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Different Organisms (different + organism)
Selected AbstractsStrategies for DNA interstrand crosslink repair: Insights from worms, flies, frogs, and slime moldsENVIRONMENTAL AND MOLECULAR MUTAGENESIS, Issue 6 2010Mitch McVey Abstract DNA interstrand crosslinks (ICLs) are complex lesions that covalently link both strands of the DNA double helix and impede essential cellular processes such as DNA replication and transcription. Recent studies suggest that multiple repair pathways are involved in their removal. Elegant genetic analysis has demonstrated that at least three distinct sets of pathways cooperate in the repair and/or bypass of ICLs in budding yeast. Although the mechanisms of ICL repair in mammals appear similar to those in yeast, important differences have been documented. In addition, mammalian crosslink repair requires other repair factors, such as the Fanconi anemia proteins, whose functions are poorly understood. Because many of these proteins are conserved in simpler metazoans, nonmammalian models have become attractive systems for studying the function(s) of key crosslink repair factors. This review discusses the contributions that various model organisms have made to the field of ICL repair. Specifically, it highlights how studies performed with C. elegans, Drosophila, Xenopus, and the social amoeba Dictyostelium serve to complement those from bacteria, yeast, and mammals. Together, these investigations have revealed that although the underlying themes of ICL repair are largely conserved, the complement of DNA repair proteins utilized and the ways in which each of the proteins is used can vary substantially between different organisms. Environ. Mol. Mutagen., 2010. © 2010 Wiley-Liss, Inc. [source] Osmoadaptation in bacteria and archaea: common principles and differencesENVIRONMENTAL MICROBIOLOGY, Issue 12 2001Markus Roeßler The availability of water is the most important prerequisite for life of any living cell, and exposure of cells to hypersaline conditions always threatens the cells with a drastic loss of water. To re-establish the essential turgor pressure, cells increase the water activity of their cytoplasm by accumulation of compatible solutes, either by synthesis or by uptake. The ability to respond to increasing osmolality is well conserved in all three lines of descent and, here, we compare the osmoadaptive strategies of Bacteria and Archaea. The temporal sequence of events after an osmotic upshock will be discussed, with a focus on the most rapid response, notably the mechanisms of transport activation at the protein level, and different signals for osmolality will be compared. The spectrum of compatible solutes used by different organisms is rather diverse and a comparison of ,bacterial' and ,archaeal' compatible solutes will be given. [source] The importance of a functional trehalose biosynthetic pathway for the life of yeasts and fungiFEMS YEAST RESEARCH, Issue 4-5 2004Carlos Gancedo Abstract The view of the role of trehalose in yeast has changed in the last few years. For a long time considered a reserve carbohydrate, it gained new importance when its function in the acquisition of thermotolerance was demonstrated. More recently the cellular processes in which the trehalose biosynthetic pathway has been implicated range from the control of glycolysis to sporulation and infectivity by certain fungal pathogens. There is now enough experimental evidence to conclude that trehalose 6-phosphate, an intermediate of trehalose biosynthesis, is an important metabolic regulator in such different organisms as yeasts or plants. Its inhibition of hexokinase plays a key role in the control of the glycolytic flux in Saccharomyces cerevisiae but other, likely important, sites of action are still unknown. We present examples of the phenotypes produced by mutations in the two steps of the trehalose biosynthetic pathway in different yeasts and fungi, and whenever possible examine the molecular explanations advanced to interpret them. [source] Morphology and wall ultrastructure of leiosphaeric and acanthomorphic acritarchs from the Ediacaran of AustraliaGEOBIOLOGY, Issue 1 2009S. WILLMANArticle first published online: 18 DEC 200 ABSTRACT Acritarchs are a group of organic-walled microfossils with unknown biological affinities. The wall ultrastructure of the unornamented, smooth Leiosphaeridia sp. and the acanthomorphic Gyalosphaeridium pulchrum from the Ediacaran Dey Dey Mudstone in the Officer Basin, South Australia, was studied by use of transmission and scanning electron microscopy, and transmitted light microscopy. The study of the ultrastructure reveals a complexity in the cell wall not seen in prokaryotes. Wall ultrastructures range from single-layered to three- or four-layered and from homogeneous to porous. Acritarchs with different wall ultrastructures may be different organisms, but may also reflect different stages in a life cycle. In this paper I review previous ultrastructure studies and discuss possible algal and metazoan affinities for the specimens studied herein. [source] Organic acids: old metabolites, new themesJOURNAL OF CHEMICAL TECHNOLOGY & BIOTECHNOLOGY, Issue 10 2006Israel Goldberg Abstract Fumaric, L -malic and citric acids are intermediates of the oxidative tricarboxylic acid (TCA) cycle which in eukaryotes is localized in mitochondria. These organic acids are synthesized and accumulated in the medium to very high concentrations by filamentous fungi such as Aspergillus spp. and Rhizopus sp. This article reviews basic research on the unusual acid production capability and the associated metabolic pathways operating under defined stress conditions in these specific fungi. In particular, we describe and discuss the importance of the cytosolic reductive TCA pathway, which includes the cytosolic activities of pyruvate carboxylase, malate dehydrogenase and fumarase, for production of fumaric and L -malic acids. This article also describes the differences between fumaric acid, L -malic acid and citric acid production by different organisms (filamentous fungi, yeast, and higher eukaryotes), and the possible application of novel technologies (genetic engineering and bioinformatics) to fungal systems which may offer new industrial potential of filamentous fungi for the production of valuable metabolites. Copyright © 2006 Society of Chemical Industry [source] miR-17, miR-19b, miR-20a, and miR-106a are down-regulated in human agingAGING CELL, Issue 2 2010Matthias Hackl Summary Aging is a multifactorial process where deterioration of body functions is driven by stochastic damage while counteracted by distinct genetically encoded repair systems. To better understand the genetic component of aging, many studies have addressed the gene and protein expression profiles of various aging model systems engaging different organisms from yeast to human. The recently identified small non-coding miRNAs are potent post-transcriptional regulators that can modify the expression of up to several hundred target genes per single miRNA, similar to transcription factors. Increasing evidence shows that miRNAs contribute to the regulation of most if not all important physiological processes, including aging. However, so far the contribution of miRNAs to age-related and senescence-related changes in gene expression remains elusive. To address this question, we have selected four replicative cell aging models including endothelial cells, replicated CD8+ T cells, renal proximal tubular epithelial cells, and skin fibroblasts. Further included were three organismal aging models including foreskin, mesenchymal stem cells, and CD8+ T cell populations from old and young donors. Using locked nucleic acid-based miRNA microarrays, we identified four commonly regulated miRNAs, miR-17 down-regulated in all seven; miR-19b and miR-20a, down-regulated in six models; and miR-106a down-regulated in five models. Decrease in these miRNAs correlated with increased transcript levels of some established target genes, especially the cdk inhibitor p21/CDKN1A. These results establish miRNAs as novel markers of cell aging in humans. [source] Transglutaminase Catalyzed Reactions: Impact on Food ApplicationsJOURNAL OF FOOD SCIENCE, Issue 8 2002G.A.H. DeJong ABSTRACT: Transglutaminases can perform various reactions that are based on cross-linking, acyl-transfer and deamidation. These enzymes are found in many different organisms where they have very specific roles. The basic reaction mechanism of these transglutaminases is similar. The reactions catalyzed by transglutaminases have proven to be useful in production of different kinds of protein ingredients and food products. In this review, we will show important aspects of transglutaminase cross-linking in respect to substrate specificity, accessibility of proteins, regulation and differences in reactions and safety. These aspects will be viewed in respect to food applications [source] Phage display screening for peptidic chitinase inhibitors,JOURNAL OF MOLECULAR RECOGNITION, Issue 6 2008Cordula Petter Abstract A phage display library with disulfide-cyclized peptides was screened for peptides binding to chitinases from Serratia marcescens. One of those peptides was found to efficiently inhibit chitinase A and two others were inhibitors of chitinase B. Complete substitutional analysis of all three peptides using cellulose-bound peptide spot synthesis revealed key interaction positions and allowed optimization of the chitinase B inhibitory peptides towards higher affinity, with inhibitory constants in the lower nanomolar range. Inhibition by all peptides proved to be competitive and highly specific for the chitinase used to select them, as shown with a series of chitinases from different organisms. Copyright © 2008 John Wiley & Sons, Ltd. [source] Advances in protein turnover analysis at the global level and biological insightsMASS SPECTROMETRY REVIEWS, Issue 5 2010Qingbo Li Abstract The concept of a dynamic state of body constituents, a precursor of the modern term of proteome dynamics, was conceived over a century ago. But, not until recently can we examine the dynamics of individual "constituents" for example, proteins at a truly global level. The path of advancement in our understanding of protein turnover at the global level is marked by the introduction of some key technological innovations. These methods include the isotopic tracer technique in the 1930s, the two-dimensional gel electrophoresis technique in the 1970s, the sector mass spectrometer that could analyze isotopomers of peptides in the early 1990s, the 2D gel/MALDI-TOF proteomics technology in the late 1990s, the booming liquid chromatography/mass spectrometry proteomics technology in this decade, and the recently emerging protein-tagging approaches that offer single-cell resolution for protein turnover measurements. The long-standing inquiry raised in the 1950s about the existence of a dynamic state in different organisms at different physiological conditions can now be answered with an individual "constituent" resolution on a truly global scale. Now it appears that protein degradation is not necessarily an end to the protein function. Rather, it can be the start of a new function because protein degradation clears the way for the action of other proteins. Protein turnover participates in a multi-layer complex regulatory network and shares equal importance with gene transcription and protein translation. The advances in technologies for protein turnover analysis and the improved understanding of the biological role of protein turnover will likely help to solve some long-standing biomedical problems such as the tuberculosis disease that at the present day still affects one-third of the world population. © 2009 Wiley Periodicals, Inc., Mass Spec Rev 29:717,736, 2010 [source] Inosine monophosphate dehydrogenase (IMPDH) as a target in drug discoveryMEDICINAL RESEARCH REVIEWS, Issue 2 2008Qingning Shu Abstract Inosine monophosphate dehydrogenase (IMPDH) is a key enzyme of de novo purine nucleotide biosynthesis and is viewed as an important target in the quest for discovery of drugs in the antiviral, antibacterial and anticancer therapeutic areas. This review focuses on the medicinal chemistry, drug discovery and chemical biology of IMPDH. Examples of IMP and cofactor site-directed inhibitors, allosteric inhibitors and isoform-selective inhibitors are presented. Comparison of IMPDHs from different organisms is also made to facilitate the design of species-selective IMPDH inhibitors for drug discovery. Special emphasis in the review is placed on IMPDH from Mycobacterium tuberculosis. © 2007 Wiley Periodicals, Inc. Med Res Rev, 28, No. 2, 219,232, 2008 [source] Nitric oxide in plants: the history is just beginningPLANT CELL & ENVIRONMENT, Issue 3 2001M. V. Beligni ABSTRACT Nitric oxide (NO) is a bioactive molecule that exerts a number of diverse activities in phylogenetically distant species, as well as opposing effects in related biological systems. It was firstly described in mammals as a major messenger in the cardiovascular, immune and nervous system, in which it plays regulatory, signalling, cytoprotective and cytotoxic effects (Ignarro, Annual Review of Pharmacology and Toxicology 30, 535,560, 1990; Anbar, Experientia 51, 545,550, 1995). This versatility is mainly achieved through interactions with targets via either a redox or an additive chemistry (Stamler, Cell 78, 931,936, 1994). For this reason, metal- and thiol-containing proteins serve as major target sites for NO: these include signalling proteins, receptors, enzymes, transcription factors and DNA, among others. Furthermore, NO is a small, highly diffusible molecule. It rapidly crosses biological membranes and triggers various different processes in a short period of time. In this context, NO can co-ordinate and regulate cellular functions of microsomes and organelles such as mitochondria. The ubiquity of NO reactions, as well as the finding that the biochemical and molecular mechanisms underlying many physiological processes are well conserved between diverse species, have opened the exploration of NO chemistry in different organisms. Among these, plants were not the exception. The research in plants has been focused on three main fields: (i) the search for NO or any source of NO generation; (ii) the examination of the effects of NO upon exogenous treatments; and (iii) the search for the same molecules involved in NO-sensitive transduction pathways as in animals (e.g. cGMP, Ca2+, calmodulin). As it is evident from this review, recent progress on NO functionality in plants has been impressive. With the use of biochemistry, molecular genetics and structural biology, together with classical physiological approaches, an explosion of new discoveries will surely begin. It is certainly a good time for plant biologists. [source] Insights into yeast adaptive response to the agricultural fungicide mancozeb: A toxicoproteomics approachPROTEINS: STRUCTURE, FUNCTION AND BIOINFORMATICS, Issue 3 2009Pedro M. Santos Abstract Toxicogenomics has the potential to elucidate gene,environment interactions to identify genes that are affected by a particular chemical at the early stages of the toxicological response and to establish parallelisms between different organisms. The fungicide mancozeb, widely used in agriculture, is an ethylene-bis-dithiocarbamate complex with manganese and zinc. Exposure to this pesticide has been linked to the development of idiopathic Parkinson's disease and cancer. Given that many signalling pathways and their molecular components are substantially conserved among eukaryotic organisms, we used Saccharomyces cerevisiae to get insights into the molecular mechanisms of mancozeb toxicity and adaptation based on expression proteomics. The early global response to mancozeb was analysed by quantitative proteomics using 2-DE. The target genes (e.g. TSA1, TSA2, SOD1, SOD2, AHP1, GRE2, GRX1, CYS3, PRE3, PRE6, PRE8, PRE9, EFT1, RPS5, TIF11, HSP31, HSP26, HSP104, HSP60, HSP70 -family) and the putative main transcription activators (e.g. Yap1, Msn2/Msn4, Met4, Hsf1, Aft1, Pdr1, Skn7, Rpn4p, Gcn4) of the complex mancozeb-induced expression changes are related with yeast response to stress, in particular to oxidative stress, protein translation initiation and protein folding, disassembling of protein aggregates and degradation of damaged proteins. Our results also suggest that this study provided powerful indications that may be useful to expand the knowledge obtained in yeast not only to the global response to mancozeb toxicity in phytopathogenic fungi but also to humans. [source] The neuropeptidome of Rhodnius prolixus brainPROTEINS: STRUCTURE, FUNCTION AND BIOINFORMATICS, Issue 3 2009Sheila Ons Abstract We show a sensitive and straightforward off-line nano-LC-MALDI-MS/MS workflow that allowed the first comprehensive neuropeptidomic analysis of an insect disease vector. This approach was applied to identify neuropeptides in the brain of Rhodnius prolixus, a vector of Chagas disease. This work will contribute to the annotation of genes in the ongoing R. prolixus genome sequence project. Peptides were identified by de novo sequencing and comparisons to known neuropeptides from different organisms by database search. By these means, we were able to identify 42 novel neuropeptides from R. prolixus. The peptides were classified as extended FMRF-amide-related peptides, sulfakinins, myosuppressins, short neuropeptide F, long neuropeptide F, SIF-amide-related peptides, tachykinins, orcokinins, allatostatins, allatotropins, calcitonin-like diuretic hormones, corazonin, and pyrokinin. Some of them were detected in multiple isoforms and/or truncated fragments. Interestingly, some of the R. prolixus peptides, as myosuppressin and sulfakinins, are unique in their characteristic C-terminal domain among insect neuropeptides identified so far. [source] A dual infection by infectious cuticular epithelial necrosis virus and a Chlamydia -like organism in cultured Litopenaeus vannamei (Boone) in EcuadorAQUACULTURE RESEARCH, Issue 11 2001R Jimenez During 1996, microscopic examinations of post larvae and juveniles of moribund Litopenaeus vannamei showed multifocal necrosis in the cuticular epithelial tissues. In addition to these severe degenerative alterations in the epithelial cells typical of infectious cuticular epithelial necrosis virus (ICENV), columnar cells of the epithelium displayed small round intracytoplasmic inclusions in the necrotic tissue. Examination by electron microscopy of affected tissues demonstrated prokaryotic organisms in the cytoplasm of epithelial cells delineated by a distinct cytoplasmic vesicle; the prokaryotic organisms were morphologically similar to the genus Chlamydia. The necrotic tissue also showed the presence of particles of ICENV; the double infection by two different organisms in cuticular epithelial cells has not been reported previously. Two distinct stages in the intracellular development of a Chlamydia -like organism were recognized: (1) pleomorphic elementary bodies (EBs) that were spherical to oval were often observed in the process of division or in forming a common chain of three cells, the cells were surrounded by a rigid cell envelope and the presence of a cap or plaque hexagonally arrayed; (2) the reticular bodies (RBs) were forms often in the process of division. These cells had an electron-dense cytoplasm and contained a loose network of nuclear fibrils and a more fragile cell envelope. Regardless of the development stages of the Chlamydia -like organism within the cytoplasmic vesicles, ICENV particles were observed, either dispersed or in clusters, surrounded or inside the vesicles. The potential adverse impact of this dual infection on shrimp culture should be considered, especially in high-density operations. [source] Use of an in-house approach to study the three-dimensional structures of various outer membrane proteins: structure of the alcaligin outer membrane transporter FauA from Bordetella pertussisACTA CRYSTALLOGRAPHICA SECTION D, Issue 4 2009Karl Brillet Bordetella pertussis is the bacterial agent of whooping cough in humans. Under iron-limiting conditions, it produces the siderophore alcaligin. Released to the extracellular environment, alcaligin chelates iron, which is then taken up as a ferric alcaligin complex via the FauA outer membrane transporter. FauA belongs to a family of TonB-dependent outer membrane transporters that function using energy derived from the proton motive force. Using an in-house protocol for membrane-protein expression, purification and crystallization, FauA was crystallized in its apo form together with three other TonB-dependent transporters from different organisms. Here, the protocol used to study FauA is described and its three-dimensional structure determined at 2.3,Ĺ resolution is discussed. [source] Origin and evolution of chromosomal sperm proteinsBIOESSAYS, Issue 10 2009José M. Eirín-López Abstract In the eukaryotic cell, DNA compaction is achieved through its interaction with histones, constituting a nucleoprotein complex called chromatin. During metazoan evolution, the different structural and functional constraints imposed on the somatic and germinal cell lines led to a unique process of specialization of the sperm nuclear basic proteins (SNBPs) associated with chromatin in male germ cells. SNBPs encompass a heterogeneous group of proteins which, since their discovery in the nineteenth century, have been studied extensively in different organisms. However, the origin and controversial mechanisms driving the evolution of this group of proteins has only recently started to be understood. Here, we analyze in detail the histone hypothesis for the vertical parallel evolution of SNBPs, involving a "vertical" transition from a histone to a protamine-like and finally protamine types (H,,,PL,,,P), the last one of which is present in the sperm of organisms at the uppermost tips of the phylogenetic tree. In particular, the common ancestry shared by the protamine-like (PL)- and protamine (P)-types with histone H1 is discussed within the context of the diverse structural and functional constraints acting upon these proteins during bilaterian evolution. [source] "Mir"acles in hox gene regulationBIOESSAYS, Issue 5 2006Vivek S. Chopra Micro RNAs (miRNAs) have been shown to control many cellular processes including developmental timing in different organisms. The prediction that miRNAs are involved in regulating hox genes of flies and mouse is quite a recent idea and is supported by the finding that mir-196 represses Hoxb8 gene expression. The non-coding regions that encode these miRNAs are also conserved across species in the same way as other mechanisms that regulate expression of hox genes. On the contrary, until now no homeotic phenotype, a hallmark of any hox gene mutation, had been associated with any hox miRNA. Recent work on bithorax complex miRNA (miR,iab-4,5p) shows, for the first time, that miRNAs can lead to homeotic transformation. This miRNA regulates Ultrabithorax (Ubx) and results in the transformation of haltere to wing.1 This study unveils a new complexity and finesse to the regulation of hox gene expression pattern that is needed for determining the anteroposterior body axis in all bilaterians. BioEssays 28: 445,448, 2006. © 2006 Wiley Periodicals, Inc. [source] Evidence-based prescription of antibiotics in urology: a 5-year review of microbiologyBJU INTERNATIONAL, Issue 6 2009Ranan DasGupta OBJECTIVE To analyse the results of positive urine cultures over a 5-year period in a large hospital and urology department (amongst both inpatients and outpatients), assess the prevalence of different organisms and the resistance profiles of a range of antibiotics, and thus provide information on which organisms are likely to cause urosepsis. METHODS The use of antibiotics should be based on knowledge of which pathogens are present and what resistance patterns are emerging, particularly relevant in surgical disciplines like urology, as antibiotics are now routinely administered peri-operatively, whereby evidence-based prescription is preferable to generic guidelines. We therefore examined almost 25 000 positive urine cultures in our hospital over a 5-year period, and focused on the infections encountered amongst urology patients during this time. RESULTS A significant proportion of inpatient urinary infection (40%) is caused by Gram-positive bacteria such as Streptococcus faecalis, underlining the need for including Gram-positive cover during urological prophylaxis. The commonest pathogen remains Escherichia coli among both inpatients and outpatients. The ineffectiveness of common antibiotics such as ciprofloxacin and trimethoprim was identified, as was the increase in gentamicin resistance. CONCLUSION We propose using an aminoglycoside with a penicillin for high-risk cases (e.g. endoscopic stone surgery) while low-risk cases (e.g. flexible cystoscopy with no risk factors) might be managed without such prophylaxis. Pathogenic patterns and resistance rates should be monitored regularly. [source] | ||||||||||||||||