Protective effect of novel substituted nicotine hydrazide analogues against hypoxic brain injury in neonatal rats via inhibition of caspase.

In hypoxic-ischemic injury of the brain of neonates, the level of caspase-3 was found to be aberrantly activated. Its overexpression leads to the alteration of cytoskeleton protein fodrin and loss of DNA repair enzyme which ultimately results in neurological impairment and disability. Concerning this, the present study was intended to develop novel nicotine hydrazide analogues as caspase inhibitors via efficient synthetic route. These compounds were subsequently tested for inhibitory activity against caspase-3 and -7 where they exhibit highly potent activity against caspase-3 revealing compound 5k as most potent inhibitor (IC50=19.4±2.5µM). In Western blot analysis, 5k considerably inhibits the overexpression of caspase-3. The aryl nicotinate of compound 5k, as indicated by molecular docking was found to engage His121 and critical enzyme thiols, i.e., Cys163 of caspase-3 for its potent activity. Moreover, histopathological examination of brain tissues and hippocampus neurons showed that compound 5k considerably improves the brain injury and exert neuroprotective effects in hypoxic-ischemic (HI). In brain homogenate, 5k significantly improves the activity of MDA, SOD, GSH-Px, CAT and T-AOC to exert its beneficial effect against oxidative stress induced by HI injury.

Archaea: the first domain of diversified life.

The study of the origin of diversified life has been plagued by technical and conceptual difficulties, controversy, and apriorism. It is now popularly accepted that the universal tree of life is rooted in the akaryotes and that Archaea and Eukarya are sister groups to each other. However, evolutionary studies have overwhelmingly focused on nucleic acid and protein sequences, which partially fulfill only two of the three main steps of phylogenetic analysis, formulation of realistic evolutionary models, and optimization of tree reconstruction. In the absence of character polarization, that is, the ability to identify ancestral and derived character states, any statement about the rooting of the tree of life should be considered suspect. Here we show that macromolecular structure and a new phylogenetic framework of analysis that focuses on the parts of biological systems instead of the whole provide both deep and reliable phylogenetic signal and enable us to put forth hypotheses of origin. We review over a decade of phylogenomic studies, which mine information in a genomic census of millions of encoded proteins and RNAs. We show how the use of process models of molecular accumulation that comply with Weston's generality criterion supports a consistent phylogenomic scenario in which the origin of diversified life can be traced back to the early history of Archaea.

[Relationship between plasma motilin level and feeding intolerance in preterm infants].

OBJECTIVE: To observe changes in plasma motilin (MOT) level among preterm infants after birth, to investigate the relationship between plasma motilin level and feeding intolerance (FI), and to clarify the possible risk factors. METHODS: A total of 112 preterm infants were divided into feeding tolerance (FT) group (n=59) and FI group (n=53). Their plasma MOT levels were measured by radioimmunoassay on days 1, 4, 7 and 14 of life. The clinical data of FI group were collected and subjected to multivariate logistic regression analysis. RESULTS: Compared with the FT group, the FI group showed significantly lower plasma MOT levels on days 1, 4, 7 and 14 of life (P<0.05), and there was a positive correlation between plasma MOT level and gestational age, age in days, and volume of enteral feeding in the FI group. The lower the gestational age, the longer the FI duration. There was a negative correlation between the plasma MOT level on day 1 of life and the FI duration (r=-0.913, P<0.001). Gestational age and prenatal use of glucocorticoid were protective factors for FI, while fetal distress, placental abnormality and perinatal infection were risk factors for FI. CONCLUSIONS: Change in plasma MOT level may be closely related to the development of FI in preterm infants. Early monitoring of plasma MOT level may be useful for predicting the occurrence of FI.

The ancient history of the structure of ribonuclease P and the early origins of Archaea.

BACKGROUND: Ribonuclease P is an ancient endonuclease that cleaves precursor tRNA and generally consists of a catalytic RNA subunit (RPR) and one or more proteins (RPPs). It represents an important macromolecular complex and model system that is universally distributed in life. Its putative origins have inspired fundamental hypotheses, including the proposal of an ancient RNA world. RESULTS: To study the evolution of this complex, we constructed rooted phylogenetic trees of RPR molecules and substructures and estimated RPP age using a cladistic method that embeds structure directly into phylogenetic analysis. The general approach was used previously to study the evolution of tRNA, SINE RNA and 5S rRNA, the origins of metabolism, and the evolution and complexity of the protein world, and revealed here remarkable evolutionary patterns. Trees of molecules uncovered the tripartite nature of life and the early origin of archaeal RPRs. Trees of substructures showed molecules originated in stem P12 and were accessorized with a catalytic P1-P4 core structure before the first substructure was lost in Archaea. This core currently interacts with RPPs and ancient segments of the tRNA molecule. Finally, a census of protein domain structure in hundreds of genomes established RPPs appeared after the rise of metabolic enzymes at the onset of the protein world. CONCLUSIONS: The study provides a detailed account of the history and early diversification of a fundamental ribonucleoprotein and offers further evidence in support of the existence of a tripartite organismal world that originated by the segregation of archaeal lineages from an ancient community of primordial organisms.

Common evolutionary trends for SINE RNA structures.

Short interspersed elements (SINEs) and long interspersed elements (LINEs) are transposable elements in eukaryotic genomes that mobilize through an RNA intermediate. Understanding their evolution is important because of their impact on the host genome. Most eukaryotic SINEs are ancestrally related to tRNA genes, although the typical tRNA cloverleaf structure is not apparent for most SINE consensus RNAs. Using a cladistic method where RNA structural components were coded as polarized and ordered multistate characters, we showed that related structural motifs are present in most SINE RNAs from mammals, fishes and plants, suggesting common selective constraints imposed at the SINE RNA structural level. Based on these results, we propose a general multistep model for the evolution of tRNA-related SINEs in eukaryotes.

The origin of modern 5S rRNA: a case of relating models of structural history to phylogenetic data.

Evolutionary models of molecular structures must incorporate molecular information at different levels of structural complexity and must be phrased within a phylogenetic perspective. In this regard, phylogenetic trees of substructures that are reconstructed from molecular features that contribute to order and thermodynamic stability show that a gradual model of evolution of 5S rRNA structure is more parsimonious than models that invoke large segmental duplications of the molecule. The search for trees of substructures that are most parsimonious, by their very nature, defines an objective strategy to select models of molecular change that best fit structural data. When combined with additional data, such as the age of protein domains that interact with RNA substructures, these trees can be used to falsify unlikely hypotheses.

Comparative genomic and phylogenetic analyses reveal the evolution of the core two-component signal transduction systems in enterobacteria.

The two-component signal transduction system (TCST) consists of a histidine kinase (HK) and a response regulator (RR). TCSTs play important roles in sensing and reacting to environmental changes, and in bacterial pathogenesis. Previously, we have identified and characterized TCSTs in Erwinia amylovora, a severe plant enterobacterial pathogen, at genome-wide level. Here we conducted a comparative genomic analysis of TCSTs in 53 genomes of 16 enterobacterial species. These species include important plant, animal, human, and insect pathogenic, saprophytic or symbiotic microorganisms. Comparative genomic analysis revealed that enterobacteria contain eight pairs of core TCSTs. Phylogenetic trees reconstructed from a concatenation of the core set of TCSTs from enterobacteria and for individual TCST proteins from species in Proteobacteria showed that most TCST protein trees in the Enterobacteriaceae or in species of the γ-Proteobacteria agreed well with that of the corresponding 16S rRNA gene. It also showed that co-evolutionary relationships existed between cognate partners of the HKs and RRs. Several core TCSTs were quite ancient and universal based on phylogenomic analysis of protein structures. These results indicate that the core TCSTs are relatively conserved, and suggest that these enterobacteria may have maintained their ancient core TCSTs and might acquire specific new TCSTs for their survival in different environments or hosts, or may have evolved new functionalities of the core TCSTs for adaptation to different ecological niches.

The evolutionary history of the structure of 5S ribosomal RNA.

5S rRNA is the smallest nucleic acid component of the large ribosomal subunit, contributing to ribosomal assembly, stability, and function. Despite being a model for the study of RNA structure and RNA-protein interactions, the evolution of this universally conserved molecule remains unclear. Here, we explore the history of the three-domain structure of 5S rRNA using phylogenetic trees that are reconstructed directly from molecular structure. A total of 46 structural characters describing the geometry of 666 5S rRNAs were used to derive intrinsically rooted trees of molecules and molecular substructures. Trees of molecules revealed the tripartite nature of life. In these trees, superkingdom Archaea formed a paraphyletic basal group, while Bacteria and Eukarya were monophyletic and derived. Trees of molecular substructures supported an origin of the molecule in a segment that is homologous to helix I (alpha domain), its initial enhancement with helix III (beta domain), and the early formation of the three-domain structure typical of modern 5S rRNA in Archaea. The delayed formation of the branched structure in Bacteria and Eukarya lends further support to the archaeal rooting of the tree of life. Remarkably, the evolution of molecular interactions between 5S rRNA and associated ribosomal proteins inferred from a census of domain structure in hundreds of genomes established a tight relationship between the age of 5S rRNA helices and the age of ribosomal proteins. Results suggest 5S rRNA originated relatively quickly but quite late in evolution, at a time when primordial metabolic enzymes and translation machinery were already in place. The molecule therefore represents a late evolutionary addition to the ribosomal ensemble that occurred prior to the early diversification of Archaea.

Evolutionary patterns in the sequence and structure of transfer RNA: early origins of archaea and viruses.

Transfer RNAs (tRNAs) are ancient molecules that are central to translation. Since they probably carry evolutionary signatures that were left behind when the living world diversified, we reconstructed phylogenies directly from the sequence and structure of tRNA using well-established phylogenetic methods. The trees placed tRNAs with long variable arms charging Sec, Tyr, Ser, and Leu consistently at the base of the rooted phylogenies, but failed to reveal groupings that would indicate clear evolutionary links to organismal origin or molecular functions. In order to uncover evolutionary patterns in the trees, we forced tRNAs into monophyletic groups using constraint analyses to generate timelines of organismal diversification and test competing evolutionary hypotheses. Remarkably, organismal timelines showed Archaea was the most ancestral superkingdom, followed by viruses, then superkingdoms Eukarya and Bacteria, in that order, supporting conclusions from recent phylogenomic studies of protein architecture. Strikingly, constraint analyses showed that the origin of viruses was not only ancient, but was linked to Archaea. Our findings have important implications. They support the notion that the archaeal lineage was very ancient, resulted in the first organismal divide, and predated diversification of tRNA function and specificity. Results are also consistent with the concept that viruses contributed to the development of the DNA replication machinery during the early diversification of the living world.

Origins and evolution of modern biochemistry: insights from genomes and molecular structure.

The survey of components in living systems at different levels of organization enables an evolutionary exploration of patterns and processes in macromolecules, networks, and genomic repertoires. Here we discuss how phylogenetic strategies that generate intrinsically rooted phylogenies impact the evolutionary study of RNA and protein components of the macromolecular machinery that is responsible for biological function. We used these methods to generate timelines of discovery of components in systems, such as substructures in RNA molecules, architectures in proteomes, domains in multi-domain proteins, enzymes in metabolic networks, and protein architectures in proteomes. These timelines unfolded remarkable patterns of origin and evolution of molecules, repertoires and networks, showing episodes of both functional specialization (e.g., rise of domains with specialized functions) and molecular simplification (e.g., reductive tendencies in molecules and proteomes). These observations have important evolutionary implications for origins of translation, the genetic code, modules in the protein world, and diversification of life, and suggest early evolution of modern biochemistry was driven by recruitment of both RNA and protein catalysts in an ancient community of complex organisms.

Transfer RNA and the origins of diversified life.

The evolution of the transfer RNA (tRNA) molecule is controversial but embeds the history of protein biosynthesis, the genetic code, and the origins of diversified life. A new phylogenetic method based on RNA structure that we developed provides new lines of evidence to support the genome tag hypothesis and confirms that the 'top half' of tRNA is more ancient than the 'bottom half'. Timelines of amino acid charging function generated from constraint analyses showed that selenocysteine, tyrosine, serine, and leucine specificities were ancient, while those related to asparagine, methionine, and arginine were more recent. The timelines also uncovered an early role of the second and then first codon bases, identified codons for alanine and proline as the most ancient, and revealed important evolutionary take-overs related to the loss of the long variable arm of tRNA. Furthermore, organismal timelines showed Archaea was the oldest superkingdom, followed by viruses, and superkingdoms Eukarya and Bacteria in that order supporting conclusions from recent phylogenomic studies of protein architecture. Strikingly, results showed that the origin of viruses was not only ancient but was linked to Archaea, supporting the notion that the archaeal lineage is the most ancient on earth and its origin predated diversification of tRNA function and specificity.

Three orthologs in rice, Arabidopsis, and Populus encoding starch branching enzymes (SBEs) are different from other SBE gene families in plants.

Starch branching enzymes (SBEs) play important roles in plant starch synthesis. Three orthologs encoding SBEs in rice, Arabidopsis thaliana, and Populus trichocarpa are described. Putative amino acid sequences of these three SBE genes show approximately 30% identity to those of SBEI and SBEII from plants such as maize, barley, and wheat. More interestingly, they share approximately 31% amino acid sequence identity with those of glycogen-branching enzymes from such animals as mouse, horse, and monkey. The three genes have similar genomic structures, but their structural features are quite different from those of genes of both SBEI and SBEII families in plants. Based on phylogenetic analysis and genomic structure comparison, it is proposed that the three SBE genes represent a new family of SBEs.

Untangling the origin of viruses and their impact on cellular evolution.

The origin and evolution of viruses remain mysterious. Here, we focus on the distribution of viral replicons in host organisms, their morphological features, and the evolution of highly conserved protein and nucleic acid structures. The apparent inability of RNA viral replicons to infect contemporary akaryotic species suggests an early origin of RNA viruses and their subsequent loss in akaryotes. A census of virion morphotypes reveals that advanced forms were unique to viruses infecting a specific supergroup, while simpler forms were observed in viruses infecting organisms in all forms of cellular life. Results hint toward an ancient origin of viruses from an ancestral virus harboring either filamentous or spherical virions. Finally, phylogenetic trees built from protein domain and tRNA structures in thousands of genomes suggest that viruses evolved via reductive evolution from ancient cells. The analysis presents a complete account of the evolutionary history of cells and viruses and identifies viruses as crucial agents influencing cellular evolution.

Recruitment of voluntary non-remunerated apheresis donors: the second five years' experience in Shenzhen.

The voluntary non-remunerated blood donation campaign in Shenzhen, China, was launched in 1993 and the smooth change from paid donors to unpaid took only a decade. In the first half the volunteer donation system and a sufficient blood supply was promoted and this paved the way for further development in the second half during which the non-remunerated donation system became substantial and integral due to recruitment for plateletapheresis and peripheral stem cells donation as well as whole blood donations. Ninety percent of the donors registered for plateletapheresis do donate and none of the twenty-three non-related donors with matched HLA genotypes broke their promise to donate their peripheral stem cells.

Evolutionary patterns in the sequence and structure of transfer RNA: a window into early translation and the genetic code.

Transfer RNA (tRNA) molecules play vital roles during protein synthesis. Their acceptor arms are aminoacylated with specific amino acid residues while their anticodons delimit codon specificity. The history of these two functions has been generally linked in evolutionary studies of the genetic code. However, these functions could have been differentially recruited as evolutionary signatures were left embedded in tRNA molecules. Here we built phylogenies derived from the sequence and structure of tRNA, we forced taxa into monophyletic groups using constraint analyses, tested competing evolutionary hypotheses, and generated timelines of amino acid charging and codon discovery. Charging of Sec, Tyr, Ser and Leu appeared ancient, while specificities related to Asn, Met, and Arg were derived. The timelines also uncovered an early role of the second and then first codon bases, identified codons for Ala and Pro as the most ancient, and revealed important evolutionary take-overs related to the loss of the long variable arm in tRNA. The lack of correlation between ancestries of amino acid charging and encoding indicated that the separate discoveries of these functions reflected independent histories of recruitment. These histories were probably curbed by co-options and important take-overs during early diversification of the living world.

The origin and evolution of tRNA inferred from phylogenetic analysis of structure.

The evolutionary history of the two structural and functional domains of tRNA is controversial but harbors the secrets of early translation and the genetic code. To explore the origin and evolution of tRNA, we reconstructed phylogenetic trees directly from molecular structure. Forty-two structural characters describing the geometry of 571 tRNAs and three statistical parameters describing thermodynamic and mechanical features of molecules quantitatively were used to derive phylogenetic trees of molecules and molecular substructures. Trees of molecules failed to group tRNA according to amino acid specificity and did not reveal the tripartite nature of life, probably due to loss of phylogenetic signal or because tRNA diversification predated organismal diversification. Trees of substructures derived from both structural and statistical characters support the origin of tRNA in the acceptor arm and the hypothesis that the top half domain composed of acceptor and pseudouridine (TPsiC) arms is more ancient than the bottom half domain composed of dihydrouridine (DHU) and anticodon arms. This constitutes the cornerstone of the genomic tag hypothesis that postulates tRNAs were ancient telomeres in the RNA world. The trees of substructures suggest a model for the evolution of the major functional and structural components of tRNA. In this model, short RNA hairpins with stems homologous to the acceptor arm of present day tRNAs were extended with regions homologous to TPsiC and anticodon arms. The DHU arm was then incorporated into the resulting three-stemmed structure to form a proto-cloverleaf structure. The variable region was the last structural addition to the molecular repertoire of evolving tRNA substructures.

Genomic isolation of genes encoding starch branching enzyme II (SBEII) in apple: toward characterization of evolutionary disparity in SbeII genes between monocots and eudicots.

Two genes encoding starch branching enzyme II (SBEII) have been identified in apple. These genes share 94 and 92% identity in coding DNA sequences and amino acid sequences, respectively; moreover, they have similar expression patterns. Both genes are expressed in vegetative and reproductive tissues, including leaves, buds, flowers, and fruits. Based on genomic Southern blots, there are two copies of SbeII genes in the apple genome. Comparisons of genomic sequences between monocots and eudicots have revealed that the genomic structure of SbeII genes is conserved. However, the 5'-terminal region of coding DNA sequences of SbeII genes shows greater divergence than the 3'-terminal region between monocots and eudicots. Phylogenetic analysis of DNA sequences has demonstrated that the duplication patterns of SbeII genes are different between monocots and eudicots. In monocots, the duplication of SbeII genes must have occurred prior to the radiation of grasses (Poaceae); while, in eudicots, the expansion of SbeII genes must have followed the process of speciation.

Gene-interleaving patterns of synteny in the Saccharomyces cerevisiae genome: are they proof of an ancient genome duplication event?

BACKGROUND: Recent comparative genomic studies claim local syntenic gene-interleaving relationships in Ashbya gossypii and Kluyveromyces waltii are compelling evidence for an ancient whole-genome duplication event in Saccharomyces cerevisiae. We here test, using Hannenhalli-Pevzner rearrangement algorithms that address the multiple genome rearrangement problem, whether syntenic patterns are proof of paleopolyploidization. RESULTS: We focus on (1) pairwise comparison of gene arrangement sequences in A. gossypii and S. cerevisiae, (2) reconstruction of gene arrangements ancestral to A. gossypii, S. cerevisiae, and K. waltii, (3) synteny patterns arising within and between lineages, and (4) expected gene orientation of duplicate gene sets. The existence of syntenic patterns between ancestral gene sets and A. gossypii, S. cerevisiae, and K. waltii, and other evidence, suggests that gene-interleaving relationships are the natural consequence of topological rearrangements in chromosomes and that a more gradual scenario of genome evolution involving segmental duplication and recombination constitutes a more parsimonious explanation. Furthermore, phylogenetic trees reconstructed under alternative hypotheses placed the putative whole-genome duplication event after the divergence of the S. cerevisiae and K. waltii lineages, but in the lineage leading to K. waltii. This is clearly incompatible with an ancient genome duplication event in S. cerevisiae. CONCLUSION: Because the presence of syntenic patterns appears to be a condition that is necessary, but not sufficient, to support the existence of the whole-genome duplication event, our results prompt careful re-evaluation of paleopolyploidization in the yeast lineage and the evolutionary meaning of syntenic patterns.