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PubMed2005

Fermi surface evolution and Luttinger theorem in Na(x)CoO2: a systematic photoemission study.

We report a systematic angle-resolved photoemission study on Na(x)CoO2 for a wide range of Na concentrations (0.3 < or = x < or = 0.72). In all the metallic samples at different x, we observed (i) only a single holelike Fermi surface centered around gamma and (ii) its area changes with x according to the Luttinger theorem. We also observed a surface state that exhibits a larger Fermi surface area. The e'(g) band and the associated small Fermi surface pockets near the K points predicted by band calculations are found to sink below the Fermi energy in a manner almost independent of the doping and temperature.

Journal Article↗
PubMed2006

Controlled synthesis of high-quality PbS star-shaped dendrites, multipods, truncated nanocubes, and nanocubes and their shape evolution process.

Well-defined single-crystalline PbS nano- and microstructures including dendrites, multipods, truncated nanocubes, and nanocubes were synthesized in high yield by a simple solution route. Novel star-shaped PbS dendrites with six symmetric arms along the 100 direction, each of which shows one trunk (long axis) and four branches (short axes), have been achieved using Pb(AC)2 and thioacetamide (TAA) as precursors, under the molar ratio Pb(AC)2/TAA = 2/1, at initial reaction temperature 80 degrees C, refluxing for 30 min at 100 degrees C, in the presence of cetyltrimethylammonium bromine (CTAB). The "nanorods" in each branch are parallel to each other in the same plane and are perpendicular to the trunk. The truncated nanocubes mainly bounded by the {100} plane were prepared under a different Pb(AC)2/TAA molar ratio, at initial reaction temperature 40 degrees C, refluxing for 12 h at 100 degrees C. Based on the systematic studies on their shape evolution, a possible growth mechanism of these PbS nano- and microstructures was proposed. The shapes of PbS nanocrystals with face-centered cubic (fcc) structure are mainly determined by the ratio (R) between the growth rates along the (100) and (111) directions. The Pb(AC)2/TAA molar ratio and the initial reaction temperature influence the growth ratio R in the formation of PbS nuclei at an early stage, which results in the final morphology of PbS nanocrystals. Under the current experimental conditions, we can control the PbS shape evolution by simply tuning the molar ratio, the initial reaction temperature, and the period of reaction. Based on the systematic studies on the shape evolution, this approach is expected to be employed for the control-shaped synthesis of other fcc structural semiconductor nanomaterials. The photoluminescence properties were investigated and the prepared nano- and microstructures displayed a very strong luminescence around 600-650 nm at room temperature.

Journal Article↗
PubMed2005

Zinc oxide nanostructures: morphology derivation and evolution.

Zinc oxide nanostructures of various types, including nanobelts, nanoplatelets, nanowires, and nanorods, have been synthesized via well-developed routes by many research groups. However, so far, the underlying mechanism for the morphology derivation and evolution of the nanostructures has not been elucidated in depth. In this article, we report the systematic investigation of the morphology evolution characteristics of ZnO nanostructures from dense rods to dense nanoplatelets, nanoplatelet flowers, dense nanobelt flowers, and nanowire flowers in an evaporation-physical transport-condensation approach. Through the use of crystal growth theory, the determining factors for the formation of different nanostructural morphologies were found to be gas-phase supersaturation and the surface energy of the growing surface planes. Other experimental parameters such as the temperature at the source and the substrate, the temperature difference and the distance between the source and the substrate, the heating rate of the furnace, the gas flow rate, the ceramic tube diameter, and the starting material are all correlated with supersaturation and impose an effect on the morphology evolution. This finding may have an important impact on the qualitative understanding of the morphology evolution of nanostructures and the achieving of desired nanostructures controllably.

Journal Article↗
PubMed2002

The evolution of transthyretin synthesis in the choroid plexus.

Choroid plexus has the highest concentration of transthyretin (TTR) mRNA in the body, 4.4 microg TTR mRNA/g wet weight tissue, compared with 0.39 microg in the liver. The proportion of TTR to total protein synthesis in choroid plexus is 12%. All newly synthesized TTR is secreted towards the ventricles. Net transfer of T4 occurs only towards the ventricle and depends on ongoing protein synthesis. Thyroxine-binding globulin (TBG), TTR and albumin form a "buffering" system for plasma [T4] because of their overlapping affinities and on/off rates for L-thyroxine (T4)-binding. The individual components of this network determining T4 distribution are functionally highly redundant. Absence of TBG (humans), or TTR (mice), or albumin (humans, rats) is not associated with hypothyroidism. Natural selection is based on small, inheritable alterations improving function. The study of these alterations can identify function. TTR genes were cloned and sequenced for a large number of vertebrate species. Systematic, stepwise changes during evolution occurred only in the N-terminal region, which became shorter and more hydrophilic. Simultaneously, a change in function occurred: TTR affinities for T4 are higher in mammals than in reptiles and birds. L-triiodothyronine (T3) affinities show the opposite trend. This favors site-specific regulation of thyroid hormones by tissue-specific deiodinases in the brain.

Animals↗
PubMed1996

Comparative analysis of a conserved zinc finger gene cluster on human chromosome 19q and mouse chromosome 7.

Several lines of evidence now suggest that many of the zinc-finger-containing (ZNF) genes in the human genome are arranged in clusters. However, little is known about the structure or function of the clusters or about their conservation throughout evolution. Here, we report the analysis of a conserved ZNF gene cluster located in human chromosome 19q13.2 and mouse chromosome 7. Our results indicate that the human cluster consists of at least 10 related Kruppel-associated box (KRAB)-containing ZNF genes organized in tandem over a distance of 350-450 kb. Two cDNA clones representing genes in the murine cluster have been studied in detail. The KRAB A domains of these genes are nearly identical and are highly similar to human 19q13.2-derived KRAB sequences, but DNA-binding ZNF domains and other portions of the genes differ considerably. The two murine genes display distinct expression patterns, but are coexpressed in some adult tissues. These studies pave the way for a systematic analysis of the evolution of structure and function of genes within the numerous clustered ZNF families located on human chromosome 19 and elsewhere in the human and mouse genomes.

Amino Acid Sequence↗
PubMed2006

An integrated view of protein evolution.

Why do proteins evolve at different rates? Advances in systems biology and genomics have facilitated a move from studying individual proteins to characterizing global cellular factors. Systematic surveys indicate that protein evolution is not determined exclusively by selection on protein structure and function, but is also affected by the genomic position of the encoding genes, their expression patterns, their position in biological networks and possibly their robustness to mistranslation. Recent work has allowed insights into the relative importance of these factors. We discuss the status of a much-needed coherent view that integrates studies on protein evolution with biochemistry and functional and structural genomics.

Animals↗
PubMed2006

Systematically assessing the influence of 3-dimensional structural context on the molecular evolution of mammalian proteomes.

The 3-dimensional (3D) structural context of amino acid residues in a protein could significantly impact the level of selective constraint on the residues. Here, by analyzing 767 mammalian proteins, we systematically investigate how various 3D structural contexts influence selective constraint. The structural contexts we examined include solvent accessibility, secondary structure, and intramolecular residue-residue interactions. Through this analysis, we offer quantitative information on how 3D structural contexts affect the level of selective constraint.

Amino Acids↗
PubMed1994

Axonal torpedoes in cerebellar Purkinje cells of two normal mouse strains during aging.

The present study systematically investigated the proportional evolution of Purkinje cell (PC) axonal swellings, also termed torpedoes, during aging of the two unrelated mouse strains B6CBA and C57BL/6J. Torpedoes were identified using monoclonal antibodies against the calcium-binding protein calbindin D-28k in mice ranging in age from 8 days postnatally up to 32 months. The relative density of PCs bearing torpedoes in animals up to 6 months of age was less than 0.1%. The number increases between 6-8 months and rises further in older mice almost linearly up to 13.7% affected PCs in the oldest animal (32 months) studied. In contrast, PC loss, as indicated by parvalbumin-immunoreactive empty baskets, is only at a very moderate level (less than 0.5%) in these strains. While the proximal axonic segments often show two and occasionally up to five swellings and frequently appear to be hypertrophied as a whole, the dendritic trees and neuronal somata of the affected PCs exhibit normal morphology. On rare occasions adaptive reactions indicated by "arciform axons" and enlarged varicosities of recurrent collaterals were observed. The results demonstrate that in addition to age-related PC loss of whatever degree, axonal disturbances of PCs, indicated by torpedoes, are present, leading most probably to a graded loss of cerebellar cortico-fungal projections.

Adaptation, Physiological↗
PubMed1998

Genomics and computational molecular biology.

There has been a dramatic increase in the number of completely sequenced bacterial genomes during the past two years as a result of the efforts both of public genome agencies and the pharmaceutical industry. The availability of completely sequenced genomes permits more systematic analyses of genes, evolution and genome function than was otherwise possible. Using computational methods - which are used to identify genes and their functions including statistics, sequence similarity, motifs, profiles, protein folds and probabilistic models - it is possible to develop characteristic genome signatures, assign functions to genes, identify pathogenic genes, identify metabolic pathways, develop diagnostic probes and discover potential drug-binding sites. All of these directions are critical to understanding bacterial growth, pathogenicity and host-pathogen interactions.

Bacterial Proteins↗
PubMed1991

Molecular evolutionary history of ancient aquatic angiosperms.

Aquatic plants are notoriously difficult to study systematically due to convergent evolution and reductionary processes that result in confusing arrays of morphological features. Plant systematists have frequently focused their attention on the "water lilies," putative descendants of the most archaic angiosperms. Classification of these 10 plant genera varies from recognition of one to three orders containing three to six families. We have used DNA sequence analysis as a means of overcoming many problems inherent in morphologically based studies of the group. Phylogenetic analyses of sequence data obtained from a 1.2-kilobase portion of the chloroplast gene rbcL provide compelling evidence for the recognition of three distinct lineages of "water lily" plants. Molecular phylogenies including woody Magnoliidae sequences and sequences of these aquatic plants depict Ceratophyllum as an early diverging genus. Our results support hypotheses that most taxonomic concepts of the order Nymphaeales reflect polyphyletic groups and that the unusual genus Ceratophyllum represents descendants of some of the earliest angiosperms.

Base Sequence↗
PubMed1959

Studies on the pathogenicity of group A Streptococci. I. Its relation to surface phagocytosis.

Four strains of Group A streptococci, possessing different degrees of virulence for both mice and rats, were tested for susceptibility to phagocytosis on glass slides, in glass roller tubes, and on the surfaces of freshly excised tissues and moistened filter paper. All of the tests were performed in the absence of serum to exclude the possible presence of opsonins. Only under conditions which allowed surface phagocytosis to take place was there a correlation between virulence and susceptibility to phagocytosis. A similar relationship between virulence and surface phagocytosis was also demonstrable in vivo during the early stages of experimental streptococcal peritonitis. Systematic study of the evolution of the peritonitis revealed that its outcome was determined by the phagocytic reaction which occurred in the first few hours of the infection.

Animals↗
PubMed2005

Using the quantitative genetic threshold model for inferences between and within species.

Sewall Wright's threshold model has been used in modelling discrete traits that may have a continuous trait underlying them, but it has proven difficult to make efficient statistical inferences with it. The availability of Markov chain Monte Carlo (MCMC) methods makes possible likelihood and Bayesian inference using this model. This paper discusses prospects for the use of the threshold model in morphological systematics to model the evolution of discrete all-or-none traits. There the threshold model has the advantage over 0/1 Markov process models in that it not only accommodates polymorphism within species, but can also allow for correlated evolution of traits with far fewer parameters that need to be inferred. The MCMC importance sampling methods needed to evaluate likelihood ratios for the threshold model are introduced and described in some detail.

Bayes Theorem↗
PubMed1994

The dynamic progression of evolved character states for aromatic amino acid biosynthesis in gram-negative bacteria.

A systematic analysis of the evolution of aromatic amino acid biosynthesis in the Proteobacteria, previously focussed mainly upon the gamma subdivision, has now been extended to the beta subdivision. Five lineages were studied, represented by Neisseria gonorrhoeae, Nitrosomonas europaea, Alcaligenes faecalis, rRNA Group-III pseudomonads/Rubrivivax gelatinosus, and rRNA Group-II pseudomonads/Rhodocyclus tenuis. Within the phenylalanine pathway, the bifunctional P-protein (chorismate mutase/prephenate dehydratase) was present in each lineage and must have evolved in a common ancestor of the beta and gamma subdivisions. Each P-protein was found to be subject to activation by L-tyrosine, and to feedback inhibition by L-phenylalanine. Phenylalanine-inhibited (DS-phe) and tyrosine-inhibited (DS-tyr) isoenzymes of 3-deoxy-D-arabino-heptulosonate-7-phosphate synthase probably existed in the common beta-subdivision ancestor, with DS-tyr being lost in N. gonorrhoeae and A. faecalis. The participation of DS-phe in a dissociable multienzyme complex with one or more other common-pathway enzymes is known to exist in N. gonorrhoeae. The same complex is indicated by two peaks of DS-phe seen in chromatographic profiles of Group-III pseudomonads and A. faecalis. It is concluded that the contemporary DS-phe species present in subdivision gamma and beta must have had independent origins. Tyrosine biosynthesis was found to be quite diverse within the beta subdivision. Nit. europaea possessed an arogenate dehydrogenase which was specific for NADP+. In all other lineages, a broad-specificity cyclohexadienyl dehydrogenase (CHD) was present. In N. gonorrhoeae the CDH was specific for NAD+ while the remaining CDH species could utilize either NAD+ or NADP+. Only the CDH species within the rRNA Group-II pseudomonad/R. tenuis lineage was feedback-inhibited by L-tyrosine, and this correlated with an allosteric pattern where activation of the prephenate dehydratase component of the P-protein by L-tyrosine was relatively poor. However, the CDH enzyme present in N. gonorrhoeae and A. faecalis was subject to inhibition by 4-hydroxyphenylpyruvate, this being competitive with respect to the cyclohexadienyl substrate. The monofunctional species of chorismate mutase (CM-F) and cyclohexadienyl dehydratase, widely distributed among the gamma-subdivision assemblage and recently shown to be periplasmic enzymes, were demonstrated in Pseudomonas pickettii, a member of rRNA homology Group-II.

Alcaligenes↗
PubMed1985

Lipid composition of the nervous system of earthworms (Lumbricus terrestris).

As part of a systematic study of the evolution of the nervous system, the lipid composition of the ventral nerves of earthworms was examined. The nerve axons are wrapped in copious layers of loosely bound membrane, superficially resembling the myelin sheath of vertebrates. However, neither galactocerebroside nor sulfatide, both of which are considered to be markers for myelin, was present, and only traces of glucocerebroside, which is abundant in shrimp nerve, were detected. The lipids were rich in cholesterol (15.3 mumol/g of fresh tissue) and phospholipids (21.7 mumol/g of fresh tissue). The phospholipids were composed of phosphatidylethanolamine, -choline, -serine, and -inositol in the ratio of 41:44:8:7. Most of the ethanolamine-containing phospholipids were in the form of plasmalogens. The fatty acid moieties of these phospholipids were predominantly 18:1, 18:0, and 20:1, whereas the aldehyde moieties of plasmalogen were mostly 18:0. Sphingomyelin, which is considered a ubiquitous component of animal membranes, was not detected. How the unique structure of the membranes of earthworm nerves may be related to the function of the nervous system in this organism is discussed.

Animals↗
PubMed2002

Rooting the eukaryote tree by using a derived gene fusion.

Single-gene trees have failed to locate the root of the eukaryote tree because of systematic biases in sequence evolution. Structural genetic data should yield more reliable insights into deep phylogenetic relationships. We searched major protist groups for the presence or absence of a gene fusion in order to locate the root of the eukaryote tree. In striking contrast to previous molecular studies, we show that all eukaryote groups ancestrally with two cilia (bikonts) are evolutionarily derived. The root lies between bikonts and opisthokonts (animals, Fungi, Choanozoa). Amoebozoa either diverged even earlier or are sister of bikonts or (less likely) opisthokonts.

Animals↗
PubMed2005

Mitochondrial haplotype diversity in the tortoise species Testudo graeca from North Africa and the Middle East.

BACKGROUND: To help conservation programs of the endangered spur-thighed tortoise and to gain better insight into its systematics, genetic variation and evolution in the tortoise species Testudo graeca (Testudines: Testudinidae) was investigated by sequence analysis of a 394-nucleotide fragment of the mitochondrial 12S rRNA gene for 158 tortoise specimens belonging to the subspecies Testudo graeca graeca, Testudo graeca ibera, Testudo graeca terrestris, and a newly recognized subspecies Testudo graeca whitei. A 411-nucleotide fragment of the mitochondrial D-loop was additionally sequenced for a subset of 22 T. graeca, chosen because of their 12S gene haplotype and/or geographical origin. RESULTS: Haplotype networks generated by maximum-likelihood and neighbor-joining analyses of both the separate and the combined sequence data sets suggested the existence of two main clades of Testudo graeca, comprising Testudo graeca from northern Africa and Testudo graeca from the Turkey and the Middle East, respectively. CONCLUSION: Mitochondrial DNA haplotyping suggests that the tortoise subspecies of T. g. graeca and T. g. ibera are genetically distinct, with a calculated divergence time in the early or middle Pleistocene. Other proposed subspecies could not clearly be recognized based upon their mt haplotypes and phylogenetic position, and were either part of the T. g. graeca or of the T. g. ibera clade, suggesting that genetic evidence for the existence of most of the 15 proposed subspecies of T. graeca is weak.

Africa, Northern↗
PubMed2026

Genome-wide identification and cold-stress-responsive expression analysis of the NOX gene family in Cucumis melo.

NADPH oxidases (NOXs) are crucial enzymes for reactive oxygen species (ROS) generation in plants and play vital roles in growth, development, and stress responses. To elucidate the sequence characteristics of the NOX gene family and its low-temperature response patterns in melon (Cucumis melo L.), this study conducted genome-wide identification and expression profiling of NOX family members using bioinformatics analysis, RNA-seq transcriptome sequencing, and real-time quantitative PCR (RT-qPCR). The results revealed that eight NOX members were identified in the melon genome, distributed across six chromosomes. All members harbored conserved domains including Ferric_reductase, FAD_binding_8, NAD_binding_6, and NADPH_Ox, and the encoded proteins were generally basic and hydrophilic. Phylogenetic analysis classified the NOX proteins into five subgroups. Synteny analysis indicated the presence of only one pair of intraspecific duplicated genes in melon, which was under purifying selection. The promoter regions contained multiple hormone- and stress-responsive cis-acting elements, with CmNOX2 and CmNOX4 harboring low-temperature responsive elements. Following treatment at 4&#x2103; for 24 h and 48 h, leaf relative electrolyte leakage (REL) increased from 28.33% to 42.67% and 52.67%, respectively; transcriptome analysis identified 5,633 and 6,882 differentially expressed genes (DEGs), respectively. Cold-responsive genes exhibited significant differential expression, with SLAC1 and CPK19 showing sustained upregulation. RT-qPCR results demonstrated that the expression of CmNOX2, CmNOX5, CmNOX6, and CmNOX7 was significantly downregulated after low-temperature treatment, whereas CmNOX4 expression was significantly upregulated at 48 h. Integrating promoter elements and expression characteristics, CmNOX4 may represent an important candidate gene involved in melon low-temperature response. This study systematically characterized the structure, evolution, and expression patterns of the melon NOX gene family, identified candidate genes responsive to low temperature, and provides a reference for further investigation into the mechanisms underlying melon cold adaptation.

Cucumis melo↗