Development, validation and application of single molecule molecular inversion probe based novel integrated genetic screening method for 29 common lysosomal storage disorders in India

BACKGROUND

Current clinical diagnosis pathway for lysosomal storage disorders (LSDs) involves sequential biochemical enzymatic tests followed by DNA sequencing, which is iterative, has low diagnostic yield and is costly due to overlapping clinical presentations. Here, we describe a novel low-cost and high-throughput sequencing assay using single-molecule molecular inversion probes (smMIPs) to screen for causative single nucleotide variants (SNVs) and copy number variants (CNVs) in genes associated with 29 common LSDs in India.

RESULTS

903 smMIPs were designed to target exon and exon-intron boundaries of targeted genes (n = 23; 53.7 kb of the human genome) and were equimolarly pooled to create a sequencing library. After extensive validation in a cohort of 50 patients, we screened 300 patients with either biochemical diagnosis (n = 187) or clinical suspicion (n = 113) of LSDs. A diagnostic yield of 83.4% was observed in patients with prior biochemical diagnosis of LSD. Furthermore, diagnostic yield of 73.9% (n = 54/73) was observed in patients with high clinical suspicion of LSD in contrast with 2.4% (n = 1/40) in patients with low clinical suspicion of LSD. In addition to detecting SNVs, the assay could detect single and multi-exon copy number variants with high confidence. Critically, Niemann-Pick disease type C and neuronal ceroid lipofuscinosis-6 diseases for which biochemical testing is unavailable, could be diagnosed using our assay. Lastly, we observed a non-inferior performance of the assay in DNA extracted from dried blood spots in comparison with whole blood.

CONCLUSION

We developed a flexible and scalable assay to reliably detect genetic causes of 29 common LSDs in India. The assay consolidates the detection of multiple variant types in multiple sample types while having improved diagnostic yield at same or lower cost compared to current clinical paradigm.

Lipoprotein glomerulopathy: a rare cause of steroid-resistant nephrotic syndrome in a child

Lipoprotein glomerulopathy (LPG) is a rare condition of renal lipidosis characterized by lipoprotein thrombi in glomeruli, an abnormal plasma lipoprotein profile, and a marked increase in serum apolipoprotein E (apo E) levels. It is a monogenic disorder with autosomal dominant inheritance and the average age of presentation is 32 years (4-69 years). It is rare in children. The presentation can be nephrotic syndrome, hematuria, or progressive renal failure. Here we report the first described case of LPG in an Indian 7.5-year-old boy who presented with steroid-resistant nephrotic syndrome with normal renal function. A renal biopsy was suggestive of lipoprotein glomerulopathy. The detection of a pathogenic variant in apo E, Kyoto type, by exome sequencing, confirmed the diagnosis of lipoprotein glomerulopathy. Complete response was achieved with Angiotensin-converting Enzyme inhibitor and fenofibrates.

Geometry-driven carrier extraction enhancement in photovoltaic cells based on arrays of subwavelength light funnels

Texturing the front surface of thin film photovoltaic cells with ordered or disordered arrangements of subwavelength structures is beneficial in terms of efficient light harvesting as well as efficient carrier extraction. Previous studies demonstrated efficient broadband absorption of solar radiation with surface arrays of subwavelength inverted cones (light funnels - LFs). In the current work, we use three-dimensional finite-difference time-domain electromagnetic calculations as well as three-dimensional device calculations to examine carrier extraction from photovoltaic cells that are composed of LF arrays on top of underlying substrates. For the selected geometry under examination, we show a broadband absorption enhancement of 14% for the LF photovoltaic cell compared with a cell based on the respective optically optimized nanopillar arrays. However, we show that the nominal power conversion efficiency is 60% higher in the LF cell which is due to the enhancement of both open-circuit voltage and short-circuit current. The higher open-circuit voltage in the LF cell is due to the higher injection of photocarriers, and the higher short-circuit current is a result of the unique LF geometry that supports efficient carrier extraction due to the naturally occurring gradients of the quasi-Fermi levels and minority carrier conductivity that allow for enhanced contact selectivity. We believe that this work paves the way towards a new approach for carrier collection in photonic devices for energy applications.

Meta-analysis of classical swine fever prevalence in pigs in India: A 5-year study

Aim:

The aim of the study was to determine the overall prevalence of classical swine fever (CSF) in pigs in India, through a systematic review and meta-analysis of published data.

Materials and Methods:

Consortium for e-Resources in Agriculture, India, Google Scholar, PubMed, annual reports of All India Coordinated Research Project on Animal Disease Monitoring and Surveillance, and All India Animal Disease database of NIVEDI (NADRES) were used for searching and retrieval of CSF prevalence data (seroprevalence, virus antigen, and virus nucleic acid detection) in India using a search strategy combining keywords and related database-specific subject terms from January 2011 to December 2015 in English only.

Results:

A total of 22 data reports containing 6,158 samples size from 18 states of India were used for the quantitative synthesis, and overall 37% (95% confidence interval [CI]=0.24, 0.51) CSF prevalence in India was estimated. The data were classified into 4 different geographical zones of the country: 20% (95% CI=0.05, 0.55), 31% (95% CI=0.18, 0.47), 55% (95% CI=0.32, 0.76), and 34% (95% CI=0.14, 0.62). CSF prevalence was estimated in northern, eastern, western, and southern regions, respectively.

Conclusion:

This study indicates that overall prevalence of CSF in India is much lower than individual published reports.

Assessment of nurses’ knowledge on rotahaler device in a teaching hospital of central Nepal

Nurses are among the key personnel for educating patients on use of inhalers. This study aimed to assess the baseline knowledge of practitioner nurses on rotahaler technique and management. A descriptive study was conducted among the practitioner nurses (n=31) in a teaching hospital of Central Nepal. Knowledge on rotahaler technique and management were assessed using questionnaire by giving ‘1’ for correct response and ‘0’ for incorrect response. Descriptive statistics was calculated for statistical analysis using IBM-SPSS 20.0. The mean knowledge score of the participants was 4.74±1.56. Majority of the participants (76.7%) were unable to respond that dry powder inhalers (DPIs) allow maximum deposition of drugs in lung than pressurised metered dose inhalers (pMDIs) and only 2 (6.5%) of them was aware of instructions to clean the rotahaler. About 50% of participants were unaware that patient with asthma and chronic obstructive pulmonary disease (COPD) should hold their breath for around 10 seconds after taking inhaled medication. Similarly, two third participants knew that a quick, forceful and deep inspiration is necessary while using rotahaler. The participating nurses had inadequate knowledge on the technique of rotahaler and its management. Nurses in hospital setting need continued education and training on inhalation technique and the management of inhalation devices.

Phylogenetic analysis of glycoprotein B gene sequences of bovine herpesvirus 1 isolates from India reveals the predominance of subtype 1.1

AIM

This study was conducted for the isolation and molecular characterization of bovine herpesvirus 1 (BoHV-1) isolated from the nasal and vaginal swabs collected from naturally infected cattle showing clinical symptoms of the respiratory disease.

MATERIALS AND METHODS

Isolation of BoHV-1 virus performed on clinical samples collected from 65 cattle from five states of India. The BoHV-1 isolates were further confirmed by polymerase chain reaction (PCR) using primers specific for glycoprotein B (gB) genomic region. PCR amplification was performed using previously published gB gene-specific primer pairs. gB PCR amplicons obtained from all isolates were sequenced, and phylogenetic analysis was performed using software.

RESULTS

A total of 12 samples were found positive in cell culture isolation. 11 isolates showed the visible cytopathic effect on Madin-Darby bovine kidney after 72 h. Partial sequence analysis of gB gene of all isolates revealed 99.0-100% homology between them. All isolates showed 99.2-99.8% homology with Cooper stain.

CONCLUSION

BoHV-1.1 is the predominant circulating subtype of BoHV in India, and all isolates have homology with Cooper stain.

Assessment of knowledge and practice of community pharmacy personnel on diabetes mellitus management in Kathmandu district: a cross sectional descriptive study

Background

Pharmacists are the most reachable healthcare professionals to many chronically ill patients. It has been found that pharmacists see patients with diabetes up to five times more often than any other healthcare provider. Therefore, to provide quality health care to patients it is important that they have appropriate knowledge and practice on diabetes mellitus management. Thus, this study was conducted to assess the knowledge and practice of diabetes mellitus management among community pharmacy personnel involved in retail community pharmacies of Kathmandu.

Methods

Three hundred and fifteen community pharmacies, selected by systematic random sampling were surveyed by using pre-validated self-administered questionnaires. The first set of questionnaire evaluated the community pharmacy personnel’s diabetes knowledge based on a pre-validated 20-item questionnaire. The second set of questionnaire documented about the practice of community pharmacy personnel on diabetes mellitus management which contained 22 questions. Data was entered in EPI Data and analyzed by using SPSS version 20.

Results

This survey demonstrated that 76.5 % respondents had poor knowledge and 86.4 % had negative practice on diabetes mellitus (DM) management. Only 26.2 % respondents had good knowledge as well as good practice. 31.4 % of respondents had poor knowledge as well as poor practice on DM management.

Conclusions

Laws and regulations regarding community pharmacy personnel need to be implemented. There should be more advanced and experiment based training. Additionally, the provision for further education curriculum in pharmacy education should be implemented which should intensively include disease and proper management. Guidelines covering diabetes care should be distributed and implemented throughout community pharmacies.

Face-to-face Training as an Effective Approach for Teaching Rotahaler Technique in Newly Diagnosed Patients of Asthma and COPD

INTRODUCTION

This study aimed to evaluate the effectiveness of face-to-face training for teaching rotahaler technique in newly diagnosed patients of asthma and chronic obstructive pulmonary disease (COPD).

METHODS

A hospital-based study was conducted among twenty patients who were prescribed rotahaler for the first time. Patients received face-to-face training on rotahaler technique from pharmacist using GINA guidelines. The patients rotahaler technique was assessed after two weeks of training and scored one for correct and zero for incorrect steps. Descriptive statistics were performed.

RESULTS

The mean age of the study population was 48.85±20.49 years. Eleven (55%) patients were females. Thirteen (65%) patient were not formally educated in school. Fourteen patients (70%) were able to perform all the steps correctly giving overall median score of eight (7-8).

CONCLUSIONS

Face-to-face training seems to be effective approach for teaching rotahaler technique in asthma and COPD patients.

Burden of schizophrenia on caregivers in Nepal

Schizophrenia is the one of the severest form of psychiatric disorder. The disorder affects not only the patient but the family also. This study is performed to assess the burden faced by care givers of schizophrenic patients. Family burden interview schedule was used in this study. There were forty patients in study, twenty six male and fourteen female. Forty caregivers were interviewed for assessment of burden, among whom thirty were female and ten male. And to compare burden forty care givers of bipolar patients were taken. Female parents were the most usual care givers, with average age of 58.3 years and most of them were housewives. The most burden were in the area of finance and family dynamics and overall burden was moderate.

Intestinal protozoan parasitic infection among school children

BACKGROUND

Intestinal protozoan parasitosis is highly prevalent among general population, majority of them are children. The objective of the study is to find out the prevalence of intestinal protozoan infection in school children of Sindhuli.

METHODS

Stool samples were collected from school children of Sindhuli in June 2011 and investigated in National Institute of Tropical Medicine and Public Health Research, Laboratory by using formal-ether concentration method. Statistical significance was analyzed by using Chi-Square test.

RESULTS

A total of 342 stool samples were collected and 68 (19.8%) protozoan parasites were identified. The prevalence rate of protozoa in boys and girls were 16.9% and 22.0% respectively. Altogether 5 species of protozoan parasites were detected. Of them Entamoeba coli was most common followed by Giardia lamblia, Entamoeba histolytica, Blastocystis hominis and Endolimax nana. Positive rate was highest in Dalit (20.3%), and least in Indo-Aryan (19.6%).

CONCLUSIONS

There is a low prevalence of intestinal protozoan parasitosis among children even though this study emphasizes the need for improved environmental hygiene i.e. clean water supplies and enhanced sanitation.

Study on carrier rate of Streptococcus pyogenes among the school children and antimicrobial susceptibility pattern of isolates

This study was done to investigate the rate of Streptococcus pyogenes or Group A streptococcus (GAS) and antimicrobial susceptibility pattern of isolates in asymptomatic school children in Kathmandu and Sindhuli districts. Pharyngeal swabs were collected and subjected to crystal violet blood agar (CVBA). A total of 468 asymptomatic school aged children were included and 51 (10.8%) were found to be GAS carrier. Among the isolates 23 (12.0%) were from boys where 28 (10.1%) were from girls. The GAS colonization rate was statistically insignificant (P > 0.05) with sex and age sub-group, although the rate was slightly higher among the boys and age sub group 10-12 years. GAS was significantly higher in large family size (p < 0.05). Out of 51 isolates, 100.0% isolates were sensitive to antibiotic penicillin where as 7.8% and 5.8% isolates were resistant to antibiotic ampicillin and erythromycin respectively.

"Imaging features of extramedullary plasmacytoma of skull base with multiple myeloma"- a rare case

Imaging features of extramedullary plasmacytoma of skull base with multiple myeloma is reported in a 65 year old woman patient presented with multiple cranial nerve palsies. Contrast Enhanced CT revealed a large homogeneously enhancing mass in the left parapharyngeal region with extension in left petrous apex, left cavernous sinus and upper two cervical vertebrae. An extramedullary plasmacytoma associated with multiple myeloma was diagnosed after biopsy from the mass and laboratory investigations.

Autologous and allogeneic mixed-lymphocyte responses following thermal injury in man: the immunomodulatory effects of interleukin 1, interleukin 2, and a prostaglandin inhibitor, WY-18251

A group of 30 burn patients with 36-87% total body surface area (TBSA) burns was studied at 24-48 hr postburn. These included studies of (1) autologous and allogeneic mixed-lymphocyte reactions (MLR); (2) the immunoregulatory influence of mitomycin C-treated T cells, non-T cells, and unfractionated peripheral blood lymphocytes (PBL) on allogeneic MLR; and (3) correlation between the proportions of T-cell subsets defined with monoclonal antibodies (OKT4 and OKT8) and autologous MLR. Studies concerning adherent cell production of thromboxane, prostaglandin E2, and prostaglandin F2a and the immunomodulatory effects of Interleukin 1 (IL-1), Interleukin 2 (IL-2), and a prostaglandin inhibitor, WY-18251, on autologous MLR are presented. The autologous mixed-lymphocyte reaction was depressed in 60% of the burn patients tested. This depressed response correlated closely to the extent of third-degree injury (P less than 0.025) and to TBSA injury greater than 60% (P less than 0.025). A linear correlation was observed between the depression in autologous MLR and a decrease in both the percentage of OKT4+ T cells and the OKT4+/OKT8+ ratio. The response of T cells from burn patients in allogeneic MLR was normal. Age, sex, TBSA of the burn, and size of second-degree burn did not correlate with the abnormalities observed in MLR. Mitomycin C-treated mononuclear cells, purified T cells, or non-T cells from burned patients did not demonstrate any suppressive influence on MLR in normals. Monocyte number and arachidonic acid metabolism were investigated. In addition to increased numbers of monocytes following thermal injury, adherent cells produced increased quantities of thromboxane, prostaglandin E2, and prostaglandin F2a. The effects of Interleukin 1, Interleukin 2, and a prostaglandin inhibitor, WY-18251, were studied in autologous MLR (AMLR) of burned and normal patients. Interleukin 1 and WY-18251 did not induce any significant changes in proliferation in burned patients or normal controls. When compared to cultures without exogenous IL-2, an increase in AMLR was observed following the addition of IL-2 to burn patient cultures at Day 6 and Day 7 of culture. Although the addition of IL-2 did increase proliferation in AMLR of normal controls at Day 6 and Day 7, the enhancement observed for the burn patient cultures represented a restoration to the level of normal control cultures without IL-2. A dose-dependent increase in AMLR was observed in T cells isolated from normal and burned patients in the presence of purified Interleukin 2.(ABSTRACT TRUNCATED AT 400 WORDS)