Drying of post-harvest rough rice with silica gel: A preliminary investigation

Rice drying operations can encounter problems of over drying and losses in head rice yield (HRY) through the formation of fissures. Typical rice drying methods also utilize large volumes of expensive fossil fuels to dry the kernels. Drying of rice with a solid desiccant such as silica gel has several potential advantages that avoid some of these problems. Two cultivars of long-grain rough rice, ‘Cheniere’ and ‘Wells’ with harvest moisture contents of 17.8% and 22.0%, respectively, were dried over a 48-h period with various ratios of rough rice-to-silica gel. It was found that an intimate mixture of 3:1 rough rice to silica gel was sufficient to dry these rice lots to 12.5% and 14.3% within 12 h, respectively. Head rice yields of desiccant-dried rice showed no considerable differences from the control. Rough-rice drying curves for all rough rice-to-silica gel mixtures followed exponential relationships

Genome Empowerment for the Puerto Rican Parrot – Amazona vittata

A unique community-funded project in Puerto Rico has launched whole-genome sequencing of the critically endangered Puerto Rican Parrot (Amazona vittata), with interpretation by genome bioinformaticians and students, and deposition into public online databases. This is the first article that focuses on the whole genome of a parrot species, one endemic to the USA and recently threatened with extinction. It provides invaluable conservation tools and a vivid example of hopeful prospects for future genome assessment of so many new species. It also demonstrates inventive ways for smaller institutions to contribute to a field largely considered the domain of large sequencing centers

The identification of long non-coding RNA ZFAS1 through an exploratory RNA-sequencing analysis and its association with epithelial-to-mesenchymal transition in colon cancer adenocarcinoma.

Colorectal adenocarcinoma is the fourth most common cancer diagnosed worldwide and is a significant cause of morbidity and mortality. This dissertation performed an exploratory RNA-sequencing analysis comparing gene expression between colon adenocarcinoma tissue and paired normal colon epithelium. After identification of a number of lncRNAs that were increased in expression in colon adenocarcinoma compared to normal colon epithelium, we aimed to validate the expression and investigate their function in vitro. Specifically, we focused on the lncRNA ZFAS1 and its association with epithelial-to-mesenchymal transition. These studies found the following: 1. Seven candidate lncRNAs were identified from the exploratory RNA-sequencing analysis to be significantly increased in expression in colon adenocarcinoma, three of which ZFAS1, GAS5, and PVT1 were found to be significantly increased in colon adenocarcinoma compared to paired normal colon epithelium as examined by laser capture microdissection. 2. Both ZFAS1 and GAS5 are significantly increased in cytoplasm of cell lines compared to the nucleus, whereas PVT1 was more represented in the nucleus. As such there was significant knockdown of both ZFAS1 and GAS5 following transfection with siRNA. 3. Knockdown of ZFAS1 leads to decreased proliferation and migration in colon adenocarcinoma cell lines. In contrast, knockdown of GAS5 did not lead to a change in proliferation. We focused our subsequent investigation on ZFAS1. 4. ZFAS1 has a reciprocal relationship with miR-200b and miR-200c expression in vitro but not with three of the other experimentally verified miRNAs that bind ZFAS1. We also validated the functional effect of miR-200b and miR-200c mimics on decreasing cell migration. 5. ZFAS1 knockdown is associated with the functional changes on cellular phenotype through decreasing ZEB1 expression through miR-200 signaling, causing a subsequent increase in the expression of the epithelial marker, E-cadherin, and a decrease in the expression of the mesenchymal marker, vimentin. These findings demonstrate an association between ZFAS1 and miR-200/ZEB1/E-cadherin, vimentin signaling in EMT signaling in colon adenocarcinoma. In contrast to typical EMT signaling, ZFAS1 knockdown also leads to decreased cell proliferation suggesting its potential value as a therapeutic agent

Bvr-1, a Restriction Locus of a Type C RNA Virus in the Feline Cellular Genome: Identification, Location, and Phenotypic Characterization in Cat X Mouse Somatic Cell Hybrids

Somatic cell hybrids were constructed between BALB/c-RAG mouse cells and feline lymphoma cells by the hypoxanthine-aminopterin-thymidine selection scheme. RAG cells spontaneously produce an endogenous B-tropic type C virus. Cat-mouse hybrids preferentially segregate feline chromosomes and retain murine chromosomes,demonstrable by karyotypic and isozyme analyses. Despite the presence of the complete mouse genome, including the viral genome, virus production was diminished to 1-5% of the levels observed in RAG parents based upon particle-associated RNA-dependent DNA polymerase (reverse transcriptase) activity in the culture fluid. Thirty-seven hybrids made on four different occasions had suppressed virus levels, and no hybrids expressed parental virus levels. Reverse selection experiments on 6-thioguanine demonstrated that a restriction gene, tentatively named Bvr-1, was linked to the feline structural genes for hypoxanthine phosphoribosyltransferase (IMP:pyrophosphate phosphoribosyltransferase; EC 2.4.2.8) and glucose-6-phosphate dehydrogenase (D-glucose-6-phosphate:NADP+ 1-oxidoreductase; EC 1.1.1.49) in cats, probably on the X-chromosome. The genetic mode of action of Bvr-1 is trans dominant in restriction of murine leukemia virus. The restriction locus results in a block late in virus maturation but prior to release, since expression of antigens for viral structural proteins and mature budding particles is apparent on surfaces of restricted hybrid cells but not in high-speed pellets from culture fluid of restricted cells

An Analysis of Gene-Enzyme Variability in Natural Populations of Drosophila melanogaster and D. simulans

Nine populations of D. melanogaster and two populations of D. simulans were analyzed for polymorphism in 10 gene-enzyme systems by the technique of gel electrophoresis. In the eight natural populations of D. melanogaster, an average of 54% of the enzymes were polymorphic, and the average heterozygosity was 22.7%. An experimental population of D. melanogaster, which has been maintained in a laboratory cage for 20 years, showed levels of polymorphism equivalent to those of natural populations. The D. simulans populations had much less variability. The possible factors involved in maintaining these polymorphisms are discussed

DNA Recombination and Natural Selection Pressure Sustain Genetic Sequence Diversity of the Feline MHC Class I Genes

Sequence comparisons of seven distinct MHC class I cDNA clones revealed that feline class I molecules have a remarkable similarity to human HLA genes in their organization of functional domains as well as in the nonrandom partitioning of genetic variability according to the functional constraints ascribed to different regions of the MHC molecule. The distribution of the pattern of sequence polymorphism in the cat as compared with genetic diversity of human and mouse class I genes provides evidence for four coordinate factors that contribute to the origin and sustenance of abundant allele diversity that characterizes the MHC in the species. These include: (a) a gradual accumulation of spontaneous mutational substitution over evolutionary time; (b) selection against mutational divergence in regions of the class I molecule involved in T cell receptor interaction and also in certain regions that interact with common features of antigens; (c) positive selection pressure in favor of persistence of polymorphism and heterozygosity at 57 nucleotide residues that comprise the antigen recognition site; and (d) periodic intragenic (interallelic) and intergenic recombination within the class I genes. We describe a highly conserved 23-bp nucleotide sequence within the coding region of the first α-helix that separates two relatively polymorphic segments located in the α1 domain that may act as a template or hot spot for homologous recombination between class I alleles

Bvr-1, a Restriction Locus of a Type C RNA Virus in the Feline Cellular Genome: Pleiotropic Restriction of Endogenous BALB Virus in Cat x Mouse Somatic Cell Hybrids

Bvr-1 is a dominant X-linked feline gene which restricts the replication of B-tropic murineleukemia virus (B-MuLV) in somatic cell hybrids between murine BALB/c-RAG cells and FL-74 feline cells. Since the hybrids were originally derived by the hypoxanthine aminopterin thymidine selection scheme, counter selection experiments on 6-thioguanine result in preferential survival of hybrid cells which have spontaneously lost the feline X-chromosome on which is located the structural gene for hypoxanthine guanine phosphoribosyl transferase (IMP: pyrophosphate phosphoribosyl transferase, E.C. 2.4.2.8) and Bvr-1. Back selected Bvr-1- cells express high parental levels of B-MuLV. Bvr-1- effectively restricts the IdU-mediated induction of the endogenous xenotropic BALB virus (BALB: virus 2) but not the endogenous N-tropic virus (BALB: virus 1). Pleiotropic restriction of B-MuLV and X-MuLV, but not N-MuLV suggests that the viral targets of Bvr-1 (either viral components or functions in viral assembly) of the B-tropic and X-tropic endogenous BALB viruses are similar to each other but distinct from the target in the N-tropic virus. Very low levels of B-MuLV are detected in restricted cells, but this residual virus is not infectious in either NIH-3T3 or BALB-3T3 mouse cells which are genotypically Fv-1N/Fv-1N and Fv-1B/Fv-1B, respectively. Passage of residual virus through host cells without Fv-1 related restriction (SC-1) results in production of infectious B-MuLV indistinguishable from that produced by RAG parent cells

Host Genomic Influences on HIV/AIDS

The AIDS era has seen multiple advances in the power of genetics research; scores of host genetic protective factors have been nominated and several have translated to the bedside. We discuss how genomics may inform HIV/AIDS prevention, treatment and eradication