Digital Absolute Gene Expression Analysis of Essential Starch-Related Genes in a Radiation Developed Amaranthus cruentus L. Variety in Comparison with Real-Time PCR

We investigated the expression pattern of four major starch genes at different seed developmental stages in the radiation-bred amaranth variety “Pribina” (Amaranthus cruentus L.) and corresponding control genotype “Ficha” (Amaranthus cruentus L.). Two platforms were used and compared for the gene expression analysis of GBSSI, SSSI, SBE, and DBE amaranth genes, including a standard quantitative real-time PCR (qPCR) technique and relatively novel droplet digital PCR (ddPCR) assay. In our conditions, both methods showed great accuracy and revealed higher expression of the investigated genes in the mutant variety than in the control genotype. Here we report for the first time, a ddPCR gene expression assay for the cultivated grain amaranth, as the most important group of the species in the genus Amaranthus.

Genetic deletion of the circadian clock transcription factor BMAL1 and chronic alcohol consumption differentially alter hepatic glycogen in mice

Multiple metabolic pathways exhibit time-of-day-dependent rhythms that are controlled by the molecular circadian clock. We have shown that chronic alcohol is capable of altering the molecular clock and diurnal oscillations in several elements of hepatic glycogen metabolism ( 19 , 44 ). Herein, we sought to determine whether genetic disruption of the hepatocyte clock differentially impacts hepatic glycogen content in chronic alcohol-fed mice. Male hepatocyte-specific BMAL1 knockout (HBK) and littermate controls were fed control or alcohol-containing diets for 5 wk to alter hepatic glycogen content. Glycogen displayed a significant diurnal rhythm in livers of control genotype mice fed the control diet. While rhythmic, alcohol significantly altered the diurnal oscillation of glycogen in livers of control genotype mice. The glycogen rhythm was mildly altered in livers of control-fed HBK mice. Importantly, glycogen content was arrhythmic in livers of alcohol-fed HBK mice. Consistent with these changes in hepatic glycogen content, we observed that some glycogen and glucose metabolism genes were differentially altered by chronic alcohol consumption in livers of HBK and littermate control mice. Diurnal rhythms in glycogen synthase (mRNA and protein) were significantly altered by alcohol feeding and clock disruption. Alcohol consumption significantly altered Gck, Glut2, and Ppp1r3g rhythms in livers of control genotype mice, with diurnal rhythms of Pklr, Glut2, Ppp1r3c, and Ppp1r3g further disrupted (dampened or arrhythmic) in livers of HBK mice. Taken together, these findings show that chronic alcohol consumption and hepatocyte clock disruption differentially influence the diurnal rhythm of glycogen and various key glycogen metabolism-related genes in the liver. NEW & NOTEWORTHY We report that circadian clock disruption exacerbates alcohol-mediated alterations in hepatic glycogen. We observed differential responsiveness in diurnal rhythms of glycogen and glycogen metabolism genes and proteins in livers of hepatocyte-specific BMAL1 knockout and littermate control mice fed alcohol. Our findings provide new insights into potential mechanisms by which alcohol alters glycogen, an important energy source for liver and other organs.

Host status and phenotypic diversity of rice genotypes in relation to Pratylenchus brachyurus resistance

The aim of this study was to assess the susceptibility of rice genotypes toPratylenchus brachyurusand investigate the inheritance of resistance in the crop. Two experiments were conducted under controlled conditions, using naturally infested soil. Twenty-six rice genotypes were assessed, with maize used to show the susceptibility pattern. The maize was cultivated for 90 days and the initial nematode population was determined. Then, rice genotypes were cultivated, and the final nematode population and the reproduction factor (RF) were estimated 90 days after germination. All genotypes were susceptible toP. brachyurusin the two experiments but only one showed statistical differences, indicating variation in susceptibility, and genotypes Linhagem L03-107 and Cateto Amarelo scored higher than the control genotype, with RF of 8.80 and 9.48, respectively. Inheritance of resistance was poorly influenced by genotype genetics. Cluster analysis allowed the identification of five different groups of genotypes but there was low genetic variability among the genotypes.

Threshold trait architecture of Hsp90-buffered variation

Common genetic variants buffered by Hsp90 are candidates for human diseases of signaling such as cancer. Like cancer, morphological abnormalities buffered by Hsp90 are discrete threshold traits with a continuous underlying basis of liability determining their probability of occurrence. QTL and deletion maps for one of the most frequent Hsp90-dependent abnormalities in Drosophila, deformed eye (dfe), were replicated across three genetically related artificial selection lines using strategies dependent on proximity to the dfe threshold and the direction of genetic and environmental effects. Up to 17 dfe loci (QTL) linked by 7 interactions were detected based on the ability of small recombinant regions of an unaffected and completely homozygous control genotype to dominantly suppress or enhance dfe penetrance at its threshold in groups of isogenic recombinant flies, and over 20 deletions increased dfe penetrance from a low expected value in one or more line, identifying a complex network of genes responsible for the dfe phenotype. Replicated comparisons of these whole-genome mapping approaches identified several QTL regions narrowly defined by deletions and 4 candidate genes, with additional uncorrelated QTL and deletions highlighting differences between the approaches and the need for caution in attributing the effect of deletions directly to QTL genes.

Post head-emergence frost resistance of barley genotypes in the northern grain region of Australia

Post head-emergence frost causes substantial losses for Australian barley producers. Varieties with improved resistance would have a significant positive impact on Australian cropping enterprises. Five barley genotypes previously tested for reproductive frost resistance in southern Australia were tested, post head-emergence, in the northern grain region of Australia and compared with the typical northern control cultivars, Gilbert and Kaputar. All tested genotypes suffered severe damage to whole heads and stems at plant minimum temperatures less than −8°C. In 2003, 2004 and 2005, frost events reaching a plant minimum temperature of ~−6.5°C did not result in the complete loss of grain yield. Rather, partial seed set was observed. The control genotype, Gilbert, exhibited seed set that was greater than or equal to that of any genotype in each year, as did Kaputar when tested in 2005. Thus, Gilbert and Kaputar were at least as resistant as any tested genotype. This contrasts with trial results from the southern grain region where Gilbert was reported to be less resistant than Franklin, Amagi Nijo and Haruna Nijo. Hence, rankings for post head-emergence frost damage in the northern grain region differ from those previously reported. These results indicate that Franklin, Amagi Nijo and Haruna Nijo are not likely to provide useful sources of frost resistance or markers to develop improved varieties for the northern grain region of Australia.

Disruption of Laminin-γ1 Expression Induces Rapid Decrease In Spleen Size.

Abstract 2596 Laminins are heterotrimeric proteins composed of an alpha, beta, and gamma subunit, and are expressed in a majority of organ systems, including hematopoietic and lymphoid tissues. Specific laminin subunits have been identified in prognostic stromal gene expression profiles from diffuse large B-cell lymphomas (Lenz et al. 2008). Laminin g1 is the gamma-subunit present in a majority of physiologically expressed laminin heterotrimers. Global laminin-g1 deficiency in mice is embryologically lethal at E5.5 and results in part from failure of the primordial basal lamina to form (Smyth et al. 1998). Conditional knockout mouse lines have therefore been developed to examine the role of laminin-g1 in specific tissues. Disruption of Schwann cell-specific expression of laminin-g1 prevents basal lamina formation within peripheral nerves, decreases glial cell proliferation, and increases glial cell apoptosis leading to a severe dysmyelinated phenotype (Chen and Strickland 2003; Yu et al. 2005). Here we present data that global disruption of laminin- g1 expression in adult animals induces involution of the spleen and suggests a fundamental role for laminins in maintenance of spleen integrity. Mice homozygous for the LoxP flanked laminin-g1 allele (floxed allele) were crossed with mice expressing a global Cre-ERT2 transgene. Mice homozygous or heterozygous for the floxed laminin-g1 allele that carry the inducible Cre transgene are hereafter referred to as homozygous and heterozygous mutant mice, respectively. Adult heterozygous and homozygous mutant animals were treated with either tamoxifen (TM) or corn oil (control), and three weeks afterwards, tissues were harvested for analysis. Treatment of homozygous mutant mice with TM, but not corn oil, induced laminin-g1 gene recombination. There was a significant decrease in spleen size in TM-treated but not control-treated homozygous mutant animals. Neither TM nor control treatment induced changes in the spleen size of heterozygous mutant animals. Similarly, TM treatment did not alter spleen size of animals that expressed Cre-transgene but were wild type with respect to the floxed laminin-g1 gene, or which were homozygous for the floxed laminin-g1 gene but lacked the Cre-transgene (Figure 1). Fig. 1. Comparison of spleen size from adult animals following treatment with TM or control. Genotype and treatment as follows (1, 5) Cre, TM: (2) F/F, TM:(3) F/F, Cre, Control: (4, 10) F/+;Cre, TM:(6, 9) F/F, Cre, TM (two animals in well 6): (7) F/F; Cre, Control and (8) F/+; Cre, Control. Fig. 1. Comparison of spleen size from adult animals following treatment with TM or control. Genotype and treatment as follows (1, 5) Cre, TM: (2) F/F, TM:(3) F/F, Cre, Control: (4, 10) F/+;Cre, TM:(6, 9) F/F, Cre, TM (two animals in well 6): (7) F/F; Cre, Control and (8) F/+; Cre, Control. This is the first animal model to show that continued expression of laminins are critical for maintenance of the normal spleen and suggests a potential new target for disorders of lymphoid or splenic hyperproliferation. Chen ZL, Strickland S. 2003. Laminin gamma1 is critical for Schwann cell differentiation, axon myelination, and regeneration in the peripheral nerve. J Cell Biol 163(4):889-99. Lenz G, Wright G, Dave SS, Xiao W, Powell J, Zhao H, Xu W, Tan B, Goldschmidt N, Iqbal J and others. 2008. Stromal gene signatures in large-B-cell lymphomas. N Engl J Med 359(22):2313–23. Smyth N, Vatansever HS, Meyer M, Frie C, Paulsson M, Edgar D. 1998. The targeted deletion of the LAMC1 gene. Ann N Y Acad Sci 857:283–6. Yu WM, Feltri ML, Wrabetz L, Strickland S, Chen ZL. 2005. Schwann cell-specific ablation of laminin gamma1 causes apoptosis and prevents proliferation. J Neurosci 25(18):4463–72. Disclosures: No relevant conflicts of interest to declare