Explore the vast range of titles available.

We study the sphaleron solutions in two deformations of the ϕ 6 model and analyze the oscillons originated from them. We find that the presence of internal modes plays a crucial role in the sphaleron collapse. The positive internal modes triggered by a squeezing of the sphaleron are able to change the direction of collapse. We provide an analytical understanding behind this phenomenon.

The bacterial second messenger bis-(3'-5') cyclic dimeric guanosine monophosphate (c-di-GMP) has emerged as a central regulator for biofilm formation. Increased cellular c-di-GMP levels lead to stable cell attachment, which in Pseudomonas fluorescens requires the transmembrane receptor LapD. LapD exhibits a conserved and widely used modular architecture containing a HAMP domain and degenerate diguanylate cyclase and phosphodiesterase domains. c-di-GMP binding to the LapD degenerate phosphodiesterase domain is communicated via the HAMP relay to the periplasmic domain, triggering sequestration of the protease LapG, thus preventing cleavage of the surface adhesin LapA. Here, we elucidate the molecular mechanism of autoinhibition and activation of LapD based on structure-function analyses and crystal structures of the entire periplasmic domain and the intracellular signaling unit in two different states. In the absence of c-di-GMP, the intracellular module assumes an inactive conformation. Binding of c-di-GMP to the phosphodiesterase domain disrupts the inactive state, permitting the formation of a trans-subunit dimer interface between adjacent phosphodiesterase domains via interactions conserved in c-di-GMP-degrading enzymes. Efficient mechanical coupling of the conformational changes across the membrane is realized through an extensively domain-swapped, unique periplasmic fold. Our structural and functional analyses identified a conserved system for the regulation of periplasmic proteases in a wide variety of bacteria, including many free-living and pathogenic species.

Bacteroidales (syn. Bacteroidetes) are prominent members of the human gastrointestinal ecosystem mainly due to their efficient glycan-degrading machinery, organized into gene clusters known as polysaccharide utilization loci (PULs). A single PUL was reported for catabolism of high-mannose (HM) N -glycan glyco-polypeptides in the gut symbiont Bacteroides thetaiotaomicron , encoding a surface endo-β-N-acetylglucosaminidase (ENGase), BT3987. Here, we discover an ENGase from the GH18 family in B. thetaiotaomicron , BT1285, encoded in a distinct PUL with its own repertoire of proteins for catabolism of the same HM N -glycan substrate as that of BT3987. We employ X-ray crystallography, electron microscopy, mass spectrometry-based activity measurements, alanine scanning mutagenesis and a broad range of biophysical methods to comprehensively define the molecular mechanism by which BT1285 recognizes and hydrolyzes HM N -glycans, revealing that the stabilities and activities of BT1285 and BT3987 were optimal in markedly different conditions. BT1285 exhibits significantly higher affinity and faster hydrolysis of poorly accessible HM N -glycans than does BT3987. We also find that two HM-processing endoglycosidases from the human gut-resident Alistipes finegoldii display condition-specific functional properties. Altogether, our data suggest that human gut microbes employ evolutionary strategies to express distinct ENGases in order to optimally metabolize the same N- glycan substrate in the gastroinstestinal tract. The human gut microbiome has a substantial impact on human health. Here, the authors find that prominent human gut microbes express functionally distinct surface endo-β-N-acetylglucosaminidases encoded by different polysaccharide utilization loci to optimally metabolize the same oligomannose N- glycan substrate in the gastrointestinal tract.

Microorganisms can switch from a planktonic, free-swimming life-style to a sessile, colonial state, called a biofilm, which confers resistance to environmental stress. Conversion between the motile and biofilm life-styles has been attributed to increased levels of the prokaryotic second messenger cyclic di-guanosine monophosphate (c-di-GMP), yet the signaling mechanisms mediating such a global switch are poorly understood. Here we show that the transcriptional regulator VpsT from Vibrio cholerae directly senses c-di-GMP to inversely control extracellular matrix production and motility, which identifies VpsT as a master regulator for biofilm formation. Rather than being regulated by phosphorylation, VpsT undergoes a change in oligomerization on c-di-GMP binding.

NASA’s InSight mission to Mars will measure seismic signals to determine the planet’s interior structure. These highly sensitive seismometers are susceptible to corruption of their measurements by environmental changes. Magnetic fields, atmosphere pressure changes, and local winds can all induce apparent changes in the seismic records that are not due to propagating ground motions. Thus, InSight carries a set of sensors called the Auxiliary Payload Sensor Suite (APSS) which includes a magnetometer, an atmospheric pressure sensor, and a pair of wind and air temperature sensors. In the case of the magnetometer, knowledge of the amplitude of the fluctuating magnetic field at the InSight lander will allow the separation of seismic signals from potentially interfering magnetic signals of either natural or spacecraft origin. To acquire such data, a triaxial fluxgate magnetometer was installed on the deck of the lander to obtain magnetic records at the same cadence as the seismometer. Similarly, a highly sensitive pressure sensor is carried by InSight to enable the removal of local ground-surface tilts due to advecting pressure perturbations. Finally, the local winds (speed and direction) and air temperature are estimated using a hot-film wind sensor with heritage from REMS on the Curiosity rover. When winds are too high, seismic signals can be ignored or discounted. Herein we describe the APSS sensor suite, the test programs for its components, and the possible additional science investigations it enables.

Understanding kinase action requires precise quantitative measurements of their activity in vivo. In addition, the ability to capture spatial information of kinase activity is crucial to deconvolute complex signaling networks, interrogate multifaceted kinase actions, and assess drug effects or genetic perturbations. Here we develop a proteomic kinase activity sensor technique (ProKAS) for the analysis of kinase signaling using mass spectrometry. ProKAS is based on a tandem array of peptide sensors with amino acid barcodes that allow multiplexed analysis for spatial, kinetic, and screening applications. We engineered a ProKAS module to simultaneously monitor the activities of the DNA damage response kinases ATR, ATM, and CHK1 in response to genotoxic drugs, while also uncovering differences between these signaling responses in the nucleus, cytosol, and replication factories. Furthermore, we developed an in silico approach for the rational design of specific substrate peptides expandable to other kinases. Overall, ProKAS is a versatile system for systematically and spatially probing kinase action in cells. Understanding kinase action requires precise quantitative and spatial measurements of their activity in vivo. Here the authors develop a proteomic kinase activity sensor technique (ProKAS) enabling multiplexed spatial, kinetic, and screening analyses of kinase activities via mass spectrometry.

Background The main aim of this study was to compare short-term results and long-term outcomes of patients who underwent intraoperative colonic lavage (IOCL) with primary anastomosis with those who had stent placement prior to scheduled surgery for obstructive left-sided colonic cancer (OLCC). Methods We conducted a prospective, controlled, randomized study of patients diagnosed with OLCC. Patients were divided into two groups: stent and deferred surgery (group 1) and emergency IOCL (group 2). Demographic variables, risk prediction models, postoperative morbidity and mortality, staging, complications due to stent placement, surgical time, clinical follow-up, health costs, and follow-up of survival were recorded. Results Twenty-eight patients (15 group 1 and 13 group 1) were enrolled. The study was suspended upon detecting excess morbidity in group 2. The two groups were homogeneous in clinical and demographic terms. Overall morbidity in group 1 was 2/15 (13.3%) compared with 7/13 (53.8%) in group 2 ( p  = 0.042). None of the 15 patients in group 1 presented anastomotic dehiscence compared with 4/13 (30.7%) in group 2 ( p  = 0.035). Surgical site infection was detected in 2 (13.3%) patients in group 1 and in 6 (46.1%) in group 2 ( p  = 0.096). Postoperative stay was 8 days (IQR 3, group 1) and 10 days (IQR 10, group 2) ( p  = 0.05). The mean follow-up period was 37.6 months (SD = 16.08) with no differences in survival between the groups. Conclusion In our setting, the use of a stent and scheduled surgery is safer than IOCL and is associated with lower morbidity, shorter hospital stay, and equally good long-term survival.

Despite meticulous monitoring of Salmonella spp. throughout the food chain to ensure safer animal food products for consumers, the number of salmonellosis cases in humans continues to rise annually in Europe. Phage therapy emerges as a promising tool for controlling and eradicating Salmonella in primary production. This study aimed to fully characterize new phage therapy candidates isolated from animal sources. To achieve this, a phenotypic and genetic characterization of five phage isolates was conducted. The five phages demonstrated physical stability across a wide range of temperatures and pH levels, effectively lysing 12 different Salmonella serovars, including the most prevalent ones in the European Union in recent years, as well as multidrug-resistant strains isolated from the field. Additionally, four of the phages exhibited depolymerase production in the host range, with genomic analysis confirming that all five possessed sequences encoding for this activity, suggesting their potential as surface-disinfecting agents. Genetic analysis further revealed that the phages belong to distinct genera: Felixounavirus , Cornellvirus , Skatevirus , Agtevirus and Berlinvirus . Notably, none of the phages contained harmful sequences that could compromise their future application, such as virulence factors, antibiotic resistance genes or temperate markers. Overall, these five phages show promise as suitable candidates for phage therapy applications or phage-based Salmonella eradication strategies, where their integration in the existing biocontrol measures may enhance both food safety and public health.

Flaviviruses are major human disease-causing pathogens, including dengue virus (DENV), Zika virus, yellow fever virus and others. DENV infects hundreds of millions of people per year around the world, causing a tremendous social and economic burden. DENV capsid (C) protein plays an essential role during genome encapsidation and viral particle formation. It has been previously shown that DENV C enters the nucleus in infected cells. However, whether DENV C protein exhibits nuclear export remains unclear. By spatially cross-correlating different regions of the cell, we investigated DENV C movement across the nuclear envelope during the infection cycle. We observed that transport takes place in both directions and with similar translocation times (in the ms time scale) suggesting a bidirectional movement of both C protein import and export. Furthermore, from the pair cross-correlation functions in cytoplasmic or nuclear regions we found two populations of C molecules in each compartment with fast and slow mobilities. While in the cytoplasm the correlation times were in the 2–6 and 40–110 ms range for the fast and slow mobility populations respectively, in the cell nucleus they were 1–10 and 25–140 ms range, respectively. The fast mobility of DENV C in cytoplasmic and nuclear regions agreed with the diffusion coefficients from Brownian motion previously reported from correlation analysis. These studies provide the first evidence of DENV C shuttling from and to the nucleus in infected cells, opening new venues for antiviral interventions.

Background Yellow lupin ( Lupinus luteus L.) is a minor legume crop characterized by its high seed protein content. Although grown in several temperate countries, its orphan condition has limited the generation of genomic tools to aid breeding efforts to improve yield and nutritional quality. In this study, we report the construction of 454-expresed sequence tag (EST) libraries, carried out comparative studies between L. luteus and model legume species, developed a comprehensive set of EST-simple sequence repeat (SSR) markers, and validated their utility on diversity studies and transferability to related species. Results Two runs of 454 pyrosequencing yielded 205 Mb and 530 Mb of sequence data for L1 (young leaves, buds and flowers) and L2 (immature seeds) EST- libraries. A combined assembly (L1L2) yielded 71,655 contigs with an average contig length of 632 nucleotides. L1L2 contigs were clustered into 55,309 isotigs. 38,200 isotigs translated into proteins and 8,741 of them were full length. Around 57% of L. luteus sequences had significant similarity with at least one sequence of Medicago , Lotus , Arabidopsis , or Glycine , and 40.17% showed positive matches with all of these species. L. luteus isotigs were also screened for the presence of SSR sequences. A total of 2,572 isotigs contained at least one EST-SSR, with a frequency of one SSR per 17.75 kbp. Empirical evaluation of the EST-SSR candidate markers resulted in 222 polymorphic EST-SSRs. Two hundred and fifty four (65.7%) and 113 (30%) SSR primer pairs were able to amplify fragments from L. hispanicus and L. mutabilis DNA, respectively. Fifty polymorphic EST-SSRs were used to genotype a sample of 64  L. luteus accessions. Neighbor-joining distance analysis detected the existence of several clusters among L. luteus accessions, strongly suggesting the existence of population subdivisions. However, no clear clustering patterns followed the accession’s origin. Conclusion L. luteus deep transcriptome sequencing will facilitate the further development of genomic tools and lupin germplasm. Massive sequencing of cDNA libraries will continue to produce raw materials for gene discovery, identification of polymorphisms (SNPs, EST-SSRs, INDELs, etc.) for marker development, anchoring sequences for genome comparisons and putative gene candidates for QTL detection.