De novo identification of viral pathogens from cell culture hologenomes

<p>Abstract</p> <p>Background</p> <p>Fast, specific identification and surveillance of pathogens is the cornerstone of any outbreak response system, especially in the case of emerging infectious diseases and viral epidemics. This process is generally tedious and time-consuming thus making it ineffective in traditional settings. The added complexity in these situations is the non-availability of pure isolates of pathogens as they are present as mixed genomes or hologenomes. Next-generation sequencing approaches offer an attractive solution in this scenario as it provides adequate depth of sequencing at fast and affordable costs, apart from making it possible to decipher complex interactions between genomes at a scale that was not possible before. The widespread application of next-generation sequencing in this field has been limited by the non-availability of an efficient computational pipeline to systematically analyze data to delineate pathogen genomes from mixed population of genomes or hologenomes.</p> <p>Findings</p> <p>We applied next-generation sequencing on a sample containing mixed population of genomes from an epidemic with appropriate processing and enrichment. The data was analyzed using an extensive computational pipeline involving mapping to reference genome sets and <it>de-novo </it>assembly. In depth analysis of the data generated revealed the presence of sequences corresponding to <it>Japanese encephalitis </it>virus. The genome of the virus was also independently <it>de-novo </it>assembled. The presence of the virus was in addition, verified using standard molecular biology techniques.</p> <p>Conclusions</p> <p>Our approach can accurately identify causative pathogens from cell culture hologenome samples containing mixed population of genomes and in principle can be applied to patient hologenome samples without any background information. This methodology could be widely applied to identify and isolate pathogen genomes and understand their genomic variability during outbreaks.</p

High Resolution Methylome Map of Rat Indicates Role of Intragenic DNA Methylation in Identification of Coding Region

DNA methylation is crucial for gene regulation and maintenance of genomic stability. Rat has been a key model system in understanding mammalian systemic physiology, however detailed rat methylome remains uncharacterized till date. Here, we present the first high resolution methylome of rat liver generated using Methylated DNA immunoprecipitation and high throughput sequencing (MeDIP-Seq) approach. We observed that within the DNA/RNA repeat elements, simple repeats harbor the highest degree of methylation. Promoter hypomethylation and exon hypermethylation were common features in both RefSeq genes and expressed genes (as evaluated by proteomic approach). We also found that although CpG islands were generally hypomethylated, about 6% of them were methylated and a large proportion (37%) of methylated islands fell within the exons. Notably, we obeserved significant differences in methylation of terminal exons (UTRs); methylation being more pronounced in coding/partially coding exons compared to the non-coding exons. Further, events like alternate exon splicing (cassette exon) and intron retentions were marked by DNA methylation and these regions are retained in the final transcript. Thus, we suggest that DNA methylation could play a crucial role in marking coding regions thereby regulating alternative splicing. Apart from generating the first high resolution methylome map of rat liver tissue, the present study provides several critical insights into methylome organization and extends our understanding of interplay between epigenome, gene expression and genome stability

Outcome of manual hemorrhoidopexy in the management of hemorrhoids

Background:&nbsp;Manual hemorrhoidopexy is a new technique of treating second degree hemorrhoids. In contrast to the conventional resectional techniques (Milligan-Morgan), manual hemorrhoidopexy is a novel technique as described by T Carlo. It does not involve excision but plication with fixation of the prolapsing hemorrhoid. Objective:&nbsp;To study the outcome of manual hemorrhoidopexy and to compare manual hemorrhoidopexy with the traditional hemorrhoidectomy. Methods:&nbsp;This is a prospective study conducted over 16 months (January 2012 to April 2013) in the College of Medical Sciences Teaching Hospital (COMS-TH), Bharatpur, Chitwan, Department of Surgery. The patients who presented with third degree internal-hemorrhoids on a random basis, and underwent either conventional hemorrhoidectomy (Group A) or Manual hemorrhoidopexy (Group B) by senior consultant surgeons were included. The patients who had external hemorrhoids in addition to internal were excluded. Preoperative, intraoperative, and postoperative characteristics were evaluated. Results:&nbsp;Twenty five patients with median age group 42.5 years underwent conventional (Milligan-Morgan) hemorrhoidectomy (Group A) and 25 patients with mean age of 40.1 years underwent manual hemorrhoidopexy (Group B). Male patients were predominant in both groups. The patients in group A had more postoperative pain as compared to group B (as assessed by the visual analogue scale and requirement of post-operative analgesic) and this was statistically significant (p&lt;0.001). There was no significant difference among the other post-operative urinary retention. Twelve percent (n=3) patients in group A had post-operative bleeding and only 4% (n=1) in group B which was statistically significant (p&lt;0.001). Mean duration of hospital stay in group A was 2.5 days as compared to 1.5 day in group B. Median follow up in both the study group was 3 (2-4) months. Conclusion:&nbsp;Manual hemorrhoidopexy has comparable outcomes in term of postoperative analgesic requirement, and post operative complications. Journal of College of Medical Sciences-Nepal, 2013, Vol-9, No-2, 15-19 DOI: http://dx.doi.org/10.3126/jcmsn.v9i2.9682</p

Caroli's Disease: A case report

Caroli's disease (CD) is a rare congenital abnormality characterized by dilatation of intra-hepatic bile ducts, recurrent cholangitis, formation of calculi inside these ducts with normal extra hepatic ducts and higher risk for cholangiocarcinoma. Association of this disease with congenital hepatic fibrosis is named as Caroli's syndrome. We reported 30 years old women with recurrent epigastric pain for 2 years with normal Liver function Test however involving both lobes of liver who developed cholangiocarcinoma approximately 6 months later. Journal of College of Medical Sciences-Nepal, 2012, Vol-8, No-3, 51-54 DOI: http://dx.doi.org/10.3126/jcmsn.v8i3.8685</p

Surgical outcome and clinical profile of emergency versus elective cases of colorectal cancer in College of Medical Sciences, Nepal

Background:&nbsp;Patients who undergo emergency colorectal cancer surgery has poor outcome compared to elective surgery, both in terms of morbidity and mortality. Approximately 15 to 30% of colorectal cancers present as an emergency, most often as obstruction or perforation. Objective:&nbsp;To compare surgical outcome and clinical profiles of emergency and elective cases for colorectal cancer. Methods:&nbsp;Retrospective analysis of 34 cases who underwent surgery for colorectal cancer between December 2011 to January 2013was carried out and their surgical outcomes, clinical presentation, demographic profile were analyzed. Results:&nbsp;The total numbers of patients included in this study were 34. Out of which 52.94 %( n=18) were emergency cases and 47.05 %( n=16) were elective. Male female ratio was 3:1 in emergency cases and 2.6:1 in elective cases. Per rectal bleeding (56%) and altered bowel habit (31.25%) was predominant clinical presentation in elective cases whereas intestinal obstruction (55.55%) and peritonitis (22.22%) were predominant clinical presentation in emergency cases. In emergency cases most of the tumors were located in left side (77.77%) and in elective cases rectum was common site (37.5%). Left hemicolectomy was the commonest surgery performed (72.22%) in emergency set up. In elective cases, right hemicolectomy, left hemicolectomy, APR and LAR was done in 31.25%, 31.25%, 25% and 25% cases respectively. In the emergency group 11.11% (n=2) developed enterocutaneous fistula and early mortality within 30 days was observed in 5% (n=1) of emergency cases only. Conclusion:&nbsp;In emergency conditions, colorectal cancer presented with intestinal obstruction where as elective cases presented with per rectal bleeding and altered bowel habits. Compared with the elective patients, the emergency patients had higher rate of morbidity and mortality. Because of higher incidence of colorectal cancer in our institution, in all emergency cases who presents with features of intestinal obstruction and peritonitis, we have to rule out colorectal cancer especially if the patients are elderly. Therefore, we should encourage screening programme for early detection of colorectal cancers for better outcome of surgery. Journal of College of Medical Sciences-Nepal, 2013, Vol-9, No-2, 25-30 DOI: http://dx.doi.org/10.3126/jcmsn.v9i2.9684</p

Retrorectal tumors: report of two cases

Retrorectal tumor is uncommon identity presenting with nonspecific sign and symptoms making difficulty in diagnosis. Benign tumors are more common than malignant. The lesion may be malignant or progress to malignancy from benign state. Retrorectal masses in young women may continue to grow and result in dystocia. Cystic lesions are also at risk of becoming infected, which renders subsequent excision more difficult and increase the risk of recurrence. Cross-sectional imaging is required to determine the extent of resection and the appropriate surgical approach. Surgical removal leads to favorable outcomes for patients with benign purely cystic retrorectal tumors. We report two such benign rectal lesions. ] Journal of College of Medical Sciences-Nepal, 2012, Vol-8, No-4, 46-50 DOI: http://dx.doi.org/10.3126/jcmsn.v8i4.8701 &nbsp;</p

Clinical profile, management and early outcome of gall bladder cancer

Objective To evaluate the clinical profile, management and early outcome of patients with gallbladder cancer. Methods This is a single institution based retrospective study of patients with gallbladder cancer who presented at College of Medical Sciences and Teaching Hospital, Bharatpur, Chitwan, Nepal. Patients presenting during one year period from August 2012 to July 2013 were reviewed. Results Twelve cases of Gall Bladder Cancer were reviewed in this series. Out of 12 patients, 9 were females (75%) and 3 were males (25%), showing female preponderance. Most of the patients (75%) were in age group of 51-70 years. Only one patient (8%) was below 50 years of age. Main symptom was pain associated with anorexia, nausea &amp; vomiting. Major signs were palpable mass, hepatomegaly and jaundice. All the cases had association with gall bladder stone. Of the total population, 50%(n=6) underwent extended cholecystectomy and rest of 6 cases were inoperable. Histopathological reports of all the operated cases were adenocarcinoma. Conclusion Prevalence of gall bladder cancer is higher in females in our series. Most of the patients were in fifth to seventh decade of life. Non specific symptoms like abdominal pain nausea and vomiting were the predominant symptoms. Only 50% of the cases were operable. So we have to do early screening by USG abdomen and CT scan to diagnose the disease earlier.&nbsp;&nbsp; Journal of College of Medical Sciences-Nepal, 2013, Vol-9, No-3, 12-16 &nbsp; DOI:&nbsp;http://dx.doi.org/10.3126/jcmsn.v9i3.10209 &nbsp;</p

ВПЛИВ ПАНДЕМІЇ COVID-19 НА ДОСТУП ДО ПРОМЕНЕВОЇ ТЕРАПІЇ ТА ОНКОЛОГІЧНИХ ПАЦІЄНТІВ У ЦЕНТРІ ТРЕТИННОЇ МЕДИЧНОЇ ДОПОМОГИ В АССАМІ, ПІВНІЧНО-СХІДНА ІНДІЯ: РЕТРОСПЕКТИВНЕ ДОСЛІДЖЕННЯ

Background. The COVID-19 pandemic has affected every sector of health care system including the cancer care. Objective. The purpose of the study is to analyse the impact of the current COVID‑19 pandemic on routine radiotherapy practice at a tertiary hospital of Northeast India. Methods. This is a retrospective study of all patients planned for radiotherapy at Assam Medical College, a tertiary care centre, in Assam, India from January 1, 2020 to May 31, 2020. The study samples are divided into two groups: group A – patients treated from January 1, 2020, to March 20, 2020 (pre-lockdown,) and group B – patients treated from March 21, 2020, to May 31, 2020 (lockdown). The department registration numbers of all the patients were collected from the entry register, and the respective paper files were then accessed to obtain the required data. Results. A total of 153 patients were planned for radiotherapy during the study period, of these 113 patients receiving radiotherapy in the pre-lockdown period and 40 patients receiving it in the lockdown period. The number of female patients decreased from 66 (58.40%) in the pre-lockdown period to 20 (50%) during the lockdown. The number of male patients also decreased from 47 to 20 but the proportion increased from 41.5% to 50%. The proportion of patients who completed radiotherapy was 90.8% in group B compare to 88.3% in group A. Conclusion. There was a decrease in number of cancer patients, especially female during the lockdown. The pandemic has severely disrupted every aspect of cancer care.Вступ. Пандемія COVID-19 вплинула на всі сектори системи надання медичної допомоги, включаючи систему надання онкологічної допомоги. Мета. Метою нашого дослідження був аналіз впливу поточної пандемії COVID‑19 на рутинну практику променевої терапії у закладі третинної медичної допомоги на північному сході Індії. Методи. Проводилося ретроспективне дослідження із залученням пацієнтів, яким запланована променева терапія, в медичному коледжі Ассама, центрі третинної медичної допомоги, в Ассамі, Індія, з 1 січня 2020 р. по 31 травня 2020 р. Вибірку дослідження поділено на дві групи, група А включає пацієнтів, які лікувалися з 1 січня 2020 р. по 20 березня 2020 р. (прелокдаун), а група Б включає пацієнтів, які проходили лікування з 21 березня 2020 р. по 31 травня 2020 р. (локдаун). Результати. Загалом 153 пацієнтам було заплановано проведення променевої терапії протягом періоду дослідження, з них 113 пацієнтів отримували променеву терапію в період до локдауну, а 40 пацієнтів отримували її у період карантину. Кількість пацієнток різко зменшилася з 66 (58,40%) у прелокдауні до 20 (50%) під час локдауну. Пацієнтів чоловічої статі також зменшилося з 47 до 20, але частка зросла з 41,5% до 50%. Частка пацієнтів, які завершили променеву терапію, становила 90,8% у групі Б порівняно з 88,3% у групі A. Висновки. Під час карантину кількість онкологічних пацієнтів, яким надавалася медчна допомога, особливо жінок, зменшилася. Пандемія серйозно порушила всі аспекти системи надання медичної допомоги онкологічним захворюванням