Genome-wide analysis of AAAG and ACGT cis-elements in Arabidopsis thaliana reveals their involvement with genes downregulated under jasmonic acid response in an orientation independent manner

Cis-regulatory elements are regions of noncoding DNA that regulate the transcription of neighboring genes. The study of cis-element architecture that functions in transcription regulation are essential. AAAG and ACGT are a class of cis-regulatory elements, known to interact with Dof and bZIP transcription factors respectively, and are known to regulate the expression of auxin response, gibberellin response, floral development, light response, seed storage proteins genes, biotic and abiotic stress genes in plants. Analysis of the frequency of occurrence of AAAG and ACGT motifs from varying spacer lengths (0–30 base pair) between these 2 motifs in both possible orientations—AAAG _(N) ACGT and ACGT _(N) AAAG, in the promoters and genome of Arabidopsis thaliana which indicated preferred orientation of AAAG _(N) ACGT over ACGT _(N) AAAG across the genome and in promoters. Further, microarray analysis revealed the involvement of these motifs in the genes downregulated under jasmonic acid response in an orientation-independent manner. These results were further confirmed by the transient expression studies with promoter-reporter cassettes carrying AAAG and ACGT motifs in both orientations. Furthermore, cluster analysis on genes with AAAG _(N) ACGT and ACGT _(N) AAAG motifs orientations revealed clusters of genes to be involved in ABA signaling, transcriptional regulation, DNA binding, and metal ion binding. These findings can be utilized in designing synthetic promoters for the development of stress-tolerant transgenic plants and also provides an insight into the roles of these motifs in transcriptional regulation.

Effect of ACGT motif in spatiotemporal regulation of AtAVT6D, which improves tolerance to osmotic stress and nitrogen-starvation

Plasma membrane-localized AtAVT6D importing aspartic acid can be targeted to develop plants with enhanced osmotic and nitrogen-starvation tolerance. AtAVT6D promoter can be exploited as a stress-inducible promoter for genetic improvements to raise stress-resilient crops. The AtAVT6 family of amino acid transporters in Arabidopsis thaliana has been predicted to export amino acids like aspartate and glutamate. However, the functional characterization of these amino acid transporters in plants remains unexplored. The present study investigates the expression patterns of AtAVT6 genes in different tissues and under various abiotic stress conditions using quantitative Real-time PCR. The expression analysis demonstrated that the member AtAVT6D was significantly induced in response to phytohormone ABA and stresses like osmotic and drought. The tissue-specific expression analysis showed that AtAVT6D was strongly expressed in the siliques. Taking together these results, we can speculate that AtAVT6D might play a vital role in silique development and abiotic stress tolerance. Further, subcellular localization study showed AtAVT6D was localized to the plasma membrane. The heterologous expression of AtAVT6D in yeast cells conferred significant tolerance to nitrogen-deficient and osmotic stress conditions. The Xenopus oocyte studies revealed that AtAVT6D is involved in the uptake of Aspartic acid. While overexpression of AtAVT6D resulted in smaller siliques in Arabidopsis thaliana. Additionally, transient expression studies were performed with the full-length AtAVT6D promoter and its deletion constructs to study the effect of ACGT-N₂₄-ACGT motifs on the reporter gene expression in response to abiotic stresses and ABA treatment. The fluorometric GUS analyses revealed that the promoter deletion construct-2 (Pro.C2) possessing a single copy of ACGT-N₂₄-ACGT motif directed the strongest GUS expression under all the abiotic conditions tested. These results suggest that Pro.C2 can be used as a stress-inducible promoter to drive a significant transgene expression.

Primer Designing for Amplifying an AT-Rich Promoter from Arabidopsis thaliana

The aim of the present study is to optimize the PCR conditions required to amplify the promoter sequence of an amino acid transporter having an AT-rich base composition with a high number of tandem repeats. The present study also covers the key parameters that need to be kept in mind while designing primers. Results show that successful can be achieved by performing a 2-step PCR reaction at a lower extension temperature of 65 ̊C for an increased extension period of 1.5 min/kb, with MgCl2 concentration ranging from 2.5 to 3.0mM. The results also suggest that the DNA concentration of around 25-30 ng/µl was essential to achieve this amplification.

In Silico Analysis of CCGAC and CATGTG Cis-regulatory Elements Across Genomes Reveals their Roles in Gene Regulation under Stress

Background:

Plant yield closely depends on its environment and is negatively affected by abiotic stress conditions like drought, salinity, heat, and cold. Analysis of the stress-inducible genes in Arabidopsis has previously shown that CCGAC and CATGTG play a crucial role in controlling the gene expression through the binding of DREB/CBF and NAC TFs under various stress conditions, mainly drought and salinity.

Methods:

The pattern of these motifs is conserved, which has been analyzed in this study to find the mechanism of gene expression through spacer specificity, inter motif distance preference, functional analysis, and statistical analysis for four different plants, namely Oryza sativa, Triticum aestivum, Arabidopsis thaliana, and Glycine max.

Results:

The spacer frequency analysis has shown a preference for particular spacer lengths among four genomes. The spacer specificity at all the spacer lengths which predicts dominance of particular base pairs over others, was analyzed to find the preference of the sequences in the flanking region. Functional analysis on stress-regulated genes for saline, osmotic, and heat stress clearly shows that these motif frequencies with inter motif distance (0-30) in the promoter region of Arabidopsis are highest in genes which are upregulated by saline and osmotic stress and downregulated by heat stress.

Conclusion:

Microarray data were analyzed to confirm the role of both motifs in stress response pathways. Transcription factors seem to prefer larger motif size with repeated CCGAC and CATGTG elements. The common preference for one spacer was further validated through Box and Whisker’s statistical analysis.

Promoter profiling of Arabidopsis amino acid transporters: clues for improving crops

The review describes the importance of amino acid transporters in plant growth, development, stress tolerance, and productivity. The promoter analysis provides valuable insights into their functionality leading to agricultural benefits. Arabidopsis thaliana genome is speculated to possess more than 100 amino acid transporter genes. This large number suggests the functional significance of amino acid transporters in plant growth and development. The current article summarizes the substrate specificity, cellular localization, tissue-specific expression, and expression of the amino acid transporter genes in response to environmental cues. However, till date functionality of a majority of amino acid transporter genes in plant development and stress tolerance is unexplored. Considering, that gene expression is mainly regulated by the regulatory motifs localized in their promoter regions at the transcriptional levels. The promoter regions ( ~ 1-kbp) of these amino acid transporter genes were analysed for the presence of cis-regulatory motifs responsive to developmental and external cues. This analysis can help predict the functionality of known and unexplored amino acid transporters in different tissues, organs, and various growth and development stages and responses to external stimuli. Furthermore, based on the promoter analysis and utilizing the microarray expression data we have attempted to identify plausible candidates (listed below) that might be targeted for agricultural benefits.

Molecular docking studies of Indian variants of pathophysiological proteins of SARS-CoV-2 with selected drug candidates

SARS-CoV-2 pandemic has recently made the entire world come to a standstill. The number of cases in the world, especially India, have been increasing exponentially. The need of the hour is to assimilate as much data as possible to fast track the pipeline of bringing in new therapeutic tools against this fatal virus. In this brief communication, we aim to throw light on the various variants of the proteins involved heavily in the pathophysiology of COVID-19, namely Spike protein, ACE2, GRP78, TMPRSS2 and NSP-12. We also portray the molecular docking studies of these proteins with specific drugs that are currently being associated with the same. In our brief study, we come across a few key findings. First of all the combinations of the variants of spike protein and ACE2 binding show overall 25% unfavourable ΔΔG. Second, NSP12 is the most mutation prone among all the NSPs of the SARS-CoV-2 genome and the most common mutations are P323L and A97V. Third, we discovered the variants found in the Indian subpopulation that have greater binding with the currently investigated drugs.

Risk factors of breast cancer and breast self-examination in early detection: systematic review of awareness among Indian women in community and health care professionals

BACKGROUND

This review aims at evaluating the awareness of risk factors for breast cancer (BC) and the knowledge of breast self-examination (BSE) among Indian women and health care professionals (HCPs).

METHODS

Literature search was conducted on multiple bibliographic databases with restrictions applied to English peer-reviewed journals.

RESULTS

We reviewed 37 published articles on this topic. The mean level of awareness for risk factors such as age at menarche (22.3%), age at menopause (27.1%) and late first pregnancy (34.6%) was low in community. The awareness was better among HCPs; however, there was still room for improvement.Knowledge of BSE varied from very poor (2%) to good (69.8%) in the community setting. The practice was similarly negligible (0%) to moderate (34.9%). Mean knowledge and practice of BSE in HCPs were 77.1 and 55.5%, respectively. A significant difference was noted in knowledge and practice of BSE between community and HCPs (P < 0.05).

CONCLUSIONS

The present review highlights the low level of awareness regarding risk factors for BC and BSE in the community as well as HCPs. Though BSE is not the ideal modality, this seems to be the best alternative for resource-limited settings.

Association of smokeless tobacco and cerebrovascular accident: a systematic review and meta-analysis of global data

BACKGROUND

The association of smokeless tobacco (SLT) with stroke has been dealt with in only a few reviews. The present meta-analysis aims to present the updated comprehensive summary risk of stroke in adult SLT users along with sub group analysis.

METHODS

A systematic literature search for articles evaluating risk of stroke in SLT users was conducted. The study characteristics and risk estimates were extracted independently by two authors (RG and SG). Random-effect model was used to estimate the summary relative risks.

RESULTS

The overall risk of stroke in SLT users was found to be significantly higher (1.17, 95% CI 1.04–1.30) compared to non-users, especially for users in Southeast Asian region. The results remained unchanged even after strict adjustment for smoking (1.18, 95% CI 1.04–1.32). SLT users had 1.34 times or 13.4% higher risk of fatal stroke, though risk of nonfatal stroke was not enhanced. Significantly higher risk of stroke was seen in users of chewing tobacco (1.35, 95% CI 1.20–1.50) in comparison to non-chewers. Gender-based analysis showed enhanced risk of fatal stroke in both male and female users. SLT-attributable fraction of fatal stroke was highest for India at 14.8%.

CONCLUSION

The significant higher risk of stroke with SLT use, even after adjustment for smoking, emphasizes the imperative need to include SLT cessation advice for control and prevention of stroke.

Role of Chromatin Architecture in Plant Stress Responses: An Update

Sessile plants possess an assembly of signaling pathways that perceive and transmit environmental signals, ultimately resulting in transcriptional reprogramming. Histone is a key feature of chromatin structure. Numerous histone-modifying proteins act under different environmental stress conditions to help modulate gene expression. DNA methylation and histone modification are crucial for genome reprogramming for tissue-specific gene expression and global gene silencing. Different classes of chromatin remodelers including SWI/SNF, ISWI, INO80, and CHD are reported to act upon chromatin in different organisms, under diverse stresses, to convert chromatin from a transcriptionally inactive to a transcriptionally active state. The architecture of chromatin at a given promoter is crucial for determining the transcriptional readout. Further, the connection between somatic memory and chromatin modifications may suggest a mechanistic basis for a stress memory. Studies have suggested that there is a functional connection between changes in nuclear organization and stress conditions. In this review, we discuss the role of chromatin architecture in different stress responses and the current evidence on somatic, intergenerational, and transgenerational stress memory.

In vitro activity of reconstituted rubisco enzyme from Gloeobacter violaceus

RuBisCO (Ribulose 1,5 bisphosphate carboxylase/oxygenase) by virtue of its dual specificity towards oxygen and carbon dioxide is an important rate-limiting step in photosynthesis and is believed to be the key factor for limited productivity of higher plants and algae. The photoautotrophic growth rate of cyanobacteria is a culmination of several factors including, rates of photosynthetic reactions, stress combating mechanisms and basic biomass generation metabolism in combination with optimal nutrient availability, irradiance, gaseous environment, etc. In case of cyanobacteria, the effect of RuBisCO in affecting the multiplication rate has been observed to show varied response. The current paper presents the RuBisCO activity of an early diverging cyanobacterium, Gloeobacter violaceus PCC 7421 and also compares the growth rates and RuBisCO activity of various cyanobacteria. A spectrophotometric estimation in a coupled enzyme assay system of the heterologous expressed G. violaceus PCC 7421 RuBisCO in E. coli, upon purification, revealed a carboxylation activity of LSu to be 5 nMol of phosphoglycerate min^-1 mg^-1 of protein, which is in coherence with the organism's slow growth rate. Further, the in vitro complementation of RbcL with RbcS in presence of RbcX of G. violaceus facilitated partial reconstitution of the protein and was hence found to cause a four-fold enhancement in its specific activity. The unique characteristics of the primitive cyanobacteria, such as, absence of thylakoids, lack of several photosystem constituting genes, slow carboxylation rate, pose limitation for its rapid multiplication. The RuBisCO carboxylation rate is observed as not the sole but an important parameter for obtaining optimal cell multiplication rates in photo-autotrophically multiplying cyanobacteria.

Co-expression network analysis of protein phosphatase 2A (PP2A) genes with stress-responsive genes in Arabidopsis thaliana reveals 13 key regulators

Abiotic and biotic stresses adversely affect plant growth and development and eventually result in less yield and threaten food security worldwide. In plants, several studies have been carried out to understand molecular responses to abiotic and biotic stresses. However, the complete circuitry of stress-responsive genes that plants utilise in response to those environmental stresses are still unknown. The protein phosphatase 2A (PP2A) gene has been known to have a crucial role in abiotic and biotic stresses; but how it regulates the stress response in plants is still not known completely. In this study, we constructed gene co-expression networks of PP2A genes with stress-responsive gene datasets from cold, drought, heat, osmotic, genotoxic, salt, and wounding stresses to unveil their relationships with the PP2A under different conditions of stress. The graph analysis identified 13 hub genes and several influential genes based on closeness centrality score (CCS). Our findings also revealed the count of unique genes present in different settings of stresses and subunits. We also formed clusters of influential genes based on the stress, CCS, and co-expression value. Analysis of cis-regulatory elements (CREs), recurring in promoters of these genes was also performed. Our study has led to the identification of 16 conserved CREs.

Glutathione S-transferase: a versatile protein family

Glutathione-S transferase (GST) is a most ancient protein superfamily of multipurpose roles and evolved principally from gene duplication of an ancestral GSH binding protein. They have implemented in diverse plant functions such as detoxification of xenobiotic, secondary metabolism, growth and development, and majorly against biotic and abiotic stresses. The vital structural features of GSTs like highly divergent functional topographies, conserved integrated architecture with separate binding pockets for substrates and ligand, the stringent structural fidelity with high Tm values (50º-60º), and stress-responsive cis-regulatory elements in the promoter region offer this protein as most flexible plant protein for plant breeding approaches, biotechnological applications, etc. This review article summarizes the recent information of GST evolution, and their distribution and structural features with emphasis on the assorted roles of Ser and Cys GSTs with the signature motifs in their active sites, alongside their recent biotechnological application in the area of agriculture, environment, and nanotechnology have been highlighted.

Evaluation of Web Portal for Improving Cancer Awareness in General Population in India

Background: With details on various cancers and recent advances in cancer prevention, a Web portal was developed to create awareness and value added education among Web-users in general population in villages, small towns and large cities of India. Aim: The Web portal aims at bringing awareness at the 3 levels of health related education program delivery success/efficacy triangle. The 1st level is cognitive learning of just being aware of cancer & basic knowledge. The 2nd level is a positive effect to be able to adopt life style changes that will lead to habit changes in diet, substance abuse and other life style habits and adherence to prescribed treatment. The 3rd level is actual behavioral change. Methods: A mixed methods study design incorporating etic-emic & qualitative research methodology and quantitative cross-sectional methods. We also used focused group discussions and in-depth interviews as part of qualitative study designs. Results: On the basis of data from the 100 participants, the Web portal was found to have improved attitudes toward accessing information related to cancer in participants. There was also an increase in the knowledge of the people, both general population and level 1 healthcare worker as compared with their previous knowledge about cancer. Also found was improvement in knowledge about the prevalent cancers, their screening procedures and general measures of prevention and treatment. Conclusion: On the basis of participants evaluated, we found that the Web portal may have a positive effect on cancer awareness of general population. Participants found the Web portal as a relevant tool to access information in the feedback. The comprehensive data which will be available after feedback from all participants, will help in understanding the nature of user´s response to Web based resources and its implications in improving lifestyle choices and promoting early screening & early detection of cancer.

Qiwam: A Potential Carcinogenic Smokeless Tobacco Product Consumed With Paan

Background: Qiwam (Kimam) is a liquid tobacco preparation consumed with paan. It is mostly consumed in southeast Asian region. Evidences suggest that it causes potentially malignant disorders (PMD), oral cancer (OC) and decreases sperm count. Qiwam was mentioned in earlier research publications, however details are not known. It is produced for self-consumption as well as for commercial purpose. Aim: To study in detail the ingredients and processing steps involved in the production of Qiwam. In addition, also study the adverse health implication of this smokeless tobacco product on humans. Methods: The information on qiwam was collected via literature search study, study tour to different geographical areas of India, where group discussions with the people involved in the production of qiwam, paan vendors and with community members of different age group were done. Results: Qiwam is prepared by the user for his/her own consumption or by industry for sale. Tobacco leaves and tobacco roots are boiled for several hours then soaked in water flavored with varied spices and additives. The resultant mixture is mashed, strained, and finally dried into a thick paste. It is consumed mostly with paan. Conclusion: Processing of qiwam is a complex and time taking process which involves various steps and components that may influence the carcinogenic property of the product. The different processing steps gives different taste and texture to the product. Qiwam increases the risk of cancer and hence needs to be banned or better avoided.

Using Social Media as an Effective Tool for Motivating Cancer Prevention

Background: Cancer is among leading cause of death (8.8 million) worldwide. Around 14.2 million new cases were recorded in 2012 and increasing each year. On the other hand there are about 2.8 billion users of different social media platforms (i.e., 37% of the world population). This tremendous power of social media can be used for disseminating effective information and communication on cancer prevention more efficiently (i.e., in less time to more people) to create awareness against the disease. Tobacco, alcohol and food industry have been using social media for aggressive advertising and marketing of their products. There is an urgent need to maximally use this medium of communication for advancing cancer prevention globally. Aim: To assess the role of social media in implementing effective health promotion strategies to advance cancer prevention. Methods: Extensive Web search has been done on the way social media (e.g., Facebook) is used for advancing public health communication and how it has been leveraged in the field of cancer prevention. Several Facebook pages and groups, YouTube channels were analyzed thoroughly. Various reports and articles on social media have been reviewed and analyzed. Results: Social media has been found very effective in terms of engaging greater number of population globally. Many Facebook pages and groups are available that provide information regarding specific cancer or provide support for cancer survivors. Several informative videos related to cancer prevention and survivors' stories are broadcast on various YouTube channels run by individuals, government, and nongovernment organizations. There have been many Instagram accounts on cancer but many of them don't provide relevant information on cancer prevention. However, genuine and relevant information are available through several Twitter handles. These social media platforms have very high penetration power. Facebook, YouTube, Instagram and Twitter have monthly reach to more than 1871, 1000, 500 and 263 million users respectively. This large number of user base can become a great source of spreading information on various aspects of cancer prevention through a comprehensive social media campaign. Conclusion: Social media platforms improve outreach and can also help carrying the relevant preventive health messages on cancer prevention, not only for the cancer patient but the public at large. Social media will help in amplifying the messages to the global mass while motivating prevention and health promotion to achieve public health objectives.

Relationship Between Smokeless Tobacco and Cervical Premalignant and Malignant Lesions Among the Patients Screened for Cervical Cancer in the Health Promotion Clinic, Noida

Background: Global Adult Tobacco Survey (GATS-2) India (2016-17), reported that 5.1 crore rural women and 1.4 crore urban women use tobacco in any form. Cervical cancer is the second most common cancer in India among women accounting for 22.86% of all cancer cases in women and 12% of all cancer cases in both men and women. One woman dies of cervical cancer every 8 minutes in India. The risk of cervical intraepithelial neoplasia (CIN) was found to be increased with the women who smoke but the association between smokeless tobacco (SLT) and areca nut have not been adequately reported in the literature; hence this study was contemplated to bridge the literature gap. Aim: To find the association between SLT use and cervical premalignant and malignant lesions among those women screened for cervical cancer at Health Promotion Clinic. Methods: Retrospective analysis was performed on the electronically maintained records of the individuals screened for cervical cancer from February 2014 - February 2018 at the Health Promotion Clinic at National Institute of Cancer Prevention and Research (NICPR), Noida. All married women above 30 years of age were eligible to be screened for cervical cancer using visual inspection with acetic acid (VIA) and Papanicolaou (PAP) test, if any abnormality was found colposcopy was done, if required biopsy was performed for confirmation. The premalignant lesions were treated with thermocoagulation or loop electrosurgical excision procedure (LEEP) and those diagnosed of malignancy were referred to a tertiary care center for further treatment. The participant's data on sociodemographic status, tobacco use and results cervical cancer screening are maintained in an online electronic data capture system. Results: Out of 6538 individuals attended the Health Promotion Clinic, for their oral, breast and cervical cancer screening from February 2014 - February 2018, 5431 (83.1%) were females and 1107 (16.9%) were males. All the females with eligible criteria were screened for cervical cancer 5431. Among which 126 (2.3%) reported with the habit of smoking, 595 (11%) reported of SLT use and 52 (1%) reported of both smoking and SLT use. The SLT users were at a higher risk [odds ratio (OR)] of developing cervical lesions compared with the non-SLT users diagnosed by the PAP test 1.02 (1.020-1.028). Conclusion: Women consuming SLT are at high risk of developing cervical premalignant and malignant lesions compared with the non-SLT users.

Unbranded Carcinogenic Products From Indian Terrain

Background: The burden of cancers caused due to tobacco-related carcinogenic products is increasing at an alarming rate in India. Unlike the western world, where cancer-causing products are mostly smoked (such as cigarettes), in India it is mostly consumed as such without combustion. Such products are produced for self-consumption or for selling in the local markets within specific geographical locations. There is very little information available in the public search engines (PubMed) about such products (i.e., dohra [mixture of areca nut, catechu, edible lime, peppermint, cardamom, and some flavoring agents], tuibur [tobacco water sipped and retained in mouth for 5-10 minutes and then spit out], kaddipudi [fine powder of tobacco plant used as such, or in processed form, as bricks and blocks made with jaggery and water], and hogesoppu [tobacco leaf used by women either as such or with betel]). Aim: To study the (i) geographical distribution, (ii) varieties, (iii) production and (iv) adverse health effects of unbranded chewable or drinkable carcinogenic products from India. Methods: The information on unbranded carcinogenic products was collected via study tour to different geographical areas of India, via group discussions or telephonic talks with community members of different age groups. Results: Dohra is found in the state of Uttar Pradesh, India. It majorly contains areca nut which contains a carcinogenic compound - arecoline known for causing histologic changes in the oral mucosa. Tuibur is found in the state of Manipur and Mizoram. Evidence suggests that it contains tobacco which is rich in N-nitroso compounds known for causing systemic tumors. Kaddipudi and hogesoppu are found in the state of Karnataka. Both of them contain tobacco. Conclusion: Dohra, Tuibur, kaddipudi and hogesoppu are unbranded cancer-causing products used at specific geographical locations in India. Since these products contain carcinogenic compounds, their use should be avoided.

Attitudes and Perceptions of Health Care Providers About the Implementation of Population Based Cancer Screening Program in India. A study From Assam

Background: India is facing noncommunicable diseases epidemic with cancer as one of the main reasons of mortality. To bring this epidemic under control and as a measure of secondary prevention, government of India has rolled out operational framework for population cancer screening. As cancer screening is a new concept for Indian health care providers, this study focuses on the attitudes and perceptions of HCP from a district in Assam. Aim: To know the attitudes and perceptions of healthcare providers in Assam about the implementation of population based cancer screening program in India. Methods: This study was a part of ongoing Indian Council of Medical Research project at Cachar district, Assam. The study was conducted at Silchar, Assam and the study participants were attendees of the master trainers' workshop which was conducted for the pilot cancer screening program rolled out in Cachar district, Assam. Self-administered questionnaires were used to collect data from the health care providers on the last day of the training. Data were gathered from 58 participants. The participants were medical officers, auxillary nurse midwives (ANM), accredited social health activists (ASHA), staff nurses, nongovernmental organization (NGO) representatives and other health care providers from public health facilities. Results: Majority of the study participants agreed with the concept of screening. Half of the study participants stated that they could conduct screening comfortably along with their other responsibilities. Lack of human resources and an overburdened human resource were the main challenges foreseen in the implementation of the program. 91% of the participants wanted GOI to implement the cancer screening program. Majority of the health personnel were in favor of primary health center (PHC) as the first preferable site of population cancer screening followed by subcenter being second on preference for screening. One-third of study participants opined that screening should be done by specialist doctors. Almost one fifth of participants stated that ASHA should do the screening and almost same number of participants thought that medical officer at PHC should do the screening. Conclusion: This is the first pilot study on the population based cancer screening guidelines released by the government of India. The organized screening program is yet to be rolled out in the country. Though many challenges were foreseen by the healthcare providers in carrying out the population based cancer screening, majority were optimistic for the implementation of this screening program.

Development of Operational Framework for Management of Common Cancers in India

Background and context: Cancers of the breast, uterine cervix, and oral cavity are the 3 most common malignancies in India. Overall, they comprise around one third of >1 million cases diagnosed with cancer in India each year. An effective operational framework (OF) for early detection and screening programs should play a key role in reducing and managing the cancer burden in India. Aim: i. To provide guidelines to the clinicians, and public health practitioners for screening and early detection of breast, uterine cervix, and lip or oral cavity cancers in India. ii. To build guide/roadmap for policymakers involved in developing and implementing strategies for cancer control in India. Strategy/Tactics: In collaboration with the Center for Global Health at the U.S. National Cancer Institute, 25 scientific experts comprising researchers, public health leaders, medical and dental professionals from France, India, United States, and Zambia met at Indian Council of Medical Research (ICMR)-National Institute of Cancer Prevention and Research, to summarize the feasible options and relevant evidence for screening and early detection of common cancers in India. They came out with the operational framework Program/Policy process: Recognizing the key role that effective early detection and screening programs could have in reducing the cancer burden, the ICMR-National Institute of Cancer Prevention and Research, in collaboration with the U.S. National Cancer Institute Center for Global Health, held a workshop to summarize feasible options and relevant evidence for screening and early detection of common cancers in India. Outcomes: a. A publication in Lancet: Rajaraman P, Anderson BO, Basu P, et al: Recommendations for screening and early detection of common cancers in India. Lancet Oncol 16(7):e352-e361, 2015. b. State and PHC level trainings on operational framework started in each state for the primary health care providers. What was learned: The OF acts as a guide for policymakers, clinicians, and public health practitioners who are developing and implementing strategies in cancer control. Common and consistent OF will go a long way to chart out the intensity of the problem and to rectify it.

Biochemical Profiling of Smokeless Tobacco Product Kiwam at Different Processing Steps

Introduction: Kiwam (qiwam) is a partially fermented tobacco product consumed with betel quid (paan). The major constituents of this product are tobacco, saffron (zaffrani) and some other additives. It contains tobacco-specific nitrosamines (TSNA) which is considered as a cancer causing agent. To elucidate the carcinogenic property of kiwam, biochemical profiling of its constituents at different stages of processing is needed. The major processing steps involved in the formation of kiwam and biochemical profiling/changes at each processing step is still unknown. Aim: To describe the major processing steps and biochemical changes that occur at each processing step during the preparation of kiwam. Methods: Tobacco leaves and stems were washed with Millipore water so as to remove the dirt particles from the leaves and stems. It is then boiled in water followed by filtering of the constituents to remove the leaves and stem residues. The filtrate was again boiled to form a thick paste residue. The resultant paste was partially fermented through sun curing, and lastly, saffron along with specific additives was added. The samples from each step were analyzed for biochemical profiling through Continuous Flow Autoanalyzer using Flow View Solution 3700 Analyzer (version 1.2.2) software. Results: The biochemical changes at TSNA levels were observed at each processing steps. The detailed chemical profiling will be presented during the meeting. Conclusion: Kiwam is rich in TSNA and hence its use should be avoided.

Prevalence of Gul Use, Its Predictors and Association With Oral Potentially Malignant Disorders and Oral Cancer Development in the Users of Noida, India: A Cross-Sectional Study

Background: Oral cancer is the third most common cancer in India which is attributed to the high tobacco burden especially due to a myriad of smokeless tobacco (SLT) products available in the market. Gul/Gul manjan is a commercially-produced, tobacco-based dentifrice, indigenous to rural India and Bangladesh, and mainly used by women. It is both highly addictive and carcinogenic; yet its prevalence, reasons for use and association with oral potentially malignant disorders (OPMDs) and oral cancer are scarcely documented in literature, making this study the first of its kind. Aim: To determine the prevalence of Gul use, its predictors and resultant OPMDs and oral cancer in such consumers. Methods: A cross-sectional study was performed among 3452 individuals visiting the Institute's Oral Health Promotion Clinic between December 2016-March 2018. Their basic demographic details, tobacco use history and abnormalities found on oral examination, were documented in the clinical record form. Data pertaining to Gul users was subjected to further statistical analysis. Results: Of the total individuals screened, 2.9% (n=101, P < 0.001) consumed Gul (89.1% current and 10.9% former users), with majority female consumers (86.1%) from peri-urban Noida. It was used (up to 5 times daily) mainly to alleviate dental pain due to caries/endodontic lesions, which were present in 35.6% users ( P = 0.004). A statistically significant positive association was seen between Gul use and development of OPMDs ( P < 0.001) and oral cancer ( P = 0.001), with 7.9% (n=10; 70% Gul alone users) of the overall leukoplakias/preleukoplakias (n=127), and 7.1% (n=1, Gul alone user) of all the oral cancer cases (n=14), found in Gul users. The duration of Gul use ranged up to 25 years, indicating its high dependency. Conclusion: Gul use is relatively uncommon than other SLT products in India, even among males (the major group of tobacco consumers). Apart from teeth cleaning, Gul is a cheap, easily accessible antidote for acute dental pain relief (owing to nicotine-induced analgesia) among rural women who apply it multiple times daily onto the affected teeth and adjacent gum/mucosa, often leading to its dependency. Courtesy its significant carcinogenic potential which has been clearly reported here (OPMDs and oral cancer development among users), combating/preventing its production, easy availability (in spite of the complete ban on tobacco use in dentifrices) and consumption, is essential. Therefore, the public health challenge of prevention of the use of this form of SLT ie tobacco-based dentifrices, warrants greater interest and action than that has been received thus far, which in turn would contribute to the overall mission of oral cancer prevention.

Capacity Building in Cancer Screening Using ECHO (Extension for Community Healthcare Outcomes): Innovative and Cost-Effective Model

Background and context: Three most common cancers in India are breast, uterine cervix and oral cavity, together accounting for approximately 34% of all cancers. Ministry of Health and Family Welfare, India has released an operational guidelines for cancer screening last year and has urged all the states to roll out population based cancer screening at various health care levels. As per these guidelines, the existing health care providers (HCPs) at various facilities would be rolling out the population based cancer screening in the country. However, the existing HCPs lack the skills and are not trained in cancer screening. Considering the size of the country, it is neither a feasible nor economically viable to provide in-person training for all cadres of HCPs. The limitation is comprehensively overcome by ECHO (Extension for Community Healthcare Outcomes) model provides a cost effective way to exponentially expand the capacity to mentor and train these HCPs in cancer screening best practices. ECHO as per the motto to “move knowledge rather than patients or doctors”, uses widely available one to many video-conferencing technology, didactic presentations and case based learning techniques to mentor and support HCPs to implement best practices in the field. In teleECHO clinics expert teams at an academic “hub” partner with willing participants to participate in knowledge networks in which all teach and all learn. Aim: To train the health care providers in cancer screening through technology assisted learning. Strategy/Tactics: A structured training program was designed using ECHO platform for all HCPs in separate batches that included, gynecologists, dentists and community health workers (CHWs), by virtual training to address all issues while they roll out cancer screening in their communities. Program/Policy process: A structured course of 20 week-sessions' virtual (online) cancer screening training program for various cadres of health care providers was undertaken. A typical one hour of ECHO session consisted of 25-30 minutes of didactics by the expert followed by 2 case presentations by the spokes. A “Beginner´s program” was well received by the participants who requested us to take it ahead with “Advanced training program” for specialists. Outcomes: 58 participants completed the course in cancer screening. The pre- and posttraining knowledge evaluation demonstrated a significant increase in the knowledge gained by participants. What was learned: In a resource constrained environment it is feasible to develop a basic curriculum in cancer screening program and train and support, all cadres of HCPs. Rolling out a technology enabled model such as ECHO for teaching and training can enable the development of a population based cancer screening program.

Regulatory Compliance: A Challenge for Unbranded Smokeless Tobacco Products

Background: Smokeless tobacco (SLT) is available in many forms in India and is widely used by all social groups. SLT market in India is the world largest market. Over the last 2 decades, the SLT industry in India has grown immensely, mostly in cottage industry sector and unorganized sector. Several SLT products are self-made or mixed by users themselves. This presents a great challenge for regulation of such unbranded and loose products. Cancer of the oral cavity and the pharynx are a major public health problem in India. At least 90% of these cancers are caused by SLT products use. Aim: To study the challenges for unbranded SLT products in implementing the mandated regulatory compliances under the Indian Tobacco Control Law that applies to all tobacco products. Methods: The information on unbranded/loose SLT products was collected through literature search, field trips, discussions with SLT product vendors and with community members of different age group. Results: Several types of unbranded SLT products are sold both in urban and rural India. These unbranded products vary from state to state. In some cases they vary from 1 place to another within a state. Most of the unbranded products do not comply with the legal mandates of the Indian tobacco control (COTPA) and food safety (FSSA) laws that regulate sale of tobacco products. The biggest fall-out of unbranded sale is that there is no pictorial health warnings to warn the users about the ill effects of these SLT products as required under section 7 of COTPA. In addition these products also do not mention the minimum requirement of the packaging and labeling under the legal metrology law. In absence of the pictorial health warnings these SLT products become more accessible and affordable to minors. The FSSA prohibits use of tobacco and nicotine as ingredient in any food item, however, most of the unbranded SLT products are sold with added flavorings, condiments and spices which are classified as food. Conclusion: Strict implementation of the mandated regulatory provisions is needed to check the unrestricted sale of unbranded products. Noncompliant unbranded/loose SLT products should be confiscated as per the prescriptions of the existing tobacco control and food safety laws. Findings from this paper calls for development of policies that will prevent sale of unbranded/loose SLT products in India to protect the unsuspecting youth and other vulnerable group of population from these cancer traps.

Alternate Splicing in Head and Neck Cancer: An Update

Background: Alternate splicing (AS) is a regulatory process during gene expression that allows a single gene to code multiple proteins. Sequencing of RNA (RNA-Seq) is a high throughput technology, which has been used in various studies to identify AS mechanisms in head and neck cancer (HNC). Until date, there is no available review that could update us with the major outcomes from these studies. Aim: To perform a comprehensive literature search for AS studies on HNC via RNA-Seq. Methods: A systematic literature search was performed following PRISMA guidelines to give a complete picture of AS in HNC identified through RNA-Seq. In addition, comprehensive search was also performed to identify the bioinformatics softwares that analyses RNA-Seq data for finding AS in cancer. Results: Six studies were found that used RNA-Seq data for identifying AS events in HNC. Five softwares were used by these studies to identify AS events, of which Suppa and AltAnalyze can also categorize all four AS events to subtypes, i.e., cassette exon skipping (ES), intron retention (IR), mutually exclusive exon (MXE), and alternative 5′ and 3′ splice site (ASS). Additionally, SplAdder, ASprofile, JuncBASE, and MATS softwares have been used to identify and categorize AS events in cancers other than HNC. Conclusion: Alternate splicing in HNC is a complex regulatory process of gene expression. It can be studied through RNA-Seq using various bioinformatics softwares. SplAdder, ASprofile, JuncBASE, and MATS have been used to identify and characterize other cancers, but not implemented in HNC, and hence could be used for studying AS in HNC.

Optimization of PCR conditions for amplifying an AT-rich amino acid transporter promoter sequence with high number of tandem repeats from Arabidopsis thaliana

OBJECTIVE

The aim of the present study is to optimize the PCR conditions required to amplify the promoter sequence of an amino acid transporter having an AT-rich base composition with a high number of tandem repeats.

RESULT

Results show that successful amplification can be achieved by performing a 2-step PCR at a lower extension temperature of 65 °C for an increased extension period of 1.5 min/kb, with MgCl₂ concentration ranging from 2.5 to 3.0 mM. The results also suggest that the DNA concentration of about 25-30 ng/µl was essential to achieve this amplification.

Regulatory components of carbon concentrating mechanisms in aquatic unicellular photosynthetic organisms

This review provides an insight into the regulation of the carbon concentrating mechanisms (CCMs) in lower organisms like cyanobacteria, proteobacteria, and algae. CCMs evolved as a mechanism to concentrate CO₂ at the site of primary carboxylating enzyme Ribulose-1, 5-bisphosphate carboxylase oxygenase (Rubisco), so that the enzyme could overcome its affinity towards O₂ which leads to wasteful processes like photorespiration. A diverse set of CCMs exist in nature, i.e., carboxysomes in cyanobacteria and proteobacteria; pyrenoids in algae and diatoms, the C₄ system, and Crassulacean acid metabolism in higher plants. Prime regulators of CCM in most of the photosynthetic autotrophs belong to the LysR family of transcriptional regulators, which regulate the activity of the components of CCM depending upon the ambient CO₂ concentrations. Major targets of these regulators are carbonic anhydrase and inorganic carbon uptake systems (CO₂ and HCO₃^- transporters) whose activities are modulated either at transcriptional level or by changes in the levels of their co-regulatory metabolites. The article provides information on the localization of the CCM components as well as their function and participation in the development of an efficient CCM. Signal transduction cascades leading to activation/inactivation of inducible CCM components on perception of low/high CO₂ stimuli have also been brought into picture. A detailed study of the regulatory components can aid in identifying the unraveled aspects of these mechanisms and hence provide information on key molecules that need to be explored to further provide a clear understanding of the mechanism under study.

Towards combinatorial transcriptional engineering

The modular nature of the transcriptional unit makes it possible to design robust modules with predictable input-output characteristics using a ‘parts- off a shelf’ approach. Customized regulatory circuits composed of multiple such transcriptional units have immense scope for application in diverse fields of basic and applied research. Synthetic transcriptional engineering seeks to construct such genetic cascades. Here, we discuss the three principle strands of transcriptional engineering: promoter and transcriptional factor engineering, and programming inducibilty into synthetic modules. In this context, we review the scope and limitations of some recent technologies that seek to achieve these ends. Our discussion emphasizes a requirement for rational combinatorial engineering principles and the promise this approach holds for the future development of this field.

Role of habitat and great oxidation event on the occurrence of three multisubunit inorganic carbon-uptake systems in cyanobacteria

The oxygenase reaction catalyzed by RuBisCO became an issue only after the evolution of the oxygenic photosynthesis in cyanobacteria. Several strategies were developed by autotrophic organisms as an evolutionary response to increase oxygen levels to help RuBisCO maximize its net carboxylation rate. One of the crucial advancements in this context was the development of more efficient inorganic carbon transporters which could help in increasing the influx of inorganic carbon (Ci) at the site of CO₂ fixation.We conducted a survey to find out the genes coding for cyanobacterial Ci transporters in 40 cyanobacterial phyla with respect to transporters present in Gloeobacter violaceous PCC 7421, an early-diverging cyanobacterium. An attempt was also made to correlate the prevalence of the kind of transporter present in the species with its habitat. Basically, two types of cyanobacterial inorganic carbon transporters exist, i.e. bicarbonate transporters and CO₂-uptake systems. The transporters also show variation in context to their structure as some exist as single subunit proteins (BicA and SbtA), while others exist as multisubunit proteins (namely BCT1, NdhI₃ and NdhI₄). The phylogeny and dist ribution of the former have been extensively studied and the present analysis provides an insight into the latter ones. The in silico analysis of the genes under study revealed that their distribution was greatly influenced by the habitat and major environmental changes such as the great oxidation event (GOE) in the course of their evolution.

PP2C-like Promoter and Its Deletion Variants Are Induced by ABA but Not by MeJA and SA in Arabidopsis thaliana

Gene expression is mediated through interaction between cis regulatory elements and its cognate transcription factors. Cis regulatory elements are defined as non-coding DNA sequences that provide the binding sites for transcription factors and are clustered in the upstream region of genes. ACGT cis regulatory element is one of the important cis regulatory elements found to be involved in diverse biological processes like auxin response, salicylic acid (SA) response, UV light response, ABA response and jasmonic acid (JA) response. We identified through in silico analysis that the upstream region of protein phosphatase 2C (PP2C) gene has a distinct genetic architecture of ACGT elements. In the present study, the activation of the full length promoter and its deletion constructs like 900 base pair, 500 base pair, 400 base pair and NRM (Nathji Rajesh Mehrotra) were examined by stable transformation in Arabidopsis thaliana using β-glucuronidase as the reporter gene. Evaluation of deletion constructs of PP2C-like promoter was carried out in the presence of phytohormones like abscisic acid (ABA), SA and JA. Our result indicated that the full length and 900 base pair promoter-reporter constructs of PP2C-like promoter was induced in response to ABA but not to methyl jasmonate and SA.

Abscisic acid and abiotic stress tolerance - different tiers of regulation

Abiotic stresses affect plant growth, metabolism and sustainability in a significant way and hinder plant productivity. Plants combat these stresses in myriad ways. The analysis of the mechanisms underlying abiotic stress tolerance has led to the identification of a highly complex, yet tightly regulated signal transduction pathway consisting of phosphatases, kinases, transcription factors and other regulatory elements. It is becoming increasingly clear that also epigenetic processes cooperate in a concerted manner with ABA-mediated gene expression in combating stress conditions. Dynamic stress-induced mechanisms, involving changes in the apoplastic pool of ABA, are transmitted by a chain of phosphatases and kinases, resulting in the expression of stress inducible genes. Processes involving DNA methylation and chromatin modification as well as post transcriptional, post translational and epigenetic control mechanisms, forming multiple tiers of regulation, regulate this gene expression. With recent advances in transgenic technology, it has now become possible to engineer plants expressing stress-inducible genes under the control of an inducible promoter, enhancing their ability to withstand adverse conditions. This review briefly discusses the synthesis of ABA, components of the ABA signal transduction pathway and the plants' responses at the genetic and epigenetic levels. It further focuses on the role of RNAs in regulating stress responses and various approaches to develop stress-tolerant transgenic plants.

Patterns and evolution of ACGT repeat cis-element landscape across four plant genomes

BACKGROUND

Transcription factor binding is regulated by several interactions, primarily involving cis-element binding. These binding sites maintain specificity by means of their sequence, and other additional factors such as inter-motif distance and spacer specificity. The ACGT core sequence has been established as a functionally important cis-element which frequently regulates gene expression in synergy with other cis-elements. In this study, we used two monocotyledonous - Oryza sativa and Sorghum bicolor, and two dicotyledonous species - Arabidopsis thaliana and Glycine max to analyze the conservation of co-occurring ACGT core elements in plant promoters with respect to spacer distance between them. Using data generated from Arabidopsis thaliana and Oryza sativa, we also identified conserved regions across all spacers and possible conditions regulating gene promoters with multiple ACGT cis-elements.

RESULTS

Our data indicated specific predominant spacer lengths between co-occurring ACGT elements, but these lengths were not universally conserved across all species under analysis. However, the frequency distribution indicated local regions of high correlation among monocots and dicots. Sequence specificity data clearly revealed a preference for G at the first and C at the terminal position of a spacer sequence, suggesting that the G-box motif is the most prevalent for the ACGT class of promoters. Using gene expression databases, we also observed trends suggesting that co-occurring ACGT elements are responsible for gene regulation in response to exogenous stress. Conservation in patterns of ACGT (N) ACGT among orthologous genes also indicated the possibility that emergence of functional significance across species was a result of parallel evolution of these cis-elements.

CONCLUSIONS

Although the importance of ACGT elements has been acknowledged for several plant species, ours is the first study that attempts to compare their occurrence across four species and analyze conservation among them. The apparent preference for particular spacer distances suggest that these motifs might be implicated in important physiological functions which are yet to be identified. Variations in correlation patterns among monocots and dicots might arise out of differences in transcriptional regulation in the two classes. In accordance with literature, we established the involvement of co-occurring ACGT elements in stress responses and showed how this regulation differs with variation in the ACGT (N) ACGT motif. We believe that our study will be an essential resource in determining optimum spacer length and spacer sequence between ACGT elements for promoter design in future.

Evidence for directed evolution of larger size motif in Arabidopsis thaliana genome

Transcription control of gene expression depends on a variety of interactions mediated by the core promoter region, sequence specific DNA-binding proteins, and their cognate promoter elements. The prominent group of cis acting elements in plants contains an ACGT core. The cis element with this core has been shown to be involved in abscisic acid, salicylic acid, and light response. In this study, genome-wide comparison of the frequency of occurrence of two ACGT elements without any spacers as well as those separated by spacers of different length was carried out. In the first step, the frequency of occurrence of the cis element sequences across the whole genome was determined by using BLAST tool. In another approach the spacer sequence was randomized before making the query. As expected, the sequence ACGTACGT had maximum occurrence in Arabidopsis thaliana genome. As we increased the spacer length, one nucleotide at a time, the probability of its occurrence in genome decreased. This trend continued until an unexpectedly sharp rise in frequency of (ACGT)N25(ACGT). The observation of higher probability of bigger size motif suggests its directed evolution in Arabidopsis thaliana genome.

Can we reduce the cardiovascular risk in peritoneal dialysis patients?

Patients with end-stage renal disease (ESRD), including those treated with peritoneal dialysis (PD), have a high risk for death, particularly from cardiovascular (CV) causes. Traditional risk factors for CV disease – like hypertension, diabetes, and dyslipidemia - are highly prevalent, often severe, and more difficult to treat in dialysis patients. Development of strategies for CV risk reduction in dialysis patients is complicated by epidemiologic studies that demonstrate paradoxical associations of some of the traditional risk factors with mortality. The difficulty is enhanced by either a paucity or negative findings of studies that have tested risk modification by targeting traditional CV risk factors. It is also clear that neither the prevalence nor the severity of traditional risk factors explains the substantial increase in risk for death associated with ESRD; this has led to identification of several nontraditional risk factors. Among these, systemic inflammation, disordered mineral metabolism, and long-term CV risk from infectious complications appear the most promising. However, the evidence in favor of the importance of these risk factors is largely limited to observational studies. In this review, we present a critical analysis of the literature to assist the clinician to reduce the CV risk of ESRD patients treated with PD.

Condensin phosphorylated by the Aurora-B-like kinase Ark1 is continuously required until telophase in a mode distinct from Top2

Condensin is a conserved protein complex that functions in chromosome condensation and segregation. It has not been previously unequivocally determined whether condensin is required throughout mitosis. Here, we examined whether Schizosaccharomyces pombe condensin continuously acts on chromosomes during mitosis and compared its role with that of DNA topoisomerase II (Top2). Using double mutants containing a temperature-sensitive allele of the condensin SMC2 subunit cut14 (cut14-208) or of top2, together with the cold-sensitive nda3-KM311 mutation (in β-tubulin), temperature-shift experiments were performed. These experiments allowed inactivation of condensin or Top2 at various stages throughout mitosis, even after late anaphase. The results established that mitotic chromosomes require condensin and Top2 throughout mitosis, even in telophase. We then showed that the Cnd2 subunit of condensin (also known as Barren) is the target subunit of Aurora-B-like kinase Ark1 and that Ark1-mediated phosphorylation of Cnd2 occurred throughout mitosis. The phosphorylation sites in Cnd2 were determined by mass spectrometry, and alanine and glutamate residue replacement mutant constructs for these sites were constructed. Alanine substitution mutants of Cnd2, which mimic the unphosphorylated protein, exhibited broad mitotic defects, including at telophase, and overexpression of these constructs caused a severe dominant-negative effect. By contrast, glutamate substitution mutants, which mimic the phosphorylated protein, alleviated the segregation defect in Ark1-inhibited cells. In telophase, the condensin subunits in cut14-208 mutant accumulated in lumps that contained telomeric DNA and proteins that failed to segregate. Condensin might thus serve to keep the segregated chromosomes apart during telophase.

Designer promoter: an artwork of cis engineering

Advances in systematic computational biology and rapid elucidation of synergistic interplay between cis and trans factors governing transcriptional control have facilitated functional annotation of gene networks. The generation of data through deconstructive, reconstructive and database assisted promoter studies, and its integration to principles of synthetic engineering has started an era of designer promoters. Exploration of natural promoter architecture and the concept of cis engineering have not only enabled fine tuning of single or multiple transgene expression in response to perturbations in the chemical, physiological and environmental stimuli but also provided researchers with a unique answer to various problems in crop improvement in the form of bidirectional promoters.