Beta-lactamase database (BLDB) – structure and function

Beta-Lactamase Database (BLDB) is a comprehensive, manually curated public resource providing up-to-date structural and functional information focused on this superfamily of enzymes with a great impact on antibiotic resistance. All the enzymes reported and characterised in the literature are presented according to the class (A, B, C and D), family and subfamily to which they belong. All three-dimensional structures of β-lactamases present in the Protein Data Bank are also shown. The characterisation of representative mutants and hydrolytic profiles (kinetics) completes the picture and altogether these four elements constitute the essential foundation for a better understanding of the structure-function relationship within this enzymes family. BLDB can be queried using different protein- and nucleotide-based BLAST searches, which represents a key feature of particular importance in the context of the surveillance of the evolution of the antibiotic resistance. BLDB is available online at http://bldb.eu without any registration and supports all modern browsers.     

Structure based docking and molecular dynamics studies: Peroxisome proliferator-activated receptors –α/γ dual agonists for treatment of metabolic disorders

Abstract

Diabetes is a foremost health problem globally susceptible to increased mortality and morbidity. The present therapies in the antidiabetic class have sound adverse effects and thus, emphasis on the further need to develop effective medication therapy. Peroxisome proliferator-activated receptor alpha-gamma dual approach represents an interesting target for developing novel anti-diabetic drug along with potential anti-hyperlipidimic activity. In the current study, the peroxisome proliferator-activated receptor alpha-gamma agonistic hits were screened by hierarchical virtual screening of drug like compounds followed by molecular dynamics simulation and knowledge-based structure-activity relation analysis. The key amino acid residues of binding pockets of both target proteins were acknowledged as essential and were found to be associated in the key interactions with the most potential dual hit. This dual targeted approach of structure based computational technique was undertaken to identify prevalent promising hits for both targets with binding energy and absorption distribution metabolism excretion prediction supported the analysis of their pharmacokinetic potential. In addition, stability analysis using molecular dynamics simulation of the target protein complexes was performed with the most promising dual targeted hit found in this study. Further, comparative analysis of binding site of both targets was done for the development of knowledge-based structure-activity relationship, which may useful for successful designing of dual agonistic candidates. Abbreviations ADME absorption distribution metabolism excretion

HTVS highthroughput virtual screening

MD molecular dynamics

MMGBSA molecular mechanics generalized bonn solvation accessible

PDB protein data bank

PPAR peroxisome proliferator-activated receptor

RMSD Root mean square deviation

RMSF Root mean square fluctuation

SAR structural activity relationship

SP simple precision

T2DM TypeII diabetes mellitus

XP Extra precision

Communicated by Ramaswamy H. Sarma     

Fluid–structure interaction (FSI) simulation for studying the impact of atherosclerosis on hemodynamics,arterial tissue remodeling,and initiation risk of intracranial aneurysms

The biomechanical and hemodynamic effects of atherosclerosis on the initiation of intracranial aneurysms (IA) are not yet clearly discovered. Also, studies for the observation of hemodynamic variation due to atherosclerotic stenosis and its impact on arterial remodeling and aneurysm genesis remain a controversial field of vascular engineering. The majority of studies performed are relevant to computational fluid dynamic (CFD) simulations. CFD studies are limited in consideration of blood and arterial tissue interactions. In this work, the interaction of the blood and vessel tissue because of atherosclerotic occlusions is studied by developing a fluid and structure interaction (FSI) analysis for the first time. The FSI presents a semi-realistic simulation environment to observe how the blood and vessels' structural interactions can increase the accuracy of the biomechanical study results. In the first step, many different intracranial vessels are modeled for an investigation of the biomechanical and hemodynamic effects of atherosclerosis in arterial tissue remodeling. Three physiological conditions of an intact artery, the artery with intracranial atherosclerosis (ICAS), and an atherosclerotic aneurysm (ACA) are employed in the models with required assumptions. Finally, the obtained outputs are studied with comparative and statistical analyses according to the intact model in a normal physiological condition. The results show that existing occlusions in the cross-sectional area of the arteries play a determinative role in changing the hemodynamic behavior of the arterial segments. The undesirable variations in blood velocity and pressure throughout the vessels increase the risk of arterial tissue remodeling and aneurysm formation.

     

Proteinase-activated receptors (PARs) – focus on receptor-receptor-interactions and their physiological and pathophysiological impact

Proteinase-activated receptors (PARs) are a subfamily of G protein-coupled receptors (GPCRs) with four members, PAR₁, PAR₂, PAR₃ and PAR₄, playing critical functions in hemostasis, thrombosis, embryonic development, wound healing, inflammation and cancer progression. PARs are characterized by a unique activation mechanism involving receptor cleavage by different proteinases at specific sites within the extracellular amino-terminus and the exposure of amino-terminal “tethered ligand“ domains that bind to and activate the cleaved receptors. After activation, the PAR family members are able to stimulate complex intracellular signalling networks via classical G protein-mediated pathways and beta-arrestin signalling. In addition, different receptor crosstalk mechanisms critically contribute to a high diversity of PAR signal transduction and receptor-trafficking processes that result in multiple physiological effects.In this review, we summarize current information about PAR-initiated physical and functional receptor interactions and their physiological and pathological roles. We focus especially on PAR homo- and heterodimerization, transactivation of receptor tyrosine kinases (RTKs) and receptor serine/threonine kinases (RSTKs), communication with other GPCRs, toll-like receptors and NOD-like receptors, ion channel receptors, and on PAR association with cargo receptors. In addition, we discuss the suitability of these receptor interaction mechanisms as targets for modulating PAR signalling in disease.     

Genetic variations in the interleukin-12/interleukin-23 receptor (β1) chain,and implications for IL-12 and IL-23 receptor structure and function

Cell-mediated immunity (CMI) plays an essential role in human host defense against intracellular bacteria. Type-1 cytokines, particularly gamma interferon (IFN-gamma), interleukin-12 (IL-12), and IL-23, the major cytokines that regulate IFN-gamma production, are essential in CMI. This is illustrated by patients with unusual severe infections caused by poorly pathogenic mycobacteria and Salmonella species, in whom genetic deficiencies have been identified in several key genes in the type-1 cytokine pathway, including IL12RB1, the gene encoding the beta1 chain of the IL-12 and IL-23 receptors. Several mutations in IL12RB1 with deleterious effects on human IL-12R function have been identified, including nonsense and missense mutations. In addition, a number of coding IL12RB1 polymorphisms have been reported. In order to gain more insight into the effect that IL12RB1 mutations and genetic variations can have on IL-12Rbeta1 function, three approaches have been followed. First, we determined the degree of conservation at the variant amino acid positions in IL-12Rbeta1 between different species, using known deleterious mutations, known variations in IL-12Rbeta1, as well as novel coding variations that we have identified at position S74R and R156H. Second, we analyzed the potential impact of these amino acid variations on the three-dimensional structure of the IL-12Rbeta1 protein. Third, we analyzed the putative functions of different IL-12Rbeta1 domains, partly based on their homology with gp130, and analyzed the possible effects of the above amino acid variations on the function of these domains. Based on these analyses, we propose an integrated model of IL-12Rbeta1 structure and function. This significantly enhances our molecular understanding of the human IL-12 and IL-23 systems.     

p73 is required for endothelial cell differentiation,migration and the formation of vascular networks regulating VEGF and TGFβ signaling

Vasculogenesis, the establishment of the vascular plexus and angiogenesis, branching of new vessels from the preexisting vasculature, involves coordinated endothelial differentiation, proliferation and migration. Disturbances in these coordinated processes may accompany diseases such as cancer. We hypothesized that the p53 family member p73, which regulates cell differentiation in several contexts, may be important in vascular development. We demonstrate that p73 deficiency perturbed vascular development in the mouse retina, decreasing vascular branching, density and stability. Furthermore, p73 deficiency could affect non endothelial cells (ECs) resulting in reduced in vivo proangiogenic milieu. Moreover, p73 functional inhibition, as well as p73 deficiency, hindered vessel sprouting, tubulogenesis and the assembly of vascular structures in mouse embryonic stem cell and induced pluripotent stem cell cultures. Therefore, p73 is necessary for EC biology and vasculogenesis and, in particular, that DNp73 regulates EC migration and tube formation capacity by regulation of expression of pro-angiogenic factors such as transforming growth factor-β and vascular endothelial growth factors. DNp73 expression is upregulated in the tumor environment, resulting in enhanced angiogenic potential of B16-F10 melanoma cells. Our results demonstrate, by the first time, that differential p73-isoform regulation is necessary for physiological vasculogenesis and angiogenesis and DNp73 overexpression becomes a positive advantage for tumor progression due to its pro-angiogenic capacity.Vascular system formation is one of the earliest events during organogenesis.¹ The original vascular plexus is established by vasculogenesis, through differentiation and assembly of mesodermal precursors.² The angiogenesis process allows the formation of new blood vessels from the existing vasculature and is perturbed in many diseases, including cancer.³ Although efforts have been made to identify factors that control vascular development, the understanding of the molecular networks remains incomplete.The formation of new capillaries and the remodeling of preexisting blood vessels is linked by signal transduction pathways.⁴ The members of the p53 family (p53, p73 and p63) coordinate cell proliferation, migration and differentiation, and could act as regulators of vascular development. TP73 function in angiogenesis is quite controversial,^{5, 6, 7} and it has never been addressed using developmental models.TP73 has a dual nature that resides in the existence of TA and DNp73 variants. TAp73 is capable of transactivating p53 targets^{8, 9, 10} whereas DNp73 can act as p53 and TAp73 repressor.^{11, 12, 13} TP73 final outcome will depend upon the differential expression of the TA/DNp73 isoforms in each cellular context, as they can execute synergic, as well as antagonist, functions.TP73 role during development is emphasized by the p73-knockout mice (Trp73−/−, p73KO from now on) multiple growth defects.¹⁴ These mice, which lack all p73 isoforms, exhibit gastrointestinal and cranial hemorrhages,¹⁴ suggestive of vascular fragility. Furthermore, TAp73 directly regulates GATA-1,⁸ which is essential for endothelial and hematopoietic differentiation.^{15, 16} This compounded information led us to hypothesize that p73 could be implicated in the regulation of vasculogenesis/angiogenesis.Regulation of these processes involves a broad range of signaling molecules essential for vascular growth and stability,¹⁷ such as vascular endothelial growth factor (VEGF)¹⁸ and transforming growth factor-β (TGF-β).¹⁹ TGF-β operates as a rheostat that controls endothelial cell (EC) differentiation, having an inhibitory effect on EC migration and proliferation by the TGF-β/TGFRI (ALK5)/Smad2/3 pathway, while the TβRII–ALK5/ALK1 complex activates Smad1/5/8, ID1 expression and a pro-angiogenic state.^{20, 21, 22}Regulation of the TGF-β and VEGF pathways by p53 family members has been documented.^{23, 24} However, p73''s function in these pathways during development remains largely unexplored. In this work, we have used mouse embryonic stem cells (mESC) and induced pluripotent stem cells (iPSCs) as models that recapitulate early vascular morphogenesis.^{25, 26, 27} ESC and iPSC form multi-cellular aggregates (embryoid bodies, EBs) that, under appropriate conditions, generate functional EC.²⁸ mESC and iPSC differentiation capacity into ECs has been fully addressed.^{29, 30} We have also performed retinal vascularization analysis to assess vascular processes in vivo.^{31, 32}We demonstrate that p73 deficiency perturbs density and stability of mouse retinal development by affecting VEGF and TGF-β signaling. Furthermore, p73 is necessary for the assembly of vascular structures under physiological conditions in mESC and iPSC. Moreover, DNp73 positively affects angiogenesis through regulation of the TGF-β pathway in human umbilical vein cells (HUVEC) and DNp73-overexpression results in enhanced angiogenic potential of B16-F10 melanoma cells.     

Roles for peroxisome proliferator-activated receptor γ (PPARγ) and PPARγ coactivators 1α and 1β in regulating response of white and brown adipocytes to hypoxia

Obese white adipose tissue is hypoxic but is incapable of inducing compensatory angiogenesis. Brown adipose tissue is highly vascularized, facilitating delivery of nutrients to brown adipocytes for heat production. In this study, we investigated the mechanisms by which white and brown adipocytes respond to hypoxia. Brown adipocytes produced lower amounts of hypoxia-inducible factor 1α (HIF-1α) than white adipocytes in response to low O(2) but induced higher levels of hypoxia-associated genes. The response of white adipocytes to hypoxia required HIF-1α, but its presence alone was incapable of inducing target gene expression under normoxic conditions. In addition to the HIF-1α targets, hypoxia also induced many inflammatory genes. Exposure of white adipocytes to a peroxisome proliferator-activated receptor γ (PPARγ) ligand (troglitazone) attenuated induction of these genes but enhanced expression of the HIF-1α targets. Knockdown of PPARγ in mature white adipocytes prevented the usual robust induction of HIF-1α targets in response to hypoxia. Similarly, knockdown of PPARγ coactivator (PGC) 1β in PGC-1α-deficient brown adipocytes eliminated their response to hypoxia. These data demonstrate that the response of white adipocytes requires HIF-1α but also depends on PPARγ in white cells and the PPARγ cofactors PGC-1α and PGC-1β in brown cells.     

Comparative anatomy of the heart–glomerulus complex of Cephalodiscus gracilis (Pterobranchia): structure,function, and phylogenetic implications

Cephalodiscus gracilis Harmer, 1905 is a semi-sessile deuterostome that shares with fish-like chordates pharyngeal gill slits and a dorsally situated brain. In order to reveal structures potentially homologous among deuterostomes and to infer their functional roles, we investigated the axial complex, associated blood vessels and structures of C. gracilis using transmission electron microscopy, light microscopy, and digital 3D reconstructions. We describe the smooth, bipartite cephalic shield retractor muscles that originate as solid compact muscles and fan out to traverse the protocoel as individual muscle cells. The axial complex consists of a cap-shaped coelomic sac, the pericardium that surrounds the central heart. The pericardium is constituted of myoepithelial cells, with the cells facing the heart being thicker and richer in myofilaments. A prominent dorsal median blood vessel opens into the heart, which gives rise to a short median ventral vessel that opens into the paired glomeruli connected to the ventral side of the stomochord. The tip of the curved stomochord rests precisely above the connection of the dorsal median vessel with the heart, a position that would allow the stomochord to function as a valve facilitating unidirectional blood flow. Glomeruli are lined by podocytes of the spacious protocoel and are considered to be the site of ultrafiltration. Two pairs of blood vessels enter the median dorsal blood vessel from the tentacles. The median dorsal blood vessel is separated from the brain by a thin basement membrane. This arrangement is consistent with the hypothesis that blood vessels in the tentacles increase oxygen supply for the brain. Based on detailed similarities, the heart–glomerulus complex of C. gracilis is considered homologous with the heart–glomerulus complex in Rhabdopleura spp., and Enteropneusta, and the axial complex in Echinodermata. In addition, we hypothesize homology to the excretory complex including Hatschek’s nephridium in Cephalochordata. Thus, the heart–glomerulus complex does not support a sister-group relationship between Echinodermata and Hemichordata, whereas the organization of the cephalic shield retractor muscles is consistent with the evolution of pterobranchs within enteropneusts.     

Genetic differentiation between Príncipe Island and mainland populations of the grey parrot (Psittacus erithacus), and implications for conservation

The range of the grey parrot (Psittacus erithacus), one of the most heavily harvested bird species for the international pet trade, spans the forest belt of Central and West Africa and includes the oceanic island of Príncipe (Gulf of Guinea). Morphological variation led to the recognition of two mainland subspecies (P. e. erithacus and P. e. timneh). The population from Príncipe was originally described as a separate species (P. princeps) but is currently included in the nominate race. We used 1932 bp of the mitochondrial genome to clarify the genealogical affinities between the two currently-recognized mainland subspecies and the Príncipe population. Sampling included 20 individuals from Príncipe, 17 from P. e. erithacus, and 13 from P. e. timneh. We found that the two mainland subspecies form two independent lineages, having diverged up to 2.4 million years ago (Ma), and that the Príncipe population is composed of two lineages that diverged in allopatry. The most common lineage is descended from the first colonizers and evolved in isolation for up to 1.4 Ma. Contrary to current understanding, this 'Príncipe lineage' is more closely related to the timneh than to the erithacus subspecies. The second lineage consists of P. e. erithacus birds from the nearby mainland that colonized the island in recent times. The evolutionary dynamics of the grey parrot population of Príncipe are primarily characterized by isolation, with new genetic variation being added through rare immigration events. The heavily harvested Príncipe grey parrot population should therefore be treated as an independent conservation unit.     

Effect of electro-acupuncture on ovarian expression of α (1)- and β (2)-adrenoceptors,and p75 neurotrophin receptors in rats with steroid-induced polycystic ovaries

Background  

Estradiol valerate (EV)-induced polycystic ovaries (PCO) in rats is associated with an increase in ovarian sympathetic outflow. Low-frequency (2 Hz) electro-acupuncture (EA) has been shown to modulate sympathetic markers as well as ovarian blood flow as a reflex response via the ovarian sympathetic nerves, in rats with EV-induced PCO.     

Genetic differentiation and trade among populations of peach palm (Bactris gasipaes Kunth) in the Peruvian Amazon—implications for genetic resource management

Peach palm (Bactris gasipaes Kunth) is cultivated for fruit and heart of palm, and is an important component of agroforestry systems in the Peruvian Amazon. In this study, AFLP was used to compare genetic diversity among domesticated populations along the Paranapura and Cuiparillo rivers, which are managed by indigenous and colonist farming communities, respectively. Gene diversity was 0.2629 for the populations in indigenous communities and 0.2534 in colonist communities. Genetic differentiation among populations (G_st) was 0.0377–0.0416 (P<0.01) among populations along both rivers. There was no relation between genetic differentiation and the geographical location of populations along the rivers. Since natural seed dispersal by birds and rodents is thought to occur only across relatively short distances (100–200 m), it is likely that exchange of material by farmers and commercial traders is responsible for most of the long-distance (over more than 20 km) gene flow among populations along the two rivers studied. This exchange of material may be important to counteract the effects of selection as well as genetic drift in small groups of trees in farmers fields, much as in a metapopulation, and may account for the weak genetic differentiation between the two rivers (G_st=0.0249, P<0.01). A comparison with samples from other landraces in Peru and Brazil showed the existence of an isolation-by-distance structure up to 3,000 km, consistent with gene flow on a regional scale, likely mediated by trade in the Amazon Basin. Results are discussed with regard to practical implications for the management of genetic resources with farming communities.Electronic Supplementary Material Supplementary material is available in the online version of this article at Communicated by H.F. Linskens     

Effects of temperature on egg and larval survival of cod (Gadus morhua) and sprat (Sprattus sprattus) in the Baltic Sea – implications for stock development

Hydrobiologia - Stock development of cod and sprat, two major fish species in the Baltic Sea, is linked by trophic interactions. Depending on recruitment success the Baltic may be pushed towards...     

Omega-3 PUFA profoundly affect neural,physiological, and behavioural competences – implications for systemic changes in trophic interactions

In recent decades, much conceptual thinking in trophic ecology has been guided by theories of nutrient limitation and the flow of elements, such as carbon and nitrogen, within and among ecosystems. More recently, ecologists have also turned their attention to examining the value of specific dietary nutrients, in particular polyunsaturated fatty acids (PUFA), among which the omega-3 PUFA, especially eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) play a central role as essential components of neuronal cell membranes in many organisms. This review focuses on a new neuro-ecological approach stemming from the biochemical (mechanistic) and physiological (functional) role of DHA in neuronal cell membranes, in particular in conjunction with G-protein coupled receptors (GPCRs). We link the co-evolution of these neurological functions to metabolic dependency on dietary omega-3 PUFA. We outline ways in which deficiencies in dietary DHA supply may affect, cognition, vision, and behaviour, and ultimately, the biological fitness of consumers. We then review emerging evidence that changes in access to dietary omega-3 PUFA may ultimately have profound impacts on trophic interactions leading to potential changes in community structure and ecosystem functioning that, in turn, may affect the supply of DHA within and across ecosystems, including the supply for human consumption.     

Peroxisome biogenesis and protein import in plants,animals and yeasts: enigma and variations? (Review)

Peroxisomes are found in virtually all eukaryotic cells, where they play varied but essential metabolic roles, exemplified by the catastrophic effects of mutations that compromise peroxisome biogenesis and function. This review will aim to provide an accessible introduction to peroxisome biogenesis and protein import for the non-specialist, and draws together recent advances in peroxisome protein targeting and import in plants, animals and yeasts, seeking to define common themes and highlight variations. Despite much progress, many aspects of peroxisome biology remain an enigma, and current questions and controversies in the field are highlighted and discussed.     

Development and validation of competition binding assays for affinity to the extracellular matrix receptors, α(v)β(3) and α(IIb)β(3) integrin

The RGD (Arg-Gly-Asp) binding integrins α(v)β(3) and α(IIb)β(3) are integral components of various pathological and physiological processes, including tumor angiogenesis, osteoclast function, and thrombus formation. Because of this, there is interest in identifying novel compounds and proteins binding to these receptors as well as investigating the mechanism of these interactions. In this article, we describe the development and validation of competition binding assays for determining the affinity of test compounds to α(v)β(3) and α(IIb)β(3) integrin. Assays were successfully developed for each receptor, and the affinity of known compounds was comparable to published results. However, the inability of binding between α(IIb)β(3) integrin and the labeled echistatin protein ligand to reach equilibrium resulted in an assay that did not meet the assumptions of the competition binding model. Nevertheless, there was good agreement between this assay and known literature values, and intra- and interassay variability was acceptable. Binding by conformation-specific antibodies provided evidence that solid-phase bound α(IIb)β(3) receptor was in an activated conformation. This study also demonstrated that current models and methods for determining receptor affinity are simplistic and fail to account for common receptor-ligand interactions such as nondissociable interactions and varying receptor activation states.     

Stromal-cell-derived factor (SDF) 1-alpha in combination with BMP-2 and TGF-β1 induces site-directed cell homing and osteogenic and chondrogenic differentiation for tissue engineering without the requirement for cell seeding

The clinical translation of tissue engineering approaches is limited by the requirement of a cell source. Cell guidance is a new concept that provides an alternative approach, obviating a requirement for an external cell source. This relies on site-specific homing and differentiation of the patient??s own cells to an implanted scaffold through controlled delivery of cytokines. In this study, we used stromal-cell-derived factor 1-alpha (SDF-1??) in combination with bone morphogenic protein (BMP)-2 or transforming growth factor (TGF)-??1 to induce cell migration and osteogenic or chondrogenic differentiation, respectively, in implanted scaffolds in a rat model. A customized cytokine microdelivery apparatus was used to ensure the constant rate and concentration of cytokine delivery around the scaffold. The formation of osteoid or early cartilage was observed after 4?weeks in specimens treated with SDF-1?? and either BMP-2 or TGF-??1. The density of cellular infiltrate and formation of differentiated tissue were lower in scaffolds treated only with BMP-2 or TGF-??1. Thus, controlled SDF-1?? delivery induces cell migration into scaffolds and can result in enhanced osteogenesis and chondrogenesis when used in combination with differentiation cytokines for purposes of tissue engineering.     

Genetic diversity and population structure of Eugenia dysenterica DC. (``cagaiteira' – Myrtaceae) in Central Brazil: Spatial analysis and implications for conservation and management

Studies about the organization of the genetic variability and population structure in natural plant populations are used to support conservation and management programs. Among the Cerrado fruit tree species that possess potential economic importance in agriculture, the “Cagaiteira” (Eugenia dysenterica DC. – Myrtaceae), deserves an special position. We obtained information about allele and genotypic frequencies in 10 local populations, situated up to 250 km apart, from six isozymes that furnished a total of 8 loci. The average within-population fixation index (f) was 0.337, and the out crossing rate was 0.835, suggesting a mixed mating system for this species, which seems to be preferably alogamous. Based on genetic diversity and analysis of variance techniques, a high degree of population differentiation (θ_P = 0.154) was found, in comparison with other tropical tree species. Genetic divergence, analyzed by Nei's genetic distances, clustered with UPGMA and ordinated by non-metric multidimensional scaling, showed spatial patterns of clusters of local populations. Explicit spatial analyses, using Mantel tests and boundary tests, basically confirmed these patterns and revealed a complex pattern of genetic variation in geographic space. The intercept of the multivariate spatial correlograms was around 120 km, an indication of the minimum distance between samples needed to conserve genetic diversity among samples. This spatial scale can be used to define population genetics units for conservation programs or to establish sampling strategies. This revised version was published online in July 2006 with corrections to the Cover Date.