Bioinformatics | News

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UF Researcher Dr. Marco Salemi Utilizes ICBR Genomics Expertise to Understand COVID19 Epidemiology

By Steven Madore, Ph.D.

In recent years, public health emergencies caused by epidemics have led to the use of genome sequencing to identify and characterize viral pathogens. Rapid acquisition of high quality viral genomic sequences is critical for understanding viral pathogen origin, transmission and epidemiological spread. Ultimately deciphering the molecular characteristics of viruses accelerates the development of diagnostic assays and vaccine development and drug design and is important in understanding the role of evolutionary variants in viral spread through the affected population.

This virus contains a single molecule of RNA that contains the genetic information to produce new progeny in infected cells. To determine the viral genome “code” viral (more…)

UF | ICBR Scientists Contribute to Clinical Trial Testing Novel Treatment for Canine Atopic Dermatitis

 

Atopic dermatitis, or AD, is a common chronic inflammatory skin disease affecting dogs, causing defects of the skin barrier and modifications of the normal cutaneous microflora. While multiple treatment options are available, there is a growing interest in the use of alternative natural ingredient products. In human AD reports show the potential benefits of topical applications of heat-killed beneficial bacteria, with some studies demonstrating the efficacy of rapidly killed beneficial lactobacilli in ameliorating clinical symptoms. A recent clinical trial led by Dr. Domenico Santoro and Clinical Trail Coordinator Lana Fagman from the UF Small Animal Clinical Sciences, College of Veterinary Medicine, and performed in collaboration with UF | ICBR scientists Drs. Yanping Zhang and Yu Fahong, investigated the efficacy of a spray version of a veterinary product containing heat killed lactobacilli (L. rhamnosus and L. reuteri) marketed as an adjuvant therapy for allergic dogs on the clinical signs of canine AD. This spray was applied once a day for 28 days on ten privately owned, mildly affected, dogs and clinical symptoms and skin microbiota analyzed. (more…)

UF Researchers to Use AI to Predict How Hurricanes Spread Invasive Plants

Courtesy of UF/IFAS
Written by Brad Buck

Scientists project hurricane intensity and frequency will increase with climate change. That leads researchers to want to better predict how storms will disperse and establish nonnative plant invaders.

Knowing where invasive plants spread will always be useful. But it may become especially handy soon as the National Hurricane Center is considering moving the official start of the Atlantic hurricane season two weeks earlier, starting it May 15, instead of June 1. Tropical Storm Arthur formed May 16 last year, marking six straight years a named storm formed before June 1. (more…)

UF offers powerful new NVIDIA supercomputer to students and researchers across State University System

Courtesy of UF NEWS
Written by Brittany Wise

University of Florida’s new supercomputer — the fastest artificial intelligence supercomputer in higher education — will soon be available for students and faculty across the State University System, UF Provost Joe Glover announced today.

The computer will give faculty and students from across the State unparalleled computing power in artificial intelligence (AI) to apply across many areas to improve lives, bolster industry, and create economic growth across the state. The supercomputer — known as HiPerGator AI — is based on an NVIDIA DGX SuperPOD of 140 DGX A100 systems and NVIDIA Mellanox HDR InfiniBand networking. (more…)

Excessive Heat Stroke Induces Long‐term Physiological Changes That are Linked to Altered Epigenetic Profiles

Epigenetics is the study of heritable phenotypic change that involves chemical modifications to the DNA genome sequence or associated DNA-binding proteins. These specific alterations affect how cells turn genes off or on. Exertional heat stroke (EHS) can cause long-term negative effects on health. Although epigenetic “reprogramming” of the genome is involved in the response to heat acclimation, it is not known whether the long-term effects of EHS are mediated by epigenetic reprogramming.

In a study supported by the Department of Defense, (more…)

BI Tongjun New Pub

Bioinformatics assistant scientist Tongjun Gu Ph.D. has developed a two-step logistic regression model for association studies where known factors can serve as controls.

The model is helpful for studies seeking to identify novel regulators in the RNA editing process where the dominant enzyme was found in the first step and served as a control in the second step.

Advantages of the model:

  • It considered the sequencing depth in the analysis.
  • It can be validated in the first step by the association of a biology phenomenon with the control gene, which is normally easy to obtain. Thus it is very useful, especially when the validation was difficult to be done in the second step.
  • It compares with the control gene, more confident and more functional novel regulators can be found.

(more…)

BI associate scientist contributes to two publications

Bioinformatics associate scientist Fahong Yu, Ph.D. provided research assistance in two recent publications (2019).

Oral epithelial cells (OEC) that line the oral cavity are the first line of defense against pathogenic organisms including viruses that infect the body through the oral route. The role of the OEC in triggering the immune response to viral infection is poorly understood. ICBR Bioinformatics expert Dr. Fahong Yu performed data analysis and was a key collaborator in a study performed in the laboratory of Dr. Gill Diamond in the UF Department of Oral Surgery. Dr. Diamond’s laboratory investigates the response of oral mucosal keratinocytes grown in culture to molecules that mimic viral infection.  OECs express basal levels of novel type I interferons IFNE and IFNK, while exposure to the viral mimic poly (I:C) induced interferon IFNB1 as well as other interferon‐stimulated genes.  These results were published in the journal Molecular Oral Microbiology and demonstrate that OECs exhibit a robust innate antiviral immune defense profile, which is primed to address a wide variety of pathogenic viruses that are transmitted orally. (more…)

BI assistant scientist develops a tool for stratifying cancer patients

Bioinformatics assistant scientist Tongjun Gu Ph.D. has developed an advanced deep learning method to stratify cancer patients into clinically relevant subgroups and further identify the potential biomarkers between the subgroups. This will help with the development of personalized treatments and prognosis.

The method can integrate multi-platform datasets like gene expression, miRNA expression, methylation, copy number alteration, and protein expression. It can also do transfer learning between different cancers. For example, in cancer types with smaller sample sizes, information can be borrowed from a cancer type with a larger sample size to subgroup it. (more…)