Exploring Molecular Energy Landscapes by Coupling the DFTB Potential with a Tree-Based Stochastic Algorithm: Investigation of the Conformational Diversity of Phthalates.

Exploring the global energy landscape of relatively large molecules at the quantum level is a challenging problem. In this work, we report the coupling of a nonredundant conformational space exploration method, namely, the robotics-inspired iterative global exploration and local optimization (IGLOO) algorithm, with the quantum-chemical density functional tight binding (DFTB) potential. The application of this fast and efficient computational approach to three close-sized molecules of the phthalate family (DBP, BBP, and DEHP) showed that they present different conformational landscapes. These differences have been rationalized by making use of descriptors based on distances and dihedral angles. Coulomb interactions, steric hindrance, and dispersive interactions have been found to drive the geometric properties. A strong correlation has been evidenced between the two dihedral angles describing the side-chain orientation of the phthalate molecules. Our approach identifies low-energy minima without prior knowledge of the potential energy surface, paving the way for future investigations into transition paths and states.

Variations Among Crop Seasons and Inoculum Availability Have a Higher Impact on Grapevine Rust Epidemics than Training Systems or Plastic Cover.

Canopy management practices can be effective as part of the integrated management of grapevine diseases. This study aimed to determine whether training systems and plastic covers can contribute to prevent Asian grapevine leaf rust (AGLR) development. Additionally, the influence of crop season and inoculum availability on AGLR development was investigated. Six-season experiments were carried out to characterize 16 epidemics that developed from natural inoculum (NI) or artificial inoculum (AI) sources (NI + AI), conducted in different training systems and with or without the plastic cover. The Richards model was fitted to each AGLR disease progress curve to estimate and compare the onsets and intensities of epidemics using eight curve elements. Principal components analysis (PCA) identified the incidence progress rate, the area under the severity progress curve, final disease severity, time to disease onset, and time to reach the inflection point as the main descriptors for AGLR epidemics. The results showed that AGLR epidemic development was related mainly to differences in inoculum availability and climatic conditions throughout the seasons and to a lower extent to the training system and plastic cover. The earliest disease onset was observed in epidemics when the NI was supplemented with an AI source. Differences in AGRL intensity were correlated to accumulated precipitation, being less severe in autumn-winter than in the spring-summer season. The present findings provided a better understanding of the structure and the seasonal variation of AGLR in cultivar 'Niagara Rosada'. The strategies for reducing and/or delaying inoculum buildup among seasons are discussed.

Ten Challenges to Understanding and Managing the Insect-Transmitted, Xylem-Limited Bacterial Pathogen Xylella fastidiosa.

An unprecedented plant health emergency in olives has been registered over the last decade in Italy, arguably more severe than what occurred repeatedly in grapes in the United States in the last 140 years. These emergencies are epidemics caused by a stealthy pathogen, the xylem-limited, insect-transmitted bacterium Xylella fastidiosa. Although these epidemics spurred research that answered many questions about the biology and management of this pathogen, many gaps in knowledge remain. For this review, we set out to represent both the U.S. and European perspectives on the most pressing challenges that need to be addressed. These are presented in 10 sections that we hope will stimulate discussion and interdisciplinary research. We reviewed intrinsic problems that arise from the fastidious growth of X. fastidiosa, the lack of specificity for insect transmission, and the economic and social importance of perennial mature woody plant hosts. Epidemiological models and predictions of pathogen establishment and disease expansion, vital for preparedness, are based on very limited data. Most of the current knowledge has been gathered from a few pathosystems, whereas several hundred remain to be studied, probably including those that will become the center of the next epidemic. Unfortunately, aspects of a particular pathosystem are not always transferable to others. We recommend diversification of research topics of both fundamental and applied nature addressing multiple pathosystems. Increasing preparedness through knowledge acquisition is the best strategy to anticipate and manage diseases caused by this pathogen, described as "the most dangerous plant bacterium known worldwide."

European Xylella fastidiosa strains can cause symptoms in blueberry.

Strains of the bacterial pathogen Xylella fastidiosa subspecies multiplex (Xfm) and pauca (Xfp) isolated from symptomatic almond and olive plants in Spain and Italy were used in this study. Due to the risk of host jump and considering the importance of southern highbush blueberry production in Spain, we tested a small set of these strains for their potential to infect and cause disease symptoms in blueberries under greenhouse experiments. Xfm IVIA5901 (isolated from almonds in Alicante, Spain) caused symptoms similar to those caused by Xfm AlmaEM3 (isolated from blueberries in Georgia, USA, and used as a reference strain capable of inducing severe symptoms in blueberry). Nevertheless, bacterial populations of Xfm IVIA5901 in planta were significantly lower than those of Xfm AlmaEm3. Xfm ESVL (isolated from almonds, Alicante, Spain) and Xfp XYL1961/18 (isolated from olives, Ibiza Island, Spain) caused limited symptoms, while Xfm XYL466/19 (isolated from wild olives, Mallorca Island, Spain) and Xfm XF3348 (isolated from almonds, Mallorca Island, Spain), and Xfp De Donno (isolated from olives, Puglia, Italy and representative of the devastating olive quick decline syndrome) did not cause symptoms nor colonize blueberries. This study suggests that certain strains already found in Europe could infect blueberry if conditions conducive for a host jump in this region are met, such as proximity of blueberries to other infected hosts and presence of insect vectors that feed on these crops. Surveys on the presence of X. fastidiosa in blueberries in Spain and other European countries are needed to anticipate possible issues.

Analyzing the Thermal Characteristics of Three Lining Materials for Plantar Orthotics.

INTRODUCTION: The choice of materials for covering plantar orthoses or wearable insoles is often based on their hardness, breathability, and moisture absorption capacity, although more due to professional preference than clear scientific criteria. An analysis of the thermal response to the use of these materials would provide information about their behavior; hence, the objective of this study was to assess the temperature of three lining materials with different characteristics. MATERIALS AND METHODS: The temperature of three materials for covering plantar orthoses was analyzed in a sample of 36 subjects (15 men and 21 women, aged 24.6 ± 8.2 years, mass 67.1 ± 13.6 kg, and height 1.7 ± 0.09 m). Temperature was measured before and after 3 h of use in clinical activities, using a polyethylene foam copolymer (PE), ethylene vinyl acetate (EVA), and PE-EVA copolymer foam insole with the use of a FLIR E60BX thermal camera. RESULTS: In the PE copolymer (material 1), temperature increases between 1.07 and 1.85 °C were found after activity, with these differences being statistically significant in all regions of interest (p < 0.001), except for the first toe (0.36 °C, p = 0.170). In the EVA foam (material 2) and the expansive foam of the PE-EVA copolymer (material 3), the temperatures were also significantly higher in all analyzed areas (p < 0.001), ranging between 1.49 and 2.73 °C for EVA and 0.58 and 2.16 °C for PE-EVA. The PE copolymer experienced lower overall overheating, and the area of the fifth metatarsal head underwent the greatest temperature increase, regardless of the material analyzed. CONCLUSIONS: PE foam lining materials, with lower density or an open-cell structure, would be preferred for controlling temperature rise in the lining/footbed interface and providing better thermal comfort for users. The area of the first toe was found to be the least overheated, while the fifth metatarsal head increased the most in temperature. This should be considered in the design of new wearables to avoid excessive temperatures due to the lining materials.

MoMA-LoopSampler: a web server to exhaustively sample protein loop conformations.

SUMMARY: MoMA-LoopSampler is a sampling method that globally explores the conformational space of flexible protein loops. It combines a large structural library of three-residue fragments and a novel reinforcement-learning-based approach to accelerate the sampling process while maintaining diversity. The method generates a set of statistically likely loop states satisfying geometric constraints, and its ability to sample experimentally observed conformations has been demonstrated. This paper presents a web user interface to MoMA-LoopSampler through the illustration of a typical use-case. AVAILABILITY AND IMPLEMENTATION: MoMA-LoopSampler is freely available at: https://moma.laas.fr/applications/LoopSampler/. We recommend users to create an account, but anonymous access is possible. In most cases, jobs are completed within a few minutes. The waiting time may increase depending on the server load, but it very rarely exceeds an hour. For users requiring more intensive use, binaries can be provided upon request. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

The sequence context in poly-alanine regions: structure, function and conservation.

MOTIVATION: Poly-alanine (polyA) regions are protein stretches mostly composed of alanines. Despite their abundance in eukaryotic proteomes and their association to nine inherited human diseases, the structural and functional roles exerted by polyA stretches remain poorly understood. In this work we study how the amino acid context in which polyA regions are settled in proteins influences their structure and function. RESULTS: We identified glycine and proline as the most abundant amino acids within polyA and in the flanking regions of polyA tracts, in human proteins as well as in 17 additional eukaryotic species. Our analyses indicate that the non-structuring nature of these two amino acids influences the α-helical conformations predicted for polyA, suggesting a relevant role in reducing the inherent aggregation propensity of long polyA. Then, we show how polyA position in protein N-termini relates with their function as transit peptides. PolyA placed just after the initial methionine is often predicted as part of mitochondrial transit peptides, whereas when placed in downstream positions, polyA are part of signal peptides. A few examples from known structures suggest that short polyA can emerge by alanine substitutions in α-helices; but evolution by insertion is observed for longer polyA. Our results showcase the importance of studying the sequence context of homorepeats as a mechanism to shape their structure-function relationships. AVAILABILITY AND IMPLEMENTATION: The datasets used and/or analyzed during the current study are available from the corresponding author onreasonable request. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Primary cutaneous mucormycosis due to Rhizopus arrhizus in an immunosuppressed patient with paroxysmal nocturnal haemoglobinuria.

OBJECTIVE: We present a case of primary cutaneous mucormycosis in a patient with bone marrow failure secondary to paroxysmal nocturnal haemoglobinuria (PNH). CLINICAL CASE: A 60-year-old male patient with a history of PNH, complicated to a severe aplastic anaemia, presented to the emergency department complaining of papules on the lower limbs that rapidly turned into necrotic plaques within 2 months. Histopathological examination showed granulomatous and suppurative dermatitis with tissue necrosis and the presence of non-septate hyphae. Molecular identification was achieved by amplification and sequencing of the 18S-ITS1-5.8S-ITS2-28S rRNA region using the polymerase chain reaction. The sequence showed 100% identity with Rhizopus arrhizus. The patient received treatment with liposomal amphotericin B and surgical debridement. Nonetheless, the patient suffered from severe low red blood cells and platelets and also underwent septic shock; he died 6 days after admission to the hospital. CONCLUSION: Mucormycosis in the setting of immunosuppression is challenging. Upon suspicion of a diagnosis, immediate treatment is required. Adjunctive therapies may be considered; however, the case fatality rate remains high.

Plant growth-promoting and heavy metal-resistant Priestia and Bacillus strains associated with pioneer plants from mine tailings.

Open mine tailings dams are extreme artificial environments containing sizeable potentially toxic elements (PTEs), including heavy metals (HMs), transition metals, and metalloids. Furthermore, these tailings have nutritional deficiencies, including assimilable phosphorus sources, organic carbon, and combined nitrogen, preventing plant colonization. Bacteria, that colonize these environments, have mechanisms to tolerate the selective pressures of PTEs. In this work, several Priestia megaterium (formerly Bacillus megaterium), Bacillus mojavensis, and Bacillus subtilis strains were isolated from bulk tailings, anthills, rhizosphere, and endosphere of pioneer plants from abandoned mine tailings in Zacatecas, Mexico. Bacillus spp. tolerated moderate HMs concentrations, produced siderophores and indole-3-acetic acid (IAA), solubilized phosphates, and reduced acetylene in the presence of HMs. The strains harbored different PIB-type ATPase genes encoding for efflux pumps and Cation Diffusion Facilitator (CDF) genes. Moreover, nifH and nifD nitrogenase genes were detected in P. megaterium and B. mojavensis genomic DNA. They showed similarity with sequences of the beta-Proteobacteria species, which may represent likely horizontal transfer events. These Bacillus species precede the colonization of mine tailings by plants. Their phenotypic and genotypic features could be essential in the natural recovery of the sites by reducing the oxidative stress of HMs, fixing nitrogen, solubilizing phosphate, and accumulating organic carbon. These traits of the strains reflect the adaptations of Bacillus species to the mine tailings environment and could contribute to the success of phytoremediation efforts.

Complete Circularized Genome Resources of Seven Strains of Xylella fastidiosa subsp. fastidiosa Using Hybrid Assembly Reveals Unknown Plasmids.

Xylella fastidiosa is a vascular plant pathogenic bacterium native to the Americas that is causing significant epidemics and economic losses in olive and almonds in Europe, where it is a quarantine pathogen. Since its first detection in 2013 in Italy, mandatory surveys across Europe revealed the presence of the bacterium also in France, Spain, and Portugal. Combining Oxford Nanopore Technologies and Illumina sequencing data, we assembled high-quality complete genomes of seven X. fastidiosa subsp. fastidiosa strains isolated from different plants in Spain, the United States, and Mexico. Comparative genomic analyses discovered differences in plasmid content among strains, including plasmids that had been overlooked previously when using the Illumina sequencing platform alone. Interestingly, in strain CFBP8073, intercepted in France from plants imported from Mexico, three plasmids were identified, including two (plasmids pXF-P1.CFBP8073 and pXF-P2.CFBP8073) not previously described in X. fastidiosa and one (pXF5823.CFBP8073) almost identical to a plasmid described in a X. fastidiosa strain from citrus. Plasmids found in the Spanish strains here were similar to those described previously in other strains from the same subspecies and ST1 isolated in the Balearic Islands and the United States. The genome resources from this work will assist in further studies on the role of plasmids in the epidemiology, ecology, and evolution of this plant pathogen.

Impact of Xylella fastidiosa subspecies pauca in European olives.

Xylella fastidiosa is the causal agent of plant diseases that cause massive economic damage. In 2013, a strain of the bacterium was, for the first time, detected in the European territory (Italy), causing the Olive Quick Decline Syndrome. We simulate future spread of the disease based on climatic-suitability modeling and radial expansion of the invaded territory. An economic model is developed to compute impact based on discounted foregone profits and losses in investment. The model projects impact for Italy, Greece, and Spain, as these countries account for around 95% of the European olive oil production. Climatic suitability modeling indicates that, depending on the suitability threshold, 95.5 to 98.9%, 99.2 to 99.8%, and 84.6 to 99.1% of the national areas of production fall into suitable territory in Italy, Greece, and Spain, respectively. For Italy, across the considered rates of radial range expansion the potential economic impact over 50 y ranges from 1.9 billion to 5.2 billion Euros for the economic worst-case scenario, in which production ceases after orchards die off. If replanting with resistant varieties is feasible, the impact ranges from 0.6 billion to 1.6 billion Euros. Depending on whether replanting is feasible, between 0.5 billion and 1.3 billion Euros can be saved over the course of 50 y if disease spread is reduced from 5.18 to 1.1 km per year. The analysis stresses the necessity to strengthen the ongoing research on cultivar resistance traits and application of phytosanitary measures, including vector control and inoculum suppression, by removing host plants.

Analysis of the Localization of Schizosaccharomyces pombe Glucan Synthases in the Presence of the Antifungal Agent Caspofungin.

In recent years, invasive fungal infections have emerged as a common source of infections in immunosuppressed patients. All fungal cells are surrounded by a cell wall that is essential for cell integrity and survival. It prevents cell death and lysis resulting from high internal turgor pressure. Since the cell wall is not present in animal cells, it is an ideal target for selective invasive fungal infection treatments. The antifungal family known as echinocandins, which specifically inhibit the synthesis of the cell wall ß(13)glucan, has been established as an alternative treatment for mycoses. To explore the mechanism of action of these antifungals, we analyzed the cell morphology and glucan synthases localization in Schizosaccharomyces pombe cells during the initial times of growth in the presence of the echinocandin drug caspofungin. S. pombe are rod-shaped cells that grow at the poles and divide by a central division septum. The cell wall and septum are formed by different glucans, which are synthesized by four essential glucan synthases: Bgs1, Bgs3, Bgs4, and Ags1. Thus, S. pombe is not only a perfect model for studying the synthesis of the fungal ß(1-3)glucan, but also it is ideal for examining the mechanisms of action and resistance of cell wall antifungals. Herein, we examined the cells in a drug susceptibility test in the presence of either lethal or sublethal concentrations of caspofungin, finding that exposure to the drug for long periods at high concentrations (>10 µg/mL) induced cell growth arrest and the formation of rounded, swollen, and dead cells, whereas low concentrations (<10 µg/mL) permitted cell growth with a mild effect on cell morphology. Interestingly, short-term treatments with either high or low concentrations of the drug induced effects contrary to those observed in the susceptibility tests. Thus, low drug concentrations induced a cell death phenotype that was not observed at high drug concentrations, which caused transient fungistatic cell growth arrest. After 3 h, high concentrations of the drug caused the following: (i) a decrease in the GFP-Bgs1 fluorescence level; (ii) altered locations of Bgs3, Bgs4, and Ags1; and (iii) a simultaneous accumulation of cells with calcofluor-stained incomplete septa, which at longer times resulted in septation uncoupling from plasma membrane ingression. The incomplete septa revealed with calcofluor were found to be complete when observed via the membrane-associated GFP-Bgs or Ags1-GFP. Finally, we found that the accumulation of incomplete septa depended on Pmk1, the last kinase of the cell wall integrity pathway.

Statistical proofs of the interdependence between nearest neighbor effects on polypeptide backbone conformations.

Backbone dihedral angles ϕ and ψ are the main structural descriptors of proteins and peptides. The distribution of these angles has been investigated over decades as they are essential for the validation and refinement of experimental measurements, as well as for structure prediction and design methods. The dependence of these distributions, not only on the nature of each amino acid but also on that of the closest neighbors, has been the subject of numerous studies. Although neighbor-dependent distributions are nowadays generally accepted as a good model, there is still some controversy about the combined effects of left and right neighbors. We have investigated this question using rigorous methods based on recently-developed statistical techniques. Our results unambiguously demonstrate that the influence of left and right neighbors cannot be considered independently. Consequently, three-residue fragments should be considered as the minimal building blocks to investigate polypeptide sequence-structure relationships.

No evidence for motor-recovery-related cortical connectivity changes after stroke using resting-state fMRI.

It has been proposed that a form of cortical reorganization (changes in functional connectivity between brain areas) can be assessed with resting-state (rs) functional MRI (fMRI). Here, we report a longitudinal data set collected from 19 patients with subcortical stroke and 11 controls. Patients were imaged up to five times over 1 year. We found no evidence, using rs-fMRI, for longitudinal poststroke cortical connectivity changes despite substantial behavioral recovery. These results could be construed as questioning the value of resting-state imaging. Here, we argue instead that they are consistent with other emerging reasons to challenge the idea of motor-recovery-related cortical reorganization poststroke when conceived of as changes in connectivity between cortical areas.NEW & NOTEWORTHY We investigated longitudinal changes in functional connectivity after stroke. Despite substantial motor recovery, we found no differences in functional connectivity patterns between patients and controls, nor any changes over time. Assuming that rs-fMRI is an adequate method to capture connectivity changes between cortical regions after brain injury, these results provide reason to doubt that changes in cortico-cortical connectivity are the relevant mechanism for promoting motor recovery.

[Coordination between primary care and a geriatrics service, 20 years later]. / Coordinación entre atención primaria y un servicio de geriatría, 20 años después.

OBJECTIVE: To describe the evolution of the care and coordination activity of a specialized hospital team (Geriatric Home Care-AGD team) in support of Primary Care (PC) for the care of geriatric patients. LOCATION: Health-5 area of the Community of Madrid. PARTICIPANTS, INTERVENTIONS AND MAIN MEASUREMENTS: Evaluation of patients attended at home at the request of PC by AGD, in 1997-1999 and twenty years later, in 2017-2019. Sociodemographic, clinical, functional and mental variables were recorded. Also care data such as time to first visit, average length of stay, origin and destination of patients, reason for consultation and main reason for disability. RESULTS: 524 patients (58% of the total) requested from AP in 1997-1999 and 1196 (72.2% of the total) in 2017-2019 were attended. Currently we show an older patient, more physically and mentally disabled, with a higher prevalence of geriatric syndromes and greater social fragility. Dementia has increased as the main reason for incapacity, with an increase in Comprehensive Geriatric Assessment and clinical control as the main reasons for referral. CONCLUSIONS: in our setting, after 20 years, AGD continues to be an important support for PC in the complex approach to frail elderly patients confined to their homes, who are increasingly vulnerable from a clinical, functional, cognitive and social point of view. It contributes to the management of geriatric syndromes, deprescription, direct hospital admissions when needed without having to go to the emergency department, and a decrease in institutionalization, facilitating the maintenance of the patient at home.

Protein loops with multiple meta-stable conformations: A challenge for sampling and scoring methods.

Flexible regions in proteins, such as loops, cannot be represented by a single conformation. Instead, conformational ensembles are needed to provide a more global picture. In this context, identifying statistically meaningful conformations within an ensemble generated by loop sampling techniques remains an open problem. The difficulty is primarily related to the lack of structural data about these flexible regions. With the majority of structural data coming from x-ray crystallography and ignoring plasticity, the conception and evaluation of loop scoring methods is challenging. In this work, we compare the performance of various scoring methods on a set of eight protein loops that are known to be flexible. The ability of each method to identify and select all of the known conformations is assessed, and the underlying energy landscapes are produced and projected to visualize the qualitative differences obtained when using the methods. Statistical potentials are found to provide considerable reliability despite their being designed to tradeoff accuracy for lower computational cost. On a large pool of loop models, they are capable of filtering out statistically improbable states while retaining those that resemble known (and thus likely) conformations. However, computationally expensive methods are still required for more precise assessment and structural refinement. The results also highlight the importance of employing several scaffolds for the protein, due to the high influence of small structural rearrangements in the rest of the protein over the modeled energy landscape for the loop.

Interdomain linkers tailor the stability of immunoglobulin repeats in polyproteins.

Linkers in polyproteins are considered as mere spacers between two adjacent domains. However, a series of studies using single-molecule force spectroscopy have recently reported distinct thermodynamic stability of I27 in polyproteins with varying linkers and indicated the vital role of linkers in domain stability. A flexible glycine rich linker (-(GGG)n, n ≥ 3) featured unfolding at lower forces than the regularly used arg-ser (RS) based linker. Interdomain interactions among I27 domains in Gly-rich linkers were suggested to lead to reduced domain stability. However, the negative impact of inter domain interactions on domain stability is thermodynamically counter-intuitive and demanded thorough investigations. Here, using an array of ensemble equilibrium experiments and in-silico measurements with I27 singlet and doublets with two aforementioned linkers, we delineate that the inter-domain interactions in fact raise the stability of the polyprotein with RS linker. More surprisingly, a highly flexible Gly-rich linker has no interference on the stability of polyprotein. Overall, we conclude that flexible linkers are preferred in a polyprotein for maintaining domain's independence.

A reinforcement-learning-based approach to enhance exhaustive protein loop sampling.

MOTIVATION: Loop portions in proteins are involved in many molecular interaction processes. They often exhibit a high degree of flexibility, which can be essential for their function. However, molecular modeling approaches usually represent loops using a single conformation. Although this conformation may correspond to a (meta-)stable state, it does not always provide a realistic representation. RESULTS: In this paper, we propose a method to exhaustively sample the conformational space of protein loops. It exploits structural information encoded in a large library of three-residue fragments, and enforces loop-closure using a closed-form inverse kinematics solver. A novel reinforcement-learning-based approach is applied to accelerate sampling while preserving diversity. The performance of our method is showcased on benchmark datasets involving 9-, 12- and 15-residue loops. In addition, more detailed results presented for streptavidin illustrate the ability of the method to exhaustively sample the conformational space of loops presenting several meta-stable conformations. AVAILABILITY AND IMPLEMENTATION: We are developing a software package called MoMA (for Molecular Motion Algorithms), which includes modeling tools and algorithms to sample conformations and transition paths of biomolecules, including the application described in this work. The binaries can be provided upon request and a web application will also be implemented in the short future. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Analysis and application of a suite of recombinant endo-ß(1,3)-D-glucanases for studying fungal cell walls.

BACKGROUND: The fungal cell wall is an essential and robust external structure that protects the cell from the environment. It is mainly composed of polysaccharides with different functions, some of which are necessary for cell integrity. Thus, the process of fractionation and analysis of cell wall polysaccharides is useful for studying the function and relevance of each polysaccharide, as well as for developing a variety of practical and commercial applications. This method can be used to study the mechanisms that regulate cell morphogenesis and integrity, giving rise to information that could be applied in the design of new antifungal drugs. Nonetheless, for this method to be reliable, the availability of trustworthy commercial recombinant cell wall degrading enzymes with non-contaminating activities is vital. RESULTS: Here we examined the efficiency and reproducibility of 12 recombinant endo-ß(1,3)-D-glucanases for specifically degrading the cell wall ß(1,3)-D-glucan by using a fast and reliable protocol of fractionation and analysis of the fission yeast cell wall. This protocol combines enzymatic and chemical degradation to fractionate the cell wall into the four main polymers: galactomannoproteins, α-glucan, ß(1,3)-D-glucan and ß(1,6)-D-glucan. We found that the GH16 endo-ß(1,3)-D-glucanase PfLam16A from Pyrococcus furiosus was able to completely and reproducibly degrade ß(1,3)-D-glucan without causing the release of other polymers. The cell wall degradation caused by PfLam16A was similar to that of Quantazyme, a recombinant endo-ß(1,3)-D-glucanase no longer commercially available. Moreover, other recombinant ß(1,3)-D-glucanases caused either incomplete or excessive degradation, suggesting deficient access to the substrate or release of other polysaccharides. CONCLUSIONS: The discovery of a reliable and efficient recombinant endo-ß(1,3)-D-glucanase, capable of replacing the previously mentioned enzyme, will be useful for carrying out studies requiring the digestion of the fungal cell wall ß(1,3)-D-glucan. This new commercial endo-ß(1,3)-D-glucanase will allow the study of the cell wall composition under different conditions, along the cell cycle, in response to environmental changes or in cell wall mutants. Furthermore, this enzyme will also be greatly valuable for other practical and commercial applications such as genome research, chromosomes extraction, cell transformation, protoplast formation, cell fusion, cell disruption, industrial processes and studies of new antifungals that specifically target cell wall synthesis.

Dense cloud cores revealed by CO in the low metallicity dwarf galaxy WLM.

Understanding stellar birth requires observations of the clouds in which they form. These clouds are dense and self-gravitating, and in all existing observations they are molecular, with H2 the dominant species and carbon monoxide (CO) the best available tracer. When the abundances of carbon and oxygen are low compared with that of hydrogen, and the opacity from dust is also low, as in primeval galaxies and local dwarf irregular galaxies, CO forms slowly and is easily destroyed, so it is difficult for it to accumulate inside dense clouds. Here we report interferometric observations of CO clouds in the local group dwarf irregular galaxy Wolf-Lundmark-Melotte (WLM), which has a metallicity that is 13 per cent of the solar value and 50 per cent lower than the previous CO detection threshold. The clouds are tiny compared to the surrounding atomic and H2 envelopes, but they have typical densities and column densities for CO clouds in the Milky Way. The normal CO density explains why star clusters forming in dwarf irregulars have similar densities to star clusters in giant spiral galaxies. The low cloud masses suggest that these clusters will also be low mass, unless some galaxy-scale compression occurs, such as an impact from a cosmic cloud or other galaxy. If the massive metal-poor globular clusters in the halo of the Milky Way formed in dwarf galaxies, as is commonly believed, then they were probably triggered by such an impact.