Topologically associating domain boundaries are required for normal genome function

Topologically associating domain (TAD) boundaries partition the genome into distinct regulatory territories. Anecdotal evidence suggests that their disruption may interfere with normal gene expression and cause disease phenotypes1,2,3, but the overall extent to which this occurs remains unknown. Here we demonstrate that targeted deletions of TAD boundaries cause a range of disruptions to normal in vivo genome function and organismal development. We used CRISPR genome editing in mice to individually delete eight TAD boundaries (11–80 kb in size) from the genome. All deletions examined resulted in detectable molecular or organismal phenotypes, which included altered chromatin interactions or gene expression, reduced viability, and anatomical phenotypes. We observed changes in local 3D chromatin architecture in 7 of 8 (88%) cases, including the merging of TADs and altered contact frequencies within TADs adjacent to the deleted boundary. For 5 of 8 (63%) loci examined, boundary deletions were associated with increased embryonic lethality or other developmental phenotypes. For example, a TAD boundary deletion near Smad3/Smad6 caused complete embryonic lethality, while a deletion near Tbx5/Lhx5 resulted in a severe lung malformation. Our findings demonstrate the importance of TAD boundary sequences for in vivo genome function and reinforce the critical need to carefully consider the potential pathogenicity of noncoding deletions affecting TAD boundaries in clinical genetics screening.This work was supported by U.S. National Institutes of Health (NIH) grants to L.A.P. and A.V. (UM1HG009421). Research was conducted at the E.O. Lawrence Berkeley National Laboratory and performed under U.S. Department of Energy Contract DE-AC02-05CH11231, University of California (UC). Phenotyping performed by the UC Davis Mouse Biology Program (MBP) (www.mousebiology.org) was funded by an NIH administrative supplement to the KOMP2 grant, 3UM1OD023221-07S1, for phenotyping non-coding elements. Adyam Akeza was supported by the NIH Bridges to Baccalaureate Program Grant R25GM095401 via UC Berkeley. J.L.-R. is supported by the Spanish Ministerio de Ciencia e Innovacion (PID2020-113497GB-I00).Peer reviewe

Single-cell, whole-embryo phenotyping of mammalian developmental disorders

Mouse models are a critical tool for studying human diseases, particularly developmental disorders. However, conventional approaches for phenotyping may fail to detect subtle defects throughout the developing mouse. Here we set out to establish single-cell RNA sequencing of the whole embryo as a scalable platform for the systematic phenotyping of mouse genetic models. We applied combinatorial indexing-based single-cell RNA sequencing to profile 101 embryos of 22 mutant and 4 wild-type genotypes at embryonic day 13.5, altogether profiling more than 1.6 million nuclei. The 22 mutants represent a range of anticipated phenotypic severities, from established multisystem disorders to deletions of individual regulatory regions. We developed and applied several analytical frameworks for detecting differences in composition and/or gene expression across 52 cell types or trajectories. Some mutants exhibit changes in dozens of trajectories whereas others exhibit changes in only a few cell types. We also identify differences between widely used wild-type strains, compare phenotyping of gain- versus loss-of-function mutants and characterize deletions of topological associating domain boundaries. Notably, some changes are shared among mutants, suggesting that developmental pleiotropy might be 'decomposable' through further scaling of this approach. Overall, our findings show how single-cell profiling of whole embryos can enable the systematic molecular and cellular phenotypic characterization of mouse mutants with unprecedented breadth and resolution

CLINICO-EPIDEMIOLOGICAL PROFILE OF ORAL CANCER: A HOSPITAL BASED STUDY

Background: India is heading towards various types of non-communicable diseases, which are also known as modern epidemics. Among these modern epidemics cancer is among the ten commonest cause of mortality in developing countries including India. Oral cancer is a major problem in India and accounts for 50-70% of all the cancers diagnosed. Ninety percent (90%) of oral cancers in South East Asia including India are linked to tobacco chewing and tobacco smoking. Research question: What is the profile of Oral cancer (Oral cavity) cases reported in the hospital? Objective: To study the clinico-epidemiological profile associated with Oral cancer cases. Methods: Study Design: Hospital based, Cross -sectional study. Settings: Shri Siddhivinayak Ganapati Cancer Hospital, Miraj, Maharashtra. Participants and Sample size: As it is a time bound study sample size comprised of all the confirmed cases of oral cancer reported in the hospital during the study period. The study was carried out from 1st March 2005 to 28th February 2006. Study variables included demographic factors, socioeconomic factors, enquiries regarding modifiable risk factors such as tobacco usage, alcohol consumption, site involved (within oral cavity), staging, histopathological examination, treatment modality used. Data entry and statistical analysis was done using Microsoft excel. Data presented in form of percentages and proportions. Results: Out of the total 160 cases, majority of the subjects were above 40 years age. 36 (22%) of subjects were young adults (below 40 years age). 125 (78%) subjects were male. Most of the subjects belonged to upper lower and lower middle socio-economic scale according to modified Kuppuswamy classification. It was observed that 139 (87%) cases consumed tobacco in all forms. Out of these, ninety cases consumed tobacco in chewable form. Tobacco was chewed mainly in the form of gutka. Only ten (10) female subjects chewed tobacco. No female subjects smoked. The most common site for oral cancer was tongue. Histopathologically 52 (32.5%) cases were well differentiated squamous cell carcinoma, 37 (23%) cases were moderately differentiated squamous cell carcinoma and 34 (21%) cases as poorly differentiated squamous cell carcinoma. 37 (23%) cases were diagnosed as Oral Verrucous Carcinoma (a rare variant of Oral Squamous Cell Carcinoma). 72% cases were in either stage II or stage III. Conclusions: The most common site for oral cancer was tongue and histopathologically majority of the cases were well differentiated squamous cell carcinoma presented in advanced stages of disease. We observed higher proportion of oral cancers among young patients (below 40 years). Proportion of Oral Verrucous Carcinoma (OVC) which is a rare variant of Oral Squamous Cell Carcinoma was also high in the study

Trends of Dengue Cases Reported at Tertiary Care Hospital of Metropolitan City of Maharashtra: A Record Based Study

Background & Objectives: Recent national data showed increasing trends of dengue prevalence but significant decrease in death rates.1Understanding trends and epidemiology of dengue outbreaks would help in effective control of dengue in city. Therefore, the research was planned to study & compare the trends of dengue cases reported at Tertiary hospital, state & district levels during 2009 to 2015. Methods: Six years data on ‘Dengue cases admitted in a tertiary care hospital’ was obtained from the Satellite Disease Surveillance Unit of Tertiary care hospital. District and state level data on dengue was mobilised from Public Health department authorities and websites. Tables and graphs were prepared. Data analysis and compilation was done with Microsoft Excel 2013. Result: A total of 56,981 patients with fever were screened for dengue at tertiary hospital during the study period. Of these, 5082 patients (8.91%) were tested positive. There was tenfold increase in the Dengue cases in six years. Rise of confirmed dengue cases was seen at District and state level. ‘Males’ and ‘Patients between 13-30 years age group’ were more affected. There was declining trend of dengue case fatality rate. Conclusion: Incresing trend of dengue indicates an alarming situation in the city and stressesmore preparedness during monsoon season

Against the overgrowth hypothesis: Shorter costal cartilage lengths in pectus excavatum

Background: Pectus excavatum is a common chest wall deformity with no known cause. A common hypothesis is that in patients with pectus excavatum, there is an overgrowth of costal cartilage relative to healthy individuals.Materials and methods: We obtained radiological curvilinear three-dimensional measurements of the fourth to eighth costal cartilage and associated ribs in 16 patients with pectus excavatum and 16 age- and gender-matched controls between the ages of 6 and 32 y. An analysis of variance was used to compare bone length, cartilage length, and their ratios between patients and controls.Results: Relative to bone length, patients with pectus excavatum overall had shorter costal cartilage lengths (P \u3c 0.001), especially on the left side (P \u3c 0.05). We were unable to localize this observation to specific ribs during post hoc analysis.Conclusions: This is the first study to empirically test the overgrowth hypothesis of pectus excavatum for ribs 4 through 8. Although we and others have found no evidence to support this hypothesis, we surprisingly found the alternate hypothesis to be true: patients with pectus excavatum tend to have shorter costal cartilages. Future studies should expand on these results with larger sample sizes and consider volumetric measurements longitudinally during thoracic development

On the effects of intra-gate resistive open defects in gates at nanoscaled CMOS

This paper presents a detailed characterization of the effects of intra-gate resistive open defects on nanoscaled CMOS gates as causing faults with timing and pattern sequence dependency. The values of the least detectable resistance are established for different feature sizes using HSPICE. It is found that as the feature size is reduced, the value of the least detectable resistance increases in the presence of a fault resulting in a delay of less than one nanosecond. The use of a low voltage testing technique is investigated for the detection of these faults. Finally, an analytical model that takes into account the gate current is proposed; this model considers the pronounced effect of the gate current at a decreasing feature size, while incurring in a small error compared with simulation results

Socio-Demographic Profile and Morbidity Pattern of Patients in a Rural Field Practice Area of Government Medical College, Miraj, Maharashtra

Introduction: The shifting trend of diseases from communicable to non-communicable diseases pose a dual threat in India will also add to the burden of morbidity. In view of this, the present study was conducted to assess the common morbidity pattern among the rural population of Maharashtra. Material and methods: A cross sectional study were conducted among the rural population of field practice area of Government Medical College, Miraj, Maharashtra. The study was conducted from 1st January 2018 to 31st December 2018. Patients attending Out Patient Department (OPD) services of Rural Health Training Centre and willing to participate in the study were included. Data on the current morbidity among the patients attending OPD services was gathered by the health workers. Analysis was conducted using the percentages. Results: It was observed that majority of patients attended the OPD services were females i.e. 54.3% and 45.7% patients were males. The most common morbidity observed among the participants was res- piratory infections i.e. 29.8%. Other morbidities seen were muscu- loskeletal diseases in 17.3% participants, nutritional problems in 17.1% participants and non-communicable diseases in 13.6% study subjects. Conclusion: The study revealed dual burden of communicable as well as chronic and non-communicable diseases in the rural population