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A gene network-driven approach to infer novel pathogenicity-associated genes: application to Pseudomonas aeruginosa PAO1 (open access)

A gene network-driven approach to infer novel pathogenicity-associated genes: application to Pseudomonas aeruginosa PAO1

Article describes how within the genome of a pathogen is the information regarding factors responsible for its pathogenicity. the authors of the article developed a novel pipeline that uses standard protocol in combination with gene co-expression network of a pathogen constructed using publicly available RNA-Seq data sets.
Date: November 3, 2023
Creator: De, Ronika; Whiteley, Marvin & Aza, Rajeev K.
Object Type: Article
System: The UNT Digital Library
Using Machine Learning to Predict Genes Underlying Differentiation of Multipartite and Unipartite Traits in Bacteria (open access)

Using Machine Learning to Predict Genes Underlying Differentiation of Multipartite and Unipartite Traits in Bacteria

Article describes how, since the discovery of the second chromosome in the Rhodobacter spaeroides 2.4.1 in 1989 and the revelation of gene sequences, multipartite genomes have been reported in over three hundred bacterial species under nine different phyla. In this study, the authors have attempted to leverage machine learning as a means to identify the genetic factors that underlie the differentiation of bacteria with multipartite and unipartite genomes.
Date: November 13, 2023
Creator: Almalki, Fatemah; Sunuwar, Janak & Azad, Rajeev K.
Object Type: Article
System: The UNT Digital Library
Silicon versus Superbug: Assessing Machine Learning's Role in the Fight against Antimicrobial Resistance (open access)

Silicon versus Superbug: Assessing Machine Learning's Role in the Fight against Antimicrobial Resistance

Article describes how, in his 1945 Nobel Prize acceptance speech, Sir Alexander Fleming warned of antimicrobial resistance (AMR) if the necessary precautions were not taken diligently. This paper explores the applications of ML in predicting and understanding AMR, highlighting its potential in revolutionizing healthcare practices.
Date: November 8, 2023
Creator: Coxe, Tallon & Azad, Rajeev K.
Object Type: Article
System: The UNT Digital Library
Lipid Droplets: Packing Hydrophobic Molecules Within the Aqueous Cytoplasm (open access)

Lipid Droplets: Packing Hydrophobic Molecules Within the Aqueous Cytoplasm

Article discusses how lipid droplets, also known as oil bodies or lipid bodies, are plant organelles that compartmentalize neutral lipids as a hydrophobic matrix covered by proteins embedded in a phospholipid monolayer. The authors review the growing body of knowledge about lipid droplets in plant cells, describe the evolutionary similarity and divergence in their associated subcellular machinery, and point to gaps that deserve future attention.
Date: November 22, 2022
Creator: Guzha, Athanas; Whitehead, Payton; Ischebeck, Till & Chapman, Kent Dean
Object Type: Article
System: The UNT Digital Library
The protein conformational basis of isoflavone biosynthesis (open access)

The protein conformational basis of isoflavone biosynthesis

Authors of the article assert that isoflavonoids play important roles in plant defense and also exhibit a range of mammalian health-promoting activities. They emphasize that understanding the structural basis of isoflavone biosynthesis will facilitate the engineering of new bioactive isoflavonoids.
Date: November 15, 2022
Creator: Wang, Xiaoqiang; Pan, Haiyun; Sagurthi, Someswar; Paris, Vincent; Zhuo, Chunliu & Dixon, R. A.
Object Type: Article
System: The UNT Digital Library
Prebiotic/probiotic supplementation resulted in reduced visceral fat and mRNA expression associated with adipose tissue inflammation, systemic inflammation, and chronic disease risk (open access)

Prebiotic/probiotic supplementation resulted in reduced visceral fat and mRNA expression associated with adipose tissue inflammation, systemic inflammation, and chronic disease risk

Article describes how prebiotic/probiotic supplementation represents a viable option for addressing elevated systemic inflammation and chronic disease risk in overweight individuals. The key findings support that 90-day prebiotic/probiotic supplementation may be associated with reduced adipose tissue inflammation, reduced systemic inflammation, and reduced chronic disease risk.
Date: November 28, 2022
Creator: McFarlin, Brian K.; Tanner, Elizabeth A.; Hill, David W. & Vingren, Jakob L.
Object Type: Article
System: The UNT Digital Library
The complexities of proanthocyanidin biosynthesis and its regulation in plants (open access)

The complexities of proanthocyanidin biosynthesis and its regulation in plants

Article describes how proanthocyanidins (PAs) are natural flavan-3-ol polymers that contribute protection to plants under biotic and abiotic stress, benefits to human health, and bitterness and astringency to food products. This review extends the conventional understanding with recent findings that provide new insights to address lingering questions and focus strategies for manipulating PA traits in plants.
Date: November 26, 2022
Creator: Yu, Keji; Song, Yushuang; Lin, Jinxing & Dixon, R. A.
Object Type: Article
System: The UNT Digital Library
Transcriptomic profiling of miR-203a inhibitor and miR-34b-injected zebrafish (Danio rerio) validates oil-induced neurological, cardiovascular and eye toxicity response pathways (open access)

Transcriptomic profiling of miR-203a inhibitor and miR-34b-injected zebrafish (Danio rerio) validates oil-induced neurological, cardiovascular and eye toxicity response pathways

Article discusses how the global sequencing of microRNA (miRNA; miR) and integration to downstream mRNA expression profiles in early life stages (ELS) of fish following exposure to crude oil determined consistently dysregulated miRNAs regardless of the oil source or fish species. The overlay of differentially expressed miRNAs and mRNAs into in silico software determined that the key roles of these miRNAs were predicted to be involved in cardiovascular, neurological and visually-mediated pathways.
Date: November 21, 2022
Creator: Maguson, Jason T.; Leads, Rachel R.; McGruer, Victoria; Qian, Le; Tanabe, Philip; Roberts, Aaron P. et al.
Object Type: Article
System: The UNT Digital Library
Reconstructing horizontal gene flow network to understand prokaryotic evolution (open access)

Reconstructing horizontal gene flow network to understand prokaryotic evolution

Article says that horizontal gene transfer (HGT) is a major source of phenotypic innovation and a mechanism of niche adaptation in prokaryotes. Methods for detecting HGT can be classified into phylogenetic-based and parametric or composition-based approaches, so authors exploited the complementary strengths of both the approaches to construct a high confidence horizontal gene flow network. The scale-free horizontal gene flow network presented here provides new insights into modes of transfer for the exchange of genetic information and also illuminates differential gene flow across phyla.
Date: November 30, 2022
Creator: Sungupta, Soham & Azad, Rajeev K.
Object Type: Article
System: The UNT Digital Library
A lipidomics platform to analyze the fatty acid compositions of non-polar and polar lipid molecular species from plant tissues: Examples from developing seeds and seedlings of pennycress (Thlaspi arvense) (open access)

A lipidomics platform to analyze the fatty acid compositions of non-polar and polar lipid molecular species from plant tissues: Examples from developing seeds and seedlings of pennycress (Thlaspi arvense)

Article describes a stepwise targeted lipidomics approach to characterize the polar and non-polar lipid classes using complementary LC-MS methods. This lipidomics workflow was applied to developing, mature, and germinated pennycress seeds/seedlings and found unexpected changes among several lipid molecular species.
Date: November 9, 2022
Creator: Romsdahl, Trevor B.; Cocuron, Jean-Christophe; Pearson, Mackenzie J.; Alonso, Ana Paula & Chapman, Kent Dean
Object Type: Article
System: The UNT Digital Library
Manipulating plasma thyroid hormone levels alters development of endothermy and ventilation in nestling red-winged blackbirds (open access)

Manipulating plasma thyroid hormone levels alters development of endothermy and ventilation in nestling red-winged blackbirds

Authors of the article propose that thyroid hormones play an important role in regulating development of endothermy during the nestling period in altricial birds. Their data suggests plasma thyroid hormone levels play an active role in the systemic development of endothermic capacity and the development of ventilatory control.
Date: November 29, 2022
Creator: Sirsat, Tushar S.; Sirsat, Sarah K. G.; Price, Edwan R.; Pineda, Megan & Dzialowski, Edward M. (Edward Michael)
Object Type: Article
System: The UNT Digital Library
Embryonic developmental oxygen preconditions cardiovascular functional response to acute hypoxic exposure and maximal β-adrenergic stimulation of anesthetized juvenile American alligators (Alligator mississippiensis) (open access)

Embryonic developmental oxygen preconditions cardiovascular functional response to acute hypoxic exposure and maximal β-adrenergic stimulation of anesthetized juvenile American alligators (Alligator mississippiensis)

Article investigating the effect of embryonic hypoxia on the cardiovascular phenotype of 4-year-old American alligators (Alligator mississippiensis). The findings indicate that embryonic hypoxia in crocodilians alters the cardiovascular phenotype, changing the juvenile response to acute hypoxia and β-adrenergic stimulation.
Date: January 26, 2018
Creator: Smith, Brandt R.; Crossley, Janna; Elsey, Ruth M.; Hicks, James W. & Crossley, Dane A., II
Object Type: Article
System: The UNT Digital Library
The future of legume genetic data resources: Challenges, opportunities, and priorities (open access)

The future of legume genetic data resources: Challenges, opportunities, and priorities

This article is a commentary on the future of legume genetic data resources and summarizes the workshop held in March of 2019 by the Legume Genomic Data Working Group that addressed questions of data resources and priorities for legumes.
Date: August 5, 2019
Creator: Legume Genomic Data Working Group
Object Type: Article
System: The UNT Digital Library
RNaseH-mediated simultaneous piggyback knockdown of multiple genes in adult zebrafish (open access)

RNaseH-mediated simultaneous piggyback knockdown of multiple genes in adult zebrafish

This article tests if it is possible to piggyback more than one antisense deoxyoligonucleotide (dO) with one vivo morpholino (VMO). The authors previously developed a piggyback knockdown method that was used to knockdown genes in adult zebrafish. In this article, the authors develop a method to knockdown three genes at one time, and by increasing the concentration of VMO by twofold, could knockdown six genes simultaneously. These multiple gene knockdowns will not only increase the efficiency of the method in whole genome-wide knockdowns but will also be useful to study multifactorial disorders.
Date: November 19, 2020
Creator: Raman, Revathi; Ryon, Mia & Jagadeeswaran, Pudur
Object Type: Article
System: The UNT Digital Library
Editorial: Biofuels and Bioenergy (open access)

Editorial: Biofuels and Bioenergy

Editorial on the research topic of biofuels and bioenergy.
Date: November 30, 2020
Creator: Barros-Rios, Jaime; Zhang, Jin & Lu, Mengzhu
Object Type: Article
System: The UNT Digital Library
Were domestic camelids present on the prehispanic South American agricultural frontier? An ancient DNA study (open access)

Were domestic camelids present on the prehispanic South American agricultural frontier? An ancient DNA study

Article testing the hypothesis that domesticated camelids occurred in prehispanic, southern Mendoza through analysis of ancient DNA.
Date: November 5, 2020
Creator: Johnson, Jeff A.; Kim, Tracy; Wolverton, Steven J.; Gil, Adolfo Fabian; Abbona, Cinthia Carolina & Adolfo, Gustavo Neme
Object Type: Article
System: The UNT Digital Library
CaMV35S promoter – A plant biology and biotechnology workhorse in the era of synthetic biology (open access)

CaMV35S promoter – A plant biology and biotechnology workhorse in the era of synthetic biology

This review article calls for establishing the CaMV 35S promoter as a quantitative reference standard for transcription activity in plants.
Date: November 18, 2020
Creator: Amack, Stephanie C. & Antunes, Mauricio S.
Object Type: Article
System: The UNT Digital Library
Role of ribosomal RNA released from red cells in blood coagulation in zebrafish and humans (open access)

Role of ribosomal RNA released from red cells in blood coagulation in zebrafish and humans

This article identifies that an rRNA released in hemolysis activates clotting in human and zebrafish plasma. Furthermore, it shows that fish Hgfac plays a role in rRNA-mediated activation of coagulation.
Date: November 17, 2021
Creator: Alharbi, Abdulmajeed; Iyer, Neha; Al Qaryoute, Ayah; Raman, Revathi; Burks, David J.; Azad, Rajeev K. et al.
Object Type: Article
System: The UNT Digital Library
Isorhamnetin Inhibits Proliferation and Invasion and Induces Apoptosis through the Modulation of Peroxisome Proliferator-activated Receptor γ Activation Pathway in Gastric Cancer (open access)

Isorhamnetin Inhibits Proliferation and Invasion and Induces Apoptosis through the Modulation of Peroxisome Proliferator-activated Receptor γ Activation Pathway in Gastric Cancer

Article investigating the potential effects of isorhamnetin (IH), a 3′-O-methylated metabolite of quercetin on the peroxisome proliferator-activated receptor γ (PPAR-γ) signaling cascade using proteomics technology platform, GC cell lines, and xenograft mice model. The study y proposes a novel agent for gastric cancer treatment.
Date: November 2, 2012
Creator: Ramachandran, Lalitha; Manu, Kanjoormana Aryan; Shanmugam, Muthu K.; Li, Feng; Siveen, Kodappully Sivaraman; Vali, Shireen et al.
Object Type: Article
System: The UNT Digital Library
Zebrafish Genetics: Functional Genomics captions transcript

Zebrafish Genetics: Functional Genomics

Video recording of Dr. Pudur Jagadeeswaran's presentation, "Zebrafish Genetics: Functional Genomics." It focuses on blood coagulation pathways in studying functional genomics. It was presented at the Transdisciplinary Ancestral Genomic Research Investigations (TAGRI) II Conference held online November 5-6, 2021.
Date: November 5, 2021
Creator: Jagadeeswaran, Pudur
Object Type: Video
System: The UNT Digital Library
Effect of increased embryonic temperature during developmental windows on survival, morphology and oxygen consumption of rainbow trout (Oncorhynchus mykiss) (open access)

Effect of increased embryonic temperature during developmental windows on survival, morphology and oxygen consumption of rainbow trout (Oncorhynchus mykiss)

This article applies a developmental 3-dimensional critical window experimental design for a vertebrate, using time, temperature, and phenotypic response (i.e., variables measured). To assess thermal effects on fish development, the authors examined trout hatchling phenotypes following rearing in constant temperatures (5, 10, 15 and 17.5 °C) and following exposure to increased temperature above 5 °C during specific developmental windows.
Date: November 2, 2020
Creator: Melendez, Christopher L. & Mueller, Casey A.
Object Type: Article
System: The UNT Digital Library
In situ cardiac performance of Atlantic cod (Gadus morhua) at cold temperatures: long-term acclimation, acute thermal challenge and the role of adrenaline (open access)

In situ cardiac performance of Atlantic cod (Gadus morhua) at cold temperatures: long-term acclimation, acute thermal challenge and the role of adrenaline

This article measures the cardiac performance of Newfoundland Atlantic cod (Gadus morhua). The results: (1) show that maximum performance of the isolated cod heart is not compromised by exposure to cold temperatures; and (2) support data from other studies, which show that, in contrast to salmonids, cod cardiac performance/myocardial contractility is not dependent upon humoral adrenergic stimulation.
Date: November 15, 2012
Creator: Lurman, Glenn J. & Petersen, L. H.
Object Type: Article
System: The UNT Digital Library
How Tiny Zebrafish and Their Surprisingly Human-Like Genome Can Benefit Medical Research captions transcript

How Tiny Zebrafish and Their Surprisingly Human-Like Genome Can Benefit Medical Research

Presentation highlighting the use of zebrafish to identify genes relating to predisposition to thromboembolism and cardiovascular disease in people with African ancestry. It was presented at the UNT Transdisciplinary Conference on Ancestral Genomics Research which was held virtually on November 20-21, 2020.
Date: November 21, 2020
Creator: Jagadeeswaran, Pudur
Object Type: Video
System: The UNT Digital Library
Targeting Peroxisome Proliferator-Activated Receptor-Gamma (PPARγ) Signaling Cascade for the Prevention and Treatment of Prostate Cancer (open access)

Targeting Peroxisome Proliferator-Activated Receptor-Gamma (PPARγ) Signaling Cascade for the Prevention and Treatment of Prostate Cancer

Article reviews PPARγ as an antitumor agent and summarizes the antineoplastic effects of PPARγ agonists in prostate cancer.
Date: November 14, 2012
Creator: Sikka, Sakshi; Chen, Luxi; Sethi, Gautam & Kumar, Alan Prem
Object Type: Article
System: The UNT Digital Library