Biology Commons^™

Gmr42a07, Anuradha Venkatakrishnan Chimata, Oorvashi Roy Puli, Amit Singh

DVE Enhancer Sequences Utilized in GMR Line

dve enhancer 45284

• ID - GMR42A07
• Location - 2R: 18146520, 18150306
• Base pairs - 3786

Gmr36a10, Anuradha Venkatakrishnan Chimata, Oorvashi Roy Puli, Amit Singh

DVE Enhancer Sequences Utilized in GMR Line

dve enhancer 49373

• ID - GMR36A10
• Location - 2R: 18116788, 18120701
• Base pairs - 3913

Gmr40c09, Anuradha Venkatakrishnan Chimata, Oorvashi Roy Puli, Amit Singh

DVE Enhancer Sequences Utilized in GMR Line

dve enhancer

• ID - GMR40C09
• Location - 2R: 18132203, 18134987
• Base pairs - 2784

Gmr41f05, Anuradha Venkatakrishnan Chimata, Oorvashi Roy Puli, Amit Singh

DVE Enhancer Sequences Utilized in GMR Line

dve enhancer 50133

• ID - GMR41F05
• Location - 2R: 18139042, 18142672
• Base pairs - 3630

Gmr35a04, Anuradha Venkatakrishnan Chimata, Oorvashi Roy Puli, Amit Singh

DVE Enhancer Sequences Utilized in GMR Line

dve enhancer

• ID - GMR35A04
• Location - 2R: 18125755, 18128365
• Base pairs - 2610

Gmr39h01, Anuradha Venkatakrishnan Chimata, Oorvashi Roy Puli, Amit Singh

DVE Enhancer Sequences Utilized in GMR Line

dve enhancer 50066

• ID - GMR39H01
• Location - 2R: 18153797, 18156108
• Base pairs - 2311

Gmr42e10, Anuradha Venkatakrishnan Chimata, Oorvashi Roy Puli, Amit Singh

DVE Enhancer Sequences Utilized in GMR Line

dve enhancer

• ID - GMR42E10
• Location - 2R: 18133506, 18137474
• Base pairs - 3968

Gmr41c04, Anuradha Venkatakrishnan Chimata, Oorvashi Roy Puli, Amit Singh

DVE Enhancer Sequences Utilized in GMR Line

dve enhancer

• ID - GMR41C04
• Location -2R: 18143594, 18147064
• Base pairs - 3470

Gmr40c05, Anuradha Venkatakrishnan Chimata, Oorvashi Roy Puli, Amit Singh

DVE Enhancer Sequences Utilized in GMR Line

dve enhancer 45682

• ID - GMR40C05
• Location - 2R: 18141630, 18144381
• Base pairs - 2751

Gmr41h07, Anuradha Venkatakrishnan Chimata, Oorvashi Roy Puli, Amit Singh

DVE Enhancer Sequences Utilized in GMR Line

dve enhancer 46241

• ID - GMR41H07
• Location - 2R: 18150920, 18154671
• Base pairs - 3751

Gmr42h01, Anuradha Venkatakrishnan Chimata, Oorvashi Roy Puli, Amit Singh

DVE Enhancer Sequences Utilized in GMR Line

dve enhancer 48150

• ID - GMR42H01
• Location - 2R: 18158419, 18162751
• Base pairs - 4332

Total Rna Extraction From Transgenic Flies Misexpressing Foreign Genes To Perform Next Generation Rna Sequencing, Abijeet Singh Mehta, Agustin Luz-Madrigal, Jian-Liang Li, Panagiotis A. Tsonis, Amit Singh

Biology Faculty Publications

Due to absence of transgenic approaches in Notopthalmus Viridescens (newt), and conservation of genetic machinery across species, we generated transgenic Drosophila melanogaster to misexpress unique genes from newt. Novel newt genes cloned, and inserted at attP site in Drosophila were misexpressed ubiquitously using tubulin Gal-4. Sample (total RNA) for RNA sequencing was collected at 3rd instar larval stage during which major developmental events takes place in Drosophila. Total RNA was extracted, and purified using RNA clean and ConcentratorTM. RNA quality was quantitated by calculating absorbance at 260 nm (A260) and 280 nm (A280) wavelengths using Nanodrop 2000 spectrophotometer. Good quality …

Comparative Transcriptomic Analysis And Structure Prediction Of Novel Newt Proteins, Abijeet Singh Mehta, Agustin Luz-Madrigal, Jian-Liang Li, Panagiotis A. Tsonis, Amit Singh

Biology Faculty Publications

Notophthalmus viridescens (Red-spotted Newt) possess amazing capabilities to regenerate their organs and other tissues. Previously, using a de novo assembly of the newt transcriptome combined with proteomic validation, our group identified a novel family of five protein members expressed in adult tissues during regeneration in Notophthalmus viridescens. The presence of a putative signal peptide suggests that all these proteins are secretory in nature. Here we employed iterative threading assembly refinement (I-TASSER) server to generate three-dimensional structure of these novel Newt proteins and predicted their function. Our data suggests that these proteins could act as ion transporters, and be involved …

Assessing The Efficacy Of Seedling Planting As A Forest Restoration Technique In Temperate Hardwood Forests Impacted By Invasive Species, Michaela J. Woods, Meredith Cobb, Katie Hickle

Biology Faculty Publications

The emerald ash borer (Agrilus planipennis Fairmaire; EAB) is an invasive insect that causes mortality of trees in the genus Fraxinus, creating canopy gaps that may facilitate invasion by exotic plants. Planting native tree seedlings under EAB-infested Fraxinus may accelerate succession and preclude invasive plant expansion; however, the effectiveness of this approach has not been experimentally tested. We assessed understory seedling planting of Quercus rubra, Carya laciniosa, and Juglans cinerea in EAB-infested forests, where the invasive shrub Lonicera maackii (Amur honeysuckle) was removed. We tested whether the use of plastic tree shelters (“tree tubes”) or planting season (fall versus spring) …

Emergence Of Oxacillin Resistance In Stealth Methicillin-Resistant Staphylococcus Aureus Due To Meca Sequence Instability, Richard V. Goering, Erin A. Swartzendriber, Anne E. Obradovich, Isabella A. Tickler, Fred C. Tenover

Biology Faculty Publications

Staphylococcus aureus strains that possess a mecA gene but are phenotypically susceptible to oxacillin and cefoxitin (OS-MRSA) have been recognized for over a decade and are a challenge for diagnostic laboratories. The mechanisms underlying the discrepancy vary from isolate to isolate. We characterized seven OS-MRSA clinical isolates of six different spa types from six different states by whole-genome sequencing to identify the nucleotide sequence changes leading to the OS-MRSA phenotype. The results demonstrated that oxacillin susceptibility was associated with mutations in regions of nucleotide repeats within mecA. Subinhibitory antibiotic exposure selected for secondary mecA mutations that restored oxacillin resistance. …

Hippo Signaling In Cancer: Lessons From Drosophila Models, Kirti Snigdha, Karishma Sanjay Gangwani, Gauri Vijay Lapalikar, Amit Singh, Madhuri Kango-Singh

Biology Faculty Publications

Hippo pathway was initially identified through genetic screens for genes regulating organ size in fruitflies. Recent studies have highlighted the role of Hippo signaling as a key regulator of homeostasis, and in tumorigenesis. Hippo pathway is comprised of genes that act as tumor suppressor genes like hippo (hpo) and warts (wts), and oncogenes like yorkie (yki). YAP and TAZ are two related mammalian homologs of Drosophila Yki that act as effectors of the Hippo pathway. Hippo signaling deficiency can cause YAP- or TAZ-dependent oncogene addiction for cancer cells. YAP and TAZ are often activated …

Streptococcus Agalactiae Strains With Chromosomal Deletions Evade Detection With Molecular Methods, Isabella A. Tickler, Fred C. Tenover, Scott Dewell, Victoria M. Le, Rachel N. Blackman, Richard V. Goering, Amy E. Rogers, Heather Piwonka, Brittney D. Jung-Hynes, Derrick J. Chen, Michael J. Loeffelholz, Devasena Gnanashanmugam, Ellen Jo Baron

Biology Faculty Publications

Surveillance of circulating microbial populations is critical for monitoring the performance of a molecular diagnostic test. In this study, we characterized 31 isolates of Streptococcus agalactiae (group B Streptococcus [GBS]) from several geographic locations in the United States and Ireland that contain deletions in or adjacent to the region of the chromosome that encodes the hemolysin gene cfb, the region targeted by the Xpert GBS and GBS LB assays. PCR-negative, culture-positive isolates were recognized during verification studies of the Xpert GBS assay in 12 laboratories between 2012 and 2018. Whole-genome sequencing of 15 GBS isolates from 11 laboratories revealed …

Diversity Of Resistance Mechanisms In Carbapenem-Resistant Enterobacteriaceae At A Health Care System In Northern California, From 2013 To 2016, Fiona Senchyna, Rajiv L. Gaur, Johanna Sandlund, Cynthia Truong, Guillaume Tremintin, Dietmar Kültz, Carlos A. Gomez, Fiona B. Tamburini, Tessa Andermann, Ami Bhatt, Isabella A. Tickler, Nancy Watz, Indre Budvytiene, Gongyi Shi, Fred C. Tenover, Niaz Banaei

Biology Faculty Publications

The mechanism of resistance in carbapenem-resistant Enterobacteriaceae (CRE) has therapeutic implications. We comprehensively characterized emerging mechanisms of resistance in CRE between 2013 and 2016 at a health system in Northern California. A total of 38.7% (24/62) of CRE isolates were carbapenemase gene-positive, comprising 25.0% (6/24) blaOXA-48 like, 20.8% (5/24) bla_KPC, 20.8% (5/24) bla_NDM, 20.8% (5/24) bla_SME, 8.3% (2/24) bla_IMP, and 4.2% (1/24) bla_VIM. Between carbapenemases and porin loss, the resistance mechanism was identified in 95.2% (59/62) of CRE isolates. Isolates expressing bla_KPC were 100% susceptible to ceftazidime–avibactam, meropenem–vaborbactam, …

Regeneration Data: Rna Sequences, Abijeet Singh Mehta, Amit Singh

Regeneration data

Abstract for paper for which this research was collected: Notophthalmus viridescens (Red-spotted Newt) possess amazing capabilities to regenerate their organs and other tissues. Previously, using a de novo assembly of the newt transcriptome combined with proteomic validation, we identified a novel family of 5 protein members expressed in adult tissues during regeneration in Notophthalmus viridescens. Due to absence of transgenic approaches in the Notophthalmus, and conservation of genetic machinery across species, we generated transgenic Drosophila melanogaster to misexpress these genes.

Samples for RNA sequencing were collected at third instar larval (L3) developmental stage. Out of the total 36,099 …

Exploring The Efficacy Of Natural Products In Alleviating Alzheimer’S Disease Using Animal Models, Prajakta Deshpande, Neha Gogia, Amit Singh

Biology Faculty Publications

Alzheimer’s disease (hereafter AD) is a progressive neurodegenerative disorder that affects the central nervous system. There are multiple factors that cause AD, viz., accumulation of extracellular Amyloid-beta 42 plaques, intracellular hyper-phosphorylated Tau tangles, generation of reactive oxygen species due to mitochondrial dysfunction and genetic mutations. The plaques and tau tangles trigger aberrant signaling, which eventually cause cell death of the neurons. As a result, there is shrinkage of brain, cognitive defects, behavioral and psychological problems. To date, there is no direct cure for AD. Thus, scientists have been testing various strategies like screening for the small inhibitor molecule library …

Characterization Of A Morphogenetic Furrow Specific Gal4 Driver In The Developing Drosophila Eye, Ankita Sarkar, Neha Gogia, Kevin Farley, Lydia C. Payton, Amit Singh

Biology Faculty Publications

The ability to express a gene of interest in a spatio-temporal manner using Gal4-UAS system has allowed the use of Drosophila model to study various biological phenomenon. During Drosophila eye development, a synchronous wave of differentiation called Morphogenetic furrow (MF) initiates at the posterior margin resulting in differentiation of retinal neurons. This synchronous differentiation is also observed in the differentiating retina of vertebrates. Since MF is highly dynamic, it can serve as an excellent model to study patterning and differentiation. However, there are not any Gal4 drivers available to observe the gain- of- function or loss- of- function of a …

45442 (Gmr18d08), Neha Gogia, Ankita Sarkar, Amit Singh

Dpp Enhancer Sequences Utilized in GMR Line

dpp enhancer - 45442

• Id - GMR 18D08
• Location - 2L:2446783,2449086
• Base pairs – 2303 bp

45437 (Gmr18b08), Neha Gogia, Ankita Sarkar, Amit Singh

Dpp Enhancer Sequences Utilized in GMR Line

dpp enhancer - 45437

• Id - GMR18B08
• Location - 2L:2455899,2457734
• Base pairs – 1835 bp

47472 (Gmr16g02), Neha Gogia, Ankita Sarkar, Amit Singh

Dpp Enhancer Sequences Utilized in GMR Line

dpp enhancer - 47472

• Id - GMR16G02
• Location 2L:2425041, 2428154
• Base pairs – 3113 bp

48770 (Gmr17e04), Neha Gogia, Ankita Sarkar, Amit Singh

Dpp Enhancer Sequences Utilized in GMR Line

dpp enhancer - 48770

• Id - GMR17E04
• Location 2L: 2428913..2432834
• Base pairs – 3921 bp

48784 (Gmr17g08), Neha Gogia, Ankita Sarkar, Amit Singh

Dpp Enhancer Sequences Utilized in GMR Line

dpp enhancer - 48784

• Id - GMR 17G08
• Location 2L:2450278,2451074
• Base pairs – 796 bp

49283 (Gmr19c03), Neha Gogia, Ankita Sarkar, Amit Singh

Dpp Enhancer Sequences Utilized in GMR Line

dpp enhancer - 49283

• Id - GMR19C03
• Location - 2L:2440970,2444735
• Base pairs – 3765 bp

48839 (Gmr19b04), Neha Gogia, Ankita Sarkar, Amit Singh

Dpp Enhancer Sequences Utilized in GMR Line

dpp enhancer - 48839

• Id - GMR19B04,
• Location - 2L:2432214,2435785
• Base pairs – 3571 bp

45833 (Gmr19d09), Neha Gogia, Ankita Sarkar, Amit Singh

Dpp Enhancer Sequences Utilized in GMR Line

dpp enhancer - 45833

• Id - GMR19D09
• Location - 2L:2435128,2438996
• Base pairs – 3868 bp

The 'Pseudomonas Aeruginosa' Psl Polysaccharide Is A Social But Noncheatable Trait In Biofilms, Yasuhiko Irie, Aled E. Roberts, Kasper N. Kragh, Vernita D. Gordon, Jaime B. Hutchison, Rosalind J. Allen, Gavin Melaugh, Thomas Bjarnsholt, Stuart A. West, Stephen P. Diggle

Biology Faculty Publications

Extracellular polysaccharides are compounds secreted by microorganisms into the surrounding environment, and they are important for surface attachment and maintaining structural integrity within biofilms. The social nature of many extracellular polysaccharides remains unclear, and it has been suggested that they could function as either cooperative public goods or as traits that provide a competitive advantage. Here, we empirically tested the cooperative nature of the PSL polysaccharide, which is crucial for the formation of biofilms in Pseudomonas aeruginosa. We show that (i) PSL is not metabolically costly to produce; (ii) PSL provides populationlevel benefits in biofilms, for both growth and antibiotic …