Identification of plant transcriptional activation domains.

Gene expression in Arabidopsis is regulated by more than 1,900 transcription factors (TFs), which have been identified genome-wide by the presence of well-conserved DNA-binding domains. Activator TFs contain activation domains (ADs) that recruit coactivator complexes; however, for nearly all Arabidopsis TFs, we lack knowledge about the presence, location and transcriptional strength of their ADs1. To address this gap, here we use a yeast library approach to experimentally identify Arabidopsis ADs on a proteome-wide scale, and find that more than half of the Arabidopsis TFs contain an AD. We annotate 1,553 ADs, the vast majority of which are, to our knowledge, previously unknown. Using the dataset generated, we develop a neural network to accurately predict ADs and to identify sequence features that are necessary to recruit coactivator complexes. We uncover six distinct combinations of sequence features that result in activation activity, providing a framework to interrogate the subfunctionalization of ADs. Furthermore, we identify ADs in the ancient AUXIN RESPONSE FACTOR family of TFs, revealing that AD positioning is conserved in distinct clades. Our findings provide a deep resource for understanding transcriptional activation, a framework for examining function in intrinsically disordered regions and a predictive model of ADs.

An Improved Toolkit of Gateway- and Gibson Assembly-Compatible Vectors for Protoplast Transfection and Agrobacterium-Mediated Plant Transformation.

Objective: Understanding the regulation and function of plant genes is essential for addressing the challenges faced by modern agriculture. Plant transformation, in conjunction with fluorescence microscopy, offers a powerful approach to investigate the dynamic behavior of plant genes and the proteins they encode. We previously developed a set of Gateway-compatible tissue-specific plant transformation vectors. In this paper we aim to expand the toolkit of vectors available for Agrobacterium-mediated plant transformation and protoplast transfection. Results: Here, we introduce new Agrobacterium-mediated plant transformation vectors by introducing additional fluorophores to create the pJRA vector series. Additionally, we introduce the pLCS series of vectors, a new set of modular Gateway- and Gibson assembly-compatible vectors designed for protoplast transfection. All described vectors are available from Addgene to serve as a resource for the plant research community.

High light and temperature reduce photosynthetic efficiency through different mechanisms in the C4 model Setaria viridis.

C4 plants frequently experience high light and high temperature conditions in the field, which reduce growth and yield. However, the mechanisms underlying these stress responses in C4 plants have been under-explored, especially the coordination between mesophyll (M) and bundle sheath (BS) cells. We investigated how the C4 model plant Setaria viridis responded to a four-hour high light or high temperature treatment at photosynthetic, transcriptomic, and ultrastructural levels. Although we observed a comparable reduction of photosynthetic efficiency in high light or high temperature treated leaves, detailed analysis of multi-level responses revealed important differences in key pathways and M/BS specificity responding to high light and high temperature. We provide a systematic analysis of high light and high temperature responses in S. viridis, reveal different acclimation strategies to these two stresses in C4 plants, discover unique light/temperature responses in C4 plants in comparison to C3 plants, and identify potential targets to improve abiotic stress tolerance in C4 crops.

Constitutive Overexpression of RAM1 Leads to an Increase in Arbuscule Density in Brachypodium distachyon.

Arbuscular mycorrhizal (AM) symbiosis is a mutually beneficial association of plants and fungi of the subphylum Glomeromycotina. Endosymbiotic AM fungi colonize the inner cortical cells of the roots, where they form branched hyphae called arbuscules that function in nutrient exchange with the plant. To support arbuscule development and subsequent bidirectional nutrient exchange, the root cortical cells undergo substantial transcriptional reprogramming. REDUCED ARBUSCULAR MYCORRHIZA1 (RAM1), previously studied in several dicot plant species, is a major regulator of this cortical cell transcriptional program. Here, we generated ram1 mutants and RAM1 overexpressors in a monocot, Brachypodium distachyon. The AM phenotypes of two ram1 lines revealed that RAM1 is only partly required to enable arbuscule development in B. distachyon Transgenic lines constitutively overexpressing BdRAM1 showed constitutive expression of AM-inducible genes even in the shoots. Following inoculation with AM fungi, BdRAM1-overexpressing plants showed higher arbuscule densities relative to controls, indicating the potential to manipulate the relative proportion of symbiotic interfaces via modulation of RAM1 However, the overexpressors also show altered expression of hormone biosynthesis genes and aberrant growth patterns, including stunted bushy shoots and poor seed set. While these phenotypes possibly provide additional clues about the scope of influence of BdRAM1, they also indicate that directed approaches to increase the density of symbiotic interfaces will require a more focused, potentially cell type specific manipulation of transcription factor gene expression.

Assessment of hospital based prevalence of oral cancer among population of Kanpur, Uttar Pradesh.

BACKGROUND: Oral cancer incidence depends on both qualitative and quantitative factors wherein the incidence of oral cancer in patients with smoking and tobacco chewing habit is 8.4 times higher than that of patients with no habit. AIM: To understand about the prevalence of oral cancer in population of Kanpur reported to the hospital and analyse the association with age, gender and tobacco habit. MATERIAL AND METHOD: All 320 cases of Squamous cell carcinoma diagnosed histopathologically, since January 2007 to December 2016, were retrieved from the archives and a retrospective study was conducted along with association with the variables such as age, gender, site, habit and histopathological type. RESULTS: A total of 71 cases were reported in the age group of 30-39 (22.18%) and 60 cases (18.75%) were seen to be below 30yrs. Among individuals with habit, 135 (42.18%) were tobacco chewers and smoking was prevalent in about 48 (15%). The prevalence was more in males 37 (15.22%). Amongst both males (44.03%) and females (48.05%) gingivo-buccal sulcus was the most common site. The least common site was seen to be lip with only 10 (3.12%) patients. Well differentiated squamous cell carcinoma was common in both males and females with 155 (63.78%) and 47 (61.03%) respectively. Poorly differentiated squamous cell carcinoma was only reported in 4(1.64%) males. CONCLUSION: Early detection of these oral cancers will enable appropriate clinical management and monitoring. Moreover, improving the incidence, mortality, and survival rates of oral cancer requires a multi-tier structural approach that targets society, dentists, communities, and the individual.

Awareness on cytology procedure in oral cancer detection among undergraduates: An institutional study.

BACKGROUND: The screening and the early detection of the premalignant and malignant lesions are the only means for controlling the oral cancer which is known to be one of the leading causes for mortality worldwide. Oral exfoliative cytology though not a substitute for biopsy can be a powerful tool for its early detection. Dental Surgeons can play a great role in this direction. AIMS AND OBJECTIVES: The present study was undertaken to assess the self-reported knowledge and attitude regarding the early detection of oral cancer and exfoliative cytology among the undergraduates of Rama Dental College, Kanpur. MATERIAL AND METHODS: A pretested questionnaire based cross sectional study consisting of twenty four questions was conducted among hundred randomly selected students from third year, final year and intern's batch. RESULTS: According to 73% of students biopsy was the special test done in oral cancer detection and only 59% had heard regarding oral cytology technique. Formalin was the fixative known for cytology smears among 61%. Significance of toluidine blue staining was not known by 62%. Seventy seven percent of students were not aware about classes of cytology reporting. Eighty six percent of students felt that the adequacy of training in cytology was lagging. CONCLUSION: This survey identified an existing gap in the knowledge among the dental students regarding cytology as a diagnostic aid in oral cancer detection. This emphasizes the need to provide training for undergraduates at clinical level on regular basis and also through CDE and oral can-cer detection workshops.