Spermidine constitutes a key determinant of motility and attachment of Salmonella Typhimurium through a novel regulatory mechanism

Spermidine is a poly-cationic molecule belonging to the family of polyamines and is ubiquitously present in all organisms. Salmonella synthesizes, and harbours specialized transporters to import spermidine. A group of polyamines have been shown to assist in Salmonella Typhimurium's virulence and regulation of Salmonella pathogenicity Inslad 1 (SPI-1) genes and stress resistance; however, the mechanism remains elusive. The virulence trait of Salmonella depends on its ability to employ multiple surface structures to attach and adhere to the surface of the target cells before invasion and colonization of the host niche. Our study discovers the mechanism by which spermidine assists in the early stages of Salmonella pathogenesis. For the first time, we report that Salmonella Typhimurium regulates spermidine transport and biosynthesis processes in a mutually inclusive manner. Using a mouse model, we show that spermidine is critical for invasion into the murine Peyer's patches, which further validated our in vitro cell line observation. We show that spermidine controls the mRNA expression of fimbrial (fimA) and non-fimbrial adhesins (siiE, pagN) in Salmonella and thereby assists in attachment to host cell surfaces. Spermidine also regulated the motility through the expression of flagellin genes by enhancing the translation of sigma-28, which features an unusual start codon and a poor Shine-Dalgarno sequence. Besides regulating the formation of the adhesive structures, spermidine tunes the expression of the two-component system BarA/SirA to regulate SPI-1 encoded genes. Thus, our study unravels a novel regulatory mechanism by which spermidine exerts critical functions during Salmonella Typhimurium pathogenesis.

Audit of Otological Diseases in Otolaryngology-Head and Neck Surgery Outpatient Department of a Tertiary Level Hospital

To find out the otological disease pattern of the patients attended at the Otolaryngology-Head & Neck Surgery outpatient department (OPD) of a tertiary level hospital, Dhaka, Bangladesh and to aware the people about the consequences of Ear diseases, necessity of prevention and early management. This study was done in the Otolaryngology-Head & Neck Surgery OPD of Shaheed Suhrawardy Medical College Hospital, Dhaka, Bangladesh from July 2014 to December 2014. Data were collected retrospectively from hospital record which were recorded by Resident Surgeon during his consultation of referral patients. Total 3686 patients were included in the study and data were analyzed. Out of 3686 OPD patients male were 1947(52.82%) and female 1739(47.17%), ratio 1.12:1. In age groups 11 to 40-year age group patients were more, among them 11-20 (17.25%), 21-30 (21.51%) and 31-40 (21.62%). 47.97% of the patients were presented with Ear diseases. Among the ear conditions CSOM (Chronic suppurative otitis media) were 19.96%, ASOM (Acute Suppurative Otitis Media) 2.54%, OME (Otitis media with effusion) 5.31%, Otomycosis 9.25%, Furunculosis 1.81%, Otosclerosis 0.57%, Foreign body ear 1.68%, Rupture TM (Tympanic membrane) 1.27% and Wax 4.74%. Prevalence of Ear diseases are more in Bangladesh like other developing countries. Most of the ear diseases can be managed in the local hospitals. For the proper management physicians working in those hospitals need training and adequate instruments. District hospitals and medical college hospitals should be well equipped with proper instruments and trained ENT surgeons.

Prevalence, Risk Factors and Microbiological Profile of Orthopaedic Surgical Site Infection in North-Eastern Peninsular Malaysia

Introduction

The devastating outcome of orthopaedic surgical site infections (SSI) are largely preventable if its risk factors, causative organisms and antimicrobial susceptibility patterns in the regional area are known.

Materials and methods

We conducted a retrospective study to address the lack of epidemiological and microbiological data on orthopaedic SSI in Malaysia. All the 80 patients diagnosed and treated for microbiologically proven orthopaedic SSIs in a tertiary hospital in Malaysia from April 2015 to March 2019 were included in a 1:2 case control study.

Results

The prevalence of SSI in clean and clean-contaminated surgeries was 1.243%, which is consistent with most of the studies worldwide, but is low compared to other studies done in Malaysia. The most common type of orthopaedics SSI were internal fixation infections (46.25%), superficial SSIs (25.2%) and Prosthetic joint infections (18.75%). Obesity and tobacco use were found to be significant risk factors of orthopaedic SSI. The most common perioperative prophylaxis used was IV cefuroxime. Majority of the cases (86.5%) received prolonged prophylactic antibiotics. The most common causative agent was Staphylococcus aureus (31.25%), followed by Pseudomonas aeruginosa (26.25%) and Enterobacter spp (7.5%). Methicillin-resistant Staphylococcus aureus (MRSA) accounted for 20% of the S. aureus infections. Up to 19.4% of the Gram-negative organisms are multidrug resistant. The higher rate of isolation of organisms resistant to the prophylactic antibiotics being used may be related to the prolonged use of prophylactic antibiotics, which exerted selective pressure for the acquisition of resistant organisms.

Conclusion

Despite its relatively low prevalence in our local institution and worldwide, the prevention of SSI in orthopaedic practice is crucial to avoid morbidity, mortality and high healthcare cost. This may be achieved by control of modifiable risk factors such as obesity and tobacco use, appropriate use of prophylactic antibiotics and implementation of good surgical and infection control practices.

Energetics of Spike Protein Opening of SARS-CoV-1 and SARS-CoV-2 and Its Variants of Concern: Implications in Host Receptor Scanning and Transmission

The receptor binding domain(s) (RBD) of spike (S) proteins of SARS-CoV-1 and SARS-CoV-2 (severe acute respiratory syndrome coronavirus) undergoes closed to open transition to engage with host ACE2 receptors. In this study, using multi atomistic (equilibrium) and targeted (non-equilibrium) molecular dynamics simulations, we have compared energetics of RBD opening pathways in full-length (modeled from cryo-EM structures) S proteins of SARS-CoV-1 and SARS-CoV-2. Our data indicate that amino acid variations at the RBD interaction interface can culminate into distinct free energy landscapes of RBD opening in these S proteins. We further report that mutations in the S protein of SARS-CoV-2 variants of concern can reduce the protein-protein interaction affinity of RBD(s) with its neighboring domains and could favor its opening to access ACE2 receptors. The findings can also aid in predicting the impact of future mutations on the rate of S protein opening for rapid host receptor scanning.

Prediction of long-term survival after gastrectomy using random survival forests

BACKGROUND

No well validated and contemporaneous tools for personalized prognostication of gastric adenocarcinoma exist. This study aimed to derive and validate a prognostic model for overall survival after surgery for gastric adenocarcinoma using a large national dataset.

METHODS

National audit data from England and Wales were used to identify patients who underwent a potentially curative gastrectomy for adenocarcinoma of the stomach. A total of 2931 patients were included and 29 clinical and pathological variables were considered for their impact on survival. A non-linear random survival forest methodology was then trained and validated internally using bootstrapping with calibration and discrimination (time-dependent area under the receiver operator curve (tAUC)) assessed.

RESULTS

The median survival of the cohort was 69 months, with a 5-year survival of 53.2 per cent. Ten variables were found to influence survival significantly and were included in the final model, with the most important being lymph node positivity, pT stage and achieving an R0 resection. Patient characteristics including ASA grade and age were also influential. On validation the model achieved excellent performance with a 5-year tAUC of 0.80 (95 per cent c.i. 0.78 to 0.82) and good agreement between observed and predicted survival probabilities. A wide spread of predictions for 3-year (14.8-98.3 (i.q.r. 43.2-84.4) per cent) and 5-year (9.4-96.1 (i.q.r. 31.7-73.8) per cent) survival were seen.

CONCLUSIONS

A prognostic model for survival after a potentially curative resection for gastric adenocarcinoma was derived and exhibited excellent discrimination and calibration of predictions.

Psychometric properties of the Malay inventory for the perception of Muslims with hearing impairment

OBJECTIVE

The aims of this study are to measure the psychometric properties of the newly developed preliminary version of hearing impairment inventory for religious duties for Muslim adults, i.e., the Inventori Persepsi Bagi Muslim Yang Memiliki Masalah Pendengaran (IPM3P), and to produce a final version of IPM3P.

METHODS

The preliminary version of IPM3P that is used to investigate the perception of Muslim adults with hearing impairment towards Islamic understanding and practice has been tested in this study. The preliminary version of IPM3P consists of three domains (obligation, practice, and difficulty) with 59 items in total. Four phases of validity and reliability testing involved were: i) Content validation, ii) Pretesting, face validity and proofreading, iii) Pilot study, and iv) Psychometric evaluation.

RESULTS

The final version of IPM3P consists of 36 items. The findings from the present study suggest that the final version of IPM3P has excellent psychometric properties manifested by: i) good content validity, ii) excellently pretested, iii) good face validity, iv) good construct validity shown by principal component analysis and convergent validity, and v) good discriminant validity showed by divergent validity.

CONCLUSION

IPM3P shows good potential to be used as a tool in investigating perception of Muslim adults towards Islamic understanding and practice.

Mycobacterium tuberculosis Specific Protein Rv1509 Evokes Efficient Innate and Adaptive Immune Response Indicative of Protective Th1 Immune Signature

Dissecting the function(s) of proteins present exclusively in Mycobacterium tuberculosis (M.tb) will provide important clues regarding the role of these proteins in mycobacterial pathogenesis. Using extensive computational approaches, we shortlisted ORFs/proteins unique to M.tb among 13 different species of mycobacteria and identified a hypothetical protein Rv1509 as a ‘signature protein’ of M.tb. This unique protein was found to be present only in M.tb and absent in all other mycobacterial species, including BCG. In silico analysis identified numerous putative T cell and B cell epitopes in Rv1509. Initial in vitro experiments using innate immune cells demonstrated Rv1509 to be immunogenic with potential to modulate innate immune responses. Macrophages treated with Rv1509 exhibited higher activation status along with substantial release of pro-inflammatory cytokines. Besides, Rv1509 protein boosts dendritic cell maturation by increasing the expression of activation markers such as CD80, HLA-DR and decreasing DC-SIGN expression and this interaction was mediated by innate immune receptor TLR2. Further, in vivo experiments in mice demonstrated that Rv1509 protein promotes the expansion of multifunctional CD4+ and CD8+T cells and induces effector memory response along with evoking a canonical Th1 type of immune response. Rv1509 also induces substantial B cell response as revealed by increased IgG reactivity in sera of immunized animals. This allowed us to demonstrate the diagnostic efficacy of this protein in sera of human TB patients compared to the healthy controls. Taken together, our results reveal that Rv1509 signature protein has immunomodulatory functions evoking immunological memory response with possible implications in serodiagnosis and TB vaccine development.

O14: RANDOM FOREST MODELS FOR PREDICTING SURVIVAL AFTER OESOPHAGECTOMY

Introduction

For patients with oesophageal cancer, producing accurate prediction models for survival after oesophagectomy has proved challenging. We investigated whether Random Survival Forests (RSF), a novel machine learning method, could produce an accurate prognostic model for overall survival after oesophagectomy.

Method

The study used data from the National Oesophago-Gastric Cancer Audit and included patients diagnosed with oesophageal adenocarcinoma or squamous cell carcinoma between 2012 and 2018 in England and Wales and who underwent a curative oesophagectomy with adequate lymphadenectomy (15 LN) and survived to discharge (n=6198). Missing data was handled using multiple imputation and the data was split into training and validation cohorts. 13 variables were selected for inclusion using Random Forest variable importance and used to train the final model. The same variables were used to develop a traditional Cox regression model.

Result

Median survival was 53 months in both cohorts. The final RSF model had good discrimination in the validation cohort with a C-index of 0.757(0.755-0.759), exceeding the Cox model; 0.748(0.746-0.750). At 3 years post-surgery, overall survival was 56.2%. The RSF yielded a mean predicted survival of 55.8%(IQR 29.5%-81.7%) compared to 55.4%(40.0%-77.7%) for the Cox model. The most important variables were lymph node involvement and pT/ypT stage, however other variables including neoadjuvant treatment completion and surgical complications were also found to be important.

Conculsion

A Random Forest survival model provided better performance in predicting survival after curative oesophagectomy. This will allow more personalised predictions to be delivered clinicians and patients.

Take-home message

Random Forest survival models can accurately predict post-operative prognosis after oesophagectomy.

Oesophageal cancer: The effect of early nutrition support on clinical outcomes

BACKGROUND AND AIMS

Malnutrition is prevalent in oesophageal cancer. Evidence for the use of nutrition support and prehabilitation in this cohort is variable. The aim of this study was to examine the effect of early nutrition support and functional measures of nutritional status on post-operative outcomes in adult patients with oesophageal cancer.

METHODS

Retrospective review of adults with oesophageal cancer undergoing oesophagectomy (n = 151). Early nutrition support was defined as: oral or enteral nutrition supplementation during neoadjuvant treatment. Late nutrition support defined as: oral or enteral nutrition supplementation prescribed post-operatively. Nutrition outcome measures were; percentage weight loss from 3 to 6 months prior to diagnosis, peri- and post-operatively, and pre-operative assessment of handgrip-strength (HGS).

RESULTS

Pre-operative weight loss ≥10% was a significant predictor of mortality at 1 year (OR 2.84, 95%CI 1.03-7.83, p = 0.04) independent of tumour stage, adjuvant treatment, age and gender. Adults prescribed early nutrition support during neoadjuvant treatment experienced less weight loss at 12-months post-oesophagectomy compared to adults prescribed late oral nutrition support (p=<0.05). Pre-operative HGS measurements were not a useful predictor of postoperative complications (p = 0.2), length of stay (p = 0.9) or 90-day mortality (p = 0.6).

CONCLUSIONS

Pre-operative weight loss ≥10% was associated with mortality. Early nutrition support was associated with less weight loss at 12-months post-operatively. Pre-operative HGS measures did not have prognostic value as a stand-alone measure. Future work should investigate the efficacy of early nutrition support in reducing both pre- and post-operative weight loss to improve nutritional status and surgical outcomes as part of a multimodal prehabilitation programme in adults with oesophageal cancer.

Structure-Function Analyses of New SARS-CoV-2 Variants B.1.1.7, B.1.351 and B.1.1.28.1: Clinical, Diagnostic, Therapeutic and Public Health Implications

SARS-CoV-2 (Severe Acute Respiratory Syndrome-Coronavirus 2) has accumulated multiple mutations during its global circulation. Recently, three SARS-CoV-2 lineages, B.1.1.7 (501Y.V1), B.1.351 (501Y.V2) and B.1.1.28.1 (P.1), have emerged in the United Kingdom, South Africa and Brazil, respectively. Here, we have presented global viewpoint on implications of emerging SARS-CoV-2 variants based on structural-function impact of crucial mutations occurring in its spike (S), ORF8 and nucleocapsid (N) proteins. While the N501Y mutation was observed in all three lineages, the 501Y.V1 and P.1 accumulated a different set of mutations in the S protein. The missense mutational effects were predicted through a COVID-19 dedicated resource followed by atomistic molecular dynamics simulations. Current findings indicate that some mutations in the S protein might lead to higher affinity with host receptors and resistance against antibodies, but not all are due to different antibody binding (epitope) regions. Mutations may, however, result in diagnostic tests failures and possible interference with binding of newly identified anti-viral candidates against SARS-CoV-2, likely necessitating roll out of recurring "flu-like shots" annually for tackling COVID-19. The functional relevance of these mutations has been described in terms of modulation of host tropism, antibody resistance, diagnostic sensitivity and therapeutic candidates. Besides global economic losses, post-vaccine reinfections with emerging variants can have significant clinical, therapeutic and public health impacts.

Development of hearing impairment inventory for religious duties of Muslim adult

OBJECTIVE

This study is a preliminary work to develop a Malay version questionnaire named 'Inventori Persepsi bagi Muslim yang Memiliki Masalah Pendengaran (IPM3P)' to assess the perception on Islamic understanding and practice among Muslim adults with hearing impairment.

METHODS

The scale development involved three phases: i) generation of domains based on the literature, ii) generation of sub-domains based on literature review and Islamic panel survey, and iii) generation of items.

RESULTS

Preliminary version of IPM3P consists of 59 items was produced, representing three domains: Obligation (18 items), Practice (21 items), and Difficulty (20 items), and seven sub-domains ('Ibadah', 'Aqidah', 'Muamalat', 'Tasawwuf', 'Akhlak','Da'wah', and 'Sirah').

CONCLUSION

The preliminary version of IPM3P needs to be psychometrically tested. This pioneering study may become an impetus towards more research pertaining to understanding the effect of hearing loss towards religious life in the future in Malaysia.

In ovo injection of black cumin (Nigella sativa) extract on hatching and post hatch performance of thermally challenged broiler chickens during incubation

The objective of this study was to investigate the effects in ovo injection of black cumin (BC) extract on chick's quality and response of thermally challenged broiler chickens. A total of 700 hatching eggs of broiler chickens (Marshall) were assigned to 7 treatments of 100 eggs each and incubated using the conventional protocol (37.8°C) for the first 10 d and then exposed to a high temperature (39.6°C) for 6 h daily from day 10 until day 18 of the incubation. At embryonic day 17.5, the eggs were randomly allotted to 7 treatment groups, viz.: eggs without in ovo injection (WA), eggs injected with 0.9% saline solution (SA), 3 mg ascorbic acid (AA), 2 mg BC (TB), 4 mg BC (FB), 6 mg BC (SB), and 8 mg BC (EB) extracts. Experiment was laid out in a Completely Randomized Design. After hatching, the chicks were reared separately according to in ovo treatments for 8 wk. Data were collected on hatchability, chick quality, internal organs, growth performance, plasma superoxide dismutase, malondialdehyde, and triiodothyronine (T₃). The results showed that the hatchability of the eggs in the AA group was similar to that of SB eggs and higher than that of the other treatment groups. The intestinal weights of SB and EB birds were significantly higher (P < 0.05) than those of TB, SA, and WA. The final weights of the birds of SB and AA were higher (P < 0.05) than those of other treatments. The feed conversion ratio of the birds of TB and FB was comparable to that of EB and WA but higher than that of SB and AA. At hatch, the creatinine of the birds in SA and WA was similar to that of EB, FB, and TB but higher (P < 0.05) than that of AA and SB. Also, the plasma malondialdehyde, T₃, and superoxide dismutase of SB and AA birds were better (P < 0.05) than those of the control groups. Overall, it was concluded that 6 mg of BC extract improved the antioxidant status and posthatch performance of thermally challenged broiler chickens.

Mycobacterium smegmatis Bacteria Expressing Mycobacterium tuberculosis-Specific Rv1954A Induce Macrophage Activation and Modulate the Immune Response

Mycobacterium tuberculosis (M. tb), the intracellular pathogen causing tuberculosis, has developed mechanisms that endow infectivity and allow it to modulate host immune response for its survival. Genomic and proteomic analyses of non-pathogenic and pathogenic mycobacteria showed presence of genes and proteins that are specific to M. tb. In silico studies predicted that M.tb Rv1954A is a hypothetical secretory protein that exhibits intrinsically disordered regions and possess B cell/T cell epitopes. Treatment of macrophages with Rv1954A led to TLR4-mediated activation with concomitant increase in secretion of pro-inflammatory cytokines, IL-12 and TNF-α. In vitro studies showed that rRv1954A protein or Rv1954A knock-in M. smegmatis (Ms_Rv1954A) activates macrophages by enhancing the expression of CD80 and CD86. An upregulation in the expression of CD40 and MHC I/II was noted in the presence of Rv1954A, pointing to its role in enhancing the association of APCs with T cells and in the modulation of antigen presentation, respectively. Ms_Rv1954A showed increased infectivity, induction of ROS and RNS, and apoptosis in RAW264.7 macrophage cells. Rv1954A imparted protection against oxidative and nitrosative stress, thereby enhancing the survival of Ms_Rv1954A inside macrophages. Mice immunized with Ms_Rv1954A showed that splenomegaly and primed splenocytes restimulated with Rv1954A elicited a Th1 response. Infection of Ms_Rv1954A in mice through intratracheal instillation leads to enhanced infiltration of lymphocytes in the lungs without formation of granuloma. While Rv1954A is immunogenic, it did not cause adverse pathology. Purified Rv1954A or Rv1954A knock-in M. smegmatis (Ms_Rv1954A) elicited a nearly two-fold higher titer of IgG response in mice, and PTB patients possess a higher IgG titer against Rv1954A, also pointing to its utility as a diagnostic marker for TB. The observed modulation of innate and adaptive immunity renders Rv1954A a vital protein in the pathophysiology of this pathogen.

Emerging genetic diversity among clinical isolates of SARS-CoV-2: Lessons for today

Considering the current pandemic of COVID-19, it is imperative to gauge the role of molecular divergence in SARS-CoV-2 with time, due to clinical and epidemiological concerns. Our analyses involving molecular phylogenetics is a step toward understanding the transmission clusters that can be correlated to pathophysiology of the disease to gain insight into virulence mechanism. As the infections are increasing rapidly, more divergence is expected followed possibly by viral adaptation. We could identify mutational hotspots which appear to be major drivers of diversity among strains, with RBD of spike protein emerging as the key region involved in interaction with ACE2 and consequently a major determinant of infection outcome. We believe that such molecular analyses correlated with clinical characteristics and host predisposition need to be evaluated at the earliest to understand viral adaptability, disease prognosis, and transmission dynamics.

Immunodominant Mycobacterium tuberculosis Protein Rv1507A Elicits Th1 Response and Modulates Host Macrophage Effector Functions

Mycobacterium tuberculosis (M. tb) persists as latent infection in nearly a quarter of the global population and remains the leading cause of death among infectious diseases. While BCG is the only vaccine for TB, its inability to provide complete protection makes it imperative to engineer BCG such that it expresses immunodominant antigens that can enhance its protective potential. In-silico comparative genomic analysis of Mycobacterium species identified M. tb Rv1507A as a “signature protein” found exclusively in M. tb. In-vitro (cell lines) and in-vivo experiments carried out in mice, using purified recombinant Rv1507A revealed it to be a pro-inflammatory molecule, eliciting significantly high levels of IL-6, TNF-α, and IL-12. There was increased expression of activation markers CD69, CD80, CD86, antigen presentation molecules (MHC I/MHCII), and associated Th1 type of immune response. Rv1507A knocked-in M. smegmatis also induced significantly higher pro-inflammatory Th1 response and higher survivability under stress conditions, both in-vitro (macrophage RAW264.7 cells) and in-vivo (mice). Sera derived from human TB patients showed significantly enhanced B-cell response against M. tb Rv1507A. The ability of M. tb Rv1507A to induce immuno-modulatory effect, B cell response, and significant memory response, renders it a putative vaccine candidate that demands further exploration.

0190 Impact of Menopause-Related Sleep Fragmentation on Daytime Sleepiness and Neurobehavioral Performance: Results of an Experimental Model

Introduction

Cognitive performance may be adversely affected during the menopause transition from hot flash-induced sleep fragmentation even without changes in sleep duration. We examined the effects of experimentally-induced sleep fragmentation without shortened sleep duration on daytime sleepiness and neurobehavioral performance in women in a high and low estradiol (E2) state.

Methods

Seven pre-menopausal women (29.4 ± 3.8 years) participated in two 6-day inpatient studies repeated in a high-E2 (mid-to-late follicular phase) then low-E2 state (gonadotropin-releasing hormone agonist-induced E2 suppression - similar to levels during menopause) ~6 weeks apart. Sleep was uninterrupted on nights 1–2 [8-h time-in-bed (TIB)] and fragmented on nights 3–5 (9-h TIB) using an auditory stimulus delivered every 15 min that sustained wake for 2 minutes, producing 1-h total wake after sleep onset. Wakefulness was confirmed by event-markers during polysomnographically-recorded sleep episodes. Daytime subjective sleepiness (Karolinska Sleepiness Scale; KSS) and neurobehavioral performance (Psychomotor Vigilance Task; PVT) were assessed every 2–3 hours on study days 2–5. The effects of study day and E2 state on KSS scores and PVT measured reaction time (RT) and attentional failures (RT&gt;500ms) were examined using linear mixed models.

Results

Participants reported feeling sleepier (+10%), had longer RTs (+22ms), and more attentional failures (+53%) after sleep fragmentation than after uninterrupted sleep (all p&lt;0.001). While there was no main effect of E2 state, there was a differential effect of sleep fragmentation by E2 state on PVT, but not sleepiness, such that the increase in RT and attentional failures in response to sleep fragmentation was only observed in the high-E2 state (p&lt;0.001).

Conclusion

Eight hours of total sleep time may not be sufficient to maintain subjective sleepiness and PVT performance levels when sleep is not consolidated. These findings have important implications for understanding the role of sleep and E2-modulated cognitive impairment during the menopause transition.

Support

This work was supported by the NIH: 5R01 AG053838-02 (HJ) and K24-HL105664 (EBK).

Vitamin D Profile in Juvenile Idiopathic Arthritis Patients in a Tertiary Care Hospital in Bangladesh

There are multi-factorial causes of decrease in bone mass in Juvenile Idiopathic Arthritis (JIA) patients who correlate with the duration of active disease. By measuring the vitamin D level we can assess the deficiency or insufficiency earlier and can predict the risk of osteoporotic bone fracture & can give appropriate supplementation of vitamin D & calcium. This study was done to determine the status of serum 25(OH)D in patients with JIA and to see the relationship among various subtypes and disease duration. In this cross sectional study 30 (Thirty) newly diagnosed cases of JIA attending the pediatric rheumatology clinic of Bangabandhu Sheikh Mujib Medical University (BSMMU), Dhaka, Bangladesh from July 2014 to December 2015 were included. Thirty age and sex matched control were selected and serum 25(OH)D was measured in cases and controls. Among JIA patients, 60% and among controls 33% had hypo-vitaminosis D. In JIA group the mean level of serum 25(OH)D was lower than control group and the result is statistically significant in cases of poly-articular JIA and systemic JIA (SJIA). There is significant difference of the mean values of vitamin D levels in JIA and control groups for the cases of hypo-vitaminosis D. Level of serum 25(OH)D significantly decreased as disease duration continue increased. More than half of JIA patients had hypo-vitaminosis D. It is more significant in cases of poly-articular JIA and systemic JIA (SJIA). There was negative relationship between serum 25(OH)D level and disease duration.

Rabies on the Indian subcontinent

The Indian subcontinent comprises Afghanistan, Bangladesh, Bhutan, India, Nepal, the Maldives, Myanmar, Pakistan and Sri Lanka. In all of these countries, except the Maldives, rabies is endemic. An estimated 59,000 people die from rabies each year; 45% of these deaths occur on the Indian subcontinent and approximately 33% take place in India. The majority of these deaths are attributable to dog bites, and those most affected are children and the poor. Access to post-exposure prophylaxis is limited and costly, the supply of immunoglobulins and vaccines can be irregular and public awareness of rabies is low. Moreover, the vaccination of domestic dogs is not widely implemented. There is a need for increased laboratory capacity and expertise across the continent, as well as better data, improved surveillance and more user-friendly and economical diagnostic tests. An animal birth control programme has met with mixed success in India. However, a greater focus on mass dog vaccination could eliminate the disease at its source, reducing the large burden of mortality for at-risk communities. In this paper, the authors examine the situation in each of the countries on the Indian subcontinent, discuss current needs, obstacles and progress, and examine future strategies, with the objective of eliminating dog-mediated rabies from the subcontinent by 2030.

Abstract 409: Dual-direction CRISPR transcriptional regulation screening uncovers gene networks driving drug resistance

Functional genomic screening with CRISPR-Cas9 has provided a powerful and precise new way to interrogate the phenotypic consequences of gene manipulation in high-throughput, unbiased analyses. Rapid development of pooled lentivirus and deep-sequencing-led approaches have allowed us and others to exploit this technology in target ID, target validation, drug MOA analysis and patient stratification.

Many screens have been conducted using loss-of-function driven by CRISPR-Cas9 knock-out. Whilst powerful, this approach is not suitable for the examination of hypomorphic phenotypes, which include essential genes. In addition, CRISPR-Cas9 knock-out does not allow the analysis of gene activation, leaving a significant hole in the functional genomic analysis. To address this, we have developed two new paired pooled screening platforms using inactivated Cas9 (dCas9) to control gene expression in both loss- and gain-of-function screens. Our CRISPRi platform uses a streamlined and high-performance approach with an improved tracrRNA sequence incorporated into a single-shot transduction protocol. Our CRISPRa platform is based on the SAM system and both platforms have been adapted to use next generation, highly optimised whole-genome libraries to enact maximum gene expression modulation. Validation analysis of both tools revealed outstanding performance and sensitivity, with greater than ten-fold improvement in detection rates compared to existing platforms, including RNAi.

We used these paired tools to explore the development of resistance mechanisms to the BRAF V600E inhibitor, vemurafenib. Both platforms allowed for the unambiguous discovery of expected hits, additional complex members not identified previously, as well as multiple novel genes involved in drug resistance. Most interestingly, simultaneous evaluation of both activating and inhibiting perturbations revealed direct and opposing phenotypic effects within complex gene networks, switching the response of affected cells to either sensitisation or resistance. In addition to providing a compelling strategy for the validation of drug resistance targets, the parallel analysis of CRISPRi and CRISPRa data sets also allows the identification of pathway modulators that affect both drug sensitivity and resistance, but in which sgRNAs are not reciprocally lost or increased in each screen.

Taken together, our data indicate that CRISPRa and CRISPRi screens in parallel provide an exceptionally powerful dataset for target identification. Dual directional approaches such as ours provide the new opportunity to achieve increased depth of hit finding in the analysis and offer novel discovery pathways by exploring opposing function and more complete gene network perturbation.

Citation Format: Carlos le Sage, Steffen Lawo, Prince Panckier, Tim M. Scales, Syed Asad Rahman, Annette S. Little, Nicola J. McCarthy, Jonathan D. Moore, Benedict C. Cross. Dual-direction CRISPR transcriptional regulation screening uncovers gene networks driving drug resistance [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 409.

Role of Red Cell Distribution Width to Platelet Ratio in Predicting Hepatic Fibrosis in Chronic Hepatitis B

Hepatitis B virus (HBV) infection is a serious global health problem. Globally more than 2 (Two) billion people are infected with Hepatitis B virus and about 400 million people are chronic carriers who are at risk of death from liver cirrhosis and liver cancer that kill more than one million people globally each year. Prevalence of HBV infection in Bangladesh is 2.3 to 9.7% and approximately 10 million people are harboring the virus as carrier. HBV infection is increasing at an alarming rate in Bangladesh due to lack of health education, poverty, illiteracy and lack of hepatitis B vaccination. This cross sectional study was carried out in the Department of Clinical Pathology, in collaboration with Department of Hepatology and Department of Pathology, Bangabandhu Sheikh Mujib Medical University (BSMMU), Dhaka, Bangladesh from September 2013 to August 2014 to assess the role of Red cell distribution width to platelet ratio (RPR) as a non invasive marker in predicting hepatic fibrosis in chronic hepatitis B patients. Total 40 patients with chronic hepatitis B virus infection who fulfilled the criteria of chronic hepatitis B were included in this study. In this study, majority of the patients belonged to 20-29 years, most of the patients were male and HBeAg negative .Histopathology was gold standard to identify the stages of hepatic fibrosis. We also measured RDW and Platelet count by automated haematology analyzer when platelet count was rechecked manually; RDW to platelet ratio was calculated to see the correlation between RPR with different stages of hepatic fibrosis. In chronic hepatitis B patients a positive and significant correlation was found between RPR and stages of hepatic fibrosis and Spearman's correlation coefficient for RPR was 0.749 which was positive and highly significant (p<0.001). Sensitivity, specificity, positive predictive value, negative predictive value and accuracy of RDW to Platelet ratio (RPR) was 62.86%, 80%, 95.65%, 23.53% and 65% respectively. To assess the diagnostic performance of RPR we also used receiver-operating curve (ROC). The area under ROC was 0.889 for identification of hepatic fibrosis. This data revealed that RPR is strongly associated with stages of hepatic fibrosis in chronic hepatitis B patients. As such RPR may be a useful diagnostic tool for assessing the hepatic fibrosis in chronic hepatitis B patients.

Enteroinsular hormones in two siblings with Donohue syndrome and complete leptin deficiency

The main biochemical hallmark of the rare and lethal condition of Donohue syndrome (DS) is hyperinsulinemia. The roles of the gut and other pancreatic hormones involved in glucose metabolism, satiety and energy expenditure have not been previously reported in DS. Two siblings with genetically confirmed DS and extremely low weight underwent a mixed meal (MM) test where pancreatic hormones insulin, C-peptide, glucagon, active amylin, pancreatic polypeptide (PP) as well as gut hormones active glucagon-like peptide 1 (GLP-1), glucose-dependent insulinotropic peptide (GIP), ghrelin, peptide YY (PYY) and leptin were analyzed using a Multiplex assay. Results were compared to those of 2 pediatric controls. As expected, concentrations of insulin, C-peptide and amylin were very high in DS cases. The serum glucagon concentration was undetectable at the time of hypoglycemia. GIPs concentrations were lower in the DS, however, this was not mimicked by the other incretin, GLP-1. Ghrelin concentrations were mainly undetectable (<13.7 pg/mL) in all participants. DS cases had higher PYY and dampened PP concentrations. Leptin levels remained completely undetectable (<137.0 pg/mL). Patients with DS have extremely high amylin levels, completely undetectable serum glucagon and leptin levels with abnormal satiety regulating hormone PP with a relatively normal ghrelin response during a MM test. The low serum GIP might be acting as physiological brake on insulin secretion. The undetectable serum leptin levels suggest the potential of using leptin analogues as therapy for DS patients.

Dual direction CRISPR transcriptional regulation screening uncovers gene networks driving drug resistance

Pooled CRISPR–Cas9 knock out screens provide a valuable addition to the methods available for novel drug target identification and validation. However, where gene editing is targeted to amplified loci, the resulting multiple DNA cleavage events can be a cause of false positive hit identification. The generation of nuclease deficient versions of Cas9 has enabled the development of two additional techniques – CRISPR interference (CRISPRi) and CRISPR activation (CRISPRa) – that enable the repression or overexpression, respectively, of target genes. Here we report the first direct combination of all three approaches (CRISPRko, CRISPRi and CRISPRa) in the context of genome-wide screens to identify components that influence resistance and sensitivity to the BRAF inhibitor, vemurafenib. The pairing of both loss- and gain-of-function datasets reveals complex gene networks which control drug response and illustrates how such data can add substantial confidence to target identification and validation analyses.

Educating medical students in oral health care: current curriculum and future needs of institutions in Malaysia and Australia

Poor oral health has been associated with compromised general health and quality of life. To promote comprehensive patient management, the role of medical professionals in oral health maintenance is compelling, thus indicating the need for educational preparation in this area of practice. This study aimed to determine the extent of training in oral health in Malaysian and Australian medical schools. An audio-recorded semi-structured phone interview involving Academic Programme Directors in Malaysian (n = 9, response rate=81.8%) and Australian (n = 7, response rate = 35.0%) medical schools was conducted during the 2014/2015 and 2014 academic years, respectively. Qualitative data was analysed via thematic analysis, involving coding and grouping into emerging themes. Quantitative data were measured for frequencies. It was found that medical schools in Malaysia and Australia offered limited teaching of various oral health-related components that were mostly integrated throughout the curriculum, in the absence of structured learning objectives, teaching methodologies and assessment approaches. Barriers to providing oral health education included having insufficient expertise and overloaded curriculum. As medical educators demonstrated support for oral health education, collaboration amongst various stakeholders is integral to developing a well-structured curriculum and practice guidelines on oral health management involving medical professionals.

Piezoresistive Effect in Plasma-Doping of Graphene Sheet for High-Performance Flexible Pressure Sensing Application

This paper presents a straightforward plasma treatment modification of graphene with an enhanced piezoresistive effect for the realization of a high-performance pressure sensor. The changes in the graphene in terms of its morphology, structure, chemical composition, and electrical properties after the NH₃/Ar plasma treatment were investigated in detail. Through a sufficient plasma treatment condition, our studies demonstrated that plasma-treated graphene sheet exhibits a significant increase in sensitivity by one order of magnitude compared to that of the unmodified graphene sheet. The plasma-doping introduced nitrogen (N) atoms inside the graphene structure and was found to play a significant role in enhancing the pressure sensing performance due to the tunneling behavior from the localized defects. The high sensitivity and good robustness demonstrated by the plasma-treated graphene sensor suggest a promising route for simple, low-cost, and ultrahigh resolution flexible sensors.

Piezoresistive Effect in Plasma-Doping of Graphene Sheet for High-Performance Flexible Pressure Sensing Application

This paper presents a straightforward plasma treatment modification of graphene with an enhanced piezoresistive effect for the realization of a high-performance pressure sensor. The changes in the graphene in terms of its morphology, structure, chemical composition, and electrical properties after the NH₃/Ar plasma treatment were investigated in detail. Through a sufficient plasma treatment condition, our studies demonstrated that plasma-treated graphene sheet exhibits a significant increase in sensitivity by one order of magnitude compared to that of the unmodified graphene sheet. The plasma-doping introduced nitrogen (N) atoms inside the graphene structure and was found to play a significant role in enhancing the pressure sensing performance due to the tunneling behavior from the localized defects. The high sensitivity and good robustness demonstrated by the plasma-treated graphene sensor suggest a promising route for simple, low-cost, and ultrahigh resolution flexible sensors.

Macrophage Activation Syndrome in Paediatric Rheumatic Diseases

Macrophage activation syndrome (MAS) is a potentially fatal complication of rheumatic disorders, which commonly occurs in systemic juvenile idiopathic arthritis (sJIA).This study was carried out with the aims of describing the clinical features, laboratory findings and outcomes of MAS associated with paediatric rheumatic diseases in the Department of Paediatrics, Bangabandhu Sheikh Mujib Medical University (BSMMU) and compare these results with previous studies on MAS. This retrospective study was conducted in the paediatric rheumatology wing of the Department of Paediatrics, Bangabandhu Sheikh Mujib Medical University (BSMMU), Dhaka, Bangladesh. Clinical and laboratory profile of all the diagnosed cases of MAS were analyzed from the medical records from January 2010 to July 2015. Among 10 MAS patients, 6 were female and 4 were male. Seven patients of systemic JIA, two patients of SLE and one patient with Kawasaki Disease developed MAS in their course of primary disease. Mean duration of primary disease prior to development of MAS was 2.9 years and mean age of onset was 9.1 years. High continued fever and new onset hepatosplenomegaly were the hallmark of the clinical presentation. White blood cell count and platelet count came down from the mean of 16.2 to 10.2×10⁹/L and 254 to 90×10⁹/L. Mean erythrocyte sedimentation rate was dropped from 56 to 29 mm/hr. Six patients had abnormal liver enzyme level (ALT) and 5 had evidence of coagulopathy (prolonged prothrombin time and APTT) at the onset of disease. Hyperferritinnemia were found in all the patients. Bone marrow study was done in 5 patients but features of hamophagocytosis were found only in 2 patients. All patients received intravenous steroid and 3 patients who did not respond to steroid received additional cyclosporine. Mortality rate was 30% in this series. Macrophage activation syndrome is a fatal complication of paediatric rheumatic diseases among which s-JIA was predominant. Early diagnosis and aggressive therapy is essential to reduce the morbidity and mortality of this illness.

Reaction Decoder Tool (RDT): extracting features from chemical reactions

Summary: Extracting chemical features like Atom–Atom Mapping (AAM), Bond Changes (BCs) and Reaction Centres from biochemical reactions helps us understand the chemical composition of enzymatic reactions. Reaction Decoder is a robust command line tool, which performs this task with high accuracy. It supports standard chemical input/output exchange formats i.e. RXN/SMILES, computes AAM, highlights BCs and creates images of the mapped reaction. This aids in the analysis of metabolic pathways and the ability to perform comparative studies of chemical reactions based on these features.

Availability and implementation: This software is implemented in Java, supported on Windows, Linux and Mac OSX, and freely available at https://github.com/asad/ReactionDecoder

Contact: asad@ebi.ac.uk or s9asad@gmail.com

Characterising Complex Enzyme Reaction Data

The relationship between enzyme-catalysed reactions and the Enzyme Commission (EC) number, the widely accepted classification scheme used to characterise enzyme activity, is complex and with the rapid increase in our knowledge of the reactions catalysed by enzymes needs revisiting. We present a manual and computational analysis to investigate this complexity and found that almost one-third of all known EC numbers are linked to more than one reaction in the secondary reaction databases (e.g., KEGG). Although this complexity is often resolved by defining generic, alternative and partial reactions, we have also found individual EC numbers with more than one reaction catalysing different types of bond changes. This analysis adds a new dimension to our understanding of enzyme function and might be useful for the accurate annotation of the function of enzymes and to study the changes in enzyme function during evolution.

The Classification and Evolution of Enzyme Function

Enzymes are the proteins responsible for the catalysis of life. Enzymes sharing a common ancestor as defined by sequence and structure similarity are grouped into families and superfamilies. The molecular function of enzymes is defined as their ability to catalyze biochemical reactions; it is manually classified by the Enzyme Commission and robust approaches to quantitatively compare catalytic reactions are just beginning to appear. Here, we present an overview of studies at the interface of the evolution and function of enzymes.

Correlation of hyperinsulinemia with hyperandrogenemia in primary infertile women with polycystic ovary syndrome

Polycystic ovary syndrome (PCOS) is the most common endocrinopathy among women of the reproductive age and is the most common form of anovulatory infertility. Hyperinsulinemia and hyperandrogenemia are the characteristic features of PCOS, but the association between hyperinsulinemia and hyperandrogenemia is not well established. To find out any causal association between Hyperinsulinemia and hyperandrogenemia, a retrospective study was done on primary infertile women suffering from PCOS in the department of Biochemistry, Bangabandhu Sheikh Mujib Medical University. A total of 80 subjects were selected, among them 60 were cases and 20 were controls. Depending on their body mass index, the cases were divide into two groups, obese (n=30) and non-obese (n=30). Age and BMI matched controls were taken for both age groups. Observations derived from the study suggested that hyperinsulinemia and hyperandrogenemia are characteristic features of PCOS but significant correlation was not found between hyperinsulinemia and hyperandrogenemia. However, we cannot negate any possible association between the two and thereby we recommend further study to be done with a larger sample size.

Poncet's disease (tubercular rheumatism) - a case report

Poncet's disease is a rare condition in childhood. It occurs due to immunological reaction to tubercular protein resulting in reactive arthritis and manifest with polyarthritis associated with features of active tuberculosis. We are reporting a case of Poncet's disease that was initially treated as a case of Juvenile Idiopathic Arthritis (JIA) without any improvement. The diagnosis was made clinically from history and physical findings with supportive radiological findings and confirmed by granulomatous changes on FNAC. Our patient improved dramatically after treatment with anti-tubercular drugs. Though very rare, Poncet's disease should be strongly considered in the differential diagnosis of fever and polyarthritis of obscure cause, especially in tubercular endemic countries like ours.

Panoramic radiography in evaluating the relationship of mandibular canal and impacted third molars in comparison with cone-beam computed tomography

This study evaluated the validity of panoramic radiography and cone beam computed tomography (CBCT) in the assessment of mandibular canal and impacted third molar. In this descriptive-analytical study, 58 mandibular third molars from 42 patients who showed a close relationship between impacted third molar and canal on panoramic radiographs were selected. They were then classified into seven radiographic markers in panoramic radiographs (superimposition, darkening of the root, interruption of the white lines, root narrowing, canal diversion, canal narrowing, and also closed distance in OPG <1mm). The groups of markers were further assessed with CBCT to see presence or absence of contact. The three most common markers seen in panoramic images are superimposition, interruption of white line and root darkening. In CBCT, superimposition marker always presented higher frequency of contact with canal compared to non-contact group. There are 31% of teeth presented with interruption of white lines and there are 29.3% of teeth presented with superimposition. About 55.6% and 35.3% of the impacted mandibular third molars which indicated interruption of white lines and superimposition also indicated contact in the CBCT respectively. Presence or absence of radiological sign in panoramic radiography was not properly predict a close relationship with third molar and it is suggested that in case of tooth-canal overlapping, the patient should be referred for CBCT assessment.

The evolution of enzyme function in the isomerases

The advent of computational approaches to measure functional similarity between enzymes adds a new dimension to existing evolutionary studies based on sequence and structure. This paper reviews research efforts aiming to understand the evolution of enzyme function in superfamilies, presenting a novel strategy to provide an overview of the evolution of enzymes belonging to an individual EC class, using the isomerases as an exemplar.

Exploring the biological and chemical complexity of the ligases

Using a novel method to map and cluster chemical reactions, we have re-examined the chemistry of the ligases [Enzyme Commission (EC) Class 6] and their associated protein families in detail. The type of bond formed by the ligase can be automatically extracted from the equation of the reaction, replicating the EC subclass division. However, this subclass division hides considerable complexities, especially for the C-N forming ligases, which fall into at least three distinct types. The lower levels of the EC classification for ligases are somewhat arbitrary in their definition and add little to understanding their chemistry or evolution. By comparing the multi-domain architecture of the enzymes and using sequence similarity networks, we examined the links between overall reaction and evolution of the ligases. These show that, whilst many enzymes that perform the same overall chemistry group together, both convergent (similar function, different ancestral lineage) and divergent (different function, common ancestor) evolution of function are observed. However, a common theme is that a single conserved domain (often the nucleoside triphosphate binding domain) is combined with ancillary domains that provide the variation in substrate binding and function.

Influence of platelet-rich plasma on dental implants. Osseointegration in well-controlled diabetic patients

The purpose of this study is to evaluate the effect of platelet-rich plasma (PRP) on the osseointegration of dental implants in diabetic patients. A split-mouth design was employed in all 14 patients, with each patient receiving two mini implants. A PRP-coated mini implant was installed in one quadrant as a trial and a plain mini implant was added in the opposite quadrant to serve as a control. Radiographic evaluation was done at 3, 6, and 9 weeks after implant placement. Radiographic density is measured at five points around the implants, repeatedly. Results showed no statistically significant difference between the two groups of implants. The minimally invasive mini implants successfully maintained integration at the end of 9 weeks. There were no cases of implant failure. The results of this study suggest that platelet-rich plasma implant coating has no significant effect in reducing the time for mini implant osseointegration in diabetic patients.

The EBI enzyme portal

The availability of comprehensive information about enzymes plays an important role in answering questions relevant to interdisciplinary fields such as biochemistry, enzymology, biofuels, bioengineering and drug discovery. At the EMBL European Bioinformatics Institute, we have developed an enzyme portal (http://www.ebi.ac.uk/enzymeportal) to provide this wealth of information on enzymes from multiple in-house resources addressing particular data classes: protein sequence and structure, reactions, pathways and small molecules. The fact that these data reside in separate databases makes information discovery cumbersome. The main goal of the portal is to simplify this process for end users.

Carpenter syndrome: a case report

Carpenter syndrome is a rare hereditary disorder known as Acrocephalopolysyndyctyly (ACPS) type II characterized by acrocephaly, facial dysmorphism, brachedyctyly, syndyctyly, preaxial polydyctyly, obesity, congenital heart disease, cryptorchidism, hypogenitalism, bony abnormalities and umbilical hernia. Carpenter syndrome is autosomal recessive disorder and prenatal diagnosis of this syndrome is possible by ultrasonogram during pregnancy. We reported a case of carpenter syndrome of 2.5 months old female infant of consanguineous parents who was admitted in the paediatric ward of Bangabandhu Sheikh Mujib Medical University (BSMMU) on 30th March 2010. She was diagnosed as a case of Carpenter syndrome having acrocephaly prominent ridge of sagital suture, polydactyly, syndyctyly on history, clinical examination findings and investigation reports.

MACiE: exploring the diversity of biochemical reactions

MACiE (which stands for Mechanism, Annotation and Classification in Enzymes) is a database of enzyme reaction mechanisms, and can be accessed from http://www.ebi.ac.uk/thornton-srv/databases/MACiE/. This article presents the release of Version 3 of MACiE, which not only extends the dataset to 335 entries, covering 182 of the EC sub-subclasses with a crystal structure available (∼90%), but also incorporates greater chemical and structural detail. This version of MACiE represents a shift in emphasis for new entries, from non-homologous representatives covering EC reaction space to enzymes with mechanisms of interest to our users and collaborators with a view to exploring the chemical diversity of life. We present new tools for exploring the data in MACiE and comparing entries as well as new analyses of the data and new searches, many of which can now be accessed via dedicated Perl scripts.

Mineral homeostasis in children with acute lymphoblastic leukemia before and after chemotherapy

A prospective study was carried out in the Bangabandhu Sheikh Mujib Medical University, Dhaka, Bangladesh to evaluate the pattern of mineral changes in children treated for acute lymphoblastic leukemia (ALL) before and after induction chemotherapy. A total number of 32 children aged 1-14 years of both sexes were evaluated. Serum calcium, phosphate, alkaline phosphatase, albumin and creatinine and urinary creatinine and calcium were estimated in cases and control. The mean calcium level at presentation and post induction was 9.50±1.48 mg/dl and 9.08±1.30 mg/dl. Serum phosphate was higher in preinduction mean of 4.83±2.71 mg/dl than post induction value of 4.75±1.38 mg/dl and it was statistically significant. Serum alkaline phosphatase was higher in the post induction period. It was 324.8±128.17 U/L in pre induction and 331.59±93.97 u/l in post induction period. It was not statistically significant. No statistically significant difference was found in pre and post induction urinary calcium and creatinine.

Acute lymphoblastic leukaemia presenting with severe hypercalcaemia

Acute lymphoblastic leukaemia (ALL) is the most common malignancy in children. Usually ALL children present with pallor, fever, bleeding, infection, lymphadenopathy and hapatosplenomegaly. Very rarely ALL patients may present with hypercalcaemia and osteolytic lesions. A five year old boy was referred and transferred to the paediatric ward of Bangabandhu Sheikh Mujib Medical University, Dhaka with the complaints of pain in the hip joint, generalized pain all over the body and very high calcium level. He was severely pale, the total leukocyte count was normal with normal distribution. Platelet count was also normal. There were some atypical lymphocytes. Radiology showed extensive osteolytic lesions. Considering all these findings, a bone marrow study was done, which was compatible with ALL. Flow-cytometry was also done and it confirmed the diagnosis as common ALL.

Effect of intragastric administration of crude aqueous leaf extract of Anacardium occidentale on gastric acid secretion in rats

The effect of an aqueous leaf extract ofAnacardium occidentale on gastric acid secretion was tested in rats. Twenty (20) Wistar albino rats were used for the gastric acid assay experiment. The rats were divided into 2 groups of 10 each. Gastric acid output was determined by continuous perfusion of rat stomach in urethane anesthetized rats. Control gastric acid output was obtained using 0.9% sodium chloride as perfusate and extract induced gastric acid output was obtained by perfusion with 0.1% solution of Anacardium occidentale Intragastric administration of the extract caused significant increase in mean gastric output (P <0.05). Atropine (5μg/100g,) lM and Cimetidine (5mg/100g), IM. significantly inhibited the extract induced gastric acid secretion via muscarinic and histaminic receptors respectively. Our findings showed that the use of the plant extract as a single anti-gastric ulcer therapy may not involve lowering of acid secretions rather it may be due to its anti Helicobacter pylori effect.

Hexamethonium produces both twitch and tetanic depression without fade in common African toad (Bufo regularis)

The study was designed to investigate the nature of the cholinoceptors at the sciatic nerve-gastrocnemius muscle junction of the common African toad (Bufo regularis). Using myographic technique, the twitch properties of the sciatic-gastrocnemius muscle preparation of the common African toad was studied. Both the twitch height and peak tetanic height were measured as a percentage of control. Hexamethonium at a concentration of 0.1 mM significantly [P<0.05] reduced the mean twitch height from 2.62 cm to 1.0 cm and mean peak tetanic height from 5.38 cm to 4.32 cm. Hexamethonium, however does not produce tetanic fade at the same concentration. We hypothesized that the cholinoceptors of the neuromuscular junction of the common African toad (Bufo regularis) resemble the developing synapse of African clawed toad (Xenopus laevis) and may contain muscarinic M1 autoreceptors at the pre juntional membrane.

Effect of the human leukocyte antigen HLA-DRB1 and anti-cyclic citrullinated peptide on the outcome of rheumatoid arthritis patients

Our objective was to determine whether the presence of the human leukocyte antigen HLA-DRB1 locus is associated with production of anti-cyclic citrullinated peptide antibodies (anti-CCP Abs) and to what extent they are associated with increased susceptibility to and severity of rheumatoid arthritis (RA) in Egyptian patients. Twenty-nine RA patients gave informed consent to participate in a case-control study that was approved by the Ain Shams University Medical Ethics Committee. RA disease activity and severity were determined using the simplified disease activity index and Larsen scores, respectively. We used a wide scale national study on the pattern of HLA typing in normal Egyptians as a control study. Anti-CCP Abs and HLA-DRB1 typing were determined for all subjects. The alleles most strongly associated with RA were HLA-DRB1 [*01 , *04 and *06] (41.4%). RA patients with serum anti-CCP Ab titers above 60 U/mL had a significantly higher frequency of HLA-DRB1*01 (58.3%) and HLA-DRB1*04 alleles (83.3%). Significant positive correlations were found between serum and synovial anti-CCP Ab titer, RA disease activity, and severity (r = 0.87, 0.66 and 0.63, respectively; P < 0.05). HLA-DRB1 SE+ alleles [*01 and *04] were highly expressed among Egyptian RA patients. The presence of these alleles was associated with higher anti-CCP Ab titer, active and severe RA disease. Early determination of HLA-DRB1 SE+ alleles and serum anti-CCP Ab could facilitate the prediction of the clinical course and prognosis of RA when first evaluated leading to better disease control.

An action research on promotion of healthy ageing and risk reduction of chronic disease: a need assessment study among rural elderly Malays, care givers and health professionals

OBJECTIVE

Prior to the development of a healthy ageing and risk reduction of chronic diseases intervention package for older people in Malaysia, a need assessment study was conducted to identify nutritional knowledge status and information needs, as part of an action research process.

DESIGN

A cross sectional study was conducted among 267 elderly people, 54 care givers and 66 health professionals in two rural areas of Peninsular of Malaysia (i.e Sabak Bernam, Selangor and Kuala Pilah, Negeri Sembilan). Information on nutritional knowledge was obtained from an interview based questionnaire for older subjects and caregiver and through self administered questionnaire from the health professionals. Anthropometric and functional measurements were also conducted among elderly subjects.

RESULTS

It was found that the elderly subjects had poor nutritional knowledge with 43.8% of them classified as having unsatisfactory nutritional knowledge, followed by moderately satisfactory (33.7%), very unsatisfactory (15.7%) and good (6.7%). Talks, counselling sessions with health professionals and electronic media such as television and radio were the most preferred nutrition education sources among elderly subjects and their care givers. The majority of health professionals studied (98.5%) had good nutritional knowledge. Although most of them (93.6%) were involved in management of the elderly, only 45.5% incorporated nutritional information component in this activity. Most of the health professionals used the guidelines for management of elderly patients (63.6%). However, nutritional knowledge was very minimal in these guidelines. Multiple regression analysis indicated that 'level education', involvement in 'social activities', presence of 'hearing problems', the Instrumental Activities of Daily Living (IADL) score, having previous 'nutritional information' and 'participation in healthy eating programme' were the major predictors of nutritional knowledge score among elderly subjects.

CONCLUSION

Based on the above findings it is thus, imperative that an appropriate nutritional intervention package and programme be developed so as to help improve nutritional knowledge and subsequently the nutritional status of the rural elderly Malays.

Small Molecule Subgraph Detector (SMSD) toolkit

BACKGROUND

Finding one small molecule (query) in a large target library is a challenging task in computational chemistry. Although several heuristic approaches are available using fragment-based chemical similarity searches, they fail to identify exact atom-bond equivalence between the query and target molecules and thus cannot be applied to complex chemical similarity searches, such as searching a complete or partial metabolic pathway.In this paper we present a new Maximum Common Subgraph (MCS) tool: SMSD (Small Molecule Subgraph Detector) to overcome the issues with current heuristic approaches to small molecule similarity searches. The MCS search implemented in SMSD incorporates chemical knowledge (atom type match with bond sensitive and insensitive information) while searching molecular similarity. We also propose a novel method by which solutions obtained by each MCS run can be ranked using chemical filters such as stereochemistry, bond energy, etc.

RESULTS

In order to benchmark and test the tool, we performed a 50,000 pair-wise comparison between KEGG ligands and PDB HET Group atoms. In both cases the SMSD was shown to be more efficient than the widely used MCS module implemented in the Chemistry Development Kit (CDK) in generating MCS solutions from our test cases.

CONCLUSION

Presently this tool can be applied to various areas of bioinformatics and chemo-informatics for finding exhaustive MCS matches. For example, it can be used to analyse metabolic networks by mapping the atoms between reactants and products involved in reactions. It can also be used to detect the MCS/substructure searches in small molecules reported by metabolome experiments, as well as in the screening of drug-like compounds with similar substructures.Thus, we present a robust tool that can be used for multiple applications, including the discovery of new drug molecules. This tool is freely available on http://www.ebi.ac.uk/thornton-srv/software/SMSD/

OIE guidelines on dog population control

At the 73rd General Session the OIE decided to develop guidance for Members on humane methods for the control of stray animal populations. In 2006, an ad hoc Group was convened under the leadership of the OIE Permanent Animal Welfare Working Group. With valuable assistance from the OIE Collaborating Centre on Animal Welfare, a Questionnaire was developed and sent to OIE Members, of which 81 countries submitted responses. In light of this information, the ad hoc Group prepared a first draft report, which notes the importance of controlling stray dog populations to help prevent zoonotic diseases and non-disease related nuisances to society and the environment. In choosing the preferred method of control, the risks to operators must be taken into account, as well as religious, cultural and economic contexts of the country concerned. Depending on the situation, methods requiring individual animal restraint or methods for use at a distance may be recommended. While activities that aim to physically reduce the numbers of stray dogs are important, achievement of the long term goals of dog population control and avoidance of risks to human health depends on the education of dog owners and the general public as to their responsibilities. The draft report notes that sub-national jurisdictions are often those responsible for the control of stray dog populations. The key role played by non-governmental organisations in stray dog management in many countries is acknowledged. The draft report emphasises that the close involvement of veterinarians and of official Veterinary Services, working in collaboration with public health authorities, is necessary to realise long term goals.