Microbiological quality of tomato (<i>Solanum lycopersicum</i> L.) produced under greenhouse conditions in five Municipalities of the State of Mexico

The aim of the current research was to determine tomato (Solanum lycopersicum L.) microbiological quality produced under greenhouse conditions in 5 municipalities of the State of Mexico. Studies were conducted during the 2013 production cycle to know the risks and apply prevention strategies prior to its consumption. A microbiological analysis of samples of irrigation water, soil and 100 tomato fruits variety cid was performed to determine Aerobic Mesophiles, Total Coliforms and Fecal Coliforms. The methodology used were those according to the Official Mexican Standards NOM- 109-SSA1-1994, NOM-110-SSA1-1994, NOM-092-SSA1-1994, NOM-113-SSA1-1994, and the Regulations of the National French Organization for Standardization (AFNOR) NF V08-60, and NOM-093-SSA1-1994, which establish the allowable limits for the study microorganisms. The results showed a zero level of pollution in water and soil samples. For fruits, levels of Aerobic Mesophilic were within the maximum limits permitted by the standards. The municipality of Texcaltitlan showed the highest average for these microorganisms (10083.80 CFU/mL). Huixquilucan showed 2266.84 CFU/mL for Total Coliforms. For Fecal Coliforms, municipalities of Coatepec and Texcaltitlan exceeded the allowed limit.     

Solution structure and dynamics of a designed hydrophobic core variant of ubiquitin.

BACKGROUND: The recent merger of computation and protein design has resulted in a burst of success in the generation of novel proteins with native-like properties. A critical component of this coupling between theory and experiment is a detailed analysis of the structures and stabilities of designed proteins to assess and improve the accuracy of design algorithms. RESULTS: Here we report the solution structure of a hydrophobic core variant of ubiquitin, referred to as 1D7, which was designed with the core-repacking algorithm ROC. As a measure of conformational specificity, we also present amide exchange protection factors and backbone and sidechain dynamics. The results indicate that 1D7 is similar to wild-type (WT) ubiquitin in backbone structure and degree of conformational specificity. We also observe a good correlation between experimentally determined sidechain structures and those predicted by ROC. However, evaluation of the core sidechain conformations indicates that, in general, 1D7 has more sidechains in less statistically favorable conformations than WT. CONCLUSIONS: Our results provide an explanation for the lower stability of 1D7 compared to WT, and suggest modifications to design algorithms that may improve the accuracy with which structure and stability are predicted. The results also demonstrate that core packing can affect conformational flexibility in subtle ways that are likely to be important for the design of function and protein-ligand interactions.     

Increased detection of structural templates using alignments of designed sequences

Protein structure prediction by comparative modeling benefits greatly from the use of multiple sequence alignment information to improve the accuracy of structural template identification and the alignment of target sequences to structural templates. Unfortunately, this benefit is limited to those protein sequences for which at least several natural sequence homologues exist. We show here that the use of large diverse alignments of computationally designed protein sequences confers many of the same benefits as natural sequences in identifying structural templates for comparative modeling targets. A large-scale massively parallelized application of an all-atom protein design algorithm, including a simple model of peptide backbone flexibility, has allowed us to generate 500 diverse, non-native, high-quality sequences for each of 264 protein structures in our test set. PSI-BLAST searches using the sequence profiles generated from the designed sequences ("reverse" BLAST searches) give near-perfect accuracy in identifying true structural homologues of the parent structure, with 54% coverage. In 41 of 49 genomes scanned using reverse BLAST searches, at least one novel structural template (not found by the standard method of PSI-BLAST against PDB) is identified. Further improvements in coverage, through optimizing the scoring function used to design sequences and continued application to new protein structures beyond the test set, will allow this method to mature into a useful strategy for identifying distantly related structural templates.     

A significant range extension and sanctuary for the rare Open Bay Island skink (Oligosoma taumakae)

Abstract

The Open Bay Island skink (Oligosoma taumakae) is one of New Zealand's rarest lizard species. Until 2010, it was known only from two small islands in the Open Bay Island Group, a Māori-owned wildlife sanctuary in South Westland, New Zealand. Skinks on these islands are threatened by predation from weka (Gallirallus australis), a flightless native rail thought to have been introduced to the Open Bay Islands c. 100 years ago. Here, we describe the discovery of Open Bay Island skinks on two vegetated rock stacks located off the coast of Barn Bay, 52 km southwest of the Open Bay Islands. Although small (c. 0.10 and 0.36 ha), the Barn Islands appear to be predator-free, providing an important sanctuary for the skinks. We recommend: (1) a survey of mainland sites with suitable habitat; and (2) an evaluation of the need for island biosecurity measures for detecting and responding to incursions of small mammals.     

Side-chain and backbone flexibility in protein core design.

We have developed a computational approach for the design and prediction of hydrophobic cores that includes explicit backbone flexibility. The program consists of a two-stage combination of a genetic algorithm and monte carlo sampling using a torsional model of the protein. Backbone structures are evaluated either by a canonical force-field or a constraining potential that emphasizes the preservation of local geometry. The utility of the method for protein design and engineering is explored by designing three novel hydrophobic core variants of the protein 434 cro. We use the new method to evaluate these and previously designed 434 cro variants, as well as a series of phage T4 lysozyme variants. In order to properly evaluate the influence of backbone flexibility, we have also analyzed the effects of varying amounts of side-chain flexibility on the performance of fixed backbone methods. Comparison of results using a fixed versus flexible backbone reveals that, surprisingly, the two methods are almost equivalent in their abilities to predict relative experimental stabilities, but only when full side-chain flexibility is allowed. The prediction of core side-chain structure can vary dramatically between methods. In some, but not all, cases the flexible backbone method is a better predictor of structure. The development of a flexible backbone approach to core design is particularly important for attempts at de novo protein design, where there is no prior knowledge of a precise backbone structure.     

Bilateral detection thresholds in dextrals and sinistrals reflect the more sensitive side of the nose, which is not lateralized [published erratum appears in Chem Senses 1998 Dec;23(6):761]

Several fundamental questions remain enigmatic concerning human olfactory sensitivity, including (i) whether detection threshold differences exist between the two sides of the nose (and, if so, whether such differences are influenced by handedness) and (ii) whether bilateral (i.e. binasal) stimulation leads to lower thresholds than unilateral stimulation (and, if so, whether the degree of facilitation is inversely related to general olfactory ability). In this study, and well-validated single staircase procedure was used to establish bilateral and unilateral detection thresholds for the cranial nerve I stimulant phenyl ethyl alcohol in 130 right- and 33 left-handed subjects. No differences in sensitivity between the left and right sides of the nose were observed in either group. Bilateral thresholds were lower, on average, than unilateral thresholds when the latter were categorized in terms of left and right nares. However, the bilateral thresholds did not differ significantly from those of the side of the nose with the lower threshold. Overall smell ability, as measured by the University of Pennsylvania Smell Identification Test, did not interact with any of the test measures. These data imply that (i) the left and right sides of the nose do not systematically differ in detection threshold sensitivity for either dextrals or sinistrals and (ii) if central integration of left:right olfactory threshold sensitivity occurs, its effects do not exceed the function of the better side of the nose.      

Morphogenic Regulation of Pathotoxin Synthesis in Cochliobolus carbonum

The fungus Cochliobolus carbonum causes leaf spot disease of maize. Highly virulent isolates of the pathogen produce a host-selective, peptide toxin that is active against susceptible genotypes of maize. Prior to infection, spores must germinate and differentiate appressoria, structures specialized for leaf penetration. Analysis of spore germination fluids by plasma desorption mass spectrometry, which allowed detection of as little as 0.5 ng toxin, revealed that spores induced to form appressoria in vitro synthesized and released the toxin at a time coincident with maturation of appressoria. Spores incubated under conditions that did not induce appressorium formation failed to produce toxin. These observations indicate that synthesis of the host-selective toxin, which is essential for successful pathogenesis of maize by C. carbonum, is regulated by infection-related morphogenesis.     

Chemical biology: Paper alert

A selection of interesting papers that were published in the two months before our press date in major journals most likely to report significant results in chemical biology.