An ncRNA transcriptomics-based approach to design siRNA molecules against SARS-CoV-2 double membrane vesicle formation and accessory genes

BACKGROUND

The corona virus SARS-CoV-2 is the causative agent of recent most global pandemic. Its genome encodes various proteins categorized as non-structural, accessory, and structural proteins. The non-structural proteins, NSP1-16, are located within the ORF1ab. The NSP3, 4, and 6 together are involved in formation of double membrane vesicle (DMV) in host Golgi apparatus. These vesicles provide anchorage to viral replicative complexes, thus assist replication inside the host cell. While the accessory genes coded by ORFs 3a, 3b, 6, 7a, 7b, 8a, 8b, 9b, 9c, and 10 contribute in cell entry, immunoevasion, and pathological progression.

METHODS

This in silico study is focused on designing sequence specific siRNA molecules as a tool for silencing the non-structural and accessory genes of the virus. The gene sequences of NSP3, 4, and 6 along with ORF3a, 6, 7a, 8, and 10 were retrieved for conservation, phylogenetic, and sequence logo analyses. siRNA candidates were predicted using siDirect 2.0 targeting these genes. The GC content, melting temperatures, and various validation scores were calculated. Secondary structures of the guide strands and siRNA-target duplexes were predicted. Finally, tertiary structures were predicted and subjected to structural validations.

RESULTS

This study revealed that NSP3, 4, and 6 and accessory genes ORF3a, 6, 7a, 8, and 10 have high levels of conservation across globally circulating SARS-CoV-2 strains. A total of 71 siRNA molecules were predicted against the selected genes. Following rigorous screening including binary validations and minimum free energies, final siRNAs with high therapeutic potential were identified, including 7, 2, and 1 against NSP3, NSP4, and NSP6, as well as 3, 1, 2, and 1 targeting ORF3a, ORF7a, ORF8, and ORF10, respectively.

CONCLUSION

Our novel in silico pipeline integrates effective methods from previous studies to predict and validate siRNA molecules, having the potential to inhibit viral replication pathway in vitro. In total, this study identified 17 highly specific siRNA molecules targeting NSP3, 4, and 6 and accessory genes ORF3a, 7a, 8, and 10 of SARS-CoV-2, which might be used as an additional antiviral treatment option especially in the cases of life-threatening urgencies.

Structural Analysis and Epitope Prediction of S2 Domain of SARS-CoV-2, Conservation Analysis Among Major Variants

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused a global pandemic. There are four structural proteins of the virus: spike, envelope, membrane, and nucleocapsid proteins. Various vaccines were designed and are effectively being used against the spike protein of the virus. However, several vaccine-related complications have been reported worldwide. Assuming that the structural integrity of the whole protein might be contributing to these complications, this study was performed to design epitopes using the S2 domain of the spike protein, which could trigger a strong immune response. We have also predicted antigenic and allergenic properties of the selected epitopes. A total of 49 B cell epitopes passing antigenicity and other assessment filters were found using three methods. Among them, RDLICAQ had the highest antigenicity score (1.1443). However, only one cytotoxic T lymphocyte epitope, RSFIEDLLF, passed the essential filters with an antigenicity score of 0.5782 to show an appropriate immune response for T cells, while among 21 helper T cell lymphocyte epitopes that were filtered, FAMQMAYRFNGIGVT showed the highest (1.3688) antigenicity score. Conservation analysis revealed that the S2 domain is significantly conserved, thus making it an ideal candidate for vaccine development. We have also designed a vaccine construct based on the best suiting components found during the whole study. This construct and S2 domain solely can be future subjects of interest or might be included in a subunit cocktail formulation for attaining unabridged immunogenicity.

E. coli expression and immunological assessment of expressed recombinant Newcastle disease virus hemagglutinin-neuraminidase protein in chickens

Every year, the poultry industry experiences significant economic losses due to epidemics of Newcastle disease virus (NDV). Developing new vaccines by identifying and using the immunogenic hemagglutinin-neuraminidase (HN) protein can protect the poultry industry. In the present study, the full-length HN protein was expressed in Escherichia coli (E. coli) BL21 (DE3) cells, purified via affinity chromatography and detected via western blot analysis using His-specific antibodies. The purified HN protein was further evaluated in chickens to study the immune response against NDV. The successful production of HN-specific IgY proved the activity of the purified HN protein. IgY was present in the serum of immunized chickens. However, the immune response was higher in chickens immunized with purified HN protein along with complete and incomplete adjuvants than in chickens immunized with only the HN protein. Keywords: protein; Newcastle disease virus; poultry; infectious diseases; vaccines.

Constitutive expression of Asparaginase in Gossypium hirsutum triggers insecticidal activity against Bemisia tabaci

Whitefly infestation of cotton crop imparts enormous damage to cotton yield by severely affecting plant health, vigour and transmitting Cotton Leaf Curl Virus (CLCuV). Genetic modification of cotton helps to overcome both the direct whitefly infestation as well as CLCuV based cotton yield losses. We have constitutively overexpressed asparaginase (ZmASN) gene in Gossypium hirsutum to overcome the cotton yield losses imparted by whitefly infestation. We achieved 2.54% transformation efficiency in CIM-482 by Agrobacterium-mediated shoot apex transformation method. The relative qRT-PCR revealed 40-fold higher transcripts of asparaginase in transgenic cotton line vs. non-transgenic cotton lines. Metabolic analysis showed higher contents of aspartic acid and glutamic acid in seeds and phloem sap of the transgenic cotton lines. Phenotypically, the transgenic cotton lines showed vigorous growth and height, greater number of bolls, and yield. Among six representative transgenic cotton lines, line 14 had higher photosynthetic rate, stomatal conductance, smooth fiber surface, increased fiber convolutions (SEM analysis) and 95% whitefly mortality as compared to non-transgenic cotton line. The gene integration analysis by fluorescence in situ hybridization showed single copy gene integration at chromosome number 1. Collectively, asparaginase gene demonstrated potential to control whitefly infestation, post-infestation damages and improve cotton plant health and yield: a pre-requisite for farmer's community.

An audit of consenting practices in a district general hospital. Can we improve?

INTRODUCTION

Informed consent, as the declaration of patients' will, forms the basis of legality of medical procedures. A standard form based on the Department of Health model is widely used in the National Health Service (NHS). The aim of this audit process was to assess the current consent practice in comparison to the UK's General Medical Council guidance and local policy and make any appropriate improvements.

PATIENTS AND METHODS

254 adult consent forms were reviewed during the patients' admission. Data collected included legible documentation, grade of health professional completing the consent form, providing additional written information, use of abbreviations, securing the consent form in the medical records and, providing a copy to the patient. After initial assessment, interventions in an attempt to improve adherence to guidelines were introduced. A repeat audit of a further set of 110 notes was completed to assess the effectiveness of our interventions.

RESULTS

Our baseline assessment of 254 consent forms comprised of 198 (78%) elective and 56 (22%) emergency procedures. 87 (34%) consent forms were secure in the medical records. Grade of health professional was recorded in 211 (83%). 191 (75%) forms were legible. 48 (19%) patients were given copy of the consent. Only 24 (9%) patients were given additional written information. Abbreviations were used in 68 (27%) forms. Only 12 (5%) of consent forms met all criteria simultaneously. Re-audit after intervention assessed 110 consent forms; 30 (27%) for elective and 80 (72%) for emergency procedures. 52 (47%) of consent forms were secure in medical records, grade of health professional was recorded in 94 (85%), 101 (75%) forms were legible, 42 (38%) patients received copy of consent and 41 (37%) of patients received additional written information.

CONCLUSION

Initially only 5% of consent forms completely met GMC guidelines. This demonstrates an alarmingly poor adherence to such guidance that plays a vital role in patient safety, patient ethics autonomy, not to mention potential medico-legal and clinical governance implications for surgical practice. Our intervention has improved the quality of consenting within our hospital according to these guidelines. With these interventions set to continue and further develop, we expect that the quality of the consenting process will continue to provide patients with all that it is designed to.

Microarray: gateway to unravel the mystery of abiotic stresses in plants

Environmental factors, such as drought, salinity, extreme temperature, ozone poisoning, metal toxicity etc., significantly affect crops. To study these factors and to design a possible remedy, biological experimental data concerning these crops requires the quantification of gene expression and comparative analyses at high throughput level. Development of microarrays is the platform to study the differential expression profiling of the targeted genes. This technology can be applied to gene expression studies, ranging from individual genes to whole genome level. It is now possible to perform the quantification of the differential expression of genes on a glass slide in a single experiment. This review documents recently published reports on the use of microarrays for the identification of genes in different plant species playing their role in different cellular networks under abiotic stresses. The regulation pattern of differentially-expressed genes, individually or in group form, may help us to study different pathways and functions at the cellular and molecular level. These studies can provide us with a lot of useful information to unravel the mystery of abiotic stresses in important crop plants.

In-Silico Determination of Insecticidal Potential of Vip3Aa-Cry1Ac Fusion Protein Against Lepidopteran Targets Using Molecular Docking

Study and research of Bt (Bacillus thuringiensis) transgenic plants have opened new ways to combat insect pests. Over the decades, however, insect pests, especially the Lepidopteran, have developed tolerance against Bt delta-endotoxins. Such issues can be addressed through the development of novel toxins with greater toxicity and affinity against a broad range of insect receptors. In this computational study, functional domains of Bacillus thuringiensis crystal delta-endotoxin (Cry1Ac) insecticidal protein and vegetative insecticidal protein (Vip3Aa) have been fused to develop a broad-range Vip3Aa-Cry1Ac fusion protein. Cry1Ac and Vip3Aa are non-homologous insecticidal proteins possessing receptors against different targets within the midgut of insects. The insecticidal proteins were fused to broaden the insecticidal activity. Molecular docking analysis of the fusion protein against aminopeptidase-N (APN) and cadherin receptors of five Lepidopteran insects (Agrotis ipsilon, Helicoverpa armigera, Pectinophora gossypiella, Spodoptera exigua, and Spodoptera litura) revealed that the Ser290, Ser293, Leu337, Thr340, and Arg437 residues of the fusion protein are involved in the interaction with insect receptors. The Helicoverpa armigera cadherin receptor, however, showed no interaction, which might be due to either loss or burial of interactive residues inside the fusion protein. These findings revealed that the Vip3Aa-Cry1Ac fusion protein has a strong affinity against Lepidopteran insect receptors and hence has a potential to be an efficient broad-range insecticidal protein.

In silico study for diversing the molecular pathway of pigment formation: an alternative to manual coloring in cotton fibers

Diversity of colors in flowers and fruits is largely due to anthocyanin pigments. The flavonoid/anthocyanin pathway has been most extensively studied. Dihydroflavonol 4-reductase (DFR) is a vital enzyme of the flavonoid pathway which displays major impact on the formation of anthocyanins, flavan 3-ols and flavonols. The substrate specificity of the DFR was found to play a crucial role in determination of type of anthocyanidins. Altering the flavonoid/anthocyanin pathway through genetic engineering to develop color of our own choice is an exciting subject of future research. In the present study, comparison among four DFR genes (Gossypium hirsutum, Iris × hollandica, Ang. DFRI and DFRII), sequence alignment for homology as well as protein modeling and docking is demonstrated. Estimation of catalytic sites, prediction of substrate preference and protein docking were the key features of this article. For specific substrate uptake, a proline rich region and positions 12 plus 26 along with other positions emphasizing the 26-amino acid residue region (132-157) was tested. Results showed that proline rich region position 12, 26, and 132-157 plays an important role in selective attachment of DFRs with respective substrates. Further, "Expasy ProtParam tool" results showed that Iris × hollandica DFR amino acids (Asn 9: Asp 23) are favorable for reducing DHQ and DHM thus accumulating delphinidin, while Gossypium hirsutum DFR has (Asn 13: Asp 21) hypothesized to consume DHK. Protein docking data showed that amino acid residues in above mentioned positions were just involved in attachment of DFR with substrate and had no role in specific substrate uptake. Advanced bioinformatics analysis has revealed that all above mentioned positions have role in substrate attachment. For substrate specificity, other residues region is involved. It will help in color manipulations in different plant species.

Orally co-administrated oleo-gum resin of Commiphora myrrha decreases the bioavailability of cyclosporine A in rats

Cyclosporine A is a narrow therapeutic indexed immunosuppressant used after organ transplantation. Several herbs have been reported to alter its pharmacokinetics. Myrrh, dried oleogum resin obtained from Commiphora myrrha (Burseraceae) has been used for many common ailments. The present study was carried out to investigate the effect of myrrh on the pharmacokinetics of cyclosporine A. The rats of the control group received 60 mg/kg, p.o. cyclosporine A, and blood samples were collected at predetermined time intervals. Rats of the test group were treated with an aqueous suspension of myrrh (380 mg/kg p.o.) for eight days and on 8th day a single dose of cyclosporine A was administered to the treated group after 1 h of myrrh administration. Blood samples were drawn at predetermined time points and the drug was analyzed in whole blood by using H-Class UPLC-TQD. Pharmacokinetic profiles of control and test group were compared. Statistically significant differences were observed between the pharmacokinetic parameters of control and treated groups. In the myrrh treated group, the AUC(0-t) and C(max) of cyclosporine A was decreased by about 45% and 48%, respectively. The time to reach maximum concentration (T(max)) remained almost unchanged in both groups. Results indicated that the bioavailability of cyclosporine A was reduced by about 45% when co-administered with myrrh. This observation suggests that concurrent consumption of myrrh and cyclosporine A should be avoided. To confirm the clinical relevance of these findings, P-gp and CYP3A based molecular investigations can be performed along with a well-planned clinical study.

Molecular docking based screening of neem-derived compounds with the NS1 protein of Influenza virus

Different strains of influenza virus are affecting a large number of people worldwide to combat with Influenza virus destruction, numerous synthetic antiviral medicines are available for influenza virus in the market. But still there was a need for the development of drug which will target all the strains of influenza virus. For this purpose conserved residues within the influenza virus NS1 protein have been found by aligning all the available sequences of existing strains from the national center of biotechnology information(NCBI) protein database. The compounds from leaf extracts of neem (Azadirachta indica), previously known to have antiviral properties, were virtually screened to identify side effects free natural drug. Molecular docking identified eight potential compounds (Tetratriacontane, 127-40-2, 6-o-ACETYLNIMBANDIOL, Rutin, Tiplasinin, Hyperoside, ( )- Nimocinolide and Quercitrin) found to have perfect binding with reported conserved residues (R19, R35, S42 and D39) of influenza virus NS1 protein involved in the binding of drugs. From, further analysis 6-o-ACETYLNIMBANDIOL, Rutin and Tiplasinin were found as drug against influenza strains because their binding residues were conserved in all strains. The potential of neem chemical against influenza virus has best been highlighted through this study and it provides direction for further consideration of these products for in-vivo and in-vitro validations.

ABBREVIATIONS

NS1 protein - Non Structural 1 protein, NA - Neuraminidase, HA - Hemagglutinin, M - Yersinia enterocolitica 8081, ypk - Yersinia pestis KIM, yps - Yersinia pseudotuberculosis Db1, KEGG - Kyoto Encyclopedia of Genes and Genomes, KO - KEGG Orthology, KOBAS - KO Based Annotation System.

Potential inhibitory effect of herbal medicines on rat hepatic cytochrome P450 2D gene expression and metabolic activity

The aim of current study was to investigate the effect of some commonly used medicinal herbs on the regulation of rat CYP2D gene expression and its metabolic activity. Wistar albino rats were treated for seven consecutive days with selected doses of five commonly used herbs (Trigonella foenum-graecum, Ferula asafoetida, Nigella sativa, Commiphora myrrha and Lepidium sativum). Thereafter, rat livers were harvested and CYP2D mRNA levels were determined by RT-PCR. The metabolic activity of CYP2D was performed on rat hepatic microsomes using dextromethorphan as specific substrate. All investigated herbs produced inhibition of CYP2D mRNA expression and metabolic activity. The inhibitory potential of investigated herbs on rat CYP2D mRNA was in the following order: Commiphora myrrha > Nigella sativa > Lepidium sativum > Trigonella foenum-graecum > Ferula asafoetida. Whereas, the inhibitory potential of investigated herbs on CYP2D mediated enzyme metabolic activity was found in following order: Nigella sativa > Lepidium sativum > Trigonella foenum-graecum > Commiphora myrrha > Ferula asafoetida. The current study shows that only used herbs reduce CYP2D activity in rat liver microsomes at the transcriptional levels. Such effects could lead to undesirable pharmacological effects of clinically used low therapeutic index CYP2D substrate drugs.

Impact of Herbal Medicines like Nigella sativa, Trigonella foenum-graecum, and Ferula asafoetida, on Cytochrome P450 2C11 Gene Expression in Rat Liver

AIM

Combined use of herbs and drugs may result in clinically important herb-drug interactions. The majorities of these interactions are thought to be metabolism-based and involve induction or inhibition of cytochrome P450 (CYP). The current study was designed to investigate the effect of some commonly used herbs on rat CYP2C11 gene expression and metabolic activity.

METHODS

Wistar rats were treated for 7 days with increasing doses of 3 herbs; Nigella sativa, Trigonella foenum-graecum, and Ferula asafoetida. Thereafter, CYP2C11 mRNA and protein levels were determined by real-time polymerase chain reaction (RT-PCR) and western blot analyses, respectively. In vitro metabolic activity of CYP2C11 was performed on rat hepatic microsomes using tolbutamide as specific substrate.

RESULTS

Our results showed that all the 3 herbs significantly inhibited the mRNA and protein expression levels of CYP2C11 in a dose-dependent manner. Furthermore, the in vitro enzyme metabolic activity study showed a significant decrease in the formation of 4-hyroxy-tolbutamide, a tolbutamide metabolite, at the higher doses. The inhibitory effects of the investigated herbs on rat CYP2C11 was in the order: Nigella Sativa > Trigonella foenum-graecum > Ferula asafoetida.

CONCLUSIONS

The 3 herbs are strong inhibitor of CYP2C11 expression, which can lead to an undesirable pharmacological effect of clinically used CYP2C11 substrate drugs with a low therapeutic index.

Investigating the Potential Effect of Commiphora myrrha on the Pharmacokinetics of Theophylline, a Narrow Therapeutic Index Drug

AIM

The present study was conducted to investigate the effect of commonly used herb Commiphora myrrha on the pharmacokinetic profile of theophylline (narrow therapeutic index drug) in rabbits.

METHODS

In the experimental groups, theophylline (16 mg/kg) was given orally to the rabbits. Where aqueous saline suspension of Commiphora myrrha (176 mg/kg, p.o.), was given to the rabbits and the blood samples were withdrawn at different time intervals (0, 0.5, 1, 1.5, 2, 3, 4, 6, 8, 12, 24 and 36 h) from marginal ear vein after dosing and theophylline in plasma was analyzed by HPLC method.

RESULTS

It was observed that there a significant differences in the Cmax, AUC, AUMC, t1/2, and MRT of theophylline when coadministered with Commiphora myrrha which indicate that the herb affect the metabolism and elimination when coadministered with theophylline.

CONCLUSION

Our results suggested that concurrent use of investigated herb alters the pharmacokinetics of theophylline. Confirmation of these results in human studies will warrant changes in theophylline dose or frequency when coadministered with herb under consideration.

An unusual tracheal foreign body - a case report

Foreign bodies in the laryngopharynx can occur without discrimination of age or sex. Their occurrence is influenced by mode of living, customs, habits and environment. T.M. Paramciwaran(1977) reported 56 cases of foreign bodies of tracheobronchial tree in the span of 5 years. A.S.A. Abdel-Salam and Alan G. Gibb (1980) mentioned that the vast majority of cases occur in young children. They have reported that undiagnosed foreign bodies cause mechanical effects, chemical reactions and may present as chronic pulmonary infection, allergic asthma, bronchiectasis, lung collapse or lung abscess. They present as emergencies and require skilful management.

Efficacy of telmisartan and atenolol in management of essential hypertension

BACKGROUND

Telmisartan and atenolol are widely used in the management of essential hypertension. This study was conducted to compare the efficacy of these two drugs in management of patients of essential hypertension.

METHODS

Diagnosed patients of essential hypertension were selected. Therapeutic option (telmisartan/atenolol) was allocated to the patients by lottery method and they were divided into two groups. The patients were followed on subsequent visits (4 in total) and their sitting systolic and diastolic blood pressures were recorded.

RESULTS

Total number of 180 patients were divided into two treatment groups (i.e., telmisaran and atenolol). Forty percent were male and 60% were female. Majority of the patients were of age group 56-75 years. Telmisartan reduced systolic and diastolic blood pressure significantly compared to atenolol at the end of 8 weeks of treatment (p = 0.000 and 0.016 respectively).

CONCLUSION

Telmisartan 80 mg once daily is more effective than atenolol 50 mg once daily in lowering systolic and diastolic blood pressure at the end of 8 weeks of treatment.

Serosurvey of five viruses in chickens on smallholdings in Bangladesh

A serologic survey was undertaken in chickens in smallholdings in Bangladesh for avian influenza A virus (AIV), egg drop syndrome '76 virus (EDS'76V), infectious bronchitis virus (IBV), Newcastle disease virus (NDV) and reovirus (RV) in three phases: January 2002-May 2003, September 2003-August 2004, and August 2005-March 2006. Four hundred thirty-six sera collected in the 2nd phase, 295 in the first phase, 755 in the 1st plus 2nd phases and 295 in the 1st phase were investigated for AIV, EDS'76V, IBV and RV, respectively, using enzyme linked immunosorbent assays. All 854 sera collected in the three phases were screened for NDV using hemagglutination inhibition test. In chickens 20% were seropositive to AIV, 3% to EDS'76V, 74% to IBV, 88% to NDV, and 47% to RV. The seroprevalence in flocks was 23% to AIV, 6% to EDS'76V, 79% to IBV, 89% to NDV and 56% to RV. Twenty-five percent chickens had > or = 10log(2)HI titers to NDV.

Survivability and causes of loss of broody-hen chicks on smallholder households in Bangladesh

We determined the flock sizes and rates of loss caused by different factors in broody-hen chicks (BHC) up to 60 days of age on 600 randomly selected smallholdings in Bangladesh. The smallholders were beneficiaries of a village poultry production chain called 'Smallholder Livestock Development Project-2' (SLDP-2) which was undertaken with the financial assistance of the Danish International Development Agency (DANIDA). For estimating survival time of BHC, we observed chicks in 80 smallholdings. SLDP-2 aims at ameliorating poverty among women by poultry rearing at village level; in total, 104,000 key rearers, constituting 96% of all of the beneficiaries of the SLDP-2 area, were enrolled in 26 upazilas (a lower administrative unit of Bangladesh). A key rearer is a smallholder who rears at least five 'Sonali' (RIR x Fayoumi) and some indigenous (desi) chickens in a semi-scavenging system. Sonali chickens are supplied from the development project, and have higher egg production while the broodiness of the desi hens is exploited to get chicks hatched for future stocks; thus, the chicks hatched and reared to 60 days old at key rearers' households are called BHC. In this study 32% of the smallholders had BHC each month. At the beginning of a month, the median number of chicks in a flock was 8, and the mean survival time was 50.5 days. Incidence rates of loss of BHC from disease, predation, selling and slaughtering were 0.102, 0.086, 0.009 and 0.002 per chick-month at risk, respectively. The major predators were crows, mongooses and eagles with incidence rates of loss being 0.018, 0.016 and 0.010 per chick-month at risk, respectively. Colibacillosis (both single and mixed infections) contributed to the death of 21% of dead BHC collected; Newcastle disease and salmonellosis contributed to the next highest (14 and 12%) proportional mortalities.

Causes of loss of Sonali chickens on smallholder households in Bangladesh

In a 1-year-long prospective longitudinal study, we determined the causes of loss of 'Sonali' (male symbol Rhode Island Red x female symbol Fayoumi) chickens at key-rearers' households of the smallholder livestock development project-2 (SLDP-2) area in Bangladesh. A key rearer is a smallholder of chickens in the 'village poultry-production chain' (undertaken by SLDP-2 under the financial assistance of the DANIDA) who rears at least five Sonali and some 'Deshi' (non-descriptive and indigenous) chickens in their homesteads based on semi-scavenging system. The aim of this program is to ameliorate poverty, especially among women. Two co-ordination centers (set at the Potuakhali and Noakhali districts) supervised the development activities. We selected two upazilas (lower administration units) randomly from each of the two districts and in every selected upazila, we selected at random 125 key-rearer households. Incidence rates of loss of Sonali chickens from disease, predation, selling and slaughtering were 0.025, 0.023, 0.081 and 0.039 per bird-month at risk, respectively. The major predators of Sonali chickens in the study area were foxes, a kind of wild cat (Felis chaus), mongooses and human thieves. Colibacillosis (both single and mixed infections) had a contributory role in the death of 28% of dead Sonali birds collected for diagnosis; salmonellosis, Newcastle disease and internal parasites contributed to the next highest (14, 11and 10%) proportional mortalities.

Measurement of radioactivity in the soil of Bahawalpur division, Pakistan

Bahawalpur is the largest division of the Punjab province in Pakistan. It is larger than many countries of the world. Gamma activity from the naturally occurring radionuclides namely 226Ra, 232Th, the primordial radionuclide 40K and the artificial radionuclide 137Cs was measured in the soil of the Bahawalpur division using gamma spectrometry technique. The mean activity of 226Ra, 232Th, 40K and 137Cs were found to be 32.9 +/- 0.9, 53.6 +/- 1.4, 647.4 +/- 14.1 and 1.5 +/- 0.2 Bq kg(-1), respectively. The mean radium equivalent activity Raeq, external hazard index, internal hazard index and terrestrial absorbed dose rate for the area under study are 158.5 +/- 4.1 Bq kg(-1), 0.4, 0.5 and 77.32 nGy h(-1), respectively. The annual effective dose equivalent to the public was found to be 0.5 mSv.

Prevalence of exercise-induced bronchospasm in national hockey players of Pakistan

OBJECTIVE

To determine prevalence of Exercise-induced Bronchospasm (EIB) in hockey players, who had represented or were aspiring to represent Pakistan at international level.

METHOD

An observational, cross-sectional study was done on the prevalence of EIB in national hockey players of Pakistan. All participants of the training camp (n = 27) players were included in this study, after obtaining permission from the Pakistan Hockey Federation. An acquaintance session was conducted to introduce the study, and for the correct recording of Peak Expiratory Flow (PEF) rate. On field-testing day, pulse and PEF rates were measured first without any exercise and warm up (pre-exercise PEF rate). After competitive 6 minute (6-min) field free running, pulse rate was measured to ensure that players heart rate has reached 70% of the predicted maximum heart rate. PEF and pulse rates were measured at 5-min, 15-min and 30-min post exercise. A player was considered EIB positive based on a post exercise decrement in PEF rate > or = 15% at any defined point of time.

RESULTS

Twenty-seven players participated in our study out of which 5 players (19%) had EIB.

CONCLUSION

Our findings indicate that a significant number of cases of EIB exist among national field hockey players. We suggest that active screening for EIB should be made part of training sessions, so that performance of players could be enhanced. Diagnosed cases should be treated as per the guidelines laid down by International Olympic Committee Medical Commission.

Indoor radon levels and lung cancer risk estimates in seven cities of the Bahawalpur Division, Pakistan

Indoor radon concentration levels were measured in seven major cities of the Bahawalpur Division, Pakistan. These included Fort Abbas, Minchin Abad, Hasilpur, Bahawalpur, Liaqatpur, Rahimyar Khan and Sadiq Abad. In order to select houses for this survey, the inhabitants were approached through their school-registered children. Due to several constraints, only those 100 houses were chosen in each city that were relatively the best representatives of the built-up area. The selected houses were then divided into live categories according to the house locations and building characteristics. CR-39 detectors, placed in polyethylene bags. were installed at head height in bedrooms and sitting rooms of all the selected houses and were exposed to radon and its daughter products for 90 days. Four such measurements were performed over a year in order to average out the seasonal variation in radon levels. After exposure, all the detectors were etched and counted under an optical microscope. The track densities of four measurements were averaged out and related to radon concentration levels. The radon levels were found to be 20, 20, 26, 28, 34, 42, 47 Bq m(-3) in the bedrooms and 24, 26, 27, 26, 37, 40, 43 Bq m(-3) in sitting rooms of Hasilpur, Rahimyar Khan, Minchin Abad, Fort Abbas, Sadiq Abad, Bahawalpur and Liaqatpur respectively. The observed variation in the radon level may be attributed to the geological variation in the area. Based on the observed data, excess lung cancer risk was assessed using the risk factors recommended by the USEPA, UNSCEAR and the ICRP. According to the EPA model, the lifetime excess lung cancer risk due to the lifetime exposure is found to vary from 12-102 per million per year in the houses surveyed. This variation is from 16-114 and 26-62 per million per year if UNSCEAR and ICRP limits are applied respectively.

Continuous quality assessment; development of a simple computer based model for audit

OBJECTIVE

Accurate assessment of quality of care is a fundamental first step in the process of quality improvement. The vast amount of data generated in a hospital mandates some form of computerization for management of information. We describe a locally developed simple computer based program to access relevant information from a hospital patient management network. The objective was to reduce the amount of manual work involved for busy clinicians attempting to audit quality of care.

METHODS

A single surgical procedure, Laparoscopic Cholecystectomy was chosen. Quality indicators were identified by literature review as conversion rate from laparoscopic to open cholecystectomy and length of hospital stay (LOS). A simple query was developed to extract the required information from hospital database. Commercially available spreadsheet software (Microsoft Excel) was used to calculate the rates. Outliers were defined as LOS more than 1 standard deviation from the mean. The second part of the study involved a manual review of case notes to validate the program and determine the causes for deviation from the mean.

RESULTS

The program was able to access and process data as planned. In a one-year period from March 1997 to February 1998, two hundred and thirty one laparoscopic cholecystectomies were attempted. Twenty-three were converted to open procedures given a conversion rate of 9.96%. On manual review of case notes no false positives or false negatives were found. The reasons for conversion were similar to those described in the literature. The mean length of stay for laparoscopic cholecystectomy was 3.39 days and 7.17 days for converted cases. The commonest reason for delay in discharge was noted to be non-availability of elective operating time.

CONCLUSION

We have successfully developed and used a simple computer based program to access information stored in hospital patient management systems. Quality of care indicators identified from literature were used as standards. Outliers with respect to these were reviewed in detail to identify causes for deviation. The program was validated by manual review.

An objective structured practical examination to test students in experimental physiology

OBJECTIVE

To develop a competency based discriminatory assessment method for physiology practical examination.

METHOD

Results from 1st professional M.B.B.S. Part I and II of three batches were taken and students performance in traditional and objective structured practical examination (OSPE) were compared. The course objective for practical examination of all three batches were same. However, Batch II appeared in the conventional examination, while Batches III and IV were examined by OSPE.

RESULTS

The mean score of Batch II was 68 +/- 6, of Batch III 53 +/- 13 and Batch IV 50 +/- 16. Batch II had thus an overall higher score as compared to Batches III and IV. The comparison of mean scores using ANOVA showed a significant (P < .001) difference between scores of Batch II as compared to Batches III and IV. Tukey's pair wise comparison of the batches showed a significant difference between batches II and III (95% CI for difference: 9.1, 20.5 with P < 0.001) and batches II and IV (95% CI for difference: 12.2, 23.6 with P < 0.001). However, no significant difference was found between batches III and IV (95% CI for difference: -2.6, 8.8 with P = 0.27). The result also showed that Batch II with conventional method of examination had a lesser spread around the mean (scores ranging from 52 to 81) as compared to Batch III (25 to 80) and Batch IV (14 to 90).

CONCLUSION

OSPE is an effective tool to discriminate between good and poor performers in physiology practical examinations.

Schwannoma of submandibular region

Tumours of the nerve sheath origin in the head and neck are not common. Schwannomas are rare. Only a few cases have been reported so far. We report a rare case of Schwannoma of Submandibular region arising from the lingual nerve.

Peripheral T cell lymphomas: an immunological study of seven unusual cases

A multiparameter study of malignant lymph node cells and peripheral blood lymphocytes of seven patients with peripheral T cell lymphoma is presented. The results of monoclonal marker studies showed three cases of helper-suppressor T cell lymphoma (OKT4+, OKT8+), one case of suppressor T cell lymphoma (OKT8+), and three cases of helper T cell lymphoma (OKT4+). Immunophenotypic heterogeneity of neoplastic T cells with expression of pan-T antigens, OKT3+, and OKT11+ (erythrocyte rosetting+) was observed in most patients. Six of the seven cases tested showed Ia and DR antigens. No relationship was detected between patterns of reactivity with T cell reagents and histological types. When tested, the in-vitro malignant T cells of five patients proliferated in response to concanavalin A (Con A), but had poor response to phytohaemagglutinin. The interleukin 2 receptors showed maximum expression on Con A-activated T cells of five patients, and phytohaemagglutinin-activated T cells of one patient. The neoplastic T cells (OKT4+, OKT8+) of one patient studied had suppressor activity for IgG and IgA, and helper activity for IgM synthesis on pokeweed mitogen-induced normal B cell differentiations.

Does a barbiturate drug given in lethal dose enter the cornea?

We wished to see whether sodium phenobarbital (one of the commonest drugs used to commit suicide) given in a lethal dose would enter the cornea. Guinea pigs and rabbits were killed with an overdose of the drug. Using gas chromatography we were able to detect the drug not only in the vascular ocular tissues and the intraocular fluids but also in the avascular tissues such as the cornea.

Pathology of malignant tumors of the nose and throat and their relationship to lymphatic metastasis

One hundred cases of malignant tumors of the larynx, pharynx, oral cavity, nose and paranasal sinuses were studied. The hypopharynx was the most frequent site and the most common type of tumor was squamous cell carcinoma. Lymph nodes were palpable in 59% of cases, of which 72.8% showed histological evidence of metastasis. The highest incidence of metastasis was found in nasopharyngeal growths and the lowest in the nose and the sinuses. In laryngeal tumors the site of the tumor was the most important factor influencing regional lymphatic metastasis. The grade of the tumor influenced the lymph node metastasis in the regions of the hypopharynx, tonsil and base of tongue. At other sites the differentiation of the tumor did not seem to have any correlation with the incidence of metastasis.