Demonstration of linkage and development of the first low-density genetic map of garlic, based on AFLP markers

Garlic (Allium sativum L.) is a long-cultivated, clonally propagated diploid plant (2n=2x=16). With routine seed production now underway, we used populations (MP1 and MP2) generated by self-pollination of unrelated plants to generate two low-density genetic maps of garlic, consisting of amplified fragment length polymorphism (AFLP) and gene-specific markers. We did not observe any two plants with identical marker patterns in either population, indicating that they were the result of amphimixis rather than apomixis. This is an important finding, since several Alliums are facultative apomicts. A total of 360 markers segregated in MP1 (12.8 AFLP markers per primer combination) and 321 markers segregated in MP2 (13.9 per primer combination) to indicate a fairly high level of genetic heterozygosity in the garlic nuclear genome. Of these markers, 15.3% in MP1 and 24.3% in MP2 had segregation ratios distorted from the expected 3:1. Interestingly, 94.7% of those distorted segregations fit a 15:1 segregation ratio for duplicated loci, suggesting extensive levels of duplication in the garlic genome and supporting similar observations for onion. The genetic map for the MP1 family with 216 markers spanned 1,166 cM of the garlic genome (5.4 cM average), while 143 markers of MP2 spanned 862 cM (6.0 cM average). Gene-specific markers for alliinase, chitinase, sucrose 1-fructosyltransferase (SST-1), and chalcone synthase (CHS) were mapped, demonstrating the immediate utility of the garlic genetic map. These two garlic families had relatively few segregating AFLP markers in common, which supports their relatively distant relationship based on diversity analysis. Of those markers that were conserved, linkages were also conserved.     

Coordination topology and stability for the native and binding conformers of chymotrypsin inhibitor 2

We demonstrate that the stabilization of the binding region is accomplished at the expense of a loss in the stability of the rest of the protein. A novel molecular mechanics (MM) approach is introduced to distinguish residue stabilities of proteins in a given conformation. As an example, the relative stabilities of folded chymotrypsin inhibitor 2 (CI2) in unbound form, and CI2 in complex with subtilisin novo is investigated. The conformation of the molecule in the two states is almost identical, with an approximately 0.6-A root-mean-square deviation (RMSD) of the Calpha atoms. On binding, the packing density changes only at the binding loop. However, residue fluctuations in the rest of the protein are greatly altered solely due to those contacts, indicating the effective propagation of perturbation and the presence of remotely controlling residues. To quantify the interplay between packing density, packing order, residue fluctuations, and residue stability, we adopt an MM approach whereby small displacements are inserted at selected residues, followed by energy minimization; the displacement of each residue in response to such perturbations are organized in a perturbation-response matrix L. We define residue stability lambda(i) = summation operator((j)L(ij))/ summation operator((j) L(ji)) as the ratio of the amount of change to which the residue is amenable, to the ability of a given residue to induce change. We then define the free energy associated with residue stability, DeltaG(lambda) = -RT ln lambda. DeltaG(lambda) intrinsically selects the residues that are in the folding core. Upon complexation, the binding loop becomes more resistant to perturbation, in contrast to the alpha-helix that favors change. Although the two forms of CI2 are structurally similar, residue fluctuations differ vastly, and the stability of many residues is altered upon binding. The decrease in entropy introduced by binding is thus compensated by these changes.     

3-Dimensional Diffusion Tensor Imaging (DTI) Atlas of the Rat Brain

Anatomical atlases play an important role in the analysis of neuroimaging data in rodent neuroimaging studies. Having a high resolution, detailed atlas not only can expand understanding of rodent brain anatomy, but also enables automatic segmentation of new images, thus greatly increasing the efficiency of future analysis when applied to new data. These atlases can be used to analyze new scans of individual cases using a variety of automated segmentation methods. This project seeks to develop a set of detailed 3D anatomical atlases of the brain at postnatal day 5 (P5), 14 (P14), and adults (P72) in Sprague-Dawley rats. Our methods consisted of first creating a template image based on fixed scans of control rats, then manually segmenting various individual brain regions on the template. Using itk-SNAP software, subcortical and cortical regions, including both white matter and gray matter structures, were manually segmented in the axial, sagittal, and coronal planes. The P5, P14, and P72 atlases had 39, 45, and 29 regions segmented, respectively. These atlases have been made available to the broader research community.     

A Proteomic Approach Provides New Insights into the Control of Soil-Borne Plant Pathogens by Bacillus Species

Beneficial microorganisms (also known as biopesticides) are considered to be one of the most promising methods for more rational and safe crop management practices. We used Bacillus strains EU07, QST713 and FZB24, and investigated their inhibitory effect on Fusarium. Bacterial cell cultures, cell-free supernatants and volatiles displayed varying degrees of suppressive effect. Proteomic analysis of secreted proteins from EU07 and FZB24 revealed the presence of lytic enzymes, cellulases, proteases, 1,4-β-glucanase and hydrolases, all of which contribute to degradation of the pathogen cell wall. Further proteomic investigations showed that proteins involved in metabolism, protein folding, protein degradation, translation, recognition and signal transduction cascade play an important role in the control of Fusarium oxysporum. Our findings provide new knowledge on the mechanism of action of Bacillus species and insight into biocontrol mechanisms.     

Optimization and enhanced production of α-amylase and protease by a newly isolated Bacillus licheniformis ZB-05 under solid-state fermentation

Eight different agro-residues were tested for α-amylase and protease production by using Bacillus licheniformis ZB-05. Among them, rice husk (RH) was proved as the best substrate for two enzymes (α-amylase 443 U/g and protease 469,000 U/g). Maximum enzyme production was observed to be 30 % initial moisture, with a growth period of 36 h in 20 and 30 % inoculum volumes for α-amylase and protease, respectively. The best enzyme recovery from solid mass was obtained when extracted with tap water. Among the tested various nitrogen sources, 1 % ammonium sulphate followed by 2 % Bacto liver, 2 % ammonium sulphate and 1 % Bacto casaminoacid served as the best inorganic and organic nitrogen sources for α-amylase and protease production, respectively. As additional carbon sources, 2 % soluble starch enhanced α-amylase production, while 1 % maltose enhanced protease production.     

Immunohistochemical evaluation of natural cases of encephalitic listeriosis in sheep

ABSTRACT

Listeriosis is an important public health problem in the world. It can cause abortion, encephalitis, septicemia, conjunctivitis and mastitis in ruminants. The development of central nervous system lesions is not fully understood in encephalitic listeriosis. We performed a retrospective analysis of 15 sheep with encephalitic listeriosis. Hyperemia and opacification of the meninges were common necropsy findings. Lesions generally were localized in the caudal part of the brain including the pons, medulla oblongata, thalamus and cerebellum. Microabscesses usually were found in the caudal brain and cerebellum, while perivascular infiltrates were found most often in other parts of the brain. Evidence of Listeria monocytogenes was detected immunohistochemically in the medulla oblongata, pons, thalamus and cerebellum. Prominent reactions for glial fibrillary acidic protein (GFAP), S100 protein, N-methyl-D-aspartate receptor-1 (NMDAR1) and inducible co-stimulatory protein (ICOS) were detected in the caudal brain, which indicates that these proteins may play roles in the pathogenesis of encephalitic listeriosis.     

A chromosome-scale genome assembly of European hazel (Corylus avellana L.) reveals targets for crop improvement

The European hazelnut (Corylus avellana L.) is a tree crop of economic importance worldwide, but especially for northern Turkey, where the majority of production takes place. Hazelnut production is currently challenged by environmental stresses, such as a recent outbreak of severe powdery mildew disease; furthermore, allergy to hazelnuts is an increasing health concern in some regions. In order to provide a foundation for using the available hazelnut genetic resources for crop improvement, we produced a fully assembled genome sequence and annotation for a hazelnut species, from C. avellana cv. ‘Tombul’, one of the most important Turkish varieties. A hybrid sequencing strategy, combining short reads, long reads and proximity ligation methods, enabled us to resolve heterozygous regions and produce a high-quality 370-Mb assembly that agrees closely with cytogenetic studies and genetic maps of the 11 C. avellana chromosomes, and covers 97.8% of the estimated genome size. The genome includes 27 270 high-confidence protein-coding genes, over 20 000 of which were functionally annotated based on homology with known plant proteins. We focused particularly on gene families encoding hazelnut allergens, and the Mildew resistance Locus O (MLO) proteins that are an important susceptibility factor for powdery mildew. The complete assembly enabled us to differentiate between members of these families and to identify homologues that may be important in mildew disease and hazelnut allergy. These findings provide examples of how the genome can be used to guide research and to develop effective strategies for crop improvement in C. avellana.     

Recaching Decisions of Florida Scrub‐Jays are Sensitive to Ecological Conditions

Food caching animals depend on their caches at times of low food availability. Because stored food is susceptible to being stolen or degraded, many species employ cache protection strategies such as ceasing caching in the presence of others or avoiding storing perishable items for long periods. Several species frequently recover their caches and recache, which may reduce pilferage or degradation of cached items. We studied the food handling decisions of Florida scrub‐jays (Aphelocoma coerulescens) after cache recovery to determine the roles that social and ecological environments play in post‐recovery decisions. Instead of reducing recaching in the presence of others, recovering jays flew away from the recovery site, allowing them to eat or recache a recovered item regardless of the social context. Microhabitat type and soil moisture of the recovery sites had a significant influence on whether recoveries were eaten or recached; most items that were recached had been recovered from bare sand sites or sites with low soil moisture. Taken together, our results suggest that food store management of Florida scrub‐jays are unaffected by the social context, but are strongly affected by the habitat conditions that influence the quality of caches.