Biomedical subjects

Yunchen Gong

Publications and source records attributed to Yunchen Gong.

4 recordsLinked to original sources

PubMed2025

The evolution of separate sexes in waterhemp is associated with surprising chromosomal diversity and complexity.

The evolution of separate sexes is hypothesized to occur through distinct pathways involving few large-effect or many small-effect alleles. However, we lack empirical evidence for how these different genetic architectures shape the transition from quantitative variation in sex expression to distinct male and female phenotypes. To explore these processes, we leveraged the recent transition of Amaranthus tuberculatus to dioecy within a predominantly monoecious genus, along with a sex-phenotyped population genomic dataset, and six newly generated chromosome-level haplotype phased assemblies. We identify a ~3 Mb region strongly associated with sex through complementary SNP genotype and sequence-depth-based analyses. Comparative genomics of these proto-sex chromosomes within the species and across the Amaranthus genus demonstrates remarkable variability in their structure and genic content, including numerous polymorphic inversions. No such inversion underlies the extended linkage we observe associated with sex determination. Instead, we identify a complex presence/absence polymorphism reflecting substantial Y-haplotype variation-structured by ancestry, geography, and habitat-but only partially explaining phenotyped sex. Just over 10% of sexed individuals show phenotype-genotype mismatch in the sex-linked region, and along with observation of leakiness in the phenotypic expression of sex, suggest additional modifiers of sex and dynamic gene content within and between the proto-X and Y. Together, this work reveals a complex genetic architecture of sex determination in A. tuberculatus characterized by the maintenance of substantial haplotype diversity, and variation in the expression of sex.

Haplotypes↗

PubMed2005

Alternative signaling pathways: when, where and why?

Alternative cell signal transduction pathways have been demonstrated in some experimental systems. The importance of their existence has not been completely appreciated. In this review we present the cases of alternative pathways resulted from a survey of the available experimental data. The alternative pathways could show different relationships, i.e., synergistic, redundant, additive, opposite and competitive effects. They could have distinct time courses and cell, organ, sex or species specification. Further, they could happen during physiological or pathological situations, and display differentiated sensitivity. These case studies together imply that alternative signal pathways could be involved in the regulation of cell functions at the pathway level. In-depth understanding of the importance of the alternative pathways will rely on building and exploration of mathematical models.

Sensitivity and Specificity↗

PubMed2003

Shc-dependent pathway is redundant but dominant in MAPK cascade activation by EGF receptors: a modeling inference.

In cell signaling cascades, one stimulus often leads to various physiological functions by multiple pathways. Perturbation of one pathway by blocking or overexpressing one of its components will result in changes in multiple pathways and multiple cell functions. Thus, it is important to reveal the relative contribution of each pathway to each function in order to assess the consequence of perturbations (e.g. drug delivery). By exploring an established mathematical model, the Shc-dependent pathway is found to be both redundant and dominant during activation of the mitogen-activated protein kinase cascade by epidermal growth factor receptor (EGFR). Its dominance results from the majority consumption of the common precursor ((EGF-EGFR*)2-GAP) by this pathway. The key steps for the dominance are the binding and phosphorylation of Shc. In conclusion, cells may prefer the long Shc-dependent pathway to the short Shc-independent pathway.

Adaptor Proteins, Vesicular Transport↗

PubMed2002

Chemical transformation is not rate-limiting in the reaction catalyzed by Escherichia coli 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase.

6-Hydroxymethyl-7,8-dihydropterin pyrophosphokinase (HPPK) catalyzes the transfer of pyrophosphate from ATP to 6-hydroxymethyl-7,8-dihydropterin (HMDP). Because HPPK is essential for microorganisms but is absent from human and animals, the enzyme is an excellent target for developing antimicrobial agent. Thermodynamic analysis shows that Mg(2+) is important not only for the binding of nucleotides but also for the binding of HMDP. Transient kinetic analysis shows that a step or steps after the chemical transformation are rate-limiting in the reaction catalyzed by HPPK. The pre-steady-state kinetics is composed of a burst phase and a steady-state phase. The rate constant for the burst phase is approximately 50 times larger than that for the steady-state phase. The latter is very similar to the k(cat) value measured by steady-state kinetics. A set of rate constants for the individual steps of the HPPK-catalyzed reaction has been determined by a combination of stopped-flow and quench-flow analyses. These results form a thermodynamic and kinetic framework for dissecting the roles of active site residues in the substrate binding and catalysis by HPPK.

Adenosine Triphosphate↗