Diversidad de Araneae (Arachnida) en la Reserva Colonia Benitez, Chaco Oriental Húmedo, Argentina

Se estudió la diversidad y composición del ensamble de arañas de la Reserva Educativa Colonia Benítez, Chaco, Argentina. Las técnicas de captura incluyeron trampas de caída, golpeteo de follaje, tamizado de hojarasca, captura manual nocturna y aspiración de la vegetación mediante el uso de G-vac. El período de muestreo abarcó octubre, noviembre y diciembre de 2011. Los resultados describen la diversidad detectada (familias, especies y morfoespecies), preferencia de ambientes, eficiencia de métodos de captura, índices de riqueza específica, diversidad y abundancia. Un total de 1527 arañas fueron recolectadas, representantes de 27 familias, 179 especies y morfoespecies. Las familias más diversas fueron Araneidae, Lycosidae, Salticidae y Anyphaenidae. La mayor abundancia se registró en el bosque (59%) donde se identificaron 21 familias, seis de ellas se encontraron solo en este ambiente (Deinopidae, Mimetidae, Selenopidae, Senoculidae, Sparassidae y Uloboridae). En el pastizal se recolectaron 629 individuos ( 41 % ) agrupados también en 21 familias, seis de ella5 no encontrada5 en el Bosque (Amphinectidae, Dictynidae, Oxyopidae, Pholcidae, Scytodidae y Trechaleidae). Las técnicas G-Yac en el pa5tizal y golpeteo de foll~je en el bosque demostraron ser muy efectivas para el muestreo de la diversidad de arañas

Refraction of a Gaussian Seaway

Refraction of a Longuet-Higgins Gaussian sea by random ocean currents creates persistent local variations in average energy and wave action. These variations take the form of lumps or streaks, and they explicitly survive dispersion over wavelength and incoming wave propagation direction. Thus, the uniform sampling assumed in the venerable Longuet-Higgins theory does not apply following refraction by random currents. Proper handling of the non-uniform sampling results in greatly increased probability of freak wave formation. The present theory represents a synthesis of Longuet-Higgins Gaussian seas and the refraction model of White and Fornberg, which considered the effect of currents on a plane wave incident seaway. Using the linearized equations for deep ocean waves, we obtain quantitative predictions for the increased probability of freak wave formation when the refractive effects are taken into account. The crest height or wave height distribution depends primarily on the ``freak index", gamma, which measures the strength of refraction relative to the angular spread of the incoming sea. Dramatic effects are obtained in the tail of this distribution even for the modest values of the freak index that are expected to occur commonly in nature. Extensive comparisons are made between the analytical description and numerical simulations.Comment: 18 pages, 10 figure

EnzymeMiner: Exploration of sequence space of enzymes

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Description of Transport Tunnel in Haloalkane Dehalogenase Variant LinB D147C+L177C from Sphingobium japonicum

The activity of enzymes with active sites buried inside their protein core highly depends on the efficient transport of substrates and products between the active site and the bulk solvent. The engineering of access tunnels in order to increase or decrease catalytic activity and specificity in a rational way is a challenging task. Here, we describe a combined experimental and computational approach to characterize the structural basis of altered activity in the haloalkane dehalogenase LinB D147C+L177C variant. While the overall protein fold is similar to the wild type enzyme and the other LinB variants, the access tunnels have been altered by introduced cysteines that were expected to form a disulfide bond. Surprisingly, the mutations have allowed several conformations of the amino acid chain in their vicinity, interfering with the structural analysis of the mutant by X-ray crystallography. The duration required for the growing of protein crystals changed from days to 1.5 years by introducing the substitutions. The haloalkane dehalogenase LinB D147C+L177C variant crystal structure was solved to 1.15 angstrom resolution, characterized and deposited to Protein Data Bank under PDB ID 6s06

DNA aptamer-based sandwich microfluidic assays for dual quantification and multi-glycan profiling of cancer biomarkers

Two novel sandwich-based immunoassays for prostate cancer (PCa) diagnosis are reported, in which the primary antibody for capture is replaced by a DNA aptamer. The assays, which can be performed in parallel, were developed in a microfluidic device and tested for the detection of free Prostate Specific Antigen (fPSA). A secondary antibody (Aptamer–Antibody Assay) or a lectin (Aptamer–Lectin Assay) is used to quantify, by chemiluminescence, both the amount of fPSA and its glycosylation levels. The use of aptamers enables a more reliable, selective and controlled sensing of the analyte. The dual approach provides sensitive detection of fPSA along with selective fPSA glycoprofiling, which is of significant importance in the diagnosis and prognosis of PCa, as tumor progression is associated with changes in fPSA glycosylation. With these approaches, we can potentially detect 0.5 ng/mL of fPSA and 3 ng/mL of glycosylated fPSA using Sambucus nigra (SNA) lectin, both within the relevant clinical range. The approach can be applied to a wide range of biomarkers, thus providing a good alternative to standard antibody-based immunoassays with significant impact in medical diagnosis and prognosis

Mechanism Based Design of Efficient PET Hydrolases

Polyethylene terephthalate PET is the most widespread synthetic polyester, having been utilized in textile fibers and packaging materials for beverages and food, contributing considerably to the global solid waste stream and environmental plastic pollution. While enzymatic PET recycling and upcycling have recently emerged as viable disposal methods for a circular plastic economy, only a handful of benchmark enzymes have been thoroughly described and subjected to protein engineering for improved properties over the last 16 years. By analyzing the specific material properties of PET and the reaction mechanisms in the context of interfacial biocatalysis, this Perspective identifies several limitations in current enzymatic PET degradation approaches. Unbalanced enzyme substrate interactions, limited thermostability, and low catalytic efficiency at elevated reaction temperatures, and inhibition caused by oligomeric degradation intermediates still hamper industrial applications that require high catalytic efficiency. To overcome these limitations, successful protein engineering studies using innovative experimental and computational approaches have been published extensively in recent years in this thriving research field and are summarized and discussed in detail here. The acquired knowledge and experience will be applied in the near future to address plastic waste contributed by other mass produced polymer types e.g., polyamides and polyurethanes that should also be properly disposed by biotechnological approache

Multiple Substrate Binding Mode Guided Engineering of a Thermophilic PET Hydrolase

[Image: see text] Thermophilic polyester hydrolases (PES-H) have recently enabled biocatalytic recycling of the mass-produced synthetic polyester polyethylene terephthalate (PET), which has found widespread use in the packaging and textile industries. The growing demand for efficient PET hydrolases prompted us to solve high-resolution crystal structures of two metagenome-derived enzymes (PES-H1 and PES-H2) and notably also in complex with various PET substrate analogues. Structural analyses and computational modeling using molecular dynamics simulations provided an understanding of how product inhibition and multiple substrate binding modes influence key mechanistic steps of enzymatic PET hydrolysis. Key residues involved in substrate-binding and those identified previously as mutational hotspots in homologous enzymes were subjected to mutagenesis. At 72 °C, the L92F/Q94Y variant of PES-H1 exhibited 2.3-fold and 3.4-fold improved hydrolytic activity against amorphous PET films and pretreated real-world PET waste, respectively. The R204C/S250C variant of PES-H1 had a 6.4 °C higher melting temperature than the wild-type enzyme but retained similar hydrolytic activity. Under optimal reaction conditions, the L92F/Q94Y variant of PES-H1 hydrolyzed low-crystallinity PET materials 2.2-fold more efficiently than LCC ICCG, which was previously the most active PET hydrolase reported in the literature. This property makes the L92F/Q94Y variant of PES-H1 a good candidate for future applications in industrial plastic recycling processes

PDBe-KB: collaboratively defining the biological context of structural data

The Protein Data Bank in Europe - Knowledge Base (PDBe-KB, https://pdbe-kb.org) is an open collaboration between world-leading specialist data resources contributing functional and biophysical annotations derived from or relevant to the Protein Data Bank (PDB). The goal of PDBe-KB is to place macromolecular structure data in their biological context by developing standardised data exchange formats and integrating functional annotations from the contributing partner resources into a knowledge graph that can provide valuable biological insights. Since we described PDBe-KB in 2019, there have been significant improvements in the variety of available annotation data sets and user functionality. Here, we provide an overview of the consortium, highlighting the addition of annotations such as predicted covalent binders, phosphorylation sites, effects of mutations on the protein structure and energetic local frustration. In addition, we describe a library of reusable web-based visualisation components and introduce new features such as a bulk download data service and a novel superposition service that generates clusters of superposed protein chains weekly for the whole PDB archive