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PubMed2005

Hypoxia-inducible factor as a physiological regulator.

Hypoxia-inducible factor (HIF) is a transcription complex which responds to changes in oxygen, providing cells with a master regulator that coordinates changes in gene transcription. HIF operates in all mammalian cell types and is ancient in evolutionary terms, being conserved in C. elegans and D. melanogaster. This review summarizes recent insights into the molecular events that link reduced oxygenation to HIF activation and emerging insights into the extensive role of HIF in a broad range of physiological processes.

Animals↗

PubMed2005

A brief history of seed size.

Improved phylogenies and the accumulation of broad comparative data sets have opened the way for phylogenetic analyses to trace trait evolution in major groups of organisms. We arrayed seed mass data for 12,987 species on the seed plant phylogeny and show the history of seed size from the emergence of the angiosperms through to the present day. The largest single contributor to the present-day spread of seed mass was the divergence between angiosperms and gymnosperms, whereas the widest divergence was between Celastraceae and Parnassiaceae. Wide divergences in seed size were more often associated with divergences in growth form than with divergences in dispersal syndrome or latitude. Cross-species studies and evolutionary theory are consistent with this evidence that growth form and seed size evolve in a coordinated manner.

Biological Evolution↗

PubMed1999

Electroreception in monotremes.

I will briefly review the history of the bill sense of the platypus, a sophisticated combination of electroreception and mechanoreception that coordinates information about aquatic prey provided from the bill skin mechanoreceptors and electroreceptors, and provide an evolutionary account of electroreception in the three extant species of monotreme (and what can be inferred of their ancestors). Electroreception in monotremes is compared and contrasted with the extensive body of work on electric fish, and an account of the central processing of mechanoreceptive and electroreceptive input in the somatosensory neocortex of the platypus, where sophisticated calculations seem to enable a complete three-dimensional fix on prey, is given.

Animals↗

PubMed2000

Spectroscopic characterization of Co(II)-, Ni(II)-, and Cd(II)-substituted wild-type and non-native retroviral-type zinc finger peptides.

The nucleocapsid protein (NCP) from Mason-Pfizer monkey virus (MPMV) contains two evolutionary invariant Cys-X2-Cys-X4-His-X4-Cys retroviral-type zinc finger structures, where the Cys and His residues provide ligands to a tetrahedrally coordinated Zn(II) ion. The N-terminal zinc finger (F1) of NCP from MPMV contains an immediately contiguous Cys in the -1 position relative to the start of this conserved motif: Cys-Cys-X2-Cys-X4-His-X4-Cys. Metal complexes of 18-amino acid peptides which model the native zinc finger sequence, SER-Cys-X2-Cys-X4-His-X4-Cys (F1-SC), and non-native Cys-SER-X2-Cys-X4-His-X4-Cys (F1-CS) and SER-SER-X2-Cys-X4-His-X4-Cys (F1-SS) sequences have been spectroscopically characterized and compared to the native two-zinc-finger protein fragment, MPMV NCP 21-80. All Co(II)-substituted peptide complexes adopt tetrahedral ligand geometries and have S- -->Co(II) ligand-to-metal charge-transfer (LMCT) transition intensities consistent with three Co(II)-S bonds for F1-SC and F1-CS. The non-native F1-CS peptide binds Co(II) with KCo= 1.5 x 10(6) M(-1), comparable to that of the native complex, and approximately 100-fold tighter than F1-SS. Like the Co(II) derivative, the absorption spectrum of Ni(II)-substituted NCP 21-80 is most consistent with tetrahedral Ni(II) complexes with multiple thiolate donors. In contrast, Ni(II) complexes of F1-SC and F1-CS exhibit a single absorption band in the 400-550 nm region (epsilon approximately 200-300 M(-1) cm (-1), distinct in the two complexes, assignable to a degenerate d-d transition envelope characteristic of non-native square-planar coordination geometry, and an intense LMCT transition in the UV (epsilon255 approximately 14,000 M(-1) cm(-1)). Cd(II) complexes have intense absorption in the UV (lambda(max)=233nm), with absolute intensities consistent with approximately 5000 M(-1) cm(-1) per Cd(II)-S bond. 113Cd NMR spectroscopy of 113Cd MPMV NCP gives delta=649 ppm, consistent with S3N coordination. Co(II) and Cd(II) complexes of non-native F1-CS peptides are more sensitive to oxidation by O2, relative to F1-SC, suggestive of a higher lability in the non-native chelate. The implications of these findings for the evolutionary conservation of this motif are discussed.

Amino Acid Sequence↗

PubMedDate not supplied

A chemical index inspired by biological plastic evolution: valence-isoelectronic series of aromatics.

Plastic evolution is a new perspective of the evolutionary process conjugating the effect, on one hand, of the acquired characters and, on the other, of the relationships that emerge among the principle of evolutionary indeterminacy, the principle of morphologic determination, and natural selection. Plastic evolution is applied to design the coordination index Ic. Ic is used to characterize the valence-isoelectronic series of cyclopentadiene, benzene, toluene, and styrene and compared to charge indices for dipole moment. The parameters needed to calculate Ic are minus the standard enthalpy of formation T, molecular surface area S, and molecular weight W. With the exception of the O heteromolecule, Ic allows differentiating quantitatively the styrene series as well as the cyclopentadiene from the toluene series. Ic improves the multivariable regression equations for dipole moment and is a predictive index when it is used together with the topological charge indices. The correction introduced in the dipole moment is produced in the correct direction. Inclusion of the heteroatom in the pi-electron system is beneficial for the description of the dipole moment, owing to either the role of additional p and/or d orbitals provided by the heteroatom or the role of steric factors in the pi-electron conjugation. Principal component analysis groups the chemical indices in three classes, which are in agreement with cluster analysis.

Journal Article↗

PubMed1976

Bursal dissections and gill pouch hormones.

The terrestrial survival of birds and mammals depends on evolutionary chantes in cloacal bursae and gill pouches. Comparative dissections of these pouches provide insight into the coordinated functions of cervical endocrine organs, especially as they affect lymphoid tissue.

Animals↗

PubMed1995

Accelerating momentum for change!

As we develop strategies to compete globally, we are challenged with integrating our resources to execute these strategies effectively. Many companies are in the midst of dramatic shifts in corporate cultures, giving more responsibility to employees while raising expectations for their performance. The extent of these changes is far reaching and brings significant challenges to both employees and corporations. This article is a continuation of the evolution (over five years) of a corrective action/continuous improvement process implemented at Exide Electronics. It discusses organizational structures, including steering committees, corrective action teams, task teams, and work cells. Specific expectations, goals, and results of the teams are presented, along with ground rules for functioning within the organization. After structuring the organization and coordinating the resources effectively, the next challenge is accelerating momentum for change. The presentation also discusses the evolutionary process required to make a culture focused on change, including ongoing communication and feedback, constant evaluation and direction of the process, and measuring and paying for performance.

Communication↗

PubMed1996

Evolutionary dynamics of non-coding sequences within the class II region of the human MHC.

About 40% (350 kb) of the human MHC class II region has been sequenced and a coordinated effort to sequence the entire MHC is underway. In addition to the coding information (22 genes/pseudogenes), the non-coding sequences reveal novel information on the organisation and evolution of the MHC as demonstrated here by the example of a 200 kb contig that has been analysed for local and global features. In conjunction with cross-species comparisons, our results present new evidence on the structure of isochores, the evolutionary dynamics of repeat-mediated recombination and its effect on certain MHC encoded genes, and a higher than average degree of natural polymorphism that has implications for sequencing the human genome. We also report the finding of a class I-related pseudogene (HLA-ZI) in the middle of the class II region, which provides the first direct evidence for DNA exchange between these two related regions in man.

Amino Acid Sequence↗

PubMed2003

MT1-MMP-dependent, apoptotic remodeling of unmineralized cartilage: a critical process in skeletal growth.

Skeletal tissues develop either by intramembranous ossification, where bone is formed within a soft connective tissue, or by endochondral ossification. The latter proceeds via cartilage anlagen, which through hypertrophy, mineralization, and partial resorption ultimately provides scaffolding for bone formation. Here, we describe a novel and essential mechanism governing remodeling of unmineralized cartilage anlagen into membranous bone, as well as tendons and ligaments. Membrane-type 1 matrix metalloproteinase (MT1-MMP)-dependent dissolution of unmineralized cartilages, coupled with apoptosis of nonhypertrophic chondrocytes, mediates remodeling of these cartilages into other tissues. The MT1-MMP deficiency disrupts this process and uncouples apoptotic demise of chondrocytes and cartilage degradation, resulting in the persistence of "ghost" cartilages with adverse effects on skeletal integrity. Some cells entrapped in these ghost cartilages escape apoptosis, maintain DNA synthesis, and assume phenotypes normally found in the tissues replacing unmineralized cartilages. The coordinated apoptosis and matrix metalloproteinase-directed cartilage dissolution is akin to metamorphosis and may thus represent its evolutionary legacy in mammals.

Animals↗

PubMed1987

Molecular evolution and nucleotide sequences of the maize plastid genes for the alpha subunit of CF1 (atpA) and the proteolipid subunit of CF0 (atpH).

The nucleotide sequences of the maize plastid genes for the alpha subunit of CF1 (atpA) and the proteolipid subunit of CF0 (atpH) are presented. The evolution of these genes among higher plants is characterized by a transition mutation bias of about 2:1 and by rates of synonymous and nonsynonymous substitution which are much lower than similar rates for genes from other sources. This is consistent with the notion that the plastid genome is evolving conservatively in primary sequence. Yet, the mode and tempo of sequence evolution of these and other plastid-encoded coupling factor genes are not the same. In particular, higher rates of nonsynonymous substitution in atpE (the gene for the epsilon subunit of CF1) and higher rates of synonymous substitution in atpH in the dicot vs. monocot lineages of higher plants indicate that these sequences are likely subject to different evolutionary constraints in these two lineages. The 5'- and 3'-transcribed flanking regions of atpA and atpH from maize, wheat and tobacco are conserved in size, but contain few putative regulatory elements which are conserved either in their spatial arrangement or sequence complexity. However, these regions likely contain variable numbers of "species-specific" regulatory elements. The present studies thus suggest that the plastid genome is not a passive participant in an evolutionary process governed by a more rapidly changing, readily adaptive, nuclear compartment, but that novel strategies for the coordinate expression of genes in the plastid genome may arise through rapid evolution of the flanking sequences of these genes.

Amino Acid Sequence↗

PubMedDate not supplied

A design improvement strategy for axial blood pumps using computational fluid dynamics.

During the initial stages of concept development of non traditional axial flow pumps, numeric simulation offers an attractive advantage. Computational fluid dynamics (CFD) provides the rationale to evolve the design numerically such that undesirable flow features may be significantly mitigated before a physical prototype is fabricated. The initial design of a novel axial flow blood pump is shown through CFD analysis to exhibit large regions of reverse flow. Such fluid dynamic behavior not only decreases the pump's hydrodynamic efficiency, but, more significantly, increases its overall potential for blood trauma and thrombogenesis. The design improvement strategy consists of creating a geometric model of the blood wetted surfaces and changing the associated geometric parameters such that more desirable fluid dynamic behavior is systematically attained with each incremental modification. The fluid flow through each new pump design is analyzed by numerically solving the incompressible Navier-Stokes equations in rotating coordinates. Marked improvements in the major fluid dynamic aspects of the axial flow pump were observed over an evolutionary sequence of four generations of pump design.

Biomechanical Phenomena↗

PubMed2006

Functional coordination between leaf gas exchange and vulnerability to xylem cavitation in temperate forest trees.

We examined functional coordination among stem and root vulnerability to xylem cavitation, plant water transport characteristics and leaf traits in 14 co-occurring temperate tree species. Relationships were evaluated using both traditional cross-species correlations and phylogenetically independent contrast (PIC) correlations. For stems, the xylem tension at which 50% of hydraulic conductivity was lost (psi50) was positively associated (P < 0.001) with specific conductivity (K(S)) and with mean hydraulically weighted xylem conduit diameter (D(h-w)), but was only marginally (P = 0.06) associated with leaf specific conductivity (K(L)). The PIC correlation for each of these relationships, however, was not statistically significant. There was also no relationship between root psi50 and root K(S) in either cross-species or PIC analysis. Photosynthetic rate (A) and stomatal conductance (g(s)) were strongly and positively correlated with root psi50 in the cross-species analysis (P < 0.001), a relationship that was robust to phylogenetic correction (P < 0.01). A and g(s) were also positively correlated with stem psi50 in the cross-species analysis (P = 0.02 and 0.10, respectively). However, only A was associated with stem psi50 in the PIC analysis (P = 0.04). Although the relationship between vulnerability to cavitation and xylem conductivity traits within specific organs (i.e. stems and roots) was weak, the strong correlation between g(s) and root psi50 across species suggests that there is a trade-off between vulnerability to cavitation and water transport capacity at the whole-plant level. Our results were therefore consistent with the expectation of coordination between vulnerability to xylem cavitation and the regulation of stomatal conductance, and highlight the potential physiological and evolutionary significance of root hydraulic properties in controlling interspecific variation in leaf function.

Biological Transport↗

PubMed2005

microRNA target predictions across seven Drosophila species and comparison to mammalian targets.

microRNAs are small noncoding genes that regulate the protein production of genes by binding to partially complementary sites in the mRNAs of targeted genes. Here, using our algorithm PicTar, we exploit cross-species comparisons to predict, on average, 54 targeted genes per microRNA above noise in Drosophila melanogaster. Analysis of the functional annotation of target genes furthermore suggests specific biological functions for many microRNAs. We also predict combinatorial targets for clustered microRNAs and find that some clustered microRNAs are likely to coordinately regulate target genes. Furthermore, we compare microRNA regulation between insects and vertebrates. We find that the widespread extent of gene regulation by microRNAs is comparable between flies and mammals but that certain microRNAs may function in clade-specific modes of gene regulation. One of these microRNAs (miR-210) is predicted to contribute to the regulation of fly oogenesis. We also list specific regulatory relationships that appear to be conserved between flies and mammals. Our findings provide the most extensive microRNA target predictions in Drosophila to date, suggest specific functional roles for most microRNAs, indicate the existence of coordinate gene regulation executed by clustered microRNAs, and shed light on the evolution of microRNA function across large evolutionary distances. All predictions are freely accessible at our searchable Web site http://pictar.bio.nyu.edu.

Journal Article↗

PubMed2002

A comparative study of odorant binding protein genes: differential expression of the PBP1-GOBP2 gene cluster in Manduca sexta (Lepidoptera) and the organization of OBP genes in Drosophila melanogaster (Diptera).

Insects discriminate odors using sensory organs called olfactory sensilla, which display a wide range of phenotypes. Sensilla express ensembles of proteins, including odorant binding proteins (OBPs), olfactory receptors (ORs) and odor degrading enzymes (ODEs); odors are thought to be transported to ORs by OBPs and subsequently degraded by ODEs. These proteins belong to multigene families. The unique combinatorial expression of specific members of each of these gene families determines, in part, the phenotype of a sensillum and what odors it can detect. Furthermore, OBPs, ORs and ODEs are expressed in different cell types, suggesting the need for cell-cell communication to coordinate their expression. This report examines the OBP gene family. In Manduca sexta, the genes encoding PBP1Msex and GOBP2Msex are sequenced, shown to be adjacent to one another, and characterized together with OBP gene structures of other lepidoptera and Drosophila melanogaster. Expression of PBP1Msex, GOBP1Msex and GOBP2Msex is characterized in adult male and female antenna and in larval antenna and maxilla. The genomic organization of 25 D. melanogaster OBPs are characterized with respect to gene locus, gene cluster, amino acid sequence similarity, exon conservation and proximity to OR loci, and their sequences are compared with 14 M. sexta OBPs. Sensilla serve as portals of important behavioral information, and genes supporting sensilla function are presumably under significant evolutionary selective pressures. This study provides a basis for studying the evolution of the OBP gene family, the regulatory mechanisms governing the coordinated expression of OBPs, ORs and ODEs, and the processes that determine specific sensillum phenotypes.

Amino Acid Sequence↗

PubMed2006

Evolutionary games on cycles.

Traditional evolutionary game theory explores frequency-dependent selection in well-mixed populations without spatial or stochastic effects. But recently there has been much interest in studying the evolutionary game dynamics in spatial settings, on lattices and other graphs. Here, we present an analytic approach for the stochastic evolutionary game dynamics on the simplest possible graph, the cycle. For three different update rules, called 'birth-death' (BD), 'death-birth' (DB) and 'imitation' (IM), we derive exact conditions for natural selection to favour one strategy over another. As specific examples, we consider a coordination game and Prisoner's Dilemma. In the latter case, selection can favour cooperators over defectors for DB and IM updating. We also study the case where the replacement graph of evolutionary updating remains a cycle, but the interaction graph for playing the game is a complete graph. In this setting, all three update rules lead to identical conditions in the limit of weak selection, where we find the '1/3-law' of well-mixed populations.

Biological Evolution↗

PubMed2026

Functions of tandem-repeat galectins and domain coordination governs galectin-4 activity in grass carp (Ctenopharyngodon idella).

Galectins are β-galactoside-binding lectins that play essential roles in innate immunity. Among them, tandem-repeat galectins (TrGals), typically composed of two distinct carbohydrate-recognition domains (CRDs) connected by a linker peptide, are well established as key regulators of pathogen recognition and host defense in mammals. However, their structural diversity and immunological functions in teleost fish remain poorly understood. In this study, five TrGals (Gal-4, Gal-8a, Gal-8b, Gal-9, and Gal-9like) were identified in grass carp. Sequence and structural analysis revealed that Gal-8a/b, Gal-9, and Gal-9like possess the canonical two-CRD architecture, whereas Gal-4 uniquely contains four highly similar tandem-repeat domains. All five TrGals were broadly expressed across examined tissues, with predominant expression in the liver. Upon Aeromonas hydrophila infection, Gal-4, Gal-8a, Gal-8b, and Gal-9 were rapidly up-regulated at early time points (3-6 h). To elucidate the functional significance of CRD number, recombinant full-length CiGal-4 (CiGal4-full) and three truncated variants containing one, two, or three CRDs (CiGal4-1CRD, CiGal4-2CRD, and CiGal4-3CRD) were generated and systematically characterized. All recombinant proteins contained the conserved β-sheet structure typical of galectin CRDs. Functional assays revealed that CiGal4-full displayed the strongest growth-inhibitory activity against all tested bacteria, whereas CiGal4-1CRD showed the weakest effect. Notably, CiGal4-2CRD exhibited the most potent bactericidal activity, surpassing the full-length protein, while CiGal4-3CRD showed no further enhancement. CiGal4-full and CiGal4-2CRD showed superior carbohydrate-binding activities compared with the other variants. Collectively, these results reveal that CRD copy number alone does not linearly determine galectin function. Instead, domain organization and conformational coordination are critical for optimizing antimicrobial activity. This study provides new insights into the structure-function relationships and evolutionary diversification of galectins in teleosts and highlights their potential as novel antimicrobial and immunomodulatory agents in aquaculture.

Animals↗

PubMed2002

The crystal structure of prokaryotic phospholipase A2.

In this study, the x-ray crystal structures of the calcium-free and calcium-bound forms of phospholipase A(2) (PLA(2)), produced extracellularly by Streptomyces violaceoruber, were determined by using the multiple isomorphous replacement and molecular replacement methods, respectively. The former and latter structures were refined to an R-factor of 18.8% at a 1.4-A resolution and an R-factor of 15.0% at a 1.6-A resolution, respectively. The overall structure of the prokaryotic PLA(2) exhibits a novel folding topology that demonstrates that it is completely distinct from those of eukaryotic PLA(2)s, which have been already determined by x-ray and NMR analyses. Furthermore, the coordination geometry of the calcium(II) ion apparently deviated from that of eukaryotic PLA(2)s. Regardless of the evolutionary divergence, the catalytic mechanism including the calcium(II) ion on secreted PLA(2) seems to be conserved between prokaryotic and eukaryotic cells. Demonstrating that the overall structure determined by x-ray analysis is almost the same as that determined by NMR analysis is useful to discuss the catalytic mechanism at the molecular level of the bacterial PLA(2).

Amino Acid Sequence↗

PubMed2002

Endothelial response to hypoxia: physiologic adaptation and pathologic dysfunction.

When subjected to a period of oxygen deprivation, endothelial cells exhibit a characteristic pattern of responses that can be considered either adaptive or pathologic, depending on the circumstances. In this review, the molecular basis for these responses is detailed. Hypoxia shifts the endothelial phenotype towards one in which anticoagulant properties are diminished, permeability and leukoadhesivity are increased, and proinflammatory features dominate the endovascular milieu. Of all the different points of intersection between the coagulation and inflammatory axes in the vasculature, perhaps most fundamentally, hypoxia alters several key transcriptional factors, including early growth response gene 1 (Egr1) and hypoxia-inducible factor (HIF) 1, which coordinate separate programs of gene activation. The preponderance of forces in the hypoxic endovascular environment, perhaps designed as an evolutionary adaptation to oxygen deprivation, can trigger severe, pathologic, clinical consequences in the setting of tissue ischemia.

Adaptation, Physiological↗