Variations In Gene Products Research Articles

Modeling noise propagation in time-delayed auto-inhibitory genetic circuits

The abundance of specific protein molecules in genetically identical cell populations exposed to the same external environment can show remarkable cell-to-cell variations as biochemical reactions are inherently stochastic and occur with low numbers of molecular copies. Such variations in gene products are commonly known as gene expression noise. One of the mechanisms for cells to reduce such noise is auto-regulatory negative feedback (auto-inhibition), commonly found across organisms. This auto-inhibition is subjected to unavoidable time-delays associated with transcriptional and translational processes. Sufficient time-delays and strong auto-inhibition can generate sustained oscillations in gene products, which is a common mechanism for precise timekeeping in many biomolecular clocks. While the importance of time-delays in the generation of oscillations is well appreciated, its role in stochastic dynamics is not well understood in the absence of sustained oscillations. Here, we investigate the interplay between the feedback strength and the time-delay to study the noise propagation in the non-oscillatory regime using linear stability analysis, the linear noise approximation, and stochastic simulations. From a simple auto-regulatory model with one protein species (no delay), we systematically introduce one-step and two-step time-delays by incorporating intermediate dynamics with additional second and third species, respectively. Interestingly, the negative feedback in the presence of time-delay can show counterintuitive noise behavior to our common perception about its role as a noise buffer.

Allocation of gene products to daughter cells is determined by the age of the mother in single Escherichia coli cells.

Gene expression and growth rate are highly stochastic in Escherichia coli. Some of the growth rate variations result from the deterministic and asymmetric partitioning of damage by the mother to its daughters. One daughter, denoted the old daughter, receives more damage, grows more slowly and ages. To determine if expressed gene products are also allocated asymmetrically, we compared the levels of expressed green fluorescence protein in growing daughters descending from the same mother. Our results show that old daughters were less fluorescent than new daughters. Moreover, old mothers, which were born as old daughters, produced daughters that were more asymmetric when compared to new mothers. Thus, variation in gene products in a clonal E. coli population also has a deterministic component. Because fluorescence levels and growth rates were positively correlated, the aging of old daughters appears to result from both the presence of both more damage and fewer expressed gene products.

On the Genetic Architecture of Cytoplasmic Incompatibility: Inference from Phenotypic Data

Numerous insects carry intracellular bacteria that manipulate the insects' reproduction and thus facilitate their own spread. Cytoplasmic incompatibility (CI) is a common form of such manipulation, where a (currently uncharacterized) bacterial modification of male sperm induces the early death of embryos unless the fertilized eggs carry the same bacteria, inherited from the mother. The death of uninfected embryos provides an indirect selective advantage to infected ones, thus enabling the spread of the bacteria. Here we use and expand recently developed algorithms to infer the genetic architecture underlying the complex incompatibility data from the mosquito Culex pipiens. We show that CI requires more genetic determinants than previously believed and that quantitative variation in gene products potentially contributes to the observed CI patterns. In line with population genetic theory of CI, our analysis suggests that toxin factors (those inducing embryo death) are present in fewer copies in the bacterial genomes than antitoxin factors (those ensuring that infected embryos survive). In combination with comparative genomics, our approach will provide helpful guidance to identify the genetic basis of CI and more generally of other toxin/antitoxin systems that can be conceptualized under the same framework.

HLA DRB1*1503 allelic haplotype predominance and associated immunodysregulation in systemic lupus erythematosus

Systemic lupus erythematosus (SLE) is a chronic, relapsing, and remitting disease affecting primarily African American females of child bearing age. Familial aggregation of this disease suggests that at least part of the susceptibility for this disease is genetic, although environmental and hormonal influences are also likely to play a role. Early studies of genetic susceptibility to SLE revealed several of the major histocompatibility complex molecules, namely HLA DR, to be linked to SLE. Meta-analysis of genome scans has yielded loci significant for lupus patients, one of which includes the MHC region. Regulatory T cells are immunoregulatory cells that modulate activated immune cells. These cells play a large role in homeostasis of the immune responses and maintenance of immunologic tolerance, i.e., prevention of autoimmunity. Decreased numbers of regulatory T cells have been described in many autoimmune diseases, including systemic lupus erythematosus. Autoantibody production in systemic lupus erythematosus and the resulting immune complex formation and complex deposition into tissues are arguably the central core of immune dysregulation leading to disease manifestations and symptoms. Inability of the immune system to recognize and inhibit autoreactive immune cells in this particular autoimmune disease may be the result of inappropriate numbers and function of regulatory T cells. This study aims to characterize the immune cell population in patients from our community suffering from systemic lupus erythematosus and to prove that these patients exhibit a unique cellular profile compared to healthy age, race and gender matched control subjects. Surprisingly, our findings demonstrate that patients from the local Mississippi area exhibit increased proportions of CD25 + FoxP3 + regulatory T cells and CD25 + FoxP3 − T cells (of CD45 + CD3 + CD4 + helper T cells) as compared to healthy controls. HLA tissue-typing of these lupus patients revealed a prominent subgroup (~ 30%) of patients possessing the HLA DRB1*1503 allele. The investigation of this subgroup demonstrated regulatory T cell composition similar to that of the total lupus group and to that of the non-HLA DRB1*1503 subgroup. Genetic analysis for molecular gene expression levels of various lupus-associated genes by real-time PCR demonstrated a unique profile as compared to healthy controls. Increased gene expression of FoxP3 together with decreased gene expression levels of GATA3, TNFAIP3, and TNFSF4 suggest that variations in gene products compared to healthy controls may be playing a role in the immune cell dysregulation and disproportionate CD25 + FoxP3 + regulatory T cells.

Protein mapping and genome expression variations in the basidiomycete Agrocybe aegerita

A procedure suitable for the extraction and mapping of total proteins from the basidiomycete, Agrocybe aegerita, was developed. A. aegerita mycelia were fragmented either with a Dangoumeau grinder, an X-press bomb or a sonicator and the efficiency of these three disruption methods were compared. The extraction buffer composition was optimized to avoid proteolytic activities. 2D-SDS-PAGE analysis of protein extracts showed that the rate of reproducibility depending on extractions and electrophoretic separations was always greater than 96% for all strains. The differences in efficiency observed between the breaking procedures indicate that the A. aegerita cell wall is more mechanically resistant than that of other basidiomycetes. The efficient action of protease inhibitors (PMSF and SDS) showed that A. aegerita mycelia contains numerous and/or highly active proteases. Reproducibility of protein extraction and separation methods allowed the establishment and the comparison of standard maps. Qualitative and quantitative variations in gene products between a wild dikaryotic strain and 11 homokaryotic strains from its progeny were examined. The genetic diversity, determined by comparing the distribution of proteic variations in 11 homokaryons from the same progeny, was comparable to that observed between co-isogenic homokaryons of another basidiomycete.