Cytokine-driven regulation of NK cell functions in tumor immunity: role of the MICA-NKG2D system

Natural killer (NK) cells are critical players during tumor growth control in immunocompetent hosts. These cells also establish a cross-talk with dendritic cells (DCs) and promote a Th1-mediated immunity. NKG2D is a pivotal receptor that directs the tumoricidal activity of NK cells through the recognition of a group of ligands such as MICA widely expressed on different tumors. Here we will review the most important tumor immune escape mechanisms that compromise the functionality of NKG2D and its cognate ligands, including TGF-beta secretion, tumor shedding of soluble MICA, and additional mechanisms that compromise the tumoricidal activity of NKG2D-expressing cells. Such mechanisms may also dampen the cross-talk between NK cells and DCs during the anti-tumor immune responses. Recent knowledge may lead to innovative approaches to promote efficient NK cell-mediated anti-tumor immune responses.     

Quality of silages from Italian farms as attested by number and identity of microbial indicators

AIMS: This study evaluated the quality and possible hygiene risks related to farm-made silages by analysing the presence and number of micro-organisms that influence the preservation and safety in samples from four Italian regions. METHODS AND RESULTS: Lactic acid bacteria, clostridia, lactate-fermenting yeasts and propionibacteria (PAB) were isolated and identified by random amplified polymorphic DNA PCR, sequencing of the V2-V3 16S rRNA gene region, 5.8S-ITS rDNA RFLP and species-specific PCR. The Lactobacillus plantarum cluster was the most numerous and comprised strains mostly isolated from alfalfa silage. The Lactobacillus buchneri cluster, second in number, comprised isolates from both alfalfa and maize silage. Anaerobic spore formers were assigned to the species Clostridium baratii, Clostridium beijerinkii, Clostridium butyricum, Clostridium perfringens, Clostridium saccharolyticum, Clostridium tyrobutyricum and Paenibacillus macerans. Yeast isolates were identified as Candida apicola, Candida mesenterica and Pichia fermentans. PAB strains, detected only in unifeed, were all identified as Propionibacterium acidipropionici. CONCLUSIONS: The occurrence of spoiling micro-organisms was frequent and the possibility of contamination by potentially pathogenic clostridia was demonstrated. SIGNIFICANCE AND IMPACT OF THE STUDY: The results suggest the need for improved ensiling practices and appropriate control measures to safeguard the hygienic and nutritional quality of silages produced in farms.     

Adaptive torsion-angle quasi-statics: a general simulation method with applications to protein structure analysis and design

MOTIVATION: The cost of molecular quasi-statics or dynamics simulations increases with the size of the simulated systems, which is a problem when studying biological phenomena that involve large molecules over long time scales. To address this problem, one has often to either increase the processing power (which might be expensive), or make arbitrary simplifications to the system (which might bias the study). RESULTS: We introduce adaptive torsion-angle quasi-statics, a general simulation method able to rigorously and automatically predict the most mobile regions in a simulated system, under user-defined precision or time constraints. By predicting and simulating only these most important regions, the adaptive method provides the user with complete control on the balance between precision and computational cost, without requiring him or her to perform a priori, arbitrary simplifications. We build on our previous research on adaptive articulated-body simulation and show how, by taking advantage of the partial rigidification of a molecule, we are able to propose novel data structures and algorithms for adaptive update of molecular forces and energies. This results in a globally adaptive molecular quasi-statics simulation method. We demonstrate our approach on several examples and show how adaptive quasi-statics allows a user to interactively design, modify and study potentially complex protein structures.     

Molecular Phylogeny of the Family Ophryscolecidae (Ciliophora,Litostomatea) Inferred from 18S rDNA Sequences

The 18S rDNA was used to infer oral ciliature patterns of evolution within the family Ophryoscolecidae, with the addition of five new sequences of ciliates from the genus Ostracodinium. Our data confirmed the monophyly of the subfamilies Entodiniinae and Ophryoscolecinae, but more analysis would be required for the definition of the status of the subfamily Diplodiniinae. The oral infraciliature patterns reflect evolutionary divergence in the family Ophryscolecidae, observing monophyly on Entodinium‐type, Diplodinium‐type, Ostracodinium‐type, Epidinium‐type, and Ophryoscolex‐type. The ancestral infraciliature of Entodinium‐type cannot be proven, however, the position of Entodinium‐type showed closer of Diplodinium‐type than Ophryoscolex‐type, corroborating previous studies using morphological characters. The observed inconsistencies reflect the need to increase the number of 18S rDNA sequences to family Ophryoscolecidae and investigate the evolution of this group using other molecular markers.     

Experimental evaluation of birds as disseminators of the cosmopolitan tick Rhipicephalus sanguineus (Acari: Ixodidae)

Rhipicephalus sanguineus is believed to be the most widespread tick species of the world and its dissemination seems to rely on the diffusion of its main host, the dog. Empirical observations indicate that several bird species in urban areas regularly steal dog food. Such circumstances create a chance for R. sanguineus ticks to climb on birds and carry ticks to another site. In this work we evaluated experimentally the likelihood of birds (chicks) to either feed and/or carry R. sanguineus ticks from an infested site to another and to infest a host (rabbit) in the new location. Chicks were not suitable hosts for R. sanguineus ticks. Not a single adult tick engorged on chicks, yield as well as weight of engorged larvae and nymphs were very low and feeding period of these ticks was very long. However, a few larvae and, chiefly, nymphs were delivered to a new location either mechanically or after attachment and engorging total or partially on chicks. A few of these ticks fed successfully on rabbits. Further evidence on the capacity of birds to introduce R. sanguineus into non-infested dog settings should be provided by systematic examination of birds from urban areas, close to tick infested households.     

Predicting urban outdoor thermal comfort by the Universal Thermal Climate Index UTCI—a case study in Southern Brazil

Recognising that modifications to the physical attributes of urban space are able to promote improved thermal outdoor conditions and thus positively influence the use of open spaces, a survey to define optimal thermal comfort ranges for passers-by in pedestrian streets was conducted in Curitiba, Brazil. We applied general additive models to study the impact of temperature, humidity, and wind, as well as long-wave and short-wave radiant heat fluxes as summarised by the recently developed Universal Thermal Climate Index (UTCI) on the choice of clothing insulation by fitting LOESS smoothers to observations from 944 males and 710 females aged from 13 to 91 years. We further analysed votes of thermal sensation compared to predictions of UTCI. The results showed that females chose less insulating clothing in warm conditions compared to males and that observed values of clothing insulation depended on temperature, but also on season and potentially on solar radiation. The overall pattern of clothing choice was well reflected by UTCI, which also provided for good predictions of thermal sensation votes depending on the meteorological conditions. Analysing subgroups indicated that the goodness-of-fit of the UTCI was independent of gender and age, and with only limited influence of season and body composition as assessed by body mass index. This suggests that UTCI can serve as a suitable planning tool for urban thermal comfort in sub-tropical regions.     

Cellulose degradation by Sulfolobus solfataricus requires a cell-anchored endo-β-1-4-glucanase

A sequence encoding a putative extracellular endoglucanase (sso1354) was identified in the complete genome sequence of Sulfolobus solfataricus. The encoded protein shares signature motifs with members of glycoside hydrolases family 12. After an unsuccessful first attempt at cloning the full-length coding sequences in Escherichia coli, an active but unstable recombinant enzyme lacking a 27-residue N-terminal sequence was generated. This 27-amino-acid sequence shows significant similarity with corresponding regions in the sugar binding proteins AraS, GlcS, and TreS of S. solfataricus that are responsible for anchoring them to the plasma membrane. A strategy based on an effective vector/host genetic system for Sulfolobus and on expression control by the promoter of the S. solfataricus gene which encodes the glucose binding protein allowed production of the enzyme in sufficient quantities for study. In fact, the enzyme expressed in S. solfataricus was stable and highly thermoresistant and showed optimal activity at low pH and high temperature. The protein was detected mainly in the plasma membrane fraction, confirming the structural similarity to the sugar binding proteins. The results of the protein expression in the two different hosts showed that the SSO1354 enzyme is endowed with an endo-β-1-4-glucanase activity and specifically hydrolyzes cellulose. Moreover, it also shows significant but distinguishable specificity toward several other sugar polymers, such as lichenan, xylan, debranched arabinan, pachyman, and curdlan.     

Complete Genome Sequence of a Variant of Campylobacter jejuni NCTC 11168

Campylobacter jejuni NCTC 11168 is widely used in research, but at least two variants have been reported. The available genome was sequenced from a variant which later showed a different phenotype and gene expression profile. Here we present the complete genome sequence of a second variant of C. jejuni NCTC 11168.     

Rodaucea, a new genus of the Laboulbeniales

The new genus Rodaucea is created for a new species of Laboulbeniales parasitic on carrion beetles from Ecuador. The new genus is characterized by the presence of two unequal secondary receptacles flanking cell II on opposite sides. The perithecia have the wall cells arranged in four tiers distinctly unequal in height and the antheridia are phialid-like structures borne terminally on branches of primary and secondary appendages.     

Fabs enable single particle cryoEM studies of small proteins

In spite of its recent achievements, the technique of single particle electron cryomicroscopy (cryoEM) has not been widely used to study proteins smaller than 100 kDa, although it is a highly desirable application of this technique. One fundamental limitation is that images of small proteins embedded in vitreous ice do not contain adequate features for accurate image alignment. We describe a general strategy to overcome this limitation by selecting a fragment antigen binding (Fab) to form a stable and rigid complex with a target protein, thus providing a defined feature for accurate image alignment. Using this approach, we determined a three-dimensional structure of an ～65 kDa protein by single particle cryoEM. Because Fabs can be readily generated against a wide range of proteins by phage display, this approach is generally applicable to study many small proteins by single particle cryoEM.