive sleep apnoea (OSA) would be challenging and full paediatric sleep services are not available in every area in Europe. The purpose of this study was to consider how well clinical features predict significant OSA in obese children in order to help prioritise the need for sleep studies and subsequent treatment.

METHODS

Consecutive children referred for obesity management aged 2-16 years with a body mass index (BMI) of >2.5 z scores for age were offered a sleep study using overnight oximetry and audiovisual recordings. Significant OSA was defined as > or = 5 dips/h of >4% oxygen saturation or > or = 5 respiratory-event related arousals/h.

RESULTS

Forty-one of 158 (26%) children (mean BMI z score 3.7) had significant OSA and 95% of these had either reported apnoea, restless sleep or tonsillar hypertrophy (TH). Nineteen percent of all children had none of these features. BMI was not related to OSA.

CONCLUSION

If only obese children with reported apnoea, restless sleep or TH have a sleep study, 95% of all obese children with significant OSA will be identified using this method.

Differential regulation of human YY1 and caspase 7 promoters by prohibitin through E2F1 and p53 binding sites

Prohibitin is a 30 kDa growth suppressive protein that has pleiotropic functions in the cell. Although prohibitin has been demonstrated to have potent transcriptional regulatory functions, it has also been proposed to facilitate protein folding in the mitochondria and promote cell migration in association with Raf-1. Our previous studies have shown that prohibitin physically interacts with the marked-box domain of E2F family members and represses their transcriptional activity; in contrast, prohibitin could bind to and enhance the transcriptional activity of p53. Here, we show that promoters of human YY1 (Yin and Yang 1) as well as caspase 7 genes are modulated by prohibitin. YY1 promoter activity was reduced upon overexpression of prohibitin, while it was enhanced when prohibitin was depleted by small interfering RNA techniques. The repressive effects of prohibitin on the YY1 promoter were mediated through E2F binding sites, as seen by mutational analysis and chromatin immunoprecipitation assays. Further, depletion of E2F1 prevented prohibitin from repressing the YY1 promoter. In contrast with YY1, prohibitin overexpression led to enhanced levels of caspase 7, whereas depletion of prohibitin reduced it. Interestingly, the caspase 7 promoter was found to have p53-binding sites and prohibitin activated this promoter through p53. These studies show that prohibitin can have diverse effects on the expression of different genes and the activity of various cellular promoters is affected by prohibitin. Further, it appears very likely that prohibitin carries out many of its cellular functions by affecting the transcription of different genes.

Diagnostic value of Elisa serological tests in childhood tuberculosis

Two separate studies (study I and study II) were conducted to evaluate the efficacy of ELISA serological test for the detection of IgG antibodies against specific glycolipid antigen (PGLTb1) and ESAT 6 antigen of Mycobacterium tuberculosis, respectively. These results were compared with bacteriological tests [Ziehl Neelson (ZN) staining for acid-fast bacilli and culture on Lowenstein Jensen (LJ) medium] and polymerase chain reaction (PCR) targeting IS6110 sequence. Both studies were carried out on children with pulmonary, central nervous system, lymph node, and gastrointestinal tuberculosis along with matching controls (65 cases and 27 controls for study I and 83 cases and 22 controls for study II). Informed consents of their parents or guardians were taken. They were subjected to clinical examination, relevant laboratory investigations, tuberculin test and chest radiograph. Relevant body fluids were subjected to bacteriological tests and PCR. Sera samples were analyzed for antibodies against PGLTbl and ESAT 6 antigen in study I and study II, respectively. ELISA tests showed a significantly higher sensitivity (49% study I; 53%, study II) as compared with LJ medium culture method (15.4%, study I; 28.9% study II) and ZN staining (27.7%, study I; 20.5%, study II) in all patients (p < 0.05). The results were comparable with PCR (40%, study I; 42.2% study II). Specificity of ELISA test was 100% in all the patients except in those with pulmonary disease (92.8%, study I; 84.8%, study II). In view of the convenience, low cost and comparable sensitivity with PCR, these ELISA tests have a promising future in the diagnosis of childhood tuberculosis.

Farnesyltransferase and geranylgeranyltransferase I inhibitors upregulate RhoB expression by HDAC1 dissociation, HAT association and histone acetylation of the RhoB promoter

Recently, we have shown that RhoB suppresses EGFR-, ErbB2-, Ras- and Akt-mediated malignant transformation and metastasis. In this paper, we demonstrate that the novel antitumor agents farnesyltransferase inhibitors (FTIs) and geranylgeranyltransferase I inhibitors (GGTIs) upregulate RhoB expression in a wide spectrum of human cancer cells including those from pancreatic, breast, lung, colon, bladder and brain cancers. RhoB induction by FTI-277 and GGTI-298 occurs at the transcriptional level and is blocked by actinomycin D. Reverse transcription-PCR experiments documented that the increase in RhoB protein levels is due to an increase in RhoB transcription. Furthermore, treatment with FTIs and GGTIs of cancer cells results in HDAC1 dissociation, HAT association and histone acetylation of the RhoB promoter. Thus, promoter acetylation is a novel mechanism by which RhoB expression levels are regulated following treatment with the anticancer agents FTIs and GGTIs.

An Unusual Penetrating Foreign Body in the Neck

A case of a penetrating injury of the neck sustained due to a flying fragment of metalis presented. The nature of the Injury and its management are discussed.Key Words: Neck Injury, Penetrating, Vascular Injury, Foreign Body.

Phosphorylation of eukaryotic initiation factor 4E (eIF4E) at Ser209 is not required for protein synthesis in vitro and in vivo

Eukaryotic translation initiation factor 4E (eIF4E) is essential for efficient translation of the vast majority of capped cellular mRNAs; it binds the 5'-methylated guanosine cap of mRNA and serves as a nucleation point for the assembly of the 48S preinitiation complex. eIF4E is phosphorylated in vivo at residue 209 of the human sequence. The phosphorylated form is often regarded as the active state of the protein, with ribosome-associated eIF4E enriched for the phosphorylated form and increased phosphorylation often correlated with upregulation of rates of protein synthesis. However, the only reported measured effect attributable to phosphorylation at the physiological site has been a relatively small increase in the affinity of eIF4E for the mRNA m7GTP cap structure. Here, we provide data to suggest that phosphorylation of eIF4E at Ser209 is not required for translation. eIF4E that is modified such that it cannot be phosphorylated (Ser209-->Ala), is unimpaired in its ability to restore translation to an eIF4E-dependent in vitro translation system. In addition, both the wild-type and mutant forms of eIF4E interact equally well with eIF4G, with the phosphorylation of eIF4E not required to effect the change in conformation of eIF4G that is required for efficient cleavage of eIF4G by L-protease. Furthermore, we show that wild-type and phosphorylation-site variants of eIF4E protein are equally able to rescue the lethal phenotype of eIF4E deletion in S. cerevisiae.

Immunological profile of treated lepromatous leprosy patients

The immune responses of 19 treated lepromatous patients who had remained smear negative for a long period were assessed for specific cell-mediated immunity (CMI), anti-Mycobacterium leprae antibodies and cytokine release in response to challenge with M. leprae soluble antigen (MLSA). All of these patients remained anergic to Mitsuda lepromin. Lymphoproliferation in response to M. leprae antigen was noted in only two patients. Significant reduction in the phenolic glycolipid I (PGL-I) antibody response in treated patients with no difference in the M. leprae 35-kDa antibody response was observed when these responses were compared with those of active lepromatous patients. More treated patients produced interleukin-2 (IL-2) and interferon gamma (IFN-gamma) than did active patients. On the other hand, fewer treated patients produced IL-10 than did active patients. These limited findings suggest that the host immune response makes an attempt toward upregulation of CMI in some treated LL/BL patients.

Acute cytokine response to systemic adenoviral vectors in mice is mediated by dendritic cells and macrophages

We investigated the cellular basis for secretion of inflammatory cytokines in mice following intravenous administration of adenoviral vectors (Ad). Serum inflammatory cytokines including interleukin-6 (IL-6), IL-12, and tumor necrosis factor-alpha (TNF-alpha) were detected as early as 6 h following intravenous injection of Ad-expressing Escherichia coli beta-galactosidase (Ad-lacZ). Ad-lacZ readily accumulated in the splenic marginal zone 1 h after intravenous infusion, where both dendritic cells (DCs) and macrophages were transduced and activated within 6 h. Flow cytometric analyses showed that the expression of Ia and CD86 antigens was markedly enhanced on splenic DCs indicating their activation in vivo by Ad-lacZ. Upon ex vivo culture, these early-activated splenic DCs spontaneously produced high levels of IL-6 and IL-12. By contrast, activated splenic macrophages spontaneously secreted only IL-6. Elimination of tissue macrophages and splenic DCs in vivo considerably reduced the early release of IL-12, IL-6, and TNF-alpha and significantly blocked the specific cellular immune response to Ad and the transgene product in vivo. Our findings indicate that preferential activation of DCs and macrophages may account for Ad-triggered acute inflammatory response in vivo in mice. Moreover, DCs and macrophages may play different roles in this process in terms of their abilities to produce distinct patterns of inflammatory cytokines.

Active case finding: understanding the burden of tuberculosis in rural South Africa

SETTING

The Agincourt demographic and health surveillance site in South Africa's rural Northern Province.

OBJECTIVES

To accurately assess the true burden of tuberculosis in a rural sub-district with a known high prevalence of human immunodeficiency virus.

DESIGN

Data on hospital registrations of tuberculosis were combined with data from an ongoing demographic health and surveillance system to accurately describe the burden of tuberculosis in a well-defined community. Undiagnosed active cases of sputum-positive disease in the community were detected among chronic coughers identified by heads of household during a single-pass census interview.

RESULTS

The incidence of hospitalised tuberculosis among the permanently resident population (n = 56 566) was 212/100,000 person-years during 1999. The average point prevalence of detected tuberculosis (all forms) among patients aged over 10 years was 133/100,000, and 81/100,000 for sputum-positive pulmonary disease. This compares with a point prevalence of 16/100,000 cases of sputum-positive disease detected through active case finding.

CONCLUSION

For every nine cases of sputum positive pulmonary tuberculosis being treated at any one time, there are two cases of undiagnosed disease in the community. This study demonstrates a modest burden of undiagnosed tuberculosis among residents in a rural sub-district in South Africa.

Purification of recombinant adeno-associated virus vectors by column chromatography and its performance in vivo

Recombinant adeno-associated virus (AAV) holds much promise for human gene therapy. While evidence indicates that AAV mediates long-term gene transfer in several different tissues, difficulty in preparing and purifying this viral vector in large quantities remains a major obstacle for evaluating AAV vectors in clinical trials. The current method of purification, based on sedimentation through cesium chloride, is not scaleable and yields product of insufficient quality. In this article we report a new technique for purifying AAV, using a fully closed two-column chromatography system. Yields of AAV vectors purified by this method are high, potency is increased, and the purity of column-purified preparations is substantially improved. We previously reported a novel method to generate AAV based on an AAV Rep/Cap-containing cell line (B50) and an Ad-AAV hybrid virus, which is amenable to scale-up in bioreactors. By combining the new, fully scaleable purification process we report here with the B50/hybrid production method, it would be feasible to prepare AAV vectors to the scale and purity required for clinical and potential commercial applications.

Alternative transcriptional initiation and splicing define the translational efficiencies of zebrafish mRNAs encoding eukaryotic initiation factor 4E

Translation initiation factor 4E (eIF4E) binds to the m7GTP cap structure of eukaryotic mRNAs and influences the overall rates of translation. The eIF4E protein is subject to regulation at a number of levels that allow it to modulate translation of maternal mRNAs in early embryos before the onset of zygotic transcription. In zebrafish eIF4E (zeIF4E) mRNA levels are elevated in specific tissues and at specific times during embryogenesis. We have characterized the organization of the zeIF4E gene to facilitate elucidation of the molecular mechanisms that influence its expression. The zeIF4E gene spans about 14 kb and like its human counterpart is comprised of seven exons. Alternative splicing between the first and second exon generates two mRNA splice-forms called SF1 and SF2. Nuclease-S1-protection and primer-extension reveal two zeIF4E transcriptional start-sites. Transcripts initiating from the distal start-site during oogenesis are exclusively SF1, while initiation from the proximal start-site generates both splice-forms. Although translation in vitro of SF1 mRNA gives rise to a protein consistent in mass with affinity-purified zeIF4E, SF2 mRNA does not. Instead, SF2 mRNA inhibits in vitro protein synthesis in a concentration-dependent manner, suggesting it functions as a translational attenuator. Thus, specific transcriptional activation from the distal start-site may provide a unique mechanism for transcriptional regulation of the levels, as well as the function of zeIF4E mRNAs.

Indian-Asian relationship: mtDNA reveals more

Recent studies on human mtDNA have identified continent-specific restriction enzyme sites and resultant haplo-groups among populations from different regions of the world. Such studies have helped in elaborating the models for human migrations. We have studied Indian mtDNAs to identify the recognized world ethnic elements present in it. The results presented here are based on the study of DdeI 10394 site along with the associated Asian-specific AluI 10397 site in the mtDNA sequences of the Indian samples. On examining all the related haplo-groups, this study suggests that the apparent affinities of Indians and East Asians (comprising Chinese, Japanese, Southeast Asians etc.) could be due to a proto-Asiatic element present in Indians.

WD-repeat protein encoding genes among prokaryotes of the Streptomyces genus

Southern hybridization with probes designed for detection of WD-repeats coding sequences gave positive results in 21 streptomycete strains indicating that WD-repeats encoding genes are massively spread among streptomycetes. One of them, the wdlA gene of Streptomyces lincolnensis, codes for a 971 amino acid protein with seven WD-repeats in its C-terminus, two transmembrane domains and an ATP/GTP binding site upstream of the WD-repeat region.

Apoptosis induction by a novel anti-prostate cancer compound, BMD188 (a fatty acid-containing hydroxamic acid), requires the mitochondrial respiratory chain

We recently developed a class of novel anti-prostate cancer compounds, cyclic hydroxamates that elicit a potent apoptotic response in many tumor cells cultured in vitro (D.G. Tang et al., Biochem. Biophys. Res. Commun., 242: 380-384, 1998). The lead compound, termed BMD188, induces programmed cell death in a variety of prostate cancer cells in vitro as well as in vivo (L. Li et al., Anticancer Res., 19: 51-70, 1999). BMD188 kills androgen-independent prostate cancer cells as well as prostate cancer cells with a multidrug-resistance phenotype. The apoptotic effect of BMD188 in prostate cancer cells does not depend on cell cycle, p53 status, or its purported target, arachidonate 12-lipoxygenase, but does require caspase activation and seems to involve mitochondria. To synthesize more specific and effective anti-prostate cancer hydroxamic acid compounds, it is important to understand their mechanism(s) of action. In the present study, we studied the role of mitochondrial respiratory chain (MRC) in BMD188-induced apoptosis in androgen-independent prostate cancer PC3 cells and compared its effect with that of staurosporine (STS), a widely used apoptosis inducer. Several lines of evidence indicate that BMD188-induced cell death depends on MRC: (a) the death could be significantly inhibited by several complex-specific respiration inhibitors; (b) respiration-deficient rho0 cells were more resistant than wild-type parent cells to apoptosis induction by BMD188; and (c) BMD188 induced a rapid increase in reactive oxygen species in mitochondria, an up-regulation of cytochrome c oxidase subunits, a biphasic alteration (i.e., an early hyperpolarization, followed by later hypopolarization) in the mitochondrial membrane potential (delta psi(m)), dramatic changes in mitochondrial morphology and distribution prior to caspase activation, and an abnormal proliferation of mitochondria at the ultrastructural level. By contrast, STS-induced PC3 apoptosis seemed not to depend on MRC. Taken together, the data suggest that the MRC represents a functional target for anti-prostate cancer hydroxamates.

Activation of the interferon-inducible (2'-5') oligoadenylate synthetase by the Epstein-Barr virus RNA, EBER-1

The 2'-5' oligoadenylate synthetases and the protein kinase PKR are both interferon-induced, double-stranded RNA-dependent proteins that play important roles in the antiviral effects of the interferons and in cellular growth control. Both enzymes are activated by natural or synthetic dsRNAs and by single-stranded RNAs that possess extensive secondary structure. This report describes the effects of the small Epstein-Barr virus-encoded RNA EBER-1 on the regulation of 2-5(A) synthetase activity. We demonstrate that EBER-1 RNA binds to and activates the human 40-kDa 2-5(A) synthetase in a dose-dependent manner. The efficiency of EBER-1 as an activator of 2-5(A) synthetase is approximately 25% of that of the synthetic double-stranded RNA poly(I)/poly(C), and poly(I)/poly(C) further stimulates enzyme activity even in the presence of a high concentration of EBER-1. Conversely, EBER-1 neither stimulates nor inhibits 2-5(A) synthetase that has been activated by a high concentration of poly(I)/poly(C). Competitive binding assays suggest that the relative affinity of the enzyme for poly(I)/poly(C) is considerably higher than that for EBER-1. Our data indicate that EBER-1, like VAI RNA of adenovirus, TAR RNA of HIV-1, and Rex-RE RNA of HTLV-1, is able to activate the 2-5(A) synthetases. The significance of why several viruses may activate the 2-5(A) synthetase/RNase L-mediated RNA degradation pathway is discussed.

A novel hydroxamic acid compound, BMD188, demonstrates anti-prostate cancer effects by inducing apoptosis. I: In vitro studies

BACKGROUND

Prostate cancer is the most frequently diagnosed malignancy in the Western countries. Apoptosis-targeted drug development could represent a specific and effective weapon against the disease (Tang and Porter, 32: 284-293, 1997). We previously demonstrated that the arachidonate 12-lipoxygenase and its metabolic products could function as survival factors for many solid tumors (Tang et al., Proc. Natl. Acad. Sci. USA 93: 5241-5246, 1996; Tang and Honn, J. Cell. Physiol. 172: 155-170, 1997).

MATERIALS AND METHODS

In this study, we synthesized a series of novel cyclic hydroxamic acid compounds that demonstrated varying degrees of inhibitory effects on the arachidonate 12-lipoxygenase. Subsequently we studied the effects of these novel compounds on human prostate cancer cells. First, all these compounds were screened on androgen-independent PC3 adenocarcinoma cells. Second, based on the results (i.e., the LD50 values) of the primary, secondary and tertiary screening, lead compounds were determined. Third, the lead compounds were utilized to study their cytotoxic effects on various prostate cancer cells as well as several types of normal cells. Finally, the molecular nature of the cell death was thoroughly characterized and the potential mechanisms of cell death were determined.

RESULTS

About 30% of the compounds screened induced a strong apoptotic death of androgen-independent prostate cancer cells, PC3, with an LD50 mostly at 10-20 microM. A lead compound, BMD188 [cis-1-hydroxy-4-(1-naphthyl)-6-octylpiperidine-2-one], was subsequently identified which inhibited the growth of PC3 cells with an LD50 at approximately 10 microM. Comparative studies indicated that BMD188 induced a more potent apoptotic response in PC3 cells than several conventional chemotherapeutic drugs. Furthermore, unlike the above drugs, BMD188 could induce 100% apoptosis in tumor cells. BMD188 also caused apoptosis of other types of prostate cancer cells including cells with multidrug resistance phenotype, independent of the androgen-dependence and p53 status. By contrast, BMD188 generally demonstrated 2-5 fold lower cytotoxicity towards several normal cell types including normal prostate epithelial cells. The growth inhibition by BMD188 was due to apoptosis induction as evidenced by DNA ladder formation, PARP [poly(ADP-ribose)polymerase] cleavage, and typical apoptotic morphology. BMD188-induced apoptosis does not depend on its inhibitory effects on lipoxygenase since target cells (i.e., PC3 and Du145) did not express the lipoxygenase mRNA and protein. In contrast, the apoptosis-inducing effect of BMD188 in PC3 cells could be significantly inhibited by serine protease inhibitors TPCK and TLCK as well as by caspase inhibitors DEVD and zVAD. The involvement of caspases in the apoptotic effects of BMD188 was further confirmed by the activation of caspase-3 (CPP32). In the accompanying paper, we show that BMD188 also inhibits the primary growth and local invasion of Du145 prostate cancer cells orthotopically implanted into the SCID or athymic nude mice.

CONCLUSION

The data presented here suggest that these novel cyclic hydroxamic acid compounds, via induction of apoptotic death, may find potential clinical applications in the treatment of human prostate cancers.

PKR, apoptosis and cancer

The double-stranded (ds) RNA-regulated serine/threonine protein kinase, PKR, is an interferon-inducible enzyme of widespread occurrence in mammalian cells. PKR is activated by dsRNA via a mechanism involving autophosphorylation. Once activated, the enzyme phosphorylates the alpha-subunit of protein synthesis initiation factor eIF2, thereby inhibiting translation. Accumulating data suggest that PKR has additional substrates, and that the kinase may also regulate gene transcription and signal transduction pathways. Although PKR plays an important role in mediating the antiviral effects of interferons, PKR is also implicated in regulating cell proliferation in uninfected cells and may have a tumor suppressor function under normal conditions. Studies of human malignancies and tumor cell lines suggest that, in general, patients bearing tumors with a higher PKR content have a more favorable prognosis. However, in human breast carcinoma cells, dysregulation of PKR may be associated with the establishment or maintenance of the transformed state.

Abnormal levels and minimal activity of the dsRNA-activated protein kinase, PKR, in breast carcinoma cells

The interferon induced, dsRNA-activated, protein kinase, PKR, is a key regulator of translational initiation, playing an important role in the regulation of cell proliferation, apoptosis and transformation. PKR levels correlate inversely with proliferative activity in several human tumor systems. This inverse relationship breaks down in human invasive ductal breast carcinomas which exhibit high levels of PKR (Haines et al., Tumor Biol. 17 (1996) 5-12). Consistent with the data from human tumors, the levels of PKR in several breast carcinoma cell lines, MCF7, T47D, BT20, MDAMB231 and MDAMB468, are paradoxically high compared to those found in the normal breast cell lines MCF10A and Hs578Bst. The activity of affinity- or immuno-purified PKR from MCF7, T47D, and BT20 cells appears to be severely attenuated, as judged by its ability to autophosphorylate, or phosphorylate eIF2 alpha. Furthermore, the activity of the kinase from breast carcinoma cells is refractory to stimulation by dsRNA or heparin. However, PKR from breast carcinoma cells remains functional with respect to its ability to bind dsRNA. The activity of PKR from MCF10A cells is reduced by prior incubation with extracts from MCF7 cells, suggesting that MCF7 extracts contain a transdominant inhibitor of PKR. Deregulation of PKR may therefore provide a mechanism for the development or maintenance of a transformed phenotype of human breast carcinomas, mimicking the effects of manipulation of PKR or eIF2 activity observed in experimental systems. Thus, breast carcinomas may provide the first indication of a role for PKR in the pathogenesis of a naturally occurring human cancer.

A novel hydroxamic acid compound, BMD188, demonstrates anti-prostate cancer effects by inducing apoptosis. II: In vivo efficacy and pharmacokinetic studies

BACKGROUND

In the preceding paper, we demonstrated that, BMD188 [cis-1-hydroxy-4-(1-naphthyl)-6-octylpiperidine-2-one], a newly synthesized cyclic hydroxamic acid compound, induces potent apoptotic death of prostate cancer cells in vitro. In this project, we studied the in vivo pharmacokinetic behavior and anti-tumor efficacy of this novel compound.

MATERIALS AND METHODS

A bioavailability/elimination study was first performed using radiolabeled BMD188 administered to rats through intraperitoneal (i.p.), intravenous (i.v). or oral (p.o.) routes. Based on these pharmacokinetic data as well as pilot experiments on in vivo toxicity, two sets of efficacy studies, with i.p. administered BMD188, were performed in SCID mice or athymic nude mice which had been orthotopically transplanted with Du145 human prostate cancer cells. Tumor growth rate was measured and the final tumor weights and sizes determined. Subsequently, histopathological data were obtained and tumor tissue sections were used for apoptosis (i.e., TUNEL) staining.

RESULTS

The pharmacokinetic studies revealed low (approximately 8%) absorption through the p.o. route and high (approximately 70%) absorption through the i.p. route. The average plasma half life (T1/2) of BMD188 was approximately 50 h. Post-absorption, plasma elimination of radioactivity was similar to that in animals given [3H]-188 intravenously. The in vivo efficacy results indicate that i.p. administered BMD188 significantly inhibited the primary growth and local invasion of Du145 prostate cancer cells orthotopically implanted into SCID or athymic nude mice. The tumor-inhibitory effect of BMD188 was due to apoptosis induction in vivo, as revealed by histological analysis as well as TUNEL staining of the tumor tissue sections.

CONCLUSION

Collectively, the preceding in vitro and the current in vivo studies suggest that BMD188 and its analogs may find clinical applications in the treatment of prostate cancer patients by inducing apoptotic death of prostate cancer cells.

The vaccinia virus E3L gene product interacts with both the regulatory and the substrate binding regions of PKR: implications for PKR autoregulation

The vaccinia virus E3L gene product, pE3, is a dsRNA binding protein that prevents activation of the interferon-induced, dsRNA-activated protein kinase, PKR. Activation of PKR, which results in phosphorylation of the translation initiation factor, eIF2alpha, leads to the inhibition of protein synthesis, a process involved in defense against virus infection. The E3L gene product has a conserved dsRNA binding domain (DRBD) in its carboxyl-terminal region and has been shown to function in vitro by sequestration of dsRNA. We have utilized in vitro binding assays and the yeast two-hybrid system to demonstrate direct interactions of pE3 with PKR. By these methods, we demonstrate that pE3 interacts with two distinct regions in PKR, the amino-terminal (amino acids 1-99) located in the regulatory domain and the carboxyl-terminal (amino acids 367-523) located in the catalytic domain. The amino-terminal region of PKR that interacts with pE3 contains a conserved DRBD, suggesting that PKR can form nonfunctional heterodimers with pE3, analogous to those seen with other dsRNA binding proteins. Interaction of pE3 with the amino-terminal region of PKR is enhanced by dsRNA. In contrast, dsRNA reduces the interaction of pE3 with the carboxyl-terminal region of PKR. Competition experiments demonstrate that the carboxyl-terminal region of PKR, to which pE3 binds, overlaps the region with which eIF2alpha and the pseudosubstrate pK3 interact, suggesting that pE3 may also prevent PKR activation by masking the substrate binding domain. Like pE3, the amino-terminal region of PKR also interacts with the carboxyl-terminal domain of PKR. These interactions increase our understanding of the mechanisms by which pE3 downregulates PKR. In addition, the PKR-PKR interactions observed leads us to suggest a novel autoregulatory mechanism for activation of PKR in which dsRNA binding to the DRBD(s) induces a conformational change that results in release of the amino terminal region from the substrate binding domain, allowing access to eIF2alpha and its subsequent phosphorylation.

Apoptosis in the absence of cytochrome c accumulation in the cytosol

Cytochrome c release from mitochondria to and subsequent accumulation in the cytosol has been considered a prerequisite for apoptosis. In this study, we present evidence for apoptosis induction without accumulation of cytochrome c in the cytosol. U937 lymphoma cells treated with staurosprine released cytochrome c from mitochondria to cytosol prior to PARP cleavage and DNA fragmentation. However, U937 cells treated with BMD188 (a hydroxamic acid and a potent apoptosis inducer) did not demonstrate any cytochrome c accumulation in the cytosol during apoptosis induction. This different pattern of cytochrome c alterations was also observed with these two inducers on leukemic HL60 cells and epithelial PC3 cells. Furthermore, when PC3 cells were treated with a panel of apoptosis-inducing agents, it was found that camptothecin, bleomycin, VP16 and TNF-alpha induced varying amounts of cytosolic accumulation of cytochrome c either prior to or concurrent with PARP cleavage while vinblastine and BHPP did not. Taken together, the present results suggest that cytochrome c accumulation in the cytosol during apoptosis is a cell type- and inducer-dependent phenomenon.

BMD188, A novel hydroxamic acid compound, demonstrates potent anti-prostate cancer effects in vitro and in vivo by inducing apoptosis: requirements for mitochondria, reactive oxygen species, and proteases

A newly synthesized cyclic hydroxamic acid compound, BMD188 [cis-1-hydroxy-4-(1-naphthyl)-6-octylpiperidine-2-one], was found to induce the apoptotic death of cultured prostate cancer cells by activating caspase-3. Orally administered BMD188 significantly inhibited the primary growth of prostate cancer cells (Du145) orthotopically implanted into SCID mice. Mechanistic studies indicated that BMD188 did not alter the protein levels of several Bcl-2 family members. In contrast, the BMD188 effect required three essential factors: reactive oxygen species (ROS), the mitochondrial respiratory chain function, and proteases. First, the apoptosis-inducing effect of BMD188 could be blocked by ROS scavengers such as Desferal. Second, both BMD188-induced PARP cleavage as well as PC3 cell apoptosis could be dramatically inhibited by several complex-specific mitochondrial respiration blockers. The involvement of mitochondria was also supported by the observations that BMD188 dramatically altered the mitochondrial distribution and morphology without affecting the cellular ATP levels. Finally, the apoptosis-inducing effect of BMD188 in PC3 cells could be significantly inhibited by serine protease inhibitors (TPCK and TLCK) as well as by caspase inhibitors (zVAD-fmk and DEVD-CHO). Collectively, the present study suggests that BMD188 and its analogs may find clinical applications in the treatment of prostate cancer patients by inducing apoptotic death of prostate cancer cells.

Levels of IgG subclasses in active and inactive cases in the disease spectrum of leprosy

The present study was carried out to establish the role of IgG subclasses in leprosy. IgG subclasses to Mycobacterium leprae sonicated antigens (MLSA) and phenolic glycolipid-I (PGL-I) were determined in 124 patients with active leprosy across the disease spectrum and in 76 cases with inactive disease after completion of chemotherapy. IgG2 antibodies were found to be the predominant subclass across the disease spectrum. Lepromatous patients showed elevated levels of IgGI. IgG3 antibody levels were higher in lepromatous than that in tuberculoid patients. Patients with erythema nodosum leprosum showed a significant fall in IgG3 antibody to MLSA. While chemotherapy induced a reduction in IgG1, IgG2 and IgG3 to PGL-I in almost all types of leprous patients, for MLSA the reduction was noticed for these subclasses only in lepromatous patients. IgG4 responses to these antigens were low through out the disease spectrum and did not alter with chemotherapy.

Purification and characterization of an extracellular lectin (Lectin I) from Agrobacterium radiobacter NCIM 2443

A lectin from culture filtrate of Agrobacterium radiobacter NCIM 2443 is purified to homogeneity by ion exchange chromatography on a DEAE cellulose column followed by hydrophobic chromatography on phenyl sepharose and hydroxyapatite column chromatography. The protein (Lectin I) is a monomer of relative molecular mass 37,000, as determined by denaturing gel electrophoresis as well as size exclusion chromatography. Lectin I is stable at pH 5.0 and its isoelectric point is pH 4.0. Amino acid analysis reveals that acidic amino acids and glycine are predominant amino acids and cysteine is absent in the lectin. Chemical modification of tryptophan residues causes more than 80% loss of haemagglutination activity of the lectin and 60% loss of activity is caused by modification of carboxyl groups. Lectin I agglutinates rabbit erythrocytes but does not agglutinate human A, B and O types of erythrocytes. It is specific for N-acetyl D-glucosamine, chitobiose, pNP-beta-mannoside as well as high mannose type glycopeptides. The relative inhibition by disaccharides, oligosaccharides and glycoproteins indicates that Lectin I recognizes Man3-GlcNAc-GlcNAc core carbohydrate structure of asparagine linked glycopeptides. Tobacco tissue extracts also inhibit the haemagglutination activity of Lectin I.

Detection of HIV in oral mucosal cells

OBJECTIVE

To determine the prevalence of HIV DNA and RNA and the morphologic localization of HIV in the oral cavity of HIV-seropositive subjects.

DESIGN

A cross-sectional analysis of saliva, buccal scrapings and buccal biopsies from HIV-seropositive injecting drug users (IDUs).

SUBJECTS AND METHODS

Whole saliva, buccal mucosal scrapings and buccal biopsies were obtained from HIV-seropositive and seronegative IDUs. Presence of HIV DNA and RNA was assessed by polymerase chain reaction (PCR) and reverse transcriptase PCR (RT-PCR). RT in situ PCR was used to detect HIV tat/rev RNA in buccal mucosal scrapings. Host-cell integrated HIV-proviral DNA in buccal biopsies was detected by in situ PCR. Presence of intact HIV viral particles in buccal scrapings was assessed by electron microscopy.

RESULTS

HIV DNA was detected in 40% (18/45) and HIV RNA in 69.2% (25/36) of saliva samples from HIV-seropositive IDUs. Viral particles consistent with HIV were localized in inter-epithelial spaces by electron microscopy. RT in situ PCR revealed the presence of HIV tat/rev RNA in 36% (8/22) of the seropositive samples tested.

CONCLUSIONS

Our results suggest that epithelial cells can be productively infected by HIV. Epithelial cells in buccal mucosa may acquire HIV in the basal layers through contact with submucosal HIV-positive lymphocytes and/or Langerhans' cells. HIV infection may also spread by inter-epithelial cell contact. As HIV infected cells mature they travel to more superficial layers and are shed into the oral cavity.

Interleukin-4 in the treatment of AIDS-related Kaposi's sarcoma

PURPOSE

To define the safety and toxicity of interleukin-4 (IL-4) when administered subcutaneously in patients with AIDS-related Kaposi's sarcoma (AIDS-KS); to evaluate the effect of IL-4 on immunologic and virologic parameters; and to preliminarily assess the response rate of IL-4 in AIDS-KS.

PATIENTS AND METHODS

Eighteen patients with mucocutaneous, non-visceral AIDS-KS were treated with IL-4 at a dose of 1 mcg/kg subcutaneously, daily until unacceptable toxicity or for a maximum period of six months. Twelve (66%) patients had extensive mucocutaneous disease with over 25 lesions. Ten patients had received prior systemic chemotherapy. Seventeen had CD4+ lymphocyte counts less than 200/mm3.

RESULTS

The most common adverse effects included headache in 78%, fever in 56%, chills in 44%, and edema in 44%. Hematologic toxicities consisted of grade 4 neutropenia (less than 500/mm3) in 33%, mild anemia in 22%. Transient elevation of liver enzymes was noted in 17%. A transient elevation in CD4+ lymphocyte counts occurred during the first two weeks of therapy. Four of eleven patients tested showed marked decline in plasma HIV RNA after four weeks. Partial remission was observed in one patient, lasting six months. Three other patients (17%) had stable disease: 7 weeks in one patient, and 10 weeks in each of the two other patients.

CONCLUSION

Grade 4 neutropenia (absolute neutrophil count < 500/mm3) was the most common hematologic adverse effect with IL-4 in patients with AIDS-KS. In contrast to in vitro findings, there was a decrease in plasma HIV RNA after four weeks of IL-4 therapy in the majority of patients tested. IL-4 produced minimal anti-tumor effects in AIDS-KS with one partial remission in a patient with CD4 lymphocyte counts over 200/mm3. Further studies of IL-4 in AIDS-KS may be considered in patients with better immune status.

Contextual constraints in the choice of synonymous codons

From EMBL Nucleotide Sequence Database, protein coding sequences of all E. coli and its DNA phages, were extracted using our computer programme. Same programme has been used to form a database of sequence of oligonucleotides of length 18 nucleotides on both sides of each of the 61 codons. From analysis of this database and study of variations in twist parameter (Tw) values, as an indicator of sequence dependent variations in B-DNA helix, a method is developed to fix the codon among the set of synonymous codons. The accuracy of the method was checked on enlarged data set by adding data from more prokaryotes. Our method assign the codon 85-90% times correctly if the selection has to be made between codons having different sequence in terms of R and Y. The accuracy of the method is somewhat lower when choice of the codon has to be made between codons having same codes in terms of R and Y. This study points out that the major factors which decide the choice of a codon from a set of synonymous codons are contextual constraints arising from flanking regions.

Characterization by arbitrary primer polymerase chain reaction of polychlorinated biphenyl (PCB)-degrading strains of Comamonas testosteroni isolated from PCB-contaminated soil

In this study, we isolated and characterized biphenyl (BP) and polychlorinated biphenyl (PCB) degrading bacterial strains found in PCB-contaminated soil from an auto manufacturing plant located in Syracuse, New York. Twenty-one BP and PCB-degrading bacteria were randomly selected to form a representative sample of the bacterial population present at the site. Of the 21 bacteria, 13 were identified as Comamonas testosteroni, constituting about 60% of the bacterial population examined. Other PCB degraders identified were Acidovorax facilis, Alcaligenes xylosoxydans, Bacillus sphericus, Hydrogenophaga pseudoflava, Pseudomonas avanae, and Rhodococcus fascians. Owing to the abundance of C. testosteroni at this site, only these isolates were further characterized for their PCB congener degradation profile, 2,3-dihydroxybiphenyl 1,2-dioxygenase activity, and genetic relatedness by polymerase chain reaction (PCR) analysis. The PCB congener degradation pattern revealed a high degree of variability among the C. testosteroni isolates. The majority of the C. testosteroni isolates tested could degrade more than 95% of the PCB congeners up to pentachlorinated biphenyl. Only four isolates could degrade more than 80% of hexachlorobiphenyl. All 12 isolates of C. testosteroni tested were able to attack 2,3,4,5,6,3',4'-heptachlorobiphenyl, indicating involvement of biphenyl 2,3-dioxygenase, while 2,3,5,6,2',3',6'-heptachlorobiphenyl was attacked by 6 strains, suggesting an oxidation reaction mediated by 3,4-dioxygenase. 2,3-Dihydroxybiphenyl 1,2-dioxygenase activity was also found to vary among the C. testosteroni isolates tested in this study. Eleven strains showed 2,3-dihydroxybiphenyl 1,2-dioxygenase activity specific for 2,3-dihydroxybiphenyl, whereas isolate BW 169 could metabolize both 2,3-dihydroxybiphenyl and 4-methylcatechol, and isolate BW74 had the ability to metabolize all three substrates (2,3-dihydroxybiphenyl, 4-chlorocatechol, and 4-methylcatechol).(ABSTRACT TRUNCATED AT 250 WORDS)

Phosphorylation of eukaryotic protein synthesis initiation factor 4E at Ser-209

Initiation factor 4E (eIF-4E) binds to the m7GTP-containing cap of eukaryotic mRNA and facilitates the entry of mRNA into the initiation cycle of protein synthesis. eIF-4E is a phosphoprotein, and the phosphorylated form binds to mRNA caps 3-4-fold more tightly than the nonphosphorylated form. A previous study indicated that the major phosphorylation site was Ser-53 (Rychlik, W., Russ, M. A., and Rhoads, R. E. (1987) J. Biol. Chem. 262, 10434-10437). In the present study, we synthesized the phosphopeptide expected to result from tryptic digestion of eIF-4E, O-phosphoseryllysine. Surprisingly, the tryptic and synthetic phosphopeptides did not comigrate electrophoretically. Accordingly, we redetermined the phosphorylation site by isolating a chymotryptic phosphopeptide on reverse phase high performance liquid chromatography. The peptide was sequenced by Edman degradation and corresponded to 198QSHADTATKSGSTTKNRF215. The site of phosphorylation was determined to be Ser-209 by four methods: the increase in the ratio of dehydroalanine to serine derivatives during Edman degradation, the release of 32P, the further digestion of the chymotryptic phosphopeptide with trypsin, Glu-C, and Asp-N, and site-directed mutagenesis of eIF-4E cDNA. The S209A variant was not phosphorylated in a rabbit reticulocyte lysate system, whereas the wild-type, S53A, and S207A variants were. This site falls within the consensus sequence for phosphorylation by protein kinase C.