Actin associates with actively elongating genes and binds directly to the Cdk9 subunit of P-TEFb

Nuclear actin has been demonstrated to be essential for optimal transcription, but the molecular mechanisms and direct binding partner for actin in the RNA polymerase complex have remained unknown. By using purified proteins in a variety of biochemical assays, we demonstrate a direct and specific interaction between monomeric actin and Cdk9, the kinase subunit of the positive transcription elongation factor b required for RNA polymerase II pause-release. This interaction efficiently prevents actin polymerization, is not dependent on kinase activity of Cdk9, and is not involved with releasing positive transcription elongation factor b from its inhibitor 7SK snRNP complex. Supporting the specific role for actin in the elongation phase of transcription, chromatin immunoprecipitation followed by deep sequencing (ChIP-seq) reveals that actin interacts with genes only upon their active transcription elongation. This study therefore provides novel insights into the mechanisms by which actin facilitates the transcription process.

Acetazolamide-responsive myotonia with a novel Ile239Thr mutation in SCN4A gene: a case report

Introduction and importance

Sodium channel myotonia (SCM) belongs to the group of sodium channelopathies with mutations involving SCN4A gene. The main feature of sodium channel myotonia is pure myotonia without episodes of weakness or paralysis. One of the sodium channel myotonia has been classified as acetazolamide-responsive myotonia because of the effectiveness of acetazolamide as an antimyotonic drug.

Case presentation

The child presented with generalized muscle hypertrophy and stiffness involving arms, thighs, calves, chest, and back muscles with unusually prominent trapezius muscle. The parents described the warm-up phenomenon as an improvement in stiffness as the day passes and with repetitive action. Percussion myotonia was illustrated in the thenar eminence and trapezius muscle. Characteristic 'dive-bomber' sound was present in electromyography, and whole-exome sequencing revealed a novel Ile239Thr mutation in the SCN4A gene. Acetazolamide was prescribed for the condition, and regular follow-up shows an excellent clinical response.

Clinical discussion

This case presents a pure myotonic phenotype without episodes of weakness or paralysis. Generalized myotonia with muscle hypertrophy and demonstrating warm-up phenomenon resembles myotonia congenita (a chloride channelopathy). However, genetic analysis revealed a novel Ile239Thr mutation involving SCN4A gene indicating this case to be a sodium channelopathy.

Conclusion

This case limelight sodium channel myotonia with a novel Ile239Thr mutation in SCN4A gene that phenotypically resembles myotonia congenita but genetically belongs to sodium channelopathy highlighting the poor correlation between genotypes and phenotypes in non-dystrophic myotonia. Acetazolamide can be a safe and cost-effective antimyotonic drug in sodium channel myotonia.

Factors affecting willingness to participate in vaccine clinical trials in an underdeveloped country: perspective from Nepal

Due to the inherent complex nature of clinical trials, individual’s willingness to participate and hence, enrollment in a clinical trial maybe challenging. When it comes to vaccine clinical trial in children, informed consent needs to be secured from the parents or legally acceptable representatives (LARs). Some of the factors which contribute to hesitancy in taking part in clinical trials are based on the level of education, living standards, part of the world they live, associated burden of disease, fear of different procedures in clinical trial, side effects, limited understanding, limited time, and mistrust with Investigational product. This study included 201 parents/LARs, who approached Kanti Children Hospital site in Kathmandu with the interest to get their children enrolled in a vaccine clinical trial with objectives of describing the reasons for agreeing or disagreeing to participate in the vaccine clinical trial, factors affecting decision making, and finding the major concerns of parents/LARs. The acceptance for the study vaccine was 136 (67.7%) whereas denial was 65 (32.3%). This study showed that age, education level, family structure, advice from family and friends, and medical guidance play important roles in willingness of parents to get their child enrolled in the trial. If a proper counseling is done, fear of blood sampling is not a big factor which is contrary to the belief among clinical researchers. Safety of vaccine, frequency of injections, and cost of vaccine were the main concerns of the parents, which need to be addressed extensively while planning for any clinical trial in children.

Relationship Between Gross Motor Function and Nutritional Status in Children with Cerebral Palsy attending a Tertiary Children’s Hospital of Nepal

Introduction: Malnutrition is a common problem in children with cerebral palsy and their management outcome is not satisfactory unless we address their nutritional aspect. The present study aims to find the relationship between gross motor function and nutritional status in these children by comparing the proportion of stunting, wasting and under-weight between the various levels of gross motor function. Methods: Our study was across- sectional study conducted on 82 cases of cerebral palsy between one to five years of age visiting Kanti Children’s Hospital, Kathmandu, Nepal from May 2017 to September 2018. Their level of gross motor function was ascertained by applying the Gross Motor Function Classification System (GMFCS) and anthropometry was done using standard methods. On the basis of their motor function, the children were divided into two categories: those with poorer motor function who had poor self-mobility even with assistance (GMFCS level 4 and 5) and those with better motor function who had self-mobility with various degrees of assistance (GMFCS level 1, 2 and 3). Wasting, stunting and under-weight were compared between the two categories and odds ratio with 95% confidence interval was estimated for malnutrition. Results: The children belonging to poorer motor function were more likely to be underweight (Odds ratio 3.41; CI 1.36-8.52; p-value 0.008) and stunted (Odds ratio 3.9; CI 1.47-10.53; p-value 0.048) than those with better motor function. Conclusions: Children with poorer motor function are more likely to develop malnutrition (Specially stunting) than those with better motor function indicating that chronic form of malnutrition is more common in these children.

Emerging Properties and Functions of Actin and Actin Filaments Inside the Nucleus

Recent years have provided considerable insights into the dynamic nature of the cell nucleus, which is constantly reorganizing its genome, controlling its size and shape, as well as spatiotemporally orchestrating chromatin remodeling and transcription. Remarkably, it has become clear that the ancient and highly conserved cytoskeletal protein actin plays a crucial part in these processes. However, the underlying mechanisms, regulations, and properties of actin functions inside the nucleus are still not well understood. Here we summarize the diverse and distinct roles of monomeric and filamentous actin as well as the emerging roles for actin dynamics inside the nuclear compartment for genome organization and nuclear architecture.

Recurrent Pneumonias and Bronchiectasis - Is it an Immunodeficiency Disorder? - A Case Report

Common Variable Immunodeficiency (CVID) is a form of primary immunodeficiency disorder characterised by hypogammaglobulinemia and recurrent sino-pulmonary infections. Its diagnosis is based on the presence of low serum IgG (< 2 SD below normal for age) with or without low IgA/ IgM levels and presentation beyond two years of age. These children also have disorders of autoimmunity with majority of them presenting as autoimmune cytopenias, predominantly thrombocytopenia and some having anaemia and neutropenias. Here we report a nine years old boy with past history of recurrent pneumonia, presenting this episode with fungal pneumonia, thrombocytopenia and anaemia eventually diagnosed as CVID.

Grey water treatment in stacked multi-layer reactors with passive aeration and particle trapping

When adequately treated, grey water represents a potent alternative water resource, as it constitutes a large proportion of household wastewater. The objective of this paper was to test a full scale version of a novel compact grey water treatment technology, based on passive aeration and particle trapping in multiple layers. Using a modified dual porosity filtration technology, grey water from a public bath was passed through a stack of eight reactors, each 0.75 m × 0.55 × 0.22 m, serially connected for gravity driven flow from top to bottom in a zig-zag pattern. The topmost reactor served as pre-filter for removal of hair and other larger debris. The lower seven reactors facilitated degradation of bulk organic contaminants in biofilm established on a stack of five fibrous polyamide nets, and trapping of particles by sedimentation on five interlaid corrugated plastic plates. By operating the reactors in a time-controlled batch-mode, the corrugated plates further served to trap air and thus ensure passive aeration of the subsequent batch. The production rate was 1.2 m³/d and the hydraulic retention time 2 h, at an aerial footprint of 0.4 m², excluding storage tanks. After two weeks of initialization, a biofilm had established and the system was monitored for additionally three weeks. Significantly improved effluent quality was obtained as measured from reductions in turbidity (95%), total suspended solids (94%), chemical oxygen demand (87%), and microbiological parameters (55-98%), and from stable level of dissolved oxygen in effluent of 3.5 mg/L. Future optimization includes custom-made reactors for maximizing production capacity, improved removal of total N and total P, and addition of final disinfection.

Nuclear actin interactome analysis links actin to KAT14 histone acetyl transferase and mRNA splicing

In addition to its essential functions within the cytoskeleton, actin also localizes to the cell nucleus, where it is linked to many important nuclear processes from gene expression to maintenance of genomic integrity. However, the molecular mechanisms by which actin operates in the nucleus remain poorly understood. Here, we have used two complementary mass spectrometry (MS) techniques, AP-MS and BioID, to identify binding partners for nuclear actin. Common high-confidence interactions highlight the role of actin in chromatin-remodeling complexes and identify the histone-modifying complex human Ada-Two-A-containing (hATAC) as a novel actin-containing nuclear complex. Actin binds directly to the hATAC subunit KAT14, and modulates its histone acetyl transferase activity in vitro and in cells. Transient interactions detected through BioID link actin to several steps of transcription as well as to RNA processing. Alterations in nuclear actin levels disturb alternative splicing in minigene assays, likely by affecting the transcription elongation rate. This interactome analysis thus identifies both novel direct binding partners and functional roles for nuclear actin, as well as forms a platform for further mechanistic studies on how actin operates during essential nuclear processes.This article has an associated First Person interview with the first author of the paper.

Nuclear Actin Is Required for Transcription during Drosophila Oogenesis

Actin has been linked to processes spanning the whole gene expression cascade, from regulating specific transcription factors, such as myocardin-related transcription factor, to chromatin remodeling and RNA polymerase function. However, whether actin controls the transcription of only specific genes or has a global role in gene expression has remained elusive. Our genome-wide analysis reveals, for the first time, that actin interacts with essentially all transcribed genes in Drosophila ovaries. Actin co-occupies the majority of gene promoters together with Pol II, and on highly expressed genes, these two proteins also associate with gene bodies. Mechanistically, actin is required for Pol II recruitment to gene bodies, and manipulation of nuclear transport factors for actin leads to the decreased expression of eggshell genes. Collectively, these results uncover a global role for actin in transcription and demonstrate the in vivo importance of balanced nucleocytoplasmic shuttling of actin in the transcriptional control of a developmental process.

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Genome-wide analysis shows actin on all transcribed genes

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Actin binds with RNA polymerase II near transcription start sites of most genes

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On highly expressed genes, actin is also found on the gene bodies

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Nuclear transport of actin is required for transcription during fly development

Predicting deaths in a resource-limited neonatal intensive care unit in Nepal

Background

This study aimed to determine whether the Neonatal Acute Physiology (SNAP) scoring system (SNAP II) and with perinatal extension (SNAP II PE) can be used to predict neonatal deaths in a resource-limited neonatal intensive care unit in Nepal.

Methods

A prospective observational study was conducted in a neonatal intensive care unit (NICU) of Kanti Children's Hospital in Kathmandu, Nepal. Data required for the SNAP II and SNAP II PE scores were collected. The relationships between the SNAP II and SNAP II PE scores and neonatal mortality were analyzed.

Results

There were 135 neonates admitted during the 6 month study period, of whom 126 met the inclusion criteria. Of these 126 neonates, 29 (23.0%) died. Mortality was 83% (5/6) when SNAP II was >40, and 66.7% (6/9) when SNAP II PE was >50. A SNAP II score of ≥12 had a sensitivity of 75.9%, and specificity of 73.2% for predicting mortality, and a SNAP II PE score of ≥14 had a sensitivity of 82.8% and specificity of 67.0% for it.

Conclusions

SNAP II and SNAP II PE scoring of neonates can be used to predict prognosis of neonates in resource-limited NICUs in Nepal.

Study of Pre-disposing Factors of Acute Exacerbation of Chronic Obstructive Pulmonary Disease and Antibiotic Prescribing Pattern with Reference to Antibiotic Sensitivity Test

Background Chronic Obstructive Pulmonary Disease (COPD) affects about 329 million people worldwide, which is nearly 5% of the entire global population. In the context of Nepal, COPD accounts for 43% of the non-communicable disease burden and 2.56% of hospitalizations. Various pre-disposing factors like bacterial, viral, fungal, smoking, occupational exposures and genetic factors have been proposed to precipitate COPD and its exacerbation though, the definitive pre-disposing factors and factors related to acute exacerbation have not been determined in the context of Nepal.Objective To find out the pre-disposing factors and the related causative agents for COPD.Method A cross sectional study was conducted in a tertiary care hospital. Patients of all age group who were diagnosed as COPD and admitted in the hospital were included in this study. Patients were interviewed using structured questionnaire. The socio-demographic data including personal and medical history were recorded from those participants. In addition, sputum from those patients was sent for culture to investigate the possible responsible pathogens as well as its antibiotic sensitivity pattern.Result A total of 150 patients having Acute Exacerbation of Chronic Obstructive Pulmonary Disease (AECOPD) who have admitted from either emergency or out-patient department of the hospital were included in this study. Among the total number of patients, more than half of them were female (n=82). In addition, analysis of occupations shows that most of them were either farmer (36.0%) or housewife (30.7%). In total studied patients (n=150), most of them were using traditional firewood (83%) for cooking purpose and majority of patients (91%) were smokers. Most of the sputum samples show growth of gram-positive cocci (26.7%) and gram negative bacilli (27.5%). Considering the overall sensitivity pattern, the higher sensitivity was recorded for Co-trimoxazole and Ciprofloxacin while higher rate of resistance was noted for Penicillin group of drugs. The most widely used antibiotics were found to be Cephalosporin group of drugs (68%).Conclusion The present study revealed that the case of COPD is more in female and the commonest pre-disposing factor is found to be smoke/firewood. Cephalosporin group of drugs is the most commonly prescribed drug.

Variation in the insertion of the latissimus dorsi & its clinical importance

The latissimus dorsi is the larger, flat, dorso-lateral muscle on the trunk, posterior to the arm, and partly covered by the trapezius on its median dorsal region. Origin of the latissimus dorsi is from spinous processes of thoracic T7-T12, thoracolumbar fascia, iliac crest and inferior 3 or 4 ribs, inferior angle of scapula and insertion on floor of intertubercular groove of the humerus. We have studied 50 cadavers in the different medical colleges in which we found 2% case of anterior and posterior slip of the muscle fibers with their extension up to the pectoralis major and teres major respectively. Usually, latissimus dorsi involve in extension, adduction, transverse extension also known as horizontal abduction, flexion from an extended position, and internal rotation of the shoulder joint. It also has a synergistic role in extension and lateral flexion of the lumbar spine. The latissimus dorsi may be used for the tendon graft surgeries. Tight latissimus dorsi has been shown to be one cause of chronic shoulder pain and chronic back pain. Because the latissimus dorsi connects the spine to the humerus, tightness in this muscle can manifest as either sub-optimal glenohumeral joint function (which leads to chronic shoulder pain) or tendinitis in the tendinous fasciae connecting the latissimus dorsi to the thoracic and lumbar spine. Latissimus dorsi used for pedicle transplant rotator cuff repair reconstruction of breast, face, scalp and cranium defect. The extra slip of the latissimus dorsi may puzzle any transplant operations. We as anatomist discuss the clinical implication of the extra slip of latissimus dorsi.

Is Antimicrobial Resistance Pattern of Enteric Fever Changing in Kathmandu Valley?

Introduction: Enteric fever is a public health problem in developing countries including Nepal. Antimicrobial sensitivity pattern of Salmonella sp causing enteric fever is changing over time and also differs according to geographical location. Periodic surveillance of antimicrobial resistance of Salmonella sp is mandatory for management of enteric fever rationally. The objective of this study was to analyze the resistance pattern of Salmonella sp to commonly used antimicrobials. Materials and Methods: This was a retrospective study undertaken reviewing the records of blood isolates of Salmonella sp over one year period at Kanti Children’s Hospital, Nepal. Antimicrobial sensitivity testing was done following Kirby Bauer’s disk diffusion technique using Muller Hinton agar. Results: Salmonella typhi was found to be 100% resistance to ampicillin and resistance to nalidixic acid and ciprofloxacin was also high. The resistance to chloramphenicol and ofloxacin was low. No resistance was found to amoxicillin, ceftriaxone, cefotaxime and amikacin. However, among the sensitive isolates of Salmonella typhi intermediate sensitivity to ceftriaxone and ceftazidime was reported to be high. Among the isolates of S paratyphi A, the resistance to nalidixic acid was 100% followed by 75% to ciprofloxacin. No resistance was found to chloramphenicol, ceftriaxone, cefixime, amikacin and low resistance to amoxicillin and ofloxacin. Among the sensitive isolates of S paratyphi A, majority of them were only moderately sensitive to cefotaxime and ceftazidime and about 1/3 of the organisms had only intermediate sensitivity to ceftriaxone. Conclusiion: Commonly used parenteral third generation cephalosporins, first line drugs like chloramphenicol and amoxicillin and ofloxacin among fluoroquinolones were found to be effective in vitro in treating enteric fever. However, Salmonella typhi was found to be highly resistant to the most frequently used drugs like ciprofloxacin and cefixime and Salmonella paratyphi A to ciprofloxacin. A comparative chart of antimicrobial sensitivity of enteric fever in children over 10 year period from different hospitals of Kathmandu valley is also presented in the study. DOI: http://dx.doi.org/10.3126/jnps.v32i3.6625 J. Nepal Paediatr. SocVol.32(3) 2012 221-228

Prevalence of Salmonella typhi and paratyphi infection in children: a hospital based study

The purpose of this study was to find out the prevalence and antibiotic sensitivity pattern of Salmonella typhi and paratyphi isolated from children presenting with fever at Kanti Children's Hospital in Kathmandu, Nepal. A total of 9,856 blood samples collected for culture during one year period (April 2007 to March 2008) were included in the study. Out of total, 235 (2.0%) were positive for S. typhi and paratyphi A. Of the total positive, 195 (83.0%) were S. typhi and 40 (17.0%) were S. paratyphi A. The growth positive rate in two genders (M: 53.2% and F: 46.8%) was not significant (P > 0.05). Over two-third of cases were clustered in the age-group of 1-10 years. The occurrence of infections was common in summer months (rainy season). S. typhi was found to be most sensitive to cefotaxime (100.0%) followed by ceftriaxone (98.9%), ofloxacin (93.5%), cotrimoxazole (93.5%) and chloramphenicol (93.2%) and was least sensitive to amoxyccilin (66.7%) followed by ciprofloxacin (86.6%). S. paratyphi also was found to be most sensitive to cefotaxime (100.0%), followed by ceftriaxone (97.4%), cotrimoxazole (97.1%) and chloramphenicol (92.5%) and was least sensitive to amoxycillin (15.0%) followed by ciprofloxacin (51.3%) and ofloxacin (70.3%).