Inference of genetic regulatory networks with regulatory hubs using vector autoregressions and automatic relevance determination with model selections

The inference of genetic regulatory networks (GRNs) reveals how genes interact with each other. A few genes can regulate many genes as targets to control cell functions. We present new methods based on the order-1 vector autoregression (VAR1) for inferring GRNs from gene expression time series. The methods use the automatic relevance determination (ARD) to incorporate the regulatory hub structure into the estimation of VAR1 in a Bayesian framework. Several sparse approximation schemes are applied to the estimated regression weights or VAR1 model to generate the sparse weighted adjacency matrices representing the inferred GRNs. We apply the proposed and several widespread reference methods to infer GRNs with up to 100 genes using simulated, DREAM4 in silico and experimental E. coli gene expression time series. We show that the proposed methods are efficient on simulated hub GRNs and scale-free GRNs using short time series simulated by VAR1s and outperform reference methods on small-scale DREAM4 in silico GRNs and E. coli GRNs. They can utilize the known major regulatory hubs to improve the performance on larger DREAM4 in silico GRNs and E. coli GRNs. The impact of nonlinear time series data on the performance of proposed methods is discussed.

Optimization of Mechanical Oil Expression from Sandbox (Hura crepitans Linn.) Seeds

Optimization of process variables has become very vital in oil extraction processes to obtain maximum oil yield from oilseeds and nuts. This work focussed on the optimization of process oil extraction process from sandbox seed by mechanical expression. Effects of moisture content, roasting temperature, roasting time, expression pressure and expression time on oil yield from sandbox seed was studied using a 5×5 Central Composite Rotatable Design of Response Surface Methodology experimental design. Results obtained were subjected to Analysis of Variance (ANOVA) and SPSS statistical tool at (p = 0.05). Optimum conditions predicted were validated by experiments. All the processing factors were significant at (p = 0.05) for the sandbox oil yield except roasting temperature. The experimental results and predicted values showed low deviation (0.01-0.62). Oil yields obtained from the sandbox seed at varying process conditions varied from 16.38-38.68%. The maximum oil yield of 38.68% was obtained when the sandbox seed was subjected to process conditions of 6% moisture content, 85°C roasting temperature, 15 min roasting time, expression pressure of 20 MPa and 8 min pressing time. Mathematical equations to predict sandbox seed oil yield at varying process conditions were developed with an R2 (0.8908). The optimum extractable oil yield of 38.95% was predicted for sandbox seed at processing conditions of 7.03% moisture content, 97.72°C roasting temperature, 11.32 min roasting time, 15.11 MPa expression pressure and 8.57 min expression time. The study results provide data for designs of process and equipment for oil extraction from sandbox and other oilseeds.

Plant-expressed virus-like particles reveal the intricate maturation process of a eukaryotic virus

Many virus capsids undergo exquisitely choreographed maturation processes in their host cells to produce infectious virions, and these remain poorly understood. As a tool for studying virus maturation, we transiently expressed the capsid protein of the insect virus Nudaurelia capensis omega virus (NωV) in Nicotiana benthamiana and were able to purify both immature procapsids and mature capsids from infiltrated leaves by varying the expression time. Cryo-EM analysis of the plant-produced procapsids and mature capsids to 6.6 Å and 2.7 Å resolution, respectively, reveals that in addition to large scale rigid body motions, internal regions of the subunits are extensively remodelled during maturation, creating the active site required for autocatalytic cleavage and infectivity. The mature particles are biologically active in terms of their ability to lyse membranes and have a structure that is essentially identical to authentic virus. The ability to faithfully recapitulate and visualize a complex maturation process in plants, including the autocatalytic cleavage of the capsid protein, has revealed a ~30 Å translation-rotation of the subunits during maturation as well as conformational rearrangements in the N and C-terminal helical regions of each subunit.

Turing–Hopf bifurcation and spatiotemporal patterns in a Gierer–Meinhardt system with gene expression delay

In this paper, we consider the dynamics of delayed Gierer–Meinhardt system, which is used as a classic example to explain the mechanism of pattern formation. The conditions for the occurrence of Turing, Hopf and Turing–Hopf bifurcation are established by analyzing the characteristic equation. For Turing–Hopf bifurcation, we derive the truncated third-order normal form based on the work of Jiang et al. [11], which is topologically equivalent to the original equation, and theoretically reveal system exhibits abundant spatial, temporal and spatiotemporal patterns, such as semistable spatially inhomogeneous periodic solutions, as well as tristable patterns of a pair of spatially inhomogeneous steady states and a spatially homogeneous periodic solution coexisting. Especially, we theoretically explain the phenomenon that time delay inhibits the formation of heterogeneous steady patterns, found by S. Lee, E. Gaffney and N. Monk [The influence of gene expression time delays on Gierer–Meinhardt pattern formation systems, Bull. Math. Biol., 72(8):2139–2160, 2010.]

Effect of leaf position and days post-infiltration on transient expression of colorectal cancer vaccine candidate proteins GA733-Fc and GA733-FcK in Nicotiana benthamiana plant

Immunization with thetumor-associated antigen GA733 glycoprotein, which is highly expressed in colorectal cancer, is considered to be a promising strategy for cancer prevention and treatment. We cloned a fusion gene of GA733 and immunoglobulin Fc fragment (GA733-Fc), and that of GA733-Fc and an endoplasmic reticulum retention motif (GA733-FcK) into the Cowpea mosaic virus (CPMV)-based transient plant expression vector, pEAQ-HT. Agrobacterium tumefaciens (LBA4404) transformed with the vectors pEAQ-HT-GA733-Fc and pEAQ-HT-GA733-FcK was infiltrated into the leaves of Nicotiana benthamiana plants. To optimize harvesting of leaf to express therapeutic glycoproteins both spatially and temporally, protein expression levels at various leaf positions (top, middle, and base) and days post-infiltration (dpi) were investigated. The GA733-Fc and GA733-FcK genes were detected in leaves at 1–10 dpi using PCR. As assessed by western blot, GA733-Fc and GA733-FcK were expressed at the highest levels in the top leaf position at 5 dpi, and GA733-FcK was expressed more than GA733-Fc. The proteins were successfully purified from infiltrated N. benthamiana leaves using protein A affinity chromatography. ELISA verified that an anti-GA733 antibody recognized both purified proteins. Thus, a functional GA733-Fc colorectal cancer vaccine protein can be transiently expressed using a CPMV virus-based vector, with an optimized expression time and leaf position post-infiltration.

Time Course of Renal Transcriptomics after Subchronic Exposure to Ochratoxin A in Fisher Rats

The mycotoxin ochratoxin A (OTA) is a potent nephrocarcinogen, mainly in male rats. The aim of this study was to determine the time course of gene expression (GeneChip® Rat Gene 2.0 ST Array, Affymetrix) in kidney samples from male and female F344 rats, treated daily (p.o) with 0.50 mg/kg b.w. (body weight) of OTA for 7 or 21 days, and evaluate if there were differences between both sexes. After OTA treatment, there was an evolution of gene expression in the kidney over time, with more differentially expressed genes (DEG) at 21 days. The gene expression time course was different between sexes with respect to the number of DEG and the direction of expression (up or down): the female response was progressive and consistent over time, whereas males had a different early response with more DEG, most of them up-regulated. The statistically most significant DEG corresponded to metabolism enzymes (Akr1b7, Akr1c2, Adh6 down-regulated in females; Cyp2c11, Dhrs7, Cyp2d1, Cyp2d5 down-regulated in males) or transporters (Slc17a9 down-regulated in females; Slco1a1 (OATP-1) and Slc51b and Slc22a22 (OAT) down-regulated in males). Some of these genes had also a basal sex difference and were over-expressed in males or females with respect to the other sex.

Effect of sampling time on somatic and germ cell mutations induced by acrylamide in gpt delta mice

Background Acrylamide (AA) is a rodent carcinogen and classified by the IARC into Group 2A (probable human carcinogen). AA has been reported to induce mutations in transgenic rodent gene mutation assays (TGR assays), the extent of which is presumed to depend on exposure length and the duration of expression after exposure. In particular, it is not clear in germ cells. To investigate mutagenicity with AA in somatic and germ cells at different sampling times, we conducted TGR assays using gpt delta transgenic mice. Results The male gpt delta mice at 8 weeks of age were treated with AA at 7.5, 15 and 30 mg/kg/day by gavage for 28 days. Peripheral blood was sampled on the last day of the treatment for micronucleus tests and tissues were sampled for gene mutation assays at day 31 and day 77, those being 3 and 49 days after the final treatment (28 + 3d and 28 + 49d), respectively. Another group of mice was treated with N-Ethyl-N-nitrosourea (ENU) at 50 mg/kg/day by intraperitoneal administration for 5 consecutive days and tissues were sampled at the day 31 and day 77 (5 + 26d and 5 + 72d). Frequencies of micronucleated erythrocytes in the peripheral blood significantly increased at AA doses of 15 and 30 mg/kg/day. Two- to three-fold increases in gpt mutation frequencies (MFs) compared to vehicle control were observed in the testes and lung treated with 30 mg/kg/day of AA at both sampling time. In the sperm, the gpt MFs and G:C to T:A transversions were significantly increased at 28 + 3d, but not at 28 + 49d. ENU induced gpt mutations in these tissues were examined at both 5 + 26d and 5 + 72d. A higher mutant frequency in the ENU-treated sperm was observed at 5 + 72d than that at 5 + 26d. Conclusions The gpt MFs in the testes, sperm and lung of the AA-treated mice were determined and compared between different sampling times (3 days or 49 days following 28 day-treatment). These results suggest that spermatogonial stem cells are less sensitive to AA mutagenicity under the experimental condition. Prolonged expression time after exposure to AA to detect mutagenicity may be effective in somatic cells but not in germ cells.