Non-equilibrium phenomena and molecular reaction dynamics: mode space, energy space and conformer space

status: publishe

The Multigeneic _Rhg1_ Locus: A Model For The Effects on Root Development, Nematode Resistance and Recombination Suppression.

Soybean (Glycine max L. Merr.) resistance to populations (HgType) of _Heterodera glycines I._, the soybean cyst nematode (SCN), requires a functional allele at rhg1. An apoptosis-like response in the giant cells formed around the nematode results 24-48 h after feeding commences. This study aimed to identify the role of the three genes within the rhg1 locus, a receptor like kinase (RLK), a laccase and an ion anti-porter. Used were near isogeneic lines (NILs) that contrasted at their rhg1 alleles. Features of the rhg1 locus, the candidate genes and their nascent transcripts and proteins in roots were elucidated. First, evidence for a syntenic gene cluster was found and the effectiveness of SNP probes for distinguishing the homeolog sequence variant on linkage group (Lg) B1 from alleles at the rhg1 locus on Lg G was shown. Analysis of plant s heterozygous at rhg1 showed that the allele for resistance was dominant. The absence of recombination events among the NILs between the RLK and other 2 genes eliminated the possibility of a monogeneic rhg1 locus. Finally, an effect on root development was discovered. A model for multigeneic resistance based on developmental control of root growth including a mechanism for segregation distortion is presented

Metabolically Engineering Aspergillus nidulans for Client Protein Production

The filamentous fungi, A. nidulans, can produce nearly 100 grams per liter of industrially relevant proteins under optimal conditions. However, many of these proteins are degraded or produced alongside other proteins, which drastically reduce their efficacy in a cellulose fermentation reaction.The aim of this work is to redesign the regulatory genetic circuitry of Aspergillus nidulans to efficiently produce client proteins. We have successfully reengineered the cellulase regulatory network to produce cellulases in the presence of the C5-sugar xylose. By replacing expensive substrates with a cheap by-product carbon source we reduce enzyme production costs and lower operational costs by eliminating the need for off-site enzyme production, purification, concentration, transport and dilution.We also propose a novel mechanism, utilizing RNA interference, to combinatorially silence genes, which degrade or contaminate client proteins. Using dual promoters, we will flank a sequence containing 30 or 40bp complementary sequences for multiple client genes. This will induce double stranded RNA production, in turn loading these individual complementary sequences into the Argonaute complex, silencing the messenger RNA for each target gene.We have also utilized LC-MS/MS to examine changes in the proteome of our silenced strains. We have seen marked decreases in our target gene sequences as well as the induction of new proteins, acting as a compensation mechanism for the fungus.Our silenced strains, when transformed to produce client proteins, have also had a marked change in the amount of protein produced, as well as how long it lasts in the media during production. We have continued this work by silencing genes responsible for unwanted amylolytic activity in client protein production

Born to Parse

An argument that children are born to assign structures to their ambient language, yielding a view of language variation not based on parameters defined at UG. In this book, David Lightfoot argues that just as some birds are born to chirp, humans are born to parse—predisposed to assign linguistic structures to their ambient external language. This approach to language acquisition makes two contributions to the development of Minimalist thinking. First, it minimizes grammatical theory, dispensing with three major entities: parameters; an evaluation metric for the selection of grammars; and any independent parsing mechanism. Instead, Lightfoot argues, children parse their ambient external language using their internal language. Universal Grammar is “open,” consistent with what children learn through parsing with their internal language system. Second, this understanding of language acquisition yields a new view of variable properties in language—properties that occur only in certain languages. Under the open UG vision, very specific language particularities arise in response to new parses. Both external and internal languages play crucial, interacting roles: unstructured, amorphous external language is parsed and an internal language system results. Lightfoot explores case studies that show such innovative parses of external language in the history of English: development of modal verbs, loss of verb movement, and nineteenth-century changes in the syntax of the verb to be. He then discusses how children learn through parsing; the role of parsing at the syntactic structure's interface with the externalization system and logical form; language change; and variable properties seen through the lens of an open UG

Soybean Genomics: Developments through the Use of Cultivar “Forrest”

Legume crops are particularly important due to their ability to support symbiotic nitrogen fixation, a key to sustainable crop production and reduced carbon emissions. Soybean (Glycine max) has a special position as a major source of increased protein and oil production in the common grass-legume rotation. The cultivar “Forrest” has saved US growers billions of dollars in crop losses due to resistances programmed into the genome. Moreover, since Forrest grows well in the north-south transition zone, breeders have used this cultivar as a bridge between the southern and northern US gene pools. Investment in Forrest genomics resulted in the development of the following research tools: (i) a genetic map, (ii) three RIL populations (96 > n > 975), (iii) ∼200 NILs, (iv) 115 220 BACs and BIBACs, (v) a physical map, (vi) 4 different minimum tiling path (MTP) sets, (vii) 25 123 BAC end sequences (BESs) that encompass 18.5 Mbp spaced out from the MTPs, and 2 000 microsatellite markers within them (viii) a map of 2408 regions each found at a single position in the genome and 2104 regions found in 2 or 4 similar copies at different genomic locations (each of >150 kbp), (ix) a map of homoeologous regions among both sets of regions, (x) a set of transcript abundance measurements that address biotic stress resistance, (xi) methods for transformation, (xii) methods for RNAi, (xiii) a TILLING resource for directed mutant isolation, and (xiv) analyses of conserved synteny with other sequenced genomes. The SoyGD portal at sprovides access to the data. To date these resources assisted in the genomic analysis of soybean nodulation and disease resistance. This review summarizes the resources and their uses

Assessment of Genetic Biodiversity of Several Traits Using SSR Markers in Rice (Oryza sativa L.)

Eight primers (RM 315, RM 318, RM 166, RM 302, RM 201, RM 234, RM 526 and RM 144) revealed different levels of polymorphism to tag the related traits of interest as tolerant to abiotic stress, resistant to biotic stress and yield-related traits. Two primers (RM 190 and RM 278) were monomorphic. The percentage of the polymorphism was nearly 80 %. The size of detected fragments ranged from 105–325 bp. A total of 186 bands were scored from the amplification products with the ten SSR primers. Genetic diversity analyses were conducted on the basis of the scores with 176 unique bands. Phylogenic tree for the fifteen rice accessions from each group were established according to the molecular data and based on ten SSRs. A marked genetic diversity was observed in these innovative accessions (Sakha 101, IR 03N137, IR 83142-12, IR 87856-10-AJY-1-B, HHZ 12-Y4-DT1-Y2 and IR 1552), which revealed higher levels of diversity and hence can be used as donors for the effective conservation, utilization and providing favorable genes in rice breeding programs

Review of the Rpt3 Genes Encoding Part of the 26S Proteasome Associated with Loci Underlying Disease Resistance in Soybean

The 26S proteasomal complex is a multifunctional proteolytic machinery of the cell. The proteasome plays role in myriad of cellular functions, which have been further diversified by its separable proteolytic and non-proteolytic sub-complexes. Protein quality control and turnover, cell cycle regulation, gene regulation and DNA repair are among the key processes controlled by the proteasome. Disease resistance in plants invokes changes in all the processes controlled by the 26S proteasome. In this review, the potential contribution of genes encoding the proteasome to disease resistance in soybean (Glycine max L. Merr.) was examined

Using A Minimum Tile Path For Plant Transformations Encompassing the Entire Soybean Genome

Genomes like Glycine max (soybean) that have been highly conserved following increases in ploidy represent a frontier for genome analysis. Many soybean QTL analyzed to date have been composed of gene clusters each with contributing a portion of the trait rather than alleles of single genes. At the Soybean Genome Database (SoyGD) http://soybeangenome.siu.edu the genome browser that integrates and served the publicly available soybean physical map, BAC fingerprint database and genetic map associated genomic data shows a minimum tile of transformation ready BIBAC-like clones in pCLD04541 (pV41; oriV; tra; bom). Sequence resources made available through the DOE genome sequencing project have allowed the minimum tile to be revised and new functional analyses to be made. There are 3,840 MTP clones that appeared to encompass 90% of the genome (see http://soybeangenome.siu.edu/cgi-bin/gbrowse/BES_scaffolds). The BIBAC-like clones (tetR) from E. coli DH10 B were transferred en masse to Agrobacterium tumefaciens by triparental matings with EHA105 (rifR) mediated by pRK2013 (oriP) in DH10B (kanR) in 384 well plates. Although not necessary the extra helper plasmid boosted efficiency 10 fold. Individual A. tumefaciens rifampicin and tetracyclin resistant strains were used for transformation of Arabidopsis thaliana flowers in 384 well arrays. Initially kanamycin selection was used to isolate transgenic plants. Because the BACs were already tetR the recA mutants of A. tumefaciens could not be used (Tn3 insertions). Consequent to this and partial transconjugation events only some inserts are transferred completely while other transformed lines contain a substitution series of deleted inserts anchored on the Ti-left border (LB). These are maintained as kanR mixtures of seed. Phenotypes found for lines transgenic for particular BACs that were repeated include seed composition (protein, oil), development (growth, senescence) and disease resistance (suddean death syndrome (SDS) and soybean cyst nematode (SCN)