Schizophrenia Risk Mapping and Functional Engineering of the 3D Genome in Three Neuronal Subtypes.

Common variants associated with schizophrenia are concentrated in non-coding regulatory sequences, but their precise target genes are context-dependent and impacted by cell-type-specific three-dimensional spatial chromatin organization. Here, we map long-range chromosomal conformations in isogenic human dopaminergic, GABAergic, and glutamatergic neurons to track developmentally programmed shifts in the regulatory activity of schizophrenia risk loci. Massive repressive compartmentalization, concomitant with the emergence of hundreds of neuron-specific multi-valent chromatin architectural stripes, occurs during neuronal differentiation, with genes interconnected to genetic risk loci through these long-range chromatin structures differing in their biological roles from genes more proximal to sequences conferring heritable risk. Chemically induced CRISPR-guided chromosomal loop-engineering for the proximal risk gene SNAP91 and distal risk gene BHLHE22 profoundly alters synaptic development and functional activity. Our findings highlight the large-scale cell-type-specific reorganization of chromosomal conformations at schizophrenia risk loci during neurodevelopment and establish a causal link between risk-associated gene-regulatory loop structures and neuronal function.

A National Survey Evaluating the Knowledge and Attitude of Health-Care Workers of Saudi Arabia about Coronavirus Infection.

Background and Objectives: Health-care workers (HCWs) are playing an instrumental role in combating coronavirus infection (COVID-19). While rendering their services, they also run the risk of cross-contamination. Hence, it is important to evaluate and correlate the knowledge and attitude of HCWs of Saudi Arabia about COVID-19. Materials and Methods: A prospective, nationwide, questionnaire-based survey was conducted after getting the approval from the institutional ethical board. A validated and reliable questionnaire was constructed, developed on the Qualtrics software, and circulated through an electronic medium across the country. The questionnaire had a total of 29 questions regarding knowledge and attitude about COVID-19. Through convenience sampling, the data were collected from a total sample of 1553 HCWs. Based on the primary area of expertise, the sample was categorized into three study groups with 1040 medical health-care professionals (MHCPs) (Group I), 318 dental health-care professionals (DHCPs) (Group II), and 195 allied health-care professionals (AHCPs) (Group III). Univariate and multivariate logistic regression analysis was done using SPSS v. 21, where P < 0.05 was considered statistically significant. Results: Female HCWs (P = 0.003) were shown to have a higher (adjusted odds ratio [aOR]: 1.46; confidence interval [CI]: 1.19-1.79) risk of inadequate knowledge in comparison to male HCWs. With respect to qualification, HCWs with doctorate qualification (P = 0.005) (aOR: 0.39; CI: 0.2-0.75) had shown to have adequate knowledge compared to their counterparts. AHCPs were shown inadequate knowledge (P < 0.001; aOR: 2.36; CI: 1.65-3.38), but adequate attitude (P < 0.001; aOR: 0.13; CI: 0.09-0.2) compared to MHCPs and DHCPs. Conclusion: MHCPs were shown to have the most appropriate level of knowledge, whereas AHCPs outscore other counterparts of HCWs with respect to attitude toward COVID-19. Emphasis should be directed to the whole community of HCWs in enhancing their awareness and practice attitude toward the novel infection of COVID-19.

CLOuD9: CRISPR-Cas9-Mediated Technique for Reversible Manipulation of Chromatin Architecture.

The spatial organization of the genome plays a critical role in cell-specific biological functions such as gene expression. Existing genome-wide technologies reveal a dynamic interplay between chromatin looping and gene regulation, but the mechanisms by which regulatory interactions between genetic elements are established or maintained remain unclear. Here, we present CLOuD9, a CRISPR-based technology that can create de novo, pairwise chromatin interactions in cells. This technique for chromatin loop reorganization employs dCas9-targeting and ABI1-PYL heterodimerization. It is reversible, but can also establish epigenetic memory under certain conditions, which provides a way to dissect gene regulation mechanisms.

Global survey-based assessment of lifestyle changes during the COVID-19 pandemic.

Along with the major impact on public health, the COVID-19 outbreak has caused unprecedented concerns ranging from sudden loss of employment to mental stress and anxiety. We implemented a survey-based data collection platform to characterize how the COVID-19 pandemic has affected the socio-economic, physical and mental health conditions of individuals. We focused on three broad areas, namely, changes in social interaction during home confinement, economic impact and their health status. We identified a substantial increase in virtual interaction among individuals, which might be a way to alleviate the sudden unprecedented mental health burden, exacerbated by general awareness about viral infections or other manifestations associated with them. The majority of participants (85%) lived with one or more companions and unemployment issues did not affect 91% of the total survey takers, which was one of the crucial consequences of the pandemic. Nevertheless, measures such as an increased frequency of technology-aided distant social interaction, focus on physical fitness and leisure activities were adopted as coping mechanisms during this period of home isolation. Collectively, these metrics provide a succinct and informative summary of the socio-economic and health impact of the COVID-19 pandemic on the individuals. Findings from our study reflect that continuous surveillance of the psychological consequences for outbreaks should become routine as part of preparedness efforts worldwide. Given the limitations of analyzing the large number of variables, we have made the raw data publicly available on the OMF ME/CFS Data Center server to facilitate further analyses (https://igenomed.stanford.edu/dataset/survey-study-on-lifestyle-changes-during-covid-19-pandemic).

Superoxide dismutase, glutathione peroxidase, and catalase antioxidant enzymes in chronic tobacco smokers and chewers: A case-control study.

OBJECTIVE: Tobacco has a time dependent effect on the antioxidant system of the body. This study was designed to determine and compare alteration in levels of erythrocyte superoxide dismutase (SOD), glutathione peroxidase (GPx) and catalase (CAT) in blood subgroups of tobacco smokers and chewers with controls. MATERIALS AND METHODS: Blood samples were collected from 30 tobacco smokers (> 20 cigarettes daily), 30 tobacco chewers (> 10 packets gutka daily) and 30 controls. These groups were further divided into three subgroups (n=10) based on duration of habit (<5 yrs, 5-10 yrs, >10 yrs). The level of erythrocyte SOD, GPx and CAT were measured using standard procedures. RESULTS: The SOD and CAT levels were significantly decreased in all subgroups of smokers and chewers whereas GPx level was significantly increased. Positive correlation was observed between SOD, GPx and CAT levels with change in duration of habit in all subgroups. No significant difference observed in SOD and CAT activity between tobacco smokers and chewers. CONCLUSIONS: The findings suggested that antioxidative enzyme activities have significant correlation with change in the duration of tobacco use. Measurement of markers of free radical activity might be useful for estimating the level of oxidative stress caused by tobacco use.

Chromatin Regulates Genome Targeting with Cisplatin.

Cisplatin derivatives can form various types of DNA lesions (DNA-Pt) and trigger pleiotropic DNA damage responses. Here, we report a strategy to visualize DNA-Pt with high resolution, taking advantage of a novel azide-containing derivative of cisplatin we named APPA, a cellular pre-extraction protocol and the labeling of DNA-Pt by means of click chemistry in cells. Our investigation revealed that pretreating cells with the histone deacetylase (HDAC) inhibitor SAHA led to detectable clusters of DNA-Pt that colocalized with the ubiquitin ligase RAD18 and the replication protein PCNA. Consistent with activation of translesion synthesis (TLS) under these conditions, SAHA and cisplatin cotreatment promoted focal accumulation of the low-fidelity polymerase Polη that also colocalized with PCNA. Remarkably, these cotreatments synergistically triggered mono-ubiquitination of PCNA and apoptosis in a RAD18-dependent manner. Our data provide evidence for a role of chromatin in regulating genome targeting with cisplatin derivatives and associated cellular responses.

ZMYM3 regulates BRCA1 localization at damaged chromatin to promote DNA repair.

Chromatin connects DNA damage response factors to sites of damaged DNA to promote the signaling and repair of DNA lesions. The histone H2A variants H2AX, H2AZ, and macroH2A represent key chromatin constituents that facilitate DNA repair. Through proteomic screening of these variants, we identified ZMYM3 (zinc finger, myeloproliferative, and mental retardation-type 3) as a chromatin-interacting protein that promotes DNA repair by homologous recombination (HR). ZMYM3 is recruited to DNA double-strand breaks through bivalent interactions with both histone and DNA components of the nucleosome. We show that ZMYM3 links the HR factor BRCA1 to damaged chromatin through specific interactions with components of the BRCA1-A subcomplex, including ABRA1 and RAP80. By regulating ABRA1 recruitment to damaged chromatin, ZMYM3 facilitates the fine-tuning of BRCA1 interactions with DNA damage sites and chromatin. Consistent with a role in regulating BRCA1 function, ZMYM3 deficiency results in impaired HR repair and genome instability. Thus, our work identifies a critical chromatin-binding DNA damage response factor, ZMYM3, which modulates BRCA1 functions within chromatin to ensure the maintenance of genome integrity.

Risks and Benefits of Total Laparoscopic Hysterectomy and the Effect of Learning Curve on Them.

STUDY OBJECTIVE: The objective of this study was to prospectively analyze the risks and benefits of total laparoscopic hysterectomy (TLH) compared with total abdominal hysterectomy (TAH) and the effects of learning curve on them over 4 years (March 2010-April 2014). DESIGN: It was a prospective randomized study. SETTING: The study was conducted in Delhi government hospital which had no staff with previous experience of advanced laparoscopic surgeries. PATIENTS: Two hundred fifty patients were operated on for benign gynecological conditions (35-65 years). The numbers of cases operated laparoscopically were as follows-22 in 2010, 25 in 2011, 32 in 2012, and 46 in 2013. Equal number. of patients operated by open surgery were taken in the study during the same time period. RESULTS: Two hundred fifty cases were operated since March 2010, by either laparoscopic or open surgery. Incidence of major complications was-1.6 % for TLH compared to 4 % in TAH. After the first year of surgery, this incidence has fallen to 0 % in subsequent years in TLH group. The incidence of minor complications declined from 14 to 4.5 % in the third year of study. Total rate of conversion to laparotomy was 9.7 %, which again had a significant decline after the first year. TLH also clearly showed superior benefits of less intraoperative blood loss, early postoperative ambulance, and shorter period of hospital stay in comparison with TAH. CONCLUSION: The study has led us to conclude that TLH is a safe, effective, and reproducible technique after the completion of a period of training necessary to standardize the procedure. This approach must be established in our real, day-to-day clinical practice.

The nucleosome: orchestrating DNA damage signaling and repair within chromatin.

DNA damage occurs within the chromatin environment, which ultimately participates in regulating DNA damage response (DDR) pathways and repair of the lesion. DNA damage activates a cascade of signaling events that extensively modulates chromatin structure and organization to coordinate DDR factor recruitment to the break and repair, whilst also promoting the maintenance of normal chromatin functions within the damaged region. For example, DDR pathways must avoid conflicts between other DNA-based processes that function within the context of chromatin, including transcription and replication. The molecular mechanisms governing the recognition, target specificity, and recruitment of DDR factors and enzymes to the fundamental repeating unit of chromatin, i.e., the nucleosome, are poorly understood. Here we present our current view of how chromatin recognition by DDR factors is achieved at the level of the nucleosome. Emerging evidence suggests that the nucleosome surface, including the nucleosome acidic patch, promotes the binding and activity of several DNA damage factors on chromatin. Thus, in addition to interactions with damaged DNA and histone modifications, nucleosome recognition by DDR factors plays a key role in orchestrating the requisite chromatin response to maintain both genome and epigenome integrity.

Acetic acid as an adjunct vital stain in diagnosis of tobacco-associated oral lesions: A pilot study.

BACKGROUND: One of the most important risk factors for oral precancer and cancer in India is the use of tobacco. In chronic tobacco users, the mucosa may appear clinically healthy, however, changes are observed histologically. Screening of such tobacco users for an early diagnosis is, therefore, of paramount importance. Several adjunctive diagnostic modalities have been used in the past, but none has been conclusively validated as confirmative and cost-effective screening methodology. The aim of this study was to evaluate the use of 5% acetic acid as a vital staining agent in tobacco-associated oral lesions. MATERIALS AND METHODS: The study subjects were divided into two groups. Group I (n = 40) subjects with a history of chronic tobacco use and clinically apparent normal mucosa. Group II (n = 40) subjects suspected of having oral cancer, 5% acetic acid was applied to the mucosa/lesions, followed by incisional biopsy for confirmatory diagnosis. RESULTS: The sensitivity and specificity for Groups I and II were 97%, 50% and 95%, 60%, respectively. Positive predictive value (PPV) and negative predictive value (NPV) of Group I were 0.95 and 0.66. Group II showed PPV and NPV of 0.95 and 0.60. CONCLUSION: The results of this study suggest that acetic acid holds promise for future. Hence, further studies are needed to be undertaken on a large scale to assess its potential as a screening tool for high-risk individuals and oral cancer.

Ubiquitin-Activated Interaction Traps (UBAITs) identify E3 ligase binding partners.

We describe a new class of reagents for identifying substrates, adaptors, and regulators of HECT and RING E3s. UBAITs (Ubiquitin-Activated Interaction Traps) are E3-ubiquitin fusion proteins and, in an E1- and E2-dependent manner, the C-terminal ubiquitin moiety forms an amide linkage to proteins that interact with the E3, enabling covalent co-purification of the E3 with partner proteins. We designed UBAITs for both HECT (Rsp5, Itch) and RING (Psh1, RNF126, RNF168) E3s. For HECT E3s, trapping of interacting proteins occurred in vitro either through an E3 thioester-linked lariat intermediate or through an E2 thioester intermediate, and both WT and active-site mutant UBAITs trapped known interacting proteins in yeast and human cells. Yeast Psh1 and human RNF126 and RNF168 UBAITs also trapped known interacting proteins when expressed in cells. Human RNF168 is a key mediator of ubiquitin signaling that promotes DNA double-strand break repair. Using the RNF168 UBAIT, we identify H2AZ--a histone protein involved in DNA repair--as a new target of this E3 ligase. These results demonstrate that UBAITs represent powerful tools for profiling a wide range of ubiquitin ligases.

Genotoxic and cytotoxic effects of X-ray on buccal epithelial cells following panoramic radiography: A pediatric study.

BACKGROUND: Ionizing radiation is a potent mutagenic agent capable of inducing both mutation and chromosomal aberrations. Non-lethal doses of ionizing radiation may induce genomic instability favoring carcinogenesis. In spite of their mutagenic potential, this kind of radiation is an important tool for diagnosis of the disease and is used in medical and dental practice. It has been believed that the number of micronucleus and increased frequency of other nuclear alterations, including karyorrhexis, condensed chromatin and pyknosis, are related to the increasing effects of carcinogens. Many approaches and techniques have been developed for the monitoring of human populations exposed to various mutagens, but the analysis of micronuclei (MN) has become a standard approach for the assessment of chromosomal damage in human populations. AIM: To assess the effects of radiation exposure from panoramic radiography on the buccal epithelial cells (BECs) of pediatric patients. MATERIALS AND METHODS: The study included 20 pediatric patients who had to undergo panoramic radiography for further dental treatment. Exfoliated BECs were obtained and examined immediately before and 10 days after radiation exposure. The cells were stained using rapid Papanicolaou (PAP) kit. Evaluation for MN and nuclear alterations was carried out by an oral pathologist and data were statistically analyzed using the "t" test. RESULTS: The mean number of MN in the BECs before exposure of pediatric patients to panoramic radiography was 4.25 and after exposure was 4.40. This difference was not found to be statistically significant (P < 0.0001). However, the mean nuclear alterations of 8.70 and 15.75 before and after exposure were statistically significant (P < 0.0001). CONCLUSION: Panoramic radiographs can induce cytotoxicity but not genotoxic effects in buccal mucosal cells. Hence, dental radiographs should be prescribed only when deemed indispensable.

Screen identifies bromodomain protein ZMYND8 in chromatin recognition of transcription-associated DNA damage that promotes homologous recombination.

How chromatin shapes pathways that promote genome-epigenome integrity in response to DNA damage is an issue of crucial importance. We report that human bromodomain (BRD)-containing proteins, the primary "readers" of acetylated chromatin, are vital for the DNA damage response (DDR). We discovered that more than one-third of all human BRD proteins change localization in response to DNA damage. We identified ZMYND8 (zinc finger and MYND [myeloid, Nervy, and DEAF-1] domain containing 8) as a novel DDR factor that recruits the nucleosome remodeling and histone deacetylation (NuRD) complex to damaged chromatin. Our data define a transcription-associated DDR pathway mediated by ZMYND8 and the NuRD complex that targets DNA damage, including when it occurs within transcriptionally active chromatin, to repress transcription and promote repair by homologous recombination. Thus, our data identify human BRD proteins as key chromatin modulators of the DDR and provide novel insights into how DNA damage within actively transcribed regions requires chromatin-binding proteins to orchestrate the appropriate response in concordance with the damage-associated chromatin context.

Assessing the association of taurodontism with numeric dentition anomalies in an adult central Indian population.

AIM: To study the association between taurodontism and numeric anomalies in adult population. MATERIALS AND METHODS: Out of 1,012; 946 panoramic radiographs and dental records were retrospectively assessed to determine the presence of dental agenesis and supernumerary and taurodont teeth. RESULTS: Taurodontism of one or more teeth was observed in 164 cases (97 females and 67 males). Hypodontia was observed in 148 patients (84 females and 64 males) with 62 patients having associated taurodontism (38 females, 24 males), oligodontia in 12 patients (five females and seven males) of whom nine patients also had taurodontism of one or more teeth (five females and four males). Forty-five patients (32 females and 13 males) presented with 57 supernumerary teeth (ST) with 12 patients having simultaneous presence of taurodontic tooth (seven females and five males). CONCLUSION: Our study suggests a preferential association between tooth agenesis and taurodontism; however, such association was not observed in individuals with hyperdontia. Understanding the nature of this preferential association may be of importance in determining the etiology of both conditions. This association may also define a subphenotype for future genetic studies on dental development. Further molecular studies are necessary to verify the etiology and mechanism of taurodontism associated with tooth agenesis.

A large multifocal aggressive osteoblastoma of mandible: an immunohistochemistry case study report.

Aggressive osteoblastoma (AO) is a benign osteoblastic tumor which is rare in the head and neck region. Clinical and histo-logical features are therefore overlap with other benign and low-grade malignant tumors. The aim of this article is to report and discuss the differential diagnosis of an aggressive osteoblastoma in the mandible. A 25-year-old male patient reported with pain and asymmetry on the left side of the face since 8 months previously. Radiographic evaluation showed a mixed lesion extending from approximately the lower left premolar to the third molar region. After incisional biopsy, resection with continuity defect was carried out. Microscopic findings showed woven bone and bony trabeculae with varied degrees of mineralization along with sheets of osteoblast cells. Immunohistochemistry showed that p53 and cytokeratin (CK) were negative and ki-67 index was 7%. Postoperative follow-up for 15 months showed no evidence of recurrence.

Odontogenic myxoma.

Odontogenic myxoma is a rare, benign, locally aggressive and non metastasizing neoplasm which is believed to arise from the odontogenic ectomesenchyme and bears a close microscopic resemblance to mesenchymal portion of a tooth germ. This is a case report of odontogenic myxoma in a 32 year old female patient and the treatment rendered to her.

Nucleosome acidic patch promotes RNF168- and RING1B/BMI1-dependent H2AX and H2A ubiquitination and DNA damage signaling.

Histone ubiquitinations are critical for the activation of the DNA damage response (DDR). In particular, RNF168 and RING1B/BMI1 function in the DDR by ubiquitinating H2A/H2AX on Lys-13/15 and Lys-118/119, respectively. However, it remains to be defined how the ubiquitin pathway engages chromatin to provide regulation of ubiquitin targeting of specific histone residues. Here we identify the nucleosome acid patch as a critical chromatin mediator of H2A/H2AX ubiquitination (ub). The acidic patch is required for RNF168- and RING1B/BMI1-dependent H2A/H2AXub in vivo. The acidic patch functions within the nucleosome as nucleosomes containing a mutated acidic patch exhibit defective H2A/H2AXub by RNF168 and RING1B/BMI1 in vitro. Furthermore, direct perturbation of the nucleosome acidic patch in vivo by the expression of an engineered acidic patch interacting viral peptide, LANA, results in defective H2AXub and RNF168-dependent DNA damage responses including 53BP1 and BRCA1 recruitment to DNA damage. The acidic patch therefore is a critical nucleosome feature that may serve as a scaffold to integrate multiple ubiquitin signals on chromatin to compose selective ubiquitinations on histones for DNA damage signaling.

Nonsyndromic familial oligodontia with multiple dens invaginatus: a case report of an unusual case.

Oligodontia is a rare dental anomaly with a prevalence of 0.3% in permanent teeth and much less frequency in the primary dentition. Familial oligodontia represents an absence of varying numbers of primary and/or secondary teeth as an isolated trait. It is a complex and multifactorial condition. Many explanations-evolutionary, genetic, and environmental-have been proposed as the etiology. Simultaneous with oligodontia are often the different positional changes of the existing teeth, their morphology, size, and growth disturbances of the maxillofacial skeleton. Early recognition is vital to provide adequate treatment and prevent squeal. Multidisciplinary referral or consultation is thus important in treatment planning to improve function and esthetics. The present paper reports a rare case of familial oligodontia associated with multiple dense invaginatus and microdontia.

Atypical case of primary intraosseous adenoid cystic carcinoma of mandible.

The Primary central salivary gland neoplasms of the mandible are infrequent. Their clinical and radiographic features may be similar to odontogenic tumors, which are otherwise common. Their accurate diagnosis becomes troublesome. Hence, diagnosis should depend on stringent diagnostic criteria. Adenoid cystic carcinoma is well known for its prolonged clinical course and its tendency for delayed onset of distant metastases. The long-term survival of these patients is therefore poor. Treatment modalities include surgery, radiotherapy and chemotherapy. The purpose of this paper is to report a case of primary central adenoid cystic carcinoma of mandible with an atypical presentation.