How the other half lives: CRISPR-Cas's influence on bacteriophages

CRISPR-Cas is a genetic adaptive immune system unique to prokaryotic cells used to combat phage and plasmid threats. The host cell adapts by incorporating DNA sequences from invading phages or plasmids into its CRISPR locus as spacers. These spacers are expressed as mobile surveillance RNAs that direct CRISPR-associated (Cas) proteins to protect against subsequent attack by the same phages or plasmids. The threat from mobile genetic elements inevitably shapes the CRISPR loci of archaea and bacteria, and simultaneously the CRISPR-Cas immune system drives evolution of these invaders. Here we highlight our recent work, as well as that of others, that seeks to understand phage mechanisms of CRISPR-Cas evasion and conditions for population coexistence of phages with CRISPR-protected prokaryotes.Comment: 24 pages, 8 figure

Uso de infravermelho próximo para estimativa das falhas no estande e produtividade do amendoim

This research aims to study the use of NIR images for peanut production estimates in three different planting processes (conventional tillage, no-tillage, and planting Rip Strip) relating productivity information with extracted parameters Orthophoto generated by an Air Vehicle No manned (UAV). The images 0.2 cm error range compounds were analyzed in extracts of two central lines launched in all replicates of the various treatments. For each line, 100 linear meters were measured and quantified the existence of faults; subsequently determined the actual planting observed in each treatment and correlated with output in the treatments. planting lines and identified failures were analyzed through the Geographic Information System (GIS) Quantum Gis. The results of the correlation tended to a positive correlation between the failure data and foliar weight and yield, is a positive indicator of the use of the tool for productivity measurements by the NIR. The studies will be repeated in different conditions and variables for an improvement in productivity analysis and estimationO presente trabalho tem por objetivo estudar o uso de imagens NIR para estimativa de produção de amendoim em três diferentes processos de Plantio (plantio convencional, plantio direto e plantio Rip Strip) relacionando informações de produtividade com parâmetros extraídos de Ortofoto gerada por um Veículo Aéreo Não Tripulado (VANT). As imagens em escala de erro de 0.2 cm foram analisadas em extratos compostos de duas linhas centrais lançados em todas as repetições dos diferentes tratamentos. Para cada linha, com 100 metros lineares foram medidas e quantificadas a existência de falhas; posteriormente determinou-se o efetivo plantio verificado em cada tratamento e correlacionou- se com a produção obtida nos tratamentos. As linhas de plantio e as falhas identificadas, foram analisadas, através do Sistema de Informação Geográfica (SIG) Quantum Gis. Os resultados da correlação tenderam a uma correlação positiva entre os dados de falhas e massa foliar e produtividade, sendo um indicador positivo de uso desta ferramenta para medições de produtividade através de NIR. Os estudos serão repetidos em diferentes condições e variáveis para um aprimoramento da análise e estimativa de produtividade

Avaliação de RPAs para pulverização em diferentes culturas

The present work had as objective to study and to validate the application of defenses through RPAs (Remotely Piloted Aircraft), commonly denominated Drones. The experiment happened at APTA East Center in Ribeirão Preto, Sao Paulo. The herbicide solution glyphosate 1.5 kg ha-1 (Roundup WG®) was used using 15 L ha-1 of syrup volume. The RPA that overflew the study area at three different altitudes together with three different spray nozzle models in a range of 50 m x 5 m, with water-sensitive papers being distributed in these bands to verify the size, quantity and distribution of drops that fell on the plants. Once the information was counted, it was expected that it would be possible to create different application models, leading to greater efficiency and effectiveness of the applications. In addition, avoid waste of defense, contributing to decrease environmental impacts and increase safety in the field (lower risk of intoxication). The results allowed to identify competitive advantages, highlighting the practicality and speed, besides allowing localized control of weeds, without the need of tractors, which increases soil compaction and requires greater investment in equipment. From these results, use protocols will beestablished for various agricultural crops, such as: Peanut (Arachis hypogaea L.), Sugarcane (Saccharum officinarum L.), Soya (Glycine max L.), Maize (Zea mays).O presente trabalho teve como objetivo estudar e validar a aplicação de defensivos através de RPAs (Aeronave Remotamente Pilotadas), comumente denominadas de Drones. O experimento foi realizado na APTA Centro Leste no município do Ribeirão Preto, SP. Foi utilizado a: solução de herbicida glifosate 1.5 kg ha-1 (Roundup WG®) utilizando 15 L ha-1 de volume de calda. O RPA que sobrevoou a área de estudo em três diferentes altitudes, juntamente com três diferentes modelos de bicos pulverizadores em uma faixa compreendida de 50 m x 5 m, sendo que nessas faixas foram distribuídos papéis sensíveis à água, para verificar o tamanho, quantidade e distribuição de gotas que caíram sobre as plantas. Uma vez contabilizadas as informações, esperou-se que fosse possível criar diferentes modelos de aplicações, levando a uma maior eficiência e eficácia das aplicações. Além disso, evitar desperdício de defensivo, contribuindo para diminuição dos impactos ambientais e aumento da segurança no campo (menor risco de intoxicações). Os resultados permitiram identificar vantagens competitivas, com destaque para a praticidade e rapidez, além de permitir controle localizado de plantas daninhas, sem a necessidade de uso de tratores, o qual aumenta compactação do solo e requer maior investimento em equipamentos. A partir destes resultados, serão estabelecidos protocolos de utilização para diversas culturas agrícolas, tais como: Amendoim (Arachis hypogaea L.), Cana-de-açúcar (Saccharum officinarum L.), Soja (Glycine max L.), Milho (Zea mays)

Avaliação de populações de soja quanto à produtividade e resistência a percevejos.

O uso de defensivos agrícolas na lavoura representa elevação no custo de produção da mesma e produz impacto ambiental indesejado, devido à contaminação do meio ambiente com produtos químicos. Nesse contexto, a utilização de genótipos com resistência a insetos é desejável, apresentando-se como uma alternativa ao uso de inseticidas no campo. Na cultura da soja, sabe-se que os percevejos causam grandes danos, afetando principalmente os grãos, que devido ao ataque de tais insetos, tornam-se manchados, deformados e até mesmo inviáveis.bitstream/item/123117/1/15-Avaliacao-de-populacoes.pd

Biabduction (and related problems) in array separation logic

We investigate array separation logic (\mathsf {ASL}), a variant of symbolic-heap separation logic in which the data structures are either pointers or arrays, i.e., contiguous blocks of memory. This logic provides a language for compositional memory safety proofs of array programs. We focus on the biabduction problem for this logic, which has been established as the key to automatic specification inference at the industrial scale. We present an \mathsf {NP} decision procedure for biabduction in \mathsf {ASL}, and we also show that the problem of finding a consistent solution is \mathsf {NP}-hard. Along the way, we study satisfiability and entailment in \mathsf {ASL}, giving decision procedures and complexity bounds for both problems. We show satisfiability to be \mathsf {NP}-complete, and entailment to be decidable with high complexity. The surprising fact that biabduction is simpler than entailment is due to the fact that, as we show, the element of choice over biabduction solutions enables us to dramatically reduce the search space

Novel interactions of transglutaminase-2 with heparan sulphate proteoglycans: reflection on physiological implications

This mini-review brings together information from publications and recent conference proceedings that have shed light on the biological interaction between transglutaminase-2 and heparan sulphate proteoglycans. We subsequently draw hypothesis of possible implications in the wound healing process. There is a substantial overlap in the action of transglutaminase-2 and the heparan sulphate proteoglycan syndecan-4 in normal and abnormal wound repair. Our latest findings have identified syndecan-4 as a possible binding and signalling partner of fibronectinbound TG2 and support the idea that transglutaminase-2 and syndecan-4 acts in synergy

Early molecular diagnosis of aspergillosis in a patient with acute myeloid leukaemia

Diagnosis of invasive fungal infection remains challenging. Here we report a case of early diagnosis of invasive aspergillosis in a neutropenic patient affected by acute myeloid leukaemia, achieved through the detection of Aspergillus fumigatus species-specific ribonucleic acid sequences by a sensitive multiplex real-time polymerase chain reaction-based molecular assay. Thanks to the early diagnosis, targeted therapy was promptly established and the severe fungal infection controlled, allowing the patient to subsequently receive allogeneic hematopoietic stem cell transplantation from a haploidentical donor, her only curative option. Also in this instance, targeted secondary antifungal prophylaxis with voriconazole avoided any other fungal infection afterwards. This report suggests how the implementation of molecular assays in combination with routine diagnostic procedures, can improve microbiological diagnosis in sepsis, particularly in case of fungal infection, difficult to detect with standard microbiological culture methods

On the Complexity of Pointer Arithmetic in Separation Logic

We investigate the complexity consequences of adding pointer arithmetic to separation logic. Specifically, we study an extension of the points-to fragment of symbolic-heap separation logic with sets of simple “difference constraints” of the form where x and y are pointer variables and k is an integer offset. This extension can be considered a practically minimal language for separation logic with pointer arithmetic. Most significantly, we find that, even for this minimal language, polynomial-time decidability is already impossible: satisfiability becomes -complete, while quantifier-free entailment becomes -complete and quantified entailment becomes -complete (where is the second class in the polynomial-time hierarchy). However, the language does satisfy the small model property, meaning that any satisfiable formula has a model, and any invalid entailment has a countermodel, of polynomial size, whereas this property fails when richer forms of arithmetical constraints are permitted

Vascular smooth muscle cells remodel collagen matrices by long-distance action and anisotropic interaction

While matrix remodeling plays a key role in vascular physiology and pathology, the underlying mechanisms have remained incompletely understood. We studied the remodeling of collagen matrices by individual vascular smooth muscle cells (SMCs), clusters and monolayers. In addition, we focused on the contribution of transglutaminase 2 (TG2), which plays an important role in the remodeling of small arteries. Single SMCs displaced fibers in collagen matrices at distances up to at least 300 μm in the course of 8–12 h. This process involved both ‘hauling up’ of matrix by the cells and local matrix compaction at a distance from the cells, up to 200 μm. This exceeded the distance over which cellular protrusions were active, implicating the involvement of secreted enzymes such as TG2. SMC isolated from TG2 KO mice still showed compaction, with changed dynamics and relaxation. The TG active site inhibitor L682777 blocked local compaction by wild type cells, strongly reducing the displacement of matrix towards the cells. At increasing cell density, cells cooperated to establish compaction. In a ring-shaped collagen matrix, this resulted in preferential displacement in the radial direction, perpendicular to the cellular long axis. This process was unaffected by inhibition of TG2 cross-linking. These results show that SMCs are capable of matrix remodeling by prolonged, gradual compaction along their short axis. This process could add to the 3D organization and remodeling of blood vessels based on the orientation and contraction of SMCs