Life Sciences Commons^™

Tgmi: An Efficient Algorithm For Identifying Pathway Regulators Through Evaluation Of Triple-Gene Mutual Interaction, Chathura J. Gunasekara, Kui Zhang, Wenping Deng, Laura E. Brown, Hairong Wei

Michigan Tech Publications

Despite their important roles, the regulators for most metabolic pathways and biological processes remain elusive. Presently, the methods for identifying metabolic pathway and biological process regulators are intensively sought after. We developed a novel algorithm called triple-gene mutual interaction (TGMI) for identifying these regulators using high-throughput gene expression data. It first calculated the regulatory interactions among triple gene blocks (two pathway genes and one transcription factor (TF)), using conditional mutual information, and then identifies significantly interacted triple genes using a newly identified novel mutual interaction measure (MIM), which was substantiated to reflect strengths of regulatory interactions within each triple gene …

Growth Performance, Organ-Level Ionic Relations And Organic Osmoregulation Of Elaeagnus Angustifolia In Response To Salt Stress, Zhengxiang Liu, Jiangfeng Zhu, Xiuyan Yang, Haiwen Wu, Qi Wei, Hairong Wei, Huaxin Zhang

Michigan Tech Publications

Elaeagnus angustifolia is one of the most extensively afforested tree species in environment-harsh regions of northern China. Despite its exceptional tolerance to saline soil, the intrinsic adaptive physiology has not been revealed. In this study, we investigated the growth, organ-level ionic relations and organic osmoregulation of the seedlings hydroponically treated with 0, 100 and 200 mM NaCl for 30 days. We found that the growth characteristics and the whole-plant dry weight were not obviously stunted, but instead, were even slightly stimulated by the treatment of 100 mM NaCl. In contrast, these traits were significantly inhibited by 200 mM NaCl treatment. …

The Effect Of Poplar Psngs1.2 Overexpression On Growth, Secondary Cell Wall, And Fiber Characteristics In Tobacco, Tingting Lu, Lulu Liu, Minjing Wei, Yingying Liu, Zianshang Qu, Chuanping Yang, Hairong Wei, Zhigang Wei

Michigan Tech Publications

The glutamine synthetase (GS1) is a key enzyme that catalyzes the reaction of glutamate and ammonia to produce glutamine in the nitrogen (N) metabolism. Previous studies on GS1s in several plant species suggest that overexpression of GS1s can enhance N utilization, accelerate plant vegetative growth, and change wood formation. In this study, we isolated a GS1 gene, termed PsnGS1.2, from Populus simonii × Populus nigra. This gene was expressed at a higher level in roots, and relatively lower but detectable levels in xylem, leaves and phloem of P. simonii × P. nigra. The protein encoded by PsnGS1.2 is …

Bottom-Up Ggm Algorithm For Constructing Multilayered Hierarchical Gene Regulatory Networks That Govern Biological Pathways Or Processes, Sapna Kupari, Wenping Deng, Chathura J. Gunasekara, Vincent Chiang, Huann-Sheng Chen, Hairong Wei, Et. Al.

Michigan Tech Publications

Background: Multilayered hierarchical gene regulatory networks (ML-hGRNs) are very important for understanding genetics regulation of biological pathways. However, there are currently no computational algorithms available for directly building ML-hGRNs that regulate biological pathways.

Results: A bottom-up graphic Gaussian model (GGM) algorithm was developed for constructing ML-hGRN operating above a biological pathway using small- to medium-sized microarray or RNA-seq data sets. The algorithm first placed genes of a pathway at the bottom layer and began to construct an ML-hGRN by evaluating all combined triple genes: two pathway genes and one regulatory gene. The algorithm retained all triple genes where a regulatory …