A new similarity principle for cardiac energetics

Similarity criteria of the functional design of the mammalian cardiovascular system are scant. For the analysis of mammalian cardiac energetics physiological parameters such as mean arterial blood pressure, stroke volume, heart rate, metabolic rate and heart and body weights are considered pertinent. Based on these parameters, a new similarity principle is established via allometric equations, dimensional analysis and Buckingham's pi-theorem. The principle states that the ratio of left ventricular external work to metabolic rate is inversely proportional to resting heart rates of mammals. The proportionality constant is dimensionless and is invariant of mammalian body weights.     

Mammalian catalase: a venerable enzyme with new mysteries

Mammalian catalase has been the subject of many classic biochemical studies. Despite our detailed knowledge of its functional mechanisms and its three-dimensional structure, however, several unexpected features of mammalian catalase have been recently discovered. For example, some mammalian catalases seem to have oxidase activity and produce reactive oxygen species when exposed to UVB light. In addition, bovine catalase uses unbound NAD(P)H to prevent substrate inactivation without displacing catalase-bound NADP(+). Coupled with the earlier discovery of catalase-bound NADPH, these developments indicate that serendipity and new investigative approaches can reveal unexpected features, even for an enzyme that has been studied for over 100 years.     

Wave-intensity analysis: a new approach to coronary hemodynamics.

In 10 anesthetized dogs, we measured high-fidelity left circumflex coronary (P(LCx)), aortic (P(Ao)), and left ventricular (P(LV)) pressures and left circumflex velocity (U(LCx); Doppler) and used wave-intensity analysis (WIA) to identify the determinants of P(LCx) and U(LCx). Dogs were paced from the right atrium (control 1) or right ventricle by use of single (control 2) and then paired pacing to evaluate the effects of left ventricular contraction on P(LCx) and U(LCx). During left ventricular isovolumic contraction, P(LCx) exceeded P(Ao), paired pacing increasing the difference. Paired pacing increased DeltaP(X) (the P(LCx)-P(Ao) difference at the P(Ao)-P(LV) crossover) and average dP(LCx)/dt (P < 0.0001 for both). During this time, WIA identified a backward-going compression wave (BCW) that increased P(LCx) and decreased U(LCx); the BCW increased during paired pacing (P < 0.0001). After the aortic valve opened, the increase in P(Ao) caused a forward-going compression wave that, when it exceeded the BCW, caused U(LCx) to increase, despite P(LV) and (presumably) elastance continuing to increase. Thus WIA identifies the contributions of upstream (aortic) and downstream (microcirculatory) effects on P(LCx) and U(LCx).     

Protein structure similarity from principle component correlation analysis

Background  

Owing to rapid expansion of protein structure databases in recent years, methods of structure comparison are becoming increasingly effective and important in revealing novel information on functional properties of proteins and their roles in the grand scheme of evolutionary biology. Currently, the structural similarity between two proteins is measured by the root-mean-square-deviation (RMSD) in their best-superimposed atomic coordinates. RMSD is the golden rule of measuring structural similarity when the structures are nearly identical; it, however, fails to detect the higher order topological similarities in proteins evolved into different shapes. We propose new algorithms for extracting geometrical invariants of proteins that can be effectively used to identify homologous protein structures or topologies in order to quantify both close and remote structural similarities.     

IntelliGO: a new vector-based semantic similarity measure including annotation origin

Background  

The Gene Ontology (GO) is a well known controlled vocabulary describing the biological process, molecular function and cellular component aspects of gene annotation. It has become a widely used knowledge source in bioinformatics for annotating genes and measuring their semantic similarity. These measures generally involve the GO graph structure, the information content of GO aspects, or a combination of both. However, only a few of the semantic similarity measures described so far can handle GO annotations differently according to their origin (i.e. their evidence codes).     

A principle of maximum topological similarity in molecular systematics

The paper deals with the problem of phylogenetic reconstruction on the basis of comparative analysis of features. Main attention is paid to comparison and classification of the biopolymer sequences. Different approaches to this task are critically reviewed. The novel principle of construction of tree-like classification schemes permitting subsequent evolutionary analysis is proposed. It concentrates on reconstruction of the tree with a topologic structure that is most close to topologic features, imprinted in the source distance matrix. Realization of this approach was made possible by development of the special formalism, enabling evaluation and comparison of topologic features of distance matrices and trees.     

CLUSS: Clustering of protein sequences based on a new similarity measure

Background  

The rapid burgeoning of available protein data makes the use of clustering within families of proteins increasingly important. The challenge is to identify subfamilies of evolutionarily related sequences. This identification reveals phylogenetic relationships, which provide prior knowledge to help researchers understand biological phenomena. A good evolutionary model is essential to achieve a clustering that reflects the biological reality, and an accurate estimate of protein sequence similarity is crucial to the building of such a model. Most existing algorithms estimate this similarity using techniques that are not necessarily biologically plausible, especially for hard-to-align sequences such as proteins with different domain structures, which cause many difficulties for the alignment-dependent algorithms. In this paper, we propose a novel similarity measure based on matching amino acid subsequences. This measure, named SMS for Substitution Matching Similarity, is especially designed for application to non-aligned protein sequences. It allows us to develop a new alignment-free algorithm, named CLUSS, for clustering protein families. To the best of our knowledge, this is the first alignment-free algorithm for clustering protein sequences. Unlike other clustering algorithms, CLUSS is effective on both alignable and non-alignable protein families. In the rest of the paper, we use the term "phylogenetic" in the sense of "relatedness of biological functions".     

Mammalian evolution and biomedicine: new views from phylogeny

Recent progress resolving the phylogenetic relationships of the major lineages of mammals has had a broad impact in evolutionary biology, comparative genomics and the biomedical sciences. Novel insights into the timing and historical biogeography of early mammalian diversification have resulted from a new molecular tree for placental mammals coupled with dating approaches that relax the assumption of the molecular clock. We highlight the numerous applications to come from a well-resolved phylogeny and genomic prospecting in multiple lineages of mammals, from identifying regulatory elements in mammalian genomes to assessing the functional consequences of mutations in human disease loci and those driving adaptive evolution.     

Systemic hypertension, headache, and ocular hemodynamics: a new hypothesis

The association between systemic hypertension and headache remains controversial and its pathophysiologic basis is uncertain. A rather characteristic early-morning pulsating headache is commonly seen in hypertensive patients, and a recent meta-analysis supports the link between these 2 entities. Epidemiologic evidence has paradoxically suggested a negative association between hypertension and headache. Unpredictable clinical association between severe hypertension and headache indicates that another cranial perfusion-related variable exerts a critical role. Neuroanatomically, head and neck pain primarily involves the ophthalmic division of the trigeminal nerve (V1). A link between systemic hypertension, pulsatile choroidal blood flow (CBF), and intraocular pressure (IOP) has been established. I propose that a trait ocular sympathetic hypofunction permits rapid episodic ocular choroidal overperfusion that stretches the ocular globe in the cohort of hypertensive patients with headache. Rapid distension of the pain-sensitive corneoscleral envelope can stimulate corneoscleral and iridial pain-sensitive V1 nerve endings and generate headache. Ocular tamponade function physiologically limits choroidal overperfusion. A higher basal IOP in some patients with moderate-to-severe hypertension may dampen pulsatile CBF and account for the negative epidemiologic link between sustained systemic hypertension and headache. Besides activation of the baroreceptor reflex, the association of hypalgesia with hypertension probably involves activation of the vasopressin-endorphin adaptive system consequent to mechanical stimulation of V1. The analogy between hypertensive headache and angle-closure glaucoma is rather limited because typical ocular and visual signs and symptoms of angle-closure glaucoma are not seen in hypertension-related headache. Hypertensive crises, including those associated with pheochromocytoma, are not accompanied by attacks of angle-closure glaucoma. Glaucoma is not associated with ocular choroidal congestion, but with reduced pulsatile CBF. The predisposition to develop angle-closure glaucoma is theoretically not associated with ocular autonomic hypofunction and should be conceptually dissociated from this hypothesis. The hypothesis can be evaluated by establishing significant circadian elevations of blood pressure, including nondipping nighttime pattern as well as circadian and periheadache measurements of IOP in patients with attacks of hypertension-related headache.     

Mammalian development: new trick for an old dog

A recent study has shown that the T-box gene eomesodermin, which was first identified in Xenopus, not only plays a conserved role in vertebrates directing gastrulation, but interestingly in mammals has acquired a new function in the development of the trophoblast.     

The cytodisk: a cytometer based upon a new principle of cell alignment

A new method is described for one-dimensional alignment of small particles such as biological cells. A drop of the particle suspension is spread out on a flat disk or plate equipped with V-shaped grooves such as are present on a gramophone disk. After drying, the particles are located on the bottom of the grooves and are thus aligned in a one-dimensional array. The new alignment procedure is demonstrated with a suspension of fluorescent polystyrene microspheres (diameter 3.8 microns) and a suspension of the unicellular algae chlorella vulgaris (diameter about 3 microns). It appears that the alignment of cells and spheres is very good. When using microspheres, more than 95% of the particles in the grooves are located within +/- 2 microns of the centre line of the groove. Based upon this cell-alignment principle, a new cytometer, named the cytodisk, is proposed. The proposed system has a number of advantages over the flow cytometer, among which is the unique ability of relocating a previously measured cell for further measurement or visual examination. A prototype of a cytodisk, developed for initial test measurements, was built in our laboratory. The apparatus, constructed from a record player and ordinary long-playing records, uses a simple mechanical tracking system and a single optical fiber for fluorescence excitation and detection. With this apparatus it is demonstrated that a cytodisk can indeed perform quite well: A histogram of fluorescing microspheres could be measured with a coefficient of variation of 4.1%. The performance of this prototype is limited by the quality of the mechanical tracking system and the optical system used.(ABSTRACT TRUNCATED AT 250 WORDS)     

Protein structure similarity as guiding principle for combinatorial library design

Proteins are modularly built from a limited set of approximately 1000 structural domains. The evolutionary relationship within a domain family suggests that the knowledge about a common fold structure can be exploited for the design of small molecule libraries in the development of inhibitors and ligands. This principle has been used for the synthesis of inhibitors for kinases sharing the same fold. It can also be applied for proteins which share the same fold architecture yet belong to different functional classes. Bestatin--originally known as an aminopeptidase inhibitor--was employed as guiding structure for the development of leukotriene A4 hydrolase inhibitors. A combinatorial approach helped to identify inhibitors for sulfotransferases which share structural similarity with nucleotide kinases using a kinase inhibitor core structure as guiding principle.     

The similarity principle underlying social bonding among female rhesus monkeys

Twenty adult female rhesus monkeys (Macaca mulatta) were observed over a three-year period. They lived in a mixed captive group with kinship relations known for three generations. The study's aim was to test Seyfarth's [J. theor. Biol. 65: 671-698, 1977] model of rank-related grooming and to investigate two other possible determinants of social bonding, i.e. relative age and the group's stratification into two social classes. Data on affiliation, coalitions, and social competition were collected by means of both focal observation and instantaneous time sampling. Whereas certain elements of the existing model were confirmed, its explanatory principles were not. Social competition did not result in more contact among close-ranking females (the opposite effect was found), and the relation between affiliative behavior and coalitions was more complex than predicted. Based on multivariate analyses and a comparison of theoretical models, we propose a simpler, more encompassing principle underlying interfemale attraction. According to this 'similarity principle', rhesus females establish bonds with females whom they most resemble. The similarity may concern genetical and social background, age, hierarchical position and social class. Effects of these four factors were independently demonstrated. The most successful model assumed that similarity factors influence female bonding in a cumulative fashion.     

Mammalian RNAi: a practical guide

Silencing of gene expression by RNA interference (RNAi) has become a powerful tool for the functional annotation of the Caenorhabditis elegans and Drosophila melanogaster genomes. Recent advances in the design and delivery of targeting molecules now permit efficient and highly specific gene silencing in mammalian systems as well. RNAi offers a simple, fast, and cost-effective alternative to existing gene targeting technologies both in cell-based and in vivo settings. Synthetic small interfering RNA (siRNA) and retroviral short hairpin RNA (shRNA) libraries targeting thousands of human and mouse genes are publicly available for high-throughput genetic screens, and knockdown animals can be rapidly generated by lentivirus-mediated transgenesis. RNAi also holds great promise as a novel therapeutic approach. This review provides insight into the current gene silencing techniques in mammalian systems.     

Mammalian hybrid zones: a review

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Mammalian meiotic recombination: a reexamination

Recombination nodules (RNs) are small electron-dense structures associated with the synaptonemal complex. Two types have been identified: early RNs present during zygonema-early pachynema, which are thought to be involved in gene conversion and synaptic initiation, and late RNs present during mid-to-late pachynema, which are thought to be involved in reciprocal recombination leading to chiasma formation. In organisms as diverse as Sodaria, Drosophila, and plants there is indeed a close correlation between the observed number of late RNs and crossovers, or their cytogenetic manifestation, chiasmata. However, as this reexamination of the human data shows, there is not a similar correlation in mammals. Instead, there is a severe deficiency in RNs in eutherian males and marsupial females near chromosome ends and other recombinational hot spots (defined genetically), or localized chiasmata (defined cytogenetically). Many of these sites of hyper-recombination correspond to sites of telomere or telomere-associated sequences. Together these observations suggest the possibility of a second, mechanistically different, recombination pathway that does not involve RNs, but may directly involve telomere or telomere-associated sequences. This pathway may be responsible for sex-specific hot-spots of recombination observed at highly localized sites throughout the genome.