Atomic-level characterization of the structural dynamics of proteins

Molecular dynamics (MD) simulations are widely used to study protein motions at an atomic level of detail, but they have been limited to time scales shorter than those of many biologically critical conformational changes. We examined two fundamental processes in protein dynamics--protein folding and conformational change within the folded state--by means of extremely long all-atom MD simulations conducted on a special-purpose machine. Equilibrium simulations of a WW protein domain captured multiple folding and unfolding events that consistently follow a well-defined folding pathway; separate simulations of the protein's constituent substructures shed light on possible determinants of this pathway. A 1-millisecond simulation of the folded protein BPTI reveals a small number of structurally distinct conformational states whose reversible interconversion is slower than local relaxations within those states by a factor of more than 1000.     

Characterization of Pectobacterium brasiliense strains from potato and vegetables in Israel

Pectobacterium brasiliense (Pbr) infects a wide range of crops worldwide, causing potato blackleg and soft rot and vegetable soft rots. This study aimed to characterize the genetic diversity and virulence variability among 68 Pbr strains isolated from either symptomless potato progeny tubers, diseased potato plants, ware potatoes wash water, or vegetables grown in Israel, as well as strains isolated from symptomless seed tubers grown in Europe, or diseased potato plants grown in France. The collection was typed using PCR and TaqMan real-time PCR analyses, dnaX sequence analysis, pulsed-field gel electrophoresis (PFGE), and pectolytic activity. dnaX phylogeny grouped almost all strains in a common genetic clade related to Pbr, which was distinct from the other Pectobacterium species. PFGE analysis identified two main clusters, including one major group of 47 strains with 95%–100% similarity. Maceration assays on two potato cultivars showed significant differences between strains but with no correlations with the source of the strains nor the status of the host (with/without symptoms). Molecular (dnaX sequences and PFGE profiles) and phenotypic analyses (tuber maceration tests) showed that the tested Pbr strains are not a homogeneous group. Analysis of the tested Pbr strains isolated from potato and vegetables grown in fields with a history of potato cultivation suggests that seed tubers imported from Europe may be the main source for Pbr in Israel. To the best of our knowledge, this is the first study that describes biodiversity and population structure of P. brasiliense isolated from potato and vegetables under hot climate conditions.     

Physicochemical Behavior of Tetracycline and 17α-Ethinylestradiol with Wastewater Sludge-Derived Humic Substances

Concentration of methylmercury (MeHg) in different habitats and associated food chains may vary because of habitat characteristics that determine methylation and MeHg transfer. We examined MeHg levels in primary consumers from littoral, pelagial and profundal habitats of a boreal humic lake, and measured total mercury (TotHg) and MeHg in surface sediments at increasing depths. MeHg concentrations in primary consumers increased from profundal to littoral, a pattern which was mirrored by the surface sediment concentrations. Methylation potential (expressed as the ratio of MeHg to TotHg) was lower in profundal than in littoral sediments, suggesting that littoral sediments have higher net methylation rates. No specific MeHg-enriched entrance point in the littoral food chain was identified, however. High MeHg concentrations in littoral primary consumers and sediments suggest that shallow lake sediments are important for MeHg transfer to the aquatic food web in boreal humic lakes. Lake morphometry, most specifically the fraction of littoral, is hence likely to add to differences in MeHg bioaccumulation rates in lake food webs.     

β-Carotene from the Alga Dunaliella bardawil Decreases Gene Expression of Adipose Tissue Macrophage Recruitment Markers and Plasma Lipid Concentrations in Mice Fed a High-Fat Diet

Vitamin A and provitamin A carotenoids are involved in the regulation of adipose tissue metabolism and inflammation. We examined the effect of dietary supplementation using all-trans and 9-cis β-carotene-rich Dunaliella bardawil alga as the sole source of vitamin A on obesity-associated comorbidities and adipose tissue dysfunction in a diet-induced obesity mouse model. Three-week-old male mice (C57BL/6) were randomly allocated into two groups and fed a high-fat, vitamin A-deficient diet supplemented with either vitamin A (HFD) or β-carotene (BC) (HFD-BC). Vitamin A levels in the liver, WATs, and BAT of the HFD-BC group were 1.5–2.4-fold higher than of the HFD group. BC concentrations were 5–6-fold greater in BAT compared to WAT in the HFD-BC group. The eWAT mRNA levels of the Mcp-1 and Cd68 were 1.6- and 2.1-fold lower, respectively, and the plasma cholesterol and triglyceride concentrations were 30% and 28% lower in the HFD-BC group compared with the HFD group. Dietary BC can be the exclusive vitamin A source in mice fed a high-fat diet, as shown by the vitamin A concentration in the plasma and tissues. Feeding BC rather than vitamin A reduces adipose tissue macrophage recruitment markers and plasma lipid concentrations.     

Experimental handling stress as infection-facilitating factor for the goldfish ulcerative disease

Experimental handling stress (EHS) was applied to clinically asymptomatic farmed goldfish (Carassius auratus L.). EHS affected the gills and skin integrity of the fish and was accompanied by increased levels of plasma glucose, cortisol and interleukin-10 (IL-10). EHS application was followed by highly significant enhancement of the rate of infection with a virulent Aeromonas salmonicida isolate. Cumulative ulceration at the initial phase of the ensuing goldfish ulcerative disease (GUD) evidenced a facilitating role of EHS in the onset of GUD. Host susceptibility to the pathogen increased from 40% in unstressed fish to 90% in the stressed fish. A. salmonicida could be reisolated from the early-stage skin lesions only, whereas opportunistic strains, other than A. salmonicida (A. sobria and A. hydrophila), were recovered from progressive-stage ulcers. The implication of these findings in fish aquaculture is discussed.     

Colonization and movement of GFP-labeled Clavibacter michiganensis subsp. michiganensis during tomato infection

The vascular pathogen Clavibacter michiganensis subsp. michiganensis is responsible for bacterial wilt and canker of tomato. Pathogenicity of this bacterium is dependent on plasmid-borne virulence factors and serine proteases located on the chromosomal chp/tomA pathogenicity island (PAI). In this study, colonization patterns and movement of C. michiganensis subsp. michiganensis during tomato infection was examined using a green fluorescent protein (GFP)-labeled strain. A plasmid expressing GFP in C. michiganensis subsp. michiganensis was constructed and found to be stable in planta for at least 1 month. Confocal laser-scanning microscopy (CLSM) of inoculated stems showed that the pathogen extensively colonizes the lumen of xylem vessels and preferentially attaches to spiral secondary wall thickening of the protoxylem. Acropetal movement of the wild-type strain C. michiganensis subsp. michiganensis NCPPB382 (Cmm382) in tomato resulted in an extensive systemic colonization of the whole plant reaching the apical region after 15 days, whereas Cmm100 (lacking the plasmids pCM1 and pCM2) or Cmm27 (lacking the chp/tomA PAI) remained confined to the area surrounding of the inoculation site. Cmm382 formed biofilm-like structures composed of large bacterial aggregates on the interior of xylem walls as observed by CLSM and scanning electron microscopy. These findings suggest that virulence factors located on the chp/tomA PAI or the plasmids are required for effective movement of the pathogen in tomato and for the formation of cellular aggregates.     

Application of DNA fingerprints for identification and genetic analysis of Carica papaya and other Carica species

Summary Various DNA fingerprint probes were applied to Carica papaya and other Carica species for both identification and genetic analysis.Each of the Carica papaya cultivars is characterized by a specific DNA fingerprints pattern. Various Carica species also have specific patterns which distinguish them from one another. Band sharing levels were used to estimate the relatedness between the various Carica species.Genetic analysis of 11 progeny from a cross between the Carica papaya cultivars 17/82 and 112 suggests that application of DNA fingerprinting to Carica papaya breeding, could make the process more efficient. Genetic analysis of the DNA fingerprint bands revealed no linkage or allelic relationship among the bands analyzed, indicating that these loci are not clustered in the Carica genome.     

Cotyledons are the main source of secondary spread of Acidovorax citrulli in melon nurseries

Acidovorax citrulli (Ac) is the causal agent of bacterial fruit blotch (BFB) disease resulting in substantial economic damage to cucurbit crops worldwide. The plant parts and cultural practices (irrigation methods and bactericidal sprays) that affect the secondary spread of Ac in melon nurseries were investigated in this study. Overhead irrigation dispersed the pathogen from infected seedlings to 95% of the neighbouring healthy seedlings, with 80% of them displaying high disease severity. In contrast, when sub‐irrigation by floating was employed, the neighbouring plants of the infected ones did not display disease symptoms and were not colonized by Ac. Foliar treatment with Kocide after cotyledon emergence reduced disease incidence to 40%, with 37% of the plants displaying low disease severity. Assessment of Ac populations in different parts of the seedlings revealed that cotyledons were the most colonized part of the plant. Images of fluorescent binocular and confocal laser‐scanning microscopy of seedlings infected with a GFP‐labelled Ac strain showed that the pathogen forms abundant aggregates on the surface of cotyledons, colonizes the intercellular spaces of the parenchymatic tissues extensively, and moves through the vascular system of the hypocotyls, leading to infection of emerging leaves. Results of this study indicate that preventing secondary spread of Ac in melon nurseries by sub‐irrigation combined with a bactericidal spray at the cotyledon stage may provide an effective means for BFB control.     

Characterization of theErwinia amylovora population in Israel

A collection of 205 strains ofErwinia amylovora isolated in Israel over a period of 12 years has been established. The strains were isolated from different varieties of pear, apple, loquat and quince grown in Israel, and collected from different locations in the country. They were characterized in respect to degree of virulence on several hosts and serological and molecular characters. Pathogenicity tests carried out on flowering branches of pear and apple, shoots of pears, and on trees of pear and loquat grown in containers outdoors, revealed no significant differences in the severity of blossom blight or shoot blight among the various strains. ELISA and immunofluorescence assays revealed no serotypic groups among the Israeli strains. Genomic diversity was studied by random amplified polymorphic DNA (RAPD) analysis using 24 arbitrary 10-base primers. All the strains examined (45 Israeli and 11 from Egypt, Cyprus and Greece) produced the same RAPD patterns with each of the primers used. Amplification patterns were indistinguishable from those produced by strains isolated from the neighboring countries. Results presented in this study suggest that the population ofE. amylovora in Israel is homogenous.