bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evolution of the Genetic Code
Authors: Yokobori Shin‐ichi , Ueda Takuya , Watanabe Kimitsuna 
Published: April 2010

AbstractFrom the present situation of genetic code so far elucidated for various species of extant organisms, it is speculated that the genetic code system had started from a limited number of amino acids and evolved to the universal genetic code which is being used by most extant organisms. During evolution, the genetic code is changeable by some factors such as directional mutational pressure on genomes, genome economization and evolution of tRNA (and its cognate aminoacyl transferribonucleic acid synthetase). The metazoan (multicellular animal) mitochondrial genetic code is interesting issue as the model case of evolution of genetic code, since the metazoan mitochondrial genetic code is greatly deviated from the universal genetic code, and varied among lineages. The present situation on the genetic code is discussed.Key Concepts:Genetic code has evolved along (with) evolution of life.Codon reassignment requires both elimination of tRNAs for sense codons or release factors for termination codons recognizing the concerned codon and creation or recruitment of ‘novel’ tRNAs or release factors that can recognize the concerned codon.Wobble base pairing between anticodon first position and codon third position is an important constraint for codon reassignment.Simple mitochondrial genetic system (small genome size, reduced number of tRNA species) allowed larger variation of genetic code than other genetic systems.
S‐Adenosylmethionine
Authors: Markham George D 
Published: April 2010

AbstractS‐adenosylmethionine is one of the few sulfonium ions found in nature and it plays essential roles in the metabolism of all known organisms. The positively charged sulfonium centre endowsS‐adenosylmethionine with a chemical versatility matched by few other biochemicals, perhaps exceeding even adenosine triphosphate (ATP).S‐adenosylmethionine is used in a multitude of metabolic pathways, and the types of chemical reactions in which it partakes are highly varied, ranging from alkylation to free‐radical formation.S‐sdenosylmethionine is methyl donor in many biosynthetic reactions, whereas methylation of bothdeoxyribonucleic acid(DNA) and proteins is part of the epigenetic control of cell growth and development. In other pathways, the propylamine moiety is incorporated into the pervasive polyamines spermidine and spermine. Unusual reactions consumeS‐adenosylmethionine in the formation of plant growth factor ethylene, of cyclopropane fatty acids and in sulfur insertion in the biosynthesis of biotin, lipoic acid and thiamine.S‐adenosylmethionine appears to be one of the molecules required for life.Key concepts:S‐adenosylmethionine is a branch point compound with components from purine, amino acid and reduced sulfur metabolism, and thus is potentially able to coordinate these three areas of metabolism.S‐adenosylmethionine appears to be required for life.The sulfonium centre ofS‐adenosylmethionine is able to transfer any of the three attached alkyl groups, providing a metabolic versatility matched by few other biological molecules.S‐adenosylmethionine is a progenitor of free radicals that occur as protein‐bound reaction intermediates in unusual chemical transformations catalysed by the ‘Radical SAM’: family of enzymes.S‐adenosylmethionine metabolism is commonly disrupted in liver disease, and hereditary defects have been found in a few patients with abnormal sulfur metabolism.S‐adenosylmethionine is under investigation as a potential drug in treatment of depression, arthritis and liver disease.
Bacterial Primosome
Authors: Tanaka Taku , Masai Hisao 
Published: April 2010

AbstractDNA (deoxyribonucleic acid) replication requires operation of a molecular machinery which efficiently synthesises of nucleotide chains on both strands. This process requires not only the enzymes synthesising DNA (DNA polymerases) but also those providing primer RNAs (ribonucleic acid) and continuously melting the duplex DNA. The primosome refers to a protein complex capable of processive unwinding of duplex DNA and primer RNA synthesis on the lagging strand at a replication fork. The prepriming proteins,DNA helicaseandprimaseare sequentially assembled on the template DNA to generate primosome. Once assembled, it, in conjunction withDNA polymerases, facilitates DNA chain elongation. The assembly of bacterial primosome is triggered by an ‘initiator’ protein includingDnaAandPriA, which recognise the site of assembly. Primosome is reassembled in replication restart process at stalled or processed replication forks, triggered byPriA. Thus, primosome constitutes an essential component for active replication fork machinery.Key concepts:Replication fork is the site of DNA replication where two replicating single‐stranded DNA separates.Primer RNA is a short stretch of RNA, the 3′‐terminus of which is utilised by DNA polymerases for DNA elongation.Primosome is a name given to the protein complex capable of duplex DNA unwinding and primer RNA synthesis at the replication fork.oriCis the replicationorigin ofchromosome. The initiation site of bacterial chromosomal DNA replication under a normal growth condition.DnaA is the initiator protein for bacterial chromosomal replication, which binds tooriCto assemble a primosome.PriA is a conserved replication factor which triggers assembly of the so‐called ϕX174‐type primosome, which is assembled at a stalled replication fork for replication restart.Stalled replication fork, the replication fork the movement of which is blocked by internal and external ‘replication stress’ including DNA damages and depletion of nucleotide precursors.Replication restart is a process of reassembly of primosome at a stalled replication fork to resume DNA chain elongation.Recombination intermediate is the intermediate structure (e.g. D‐loop structure) of homologous recombination reaction.DNA helicase is a protein capable of unwinding a duplex DNA at a replication fork by using the energy derived from the hydrolysis of nucleotides.Prepriming proteins are proteins required for the stage preceding the association of the primase (an enzyme synthesising primer RNAs) during the assembly of a primosome.
Protein–Ligand Interactions: General Description
Authors: Dunn Michael F 
Published: April 2010

AbstractProtein–ligand interactions are fundamental to almost all processes occuring in living organisms. Ligand‐mediated signal transmission via molecular complementarity is essential to all life processes; these chemical interactions comprise biological recognition at the molecular level. The evolution of protein function is dependent in part on the development of highly specific sites designed to bind small‐molecule ligands with affinities tuned to the needs of the cell. Cooperativity in ligand binding is critically important to the regulation of competing biological functions. Regulation of cellular processes via cooperative protein–ligand interactions occurs through molecular mechanisms involving protein conformational transitions among low‐ and high‐affinity states. Consequently, ligand‐binding interactions are used to switch proteins among states of different function. Examples ranging from dioxygen transport to gene expression are presented. The structures of protein–ligand complexes at atomic resolution make possible the design of small‐molecule drugs for the treatment of disease.Key Concepts:Molecular recognition via protein–ligand interactions is of fundamental importance to most processes occurring within living organisms.Transmission of signals via molecular complementarity is essential to all life processes.The evolution of protein function includes the development of highly specific sites for the binding of ligands with affinities tailored to meet the needs of biological function.Cooperativity in ligand binding plays an important role in the regulation of biological function.Cooperativity in ligand binding is linked to conformational change in the protein.Well‐defined mathematical expressions based on the stoichiometry of the binding equilibrium provide a means for quantifying ligand‐binding interactions.The equilibrium constants of ligand–macromolecule interactions provide a thermodynamic measure of the strength of the interaction.The atomic resolution structures of ligand complexes provide a chemical basis for understanding protein–ligand interactions and these structures are often used as the basis for the design of small‐molecule drugs for the treatment of disease.
Haemoglobin: Cooperativity in Protein–Ligand Interactions
Authors: Ho Chien , Yuan Yue 
Published: April 2010

AbstractHaemoglobin(Hb) is an essential component of the circulatory system of vertebrates. Its chief physiological function is to transport oxygen from the lungs to the tissues. Hb binds oxygen cooperatively, that is the affinity of the protein for the first oxygen molecule is less than that for subsequent oxygen molecules. Human adult Hb was among the first proteins whose complete three‐dimensional structure was determined by X‐ray crystallography and it has been used as a model for understanding allosteric proteins. Recent X‐ray crystallographic and multinuclear NMR (nuclear magnetic resonance) studies of both ligated and unligated forms of Hb have shown that many structures exist in crystalline and solution states. These results have challenged the classical two‐structure allosteric model of this protein. To understand Hb at the atomic level, we need to correlate the structural, dynamic and functional properties of hemoglobin in solution.Key Concepts:There are many T‐ and R‐types of crystal structures of unligated and ligated forms of haemoglobin, in contrast to the classical two‐structure model for haemoglobin allostery.The structures of haemoglobin in both unligated and ligated forms in solution are different from those in crystals and exist as dynamic ensembles of various structures.The ligand‐binding data for proximal histidyl‐detached recombinant haemoglobins show that Perutz's proximal histidyl coupling mechanism contributes approximately two‐thirds to the total interaction energy between haems and that there are alternative coupling pathways for the remaining third.The Bohr effect, a heterotropic effect, is an excellent example of a global network of electrostatic interactions, rather than a few specific amino acid residues, that play a dominant role in an important physiological function of haemoglobin.Recent experimental results strongly suggest that allosteric proteins, such as haemoglobin, may require multiple pathways for signal communication, as is illustrated in the cooperative oxygenation and in the Bohr effect.Haemoglobin is a molecule with considerable plasticity.The classical two‐structure mechanism for haemoglobin allostery cannot account for the structure, dynamics and function of the haemoglobin molecule and needs revision.
Eusociality and Cooperation
Authors: Keller Laurent , Chapuisat Michel 
Published: April 2010

AbstractThe evolution of eusociality, here defined as the emergence of societies with reproductive division of labour and cooperative brood care, was first seen as a challenge to Darwin's theory of evolution by natural selection. Why should individuals permanently forgo direct reproduction to help other individuals to reproduce? Kin selection, the indirect transmission of genes through relatives, is the key process explaining the evolution of permanently nonreproductive helpers. However, in some taxa helpers delay reproduction until a breeding opportunity becomes available. Overall, eusociality evolved when ecological conditions promote stable associations of related individuals that benefit from jointly exploiting and defending common resources. High levels of cooperation and robust mechanisms of division of labour are found in many animal societies. However, conflicts among individuals are still frequent when group members that are not genetically identical compete over reproduction or resource allocation.Key Concepts:Eusociality is a form of highly integrated social organisation that is characterised by reproductive division of labour, cooperative brood care and overlap of generations.Eusociality confers a great ecological success, but has a scattered taxonomic distribution.Kin selection is the key process explaining the evolution of permanently nonreproductive helpers. However, in some taxa helpers delay reproduction until a breeding opportunity becomes available.Eusociality evolved in family groups under ecological conditions promoting the joint exploitation and defence of common resources.Eusociality is linked with division of labour, which is sometimes associated with morphological castes.The allocation of workers to tasks is a self‐organising process that occurs without central control and emerges from local interactions.In social insects, division of labour is remarkably robust and flexible to cope with unpredictable changes in the environment.Individuals in animal societies are not clones: they have partially divergent genetic interests, which can lead to various forms of conflicts.Some types of conflicts can be controlled by social means such as bribing, coercion or punishment.
Molecular Genetics of Ischaemic Stroke
Authors: Floßmann Enrico 
Published: April 2010

AbstractRare examples of single gene disorders have been described for all major subtypes of ischaemic stroke; accelerated atherosclerosis and subsequent thrombo‐embolism (e.g. homocysteinuria), connective tissue disease resulting in arterial dissections (e.g. Ehler‐Danlos type IV), disorders of cerebral small vessels (e.g. CADASIL), cardiac embolism (e.g. hypertrophic cardiomyopathy), mitochondrial cytopathies increasing cerebral tissue susceptibility to insults (e.g. MELAS) and coagulopathies (e.g. sickle cell disease).Although animal models, family history and twin studies suggest that hereditary factors might contribute to the risk of sporadic stroke, no single gene has so far been conclusively shown to do so. It is unlikely that the direct genetic contribution of any single gene towards stroke is more than modest and it is likely that the effects are mainly mediated through genetic influences on risk factors and intermediate phenotypes. Single genes are unlikely to be helpful for any risk stratification in clinical practice.Key Concepts:Rare examples of single gene disorders have been described for all major subtypes of ischaemic stroke.Although animal models, family history and twin studies suggest that hereditary factors might contribute to the risk of sporadic stroke, no single gene has so far been conclusively shown to do so.It is unlikely that the direct genetic contribution of any single gene towards stroke is more than modest.It is likely that genetic effects are mainly mediated through genetic influences on risk factors and intermediate phenotypes.Single genes are unlikely to be helpful for any risk stratification in clinical practice.
Molecular Genetics of Chronic Obstructive Pulmonary Disease
Authors: Chappell Sally , Kalsheker Noor A 
Published: April 2010

AbstractIt is well recognized that while smoking is a significant environmental cause of chronic obstructive pulmonary disease (COPD), not all smokers will develop disease. Family studies show an increased risk to relatives of patients with COPD, and linkage analysis highlighted areas of the genome which appear to be associated with COPD and measures of lung function. This all suggests that there is a genetic contribution to COPD susceptibility and severity. A variety of candidate genes have been suggested over the years, many with conflicting results. This may represent population differences or spurious results caused by underpowered studies. Genome‐wide methods for gene identification have also been reported, either based on analysis of gene expression, or on genome‐wide assessment of variation. These studies have revealed novel genes which warrant further investigation.Key ConceptsThere is a genetic contribution to the susceptibility of developing chronic obstructive pulmonary disease.Candidate gene studies in COPD often report conflicting results.Genome‐wide association studies provide an unbiased method for identifying new genes involved in COPD.Differences in gene‐expression may provide clues about other genes involved in COPD.
Simultaneous determination of nine nucleosides and nucleobases in differentFritillariaspecies by HPLC‐diode array detector
Authors: Cao Xin‐Wei , Li Jun , Chen Si‐Bao , Li Xiao‐Bo , Xiao Pei‐Gen , Chen Shi‐Lin , Yang Da‐Jian 
Published: April 2010

AbstractA sensitive and reliable HPLC‐diode‐array detector method was developed for the first time to simultaneously determine nine nucleosides and nucleobases including uracil, cytidine, guanine, uridine, thymine, inosine, guanosine, thymidine and adenosine in 13 differentFritillariaspecies. The analysis was performed on a BaseLine C18 column with a gradient of acetonitrile in water at a flow rate of 0.8 mL/min. The diode‐array detector wavelength was set at 260 nm for the UV detection of nucleosides and nucleobases. Satisfactory separation of these compounds was obtained in less than 40 min. The optimized method provided good linear relation (r2 >0.9995 for all the investigated analytes), satisfactory precision (RSD <1.51%) and good recovery (from 97.64 to 101.16%). The established method was successfully applied to simultaneous determination of nine nucleosides and nucleobases in 61 batches of samples from 13Fritillariaspecies collected from different habitats in China, which could be helpful to control the quality ofFritillariabulbs.
Tragfähigkeit — ein unscharfer Schlüsselbegriff im Schnittpunkt von Raumordnung und Regional-Demographie
Authors: Weiß Wolfgang 
Published: April 2010

To the extent in which demographic change and selected resulting problems are considered in public, the specialist terms of demography are also losing their isolation. One such term is “carrying capacity”. Problematic are the multiple connotations with which the respective underlying problem is considered, often depending on the respective viewpoint. Like other terms it is moreover used in several disciplines and to top it all in colloquial language.
This contribution understands itself as an attempt to explain carrying capacity from the perspective of regional demography, to establish linkages and also to follow a historical line. Remarkable is the variety of aspects of the term that can hardly be reconstructed but also its change in terms of content when it is occupied by political language following strategic objectives.
Correlates of sport participation among community-dwelling elderly people in Germany: a cross-sectional study
Authors: Hinrichs Timo , Trampisch Ulrike , Burghaus Ina , Endres Heinz G. , Klaaßen-Mielke Renate , Moschny Anna , Platen Petra 
Published: April 2010

Abstract
The aims of this study were (1) to analyze the sport participation in a cohort of community-dwelling elderly people in Germany and (2) to evaluate associations between sport participation, sociodemographic factors, cardiovascular risk factors, and health status. In a monitored prospective cohort study (getABI), 6,880 unselected patients ≥65 years have been followed up by 344 general practitioners beginning in 2001. As part of the 5-year follow-up telephone interview, a sample of 1,376 participants was interviewed on sport participation. The association between participation in at least one sporting activity (“sporty” yes/no) during the past week (cycling) or month (other sports) and the following parameters was analyzed by logistic regression: age, sex, immigration background, education, waist circumference, smoking, self-reported health, history of vascular events, diabetes mellitus, lipometabolic disorder, and arterial hypertension. Analysis of activities (n = 1,304; median age 76 (70–94) years; 55.1% women) showed that 27.6% of participants rode a bicycle during the previous week. During the previous month, 24.9% of participants did gymnastics or strength training, and 16.5% swam. Of all participants, 53.8% were sporty. Multivariate analysis revealed several independent factors to be associated with being sporty (p < 0.05): younger age, male sex, higher education, nonsmoking, better self-reported health, and not being diagnosed with diabetes. Immigration background, waist circumference, history of vascular events, lipometabolic disorder, and hypertension did not show a statistically significant association (p ≥ 0.05) with sport participation. Summing up, the most frequently performed sporting activities were cycling, gymnastics or strength training, and swimming. Sport participation was associated with, for example, age and sex.
New Nortriterpenoid and Ceramides From Stems and Leaves of Cultivated Triumfetta cordifolia A Rich (Tiliaceae)
Authors: Sandjo Louis Pergaud , Tchoukoua Abdou , Ntede Hippolyte Nga , Yemloul Mehdi , Perspicace Enrico , Keumedjio Felix , Couty François , Kirsch Gilbert , Ngadjui Bonaventure Tchaleu 
Published: April 2010

AbstractTo highlight the role of plants in traditional healing, the leaves and the stems of cultivated Triumfetta cordifolia were phytochemically studied yielding a new nor‐ursane type (1), a new ceramide (2) and a new piperidinic ceramide derivative (3) named, respectively, 2α,19α‐dihydroxy‐3‐oxo‐23‐nor‐urs‐12‐en‐28‐oic acid, (2R)‐2‐hydroxy‐N‐[(2S,3S,4R,26E)‐1,3,4‐trihydroxy‐26‐triaconten‐2‐yl] tetradecanamide and (2R,8Z)‐2‐hydroxy‐{(2S,3R,5R,6S)‐3,5‐dihydroxy‐6‐[(1E,5Z)‐hexadeca‐1,5‐dienyl]‐2‐(β‐d‐glucopyranosyloxy)methyl piperidine‐1‐yl} tetracos‐8‐enamide (3). These were obtained together with lupeol (4), stigmasterol (5), 3‐O‐β‐d‐glucopyranoside of β‐sitosterol (6), tormentic acid (7) from stems and heptadecanoic acid (8), β‐carotene (9), oleanolic acid (10), and 24‐hydroxytormentic acid (11) from leaves. The structures were determined on the basis of NMR data (1H‐, 13C‐, 2D‐NMR analyses), mass spectrometry and confirmed by chemical transformations as well as comparison of spectral data with those reported in the literature. The FRAP method was used to evaluate the antioxidant activity of fractions collected from flash chromatography and isolated compounds. Among the fractions, four reduced FeIII‐TPTZ to FeII‐TPTZ while isolated pure compounds showed no activity.