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On the evolution of the physiological model.

Most of us who have concerned ourselves with models can perceive outlines like those above to catalog the future evolution of the expository function of models. In the context of a single class of computerized mathematical models of respiratory physiology, we can observe at once the burgeoning interest among scientists, and the similarities between model activity and the general organization of scientific information for use. Although physiological models have become quite advanced in their subject control, there is relatively little coordinated activity in the mechanization of the purposes and philosophical potential of automata. The outlines, however, are visible. An assiduous pursuit of the notion of "explanation" by machine is a major evolutionary step next to occur. It appears to us that various diagrams similar to Figures 5 or 6 can be created and investigated in terms of their relation to the human mind and in terms of formalizing rules for traversing from one plane to the next. The evolution of models will require program-making programs which can decide when and how to aggregate for deductive inference, and how far to penetrate top-down for explanation. The rules for identifying "second order" effects must be established. The decision to ignore or use these rules will be crucial. These are the means whereby the systems are traversed from plane to plane. In a word, models need to synthesize the means to ignore, "forget," and gloss over; only then will we have useful tools for taking informed action in physiology, diagnosis in medicine, or the writing of "scholarly" reviews.

Computers↗

A 60-year tale of spots, maps, and genes.

This is an account of almost 60 years' experience in the clinical delineation of genetic disorders, mapping genes on chromosomes, and cataloging human disease-related genes and genetic disorders. The origins of medical genetics as a clinical specialty, of the Human Genome Project, of genomics (including the term), and of HUGO are recounted.

Chromosome Mapping↗

The cytoskeleton of trypanosomatid parasites.

Species of the trypanosomatid parasite genera Trypanosoma and Leishmania exhibit a particular range of cell shapes that are defined by their internal cytoskeletons. The cytoskeleton is characterized by a subpellicular corset of microtubules that are cross-linked to each other and to the plasma membrane. Trypanosomatid cells possess an extremely precise organization of microtubules and filaments, with some of their organelles, such as the mitochondria, kinetoplasts, basal bodies, and flagella, present as single copies in each cell. The duplication of these structures and changes in their position during life cycle differentiations provide markers and insight into events involved in determining cell form and division. We have a rapidly increasing catalog of these structures, their molecular cytology, and their ontogeny. The current sophistication of available molecular genetic techniques for use in these organisms has allowed a new functional analysis of the cytoskeleton, including functions that are intrinsic to the proliferation and pathogenicity of these parasites.

Animals↗

ALGINATE LYASE: review of major sources and enzyme characteristics, structure-function analysis, biological roles, and applications.

Alginate lyases, characterized as either mannuronate (EC 4.2.2.3) or guluronate lyases (EC 4.2.2.11), catalyze the degradation of alginate, a complex copolymer of alpha-L-guluronate and its C5 epimer beta-D-mannuronate. Lyases have been isolated from a wide range of organisms, including algae, marine invertebrates, and marine and terrestrial microorganisms. This review catalogs the major characteristics of these lyases, the methods for analyzing these enzymes, as well as their biological roles. Analysis of primary sequence data identifies some markedly conserved motifs that should help elucidate functional domains. Information about the three-dimensional structure of a mannuronate lyase from Sphingomonas sp., combined with various mutagenesis studies, has identified residues that are important for catalytic activity in several lyases. Characterization of alginate lyases will enhance and expand the use of these enzymes to engineer novel alginate polymers for applications in various industrial, agricultural, and medical fields. In this review, we explore both past and present applications of this important enzyme and discuss its future prospects.

Alginates↗

Microbial communities and their interactions in soil and rhizosphere ecosystems.

Since the first estimate of prokaryotic abundance in soil was published, researchers have attempted to assess the abundance and distribution of species and relate this information on community structure to ecosystem function. Culture-based methods were found to be inadequate to the task, and as a consequence a number of culture-independent approaches have been applied to the study of microbial diversity in soil. Applications of various culture-independent methods to descriptions of soil and rhizosphere microbial communities are reviewed. Culture-independent analyses have been used to catalog the species present in various environmental samples and also to assess the impact of human activity and interactions with plants or other microbes on natural microbial communities. Recent work has investigated the linkage of specific organisms to ecosystem function. Prospects for increased understanding of the ecological significance of particular populations through the use of genomics and microarrays are discussed.

Archaea↗

Pervasive media violence.

In this review, we focus our discussion on studies examining effects on children and young adults. We believe that the current epidemic of youth violence in the United States justifies a focus on this vulnerable segment of society. We consider media effects on individual children's behaviors, such as imitating aggressive acts. In addition, we examine how the media influence young people's perceptions of norms regarding interpersonal relationships. Next, we assess mass media effects on societal beliefs, or what children and adolescents think the "real world" is like. We suggest these media influences are cumulative and mutually reinforcing, and discuss the implications of repeated exposure to prominent and prevalent violent media messages. Finally, we catalog multiple intervention possibilities ranging from education to regulation. From a public health perspective, therefore, we evaluate the effects that pervasive media messages depicting violence have on young people and present multiple strategies to promote more healthful outcomes.

Adolescent↗

Antibiotic prophylaxis in vascular and interventional radiology: a rational approach.

The current medical and surgical literature was reviewed to determine the rationale for the use of prophylactic antibiotics during surgical procedures. Specifically, the experimental basis for the timing and duration of administration of the antibiotics was considered, and the expected pathogens in each type of surgery were cataloged. High-risk patient groups were identified. The risk of infectious complications during interventional radiologic procedures was reviewed, and appropriate choices of drugs were determined by analogy to the corresponding surgical procedures.

Angiography↗

Gene expression studies using microarrays: principles, problems, and prospects.

A number of mammalian genomes having been sequenced, an important next step is to catalog the expression patterns of all transcription units in health and disease by use of microarrays. Such discovery programs are crucial to our understanding of the gene networks that control developmental, physiological, and pathological processes. However, despite the excitement, the full promise of microarray technology has yet to be realized, as the superficial simplicity of the concept belies considerable problems. Microarray technology is very new; methodologies are still evolving, common standards have yet to be established, and many problems with experimental design and variability have still to be fully understood and overcome. This review will describe the time course of a microarray experiment-RNA isolation from sample, target preparation, hybridization to the microarray probe, data capture, and bioinformatic analysis. For each stage, the advantages and disadvantages of competing techniques are compared, and inherent sources of error are identified and discussed.

Animals↗

Regulation of Triglyceride Metabolism. III. Emerging role of lipid droplet protein ADFP in health and disease.

ADFP is the major lipid droplet protein present in all cells that accumulate lipids either normally or abnormally. Although discovered about 15 years ago, it was only in the last few years that we began to have a working knowledge of its possible role in lipid droplet homeostasis at the whole organism level. In this perspective, we concentrate on the potential function of ADFP in various tissues. Space limitation has precluded a complete cataloging of all publications on the topic. We instead highlight some of the salient developments in the last few years.

Adipose Tissue↗

AIDS-related vasculopathy: evidence for oxidative and inflammatory pathways in murine and human AIDS.

Increased life expectancy of human immunodeficiency virus (HIV)-positive patients has led to evidence of complications apparently not directly related to immunodeficiency or opportunistic infection, including increased cardiovascular risk. We tested the hypothesis that vascular dysfunction occurs in the murine acquired immune deficiency syndrome (AIDS) model and evaluated potential mechanisms in murine AIDS tissues and relevant human HIV/AIDS vascular tissues. We also investigated endothelial activation and/or endothelial protein nitration and their association with time-dependent vascular dysfunction. At 1 and 5 wk of murine AIDS, statistically significant decreases in KCl contractility and time-dependent contractile deficits in response to phenylephrine were observed. The maximal response (E(max)) was reduced by approximately 40% at 10 wk, and EC(50) values were significantly changed: 102 +/- 7.3 ng for control vs. 190 +/- 37 and 130 +/- 22 ng at 5 and 10 wk, respectively (P < 0.05). Endothelium-dependent relaxation to ACh was decreased (EC(50) = 120 +/- 27 and 343 +/- 94 nM for control and at 10 wk, respectively), whereas the response to an exogenous nitric oxide donor, sodium nitroprusside, remained unchanged, suggesting a specific endothelial dysfunction. Histochemical investigations of the same vascular tissues as well as corresponding coronary endothelium showed an increase in protein 3-nitrotyrosine, intercellular adhesion molecule, and nitric oxide synthase isoforms 2 and 3. These findings were corroborated in concurrent experiments in a cohort of well-cataloged human cardiac microvascular tissues. We have demonstrated, for the first time, a specific functional vasculopathy with endothelial involvement in a murine model of AIDS that was also associated with and correlated to increased oxidative stress and specific endothelial activation. This finding was echoed in a relevant population of human HIV/AIDS patients. Research into sources and intracellular targets of oxidants in this disease could provide important mechanistic insights and may reveal new therapeutic opportunities for this increasingly important cardiovascular disease state.

Acquired Immunodeficiency Syndrome↗

Airway branching morphology of mature and immature rabbit lungs.

The scheme of Horsfield et al. for describing the pulmonary airway tree (J Appl Physiol 52: 21-26, 1982) catalogs each airway according to its order and the difference in order of its two daughters (denoted Delta). Although this scheme captures the natural asymmetry in the airway tree, it is still deterministic, because it assumes that all airways of a given order are the same; yet such variability is extremely important in determining the overall behavior of the lungs. We therefore analyzed complete lung lobes from three mature and two immature rabbits and determined the Horsfield order and Delta of every airway down to the terminal bronchioles. We also measured the diameter of each airway. This allowed us to determine the average structure of the rabbit airway tree, the variation about this average, and also how the structures of mature and immature airway trees compare. We found some variation in branching asymmetry and airway diameter at a given order between animals but no evidence of systematic differences in structure between mature and immature lungs. We found evidence of a difference in the branching structure of the peripheral vs. the central part of the airway tree (the break point being around order 20). We also determined the nature of the variation in Delta and diameter as a function of order, which should be valuable for the development of computer models seeking to encapsulate the naturally occurring regional variation in airway geometry in the normal rabbit lung.

Animals↗

DNA microarray analysis of vitamin D-induced gene expression in a human colon carcinoma cell line.

The full extent to which 1,25-dihydroxyvitamin D(3) affects gene expression in human intestinal epithelial cells is unknown. We used oligonucleotide arrays to catalog vitamin D-induced changes in gene expression in Caco-2 cells, a human colon carcinoma cell line. Five paired sets of Caco-2 cell cultures were subjected to either control conditions or 1,25-dihydroxyvitamin D (10(-7) mol/l x 24 h), and RNA was analyzed on an Affymetrix cDNA array containing 12,625 human sequences. Only 13 sequences representing 12 distinct genes exhibited statistically significant changes in expression of twofold or greater and were also called as "present" or "marginal" by the array-reading software in all five experiments. Genes regulated by 1,25-dihydroxyvitamin D included two previously known genes (25-hydroxyvitamin D-24-hydroxylase and amphiregulin) and 10 genes (sorcin, Gem, adaptin-gamma, TIG1, CEACAM6, carbonic anhydrase XII, junB, ceruloplasmin, and two unidentified sequences) that were novel. We tested and independently confirmed the effect of 1,25-dihydroxyvitamin D on 11 of these genes by RT-PCR. Increased protein expression was tested and confirmed in two of the novel 1,25-dihydroxyvitamin D-regulated genes, ceruloplasmin and sorcin. The known function of these genes suggests that many of them could be involved in the antiproliferative effects of 1,25-dihydroxyvitamin D3.

Caco-2 Cells↗

Novel and nondetected human signaling protein polymorphisms.

The frequency of single nucleotide polymorphisms (SNPs) in downstream signaling proteins was determined by combination heteroduplex HPLC and double-stranded sequencing of genomic DNA from 96-144 congestive heart failure (CHF) patients. Analysis of 56 coding exons in 9 signaling genes revealed 17 novel and 8 previously reported synonymous (no change in amino acid) SNPs, as well as one novel nonsynonymous SNP in the Rad small G protein. Because this initial analysis failed to detect numerous SNPs reported in the NCBI and Celera databases, double-strand sequencing of relevant exons from 74-91 CHF patients was used to confirm the absence of 10 previously reported nonsynonymous SNPs. Our results show that synonymous SNPs are frequent in signaling protein genes, whereas nonsynonymous SNPs are rare, suggesting a high degree of evolutionary conservation among these downstream signaling molecules. Comparisons of our results to the NCBI and Celera databases indicates that 56% of their SNP entries are not detected in our cohort. Importantly, while 31% of database SNPs were verified, 69% of SNPs detected in our cohort are not included in these databases. These findings indicate that caution may be warranted in relying exclusively on SNP databases as catalogs for polymorphic signaling protein genes.

Age of Onset↗

Quest for arthritis-causative genetic factors in the rat.

Experimental rat models of arthritis are extensively studied with a view to understand the genetic underpinnings of rheumatoid arthritis (RA). Genome scans using these models have led to the detection of arthritis regulatory quantitative trait loci (QTLs) on all but three chromosomes of the rat. Whereas some of the QTLs are model specific, others overlap between models. Some arthritis susceptibility and/or severity QTLs identified by genetic linkage analyses are corroborated by substitution mapping using congenic strains, whereas others are not. In these cases, testing alternate arthritis models proved to be useful to identify QTL effects. Nevertheless, development and testing of congenic substrains containing progressively shorter introgressed regions have not only fine mapped the location of the arthritis QTLs but also resulted in the identification of multiple QTLs within several originally identified individual QTL. Most of these studies progressed rapidly since 2001, when the rat genome sequence was published. Proof of principle for substitution mapping as a successful method for QTL gene discovery is provided by the positional cloning of Ncf1 as one of the arthritis QTLs in rats. This finding is encouraging for similar sustained dissection of all the other arthritis QTLs mapped in the rat. Identification of rat arthritis QTLs is expected to pave the way for discovery of yet-unidentified arthritis-causative genetic elements and/or pathways for RA in humans and potential development of targeted therapeutics. This review catalogs some of the recent advances made in QTL discovery projects of experimentally induced rat models of arthritis.

Animals↗

Effect of hypoxia on gene expression by human hepatocytes (HepG2).

The full extent to which hypoxia produces gene expression changes in human cells is unknown. We used late-generation oligonucleotide arrays to catalog hypoxia-induced changes in gene expression in HepG2 cells. Five paired sets of cultures were subjected to either control (room air-5% CO(2)) or hypoxic (1% O(2)-5% CO(2)) conditions for 24 h, and RNA was analyzed on an Affymetrix cDNA array containing approximately 12,600 sequences. A statistically significant change in expression was shown by 2,908 sequences (1,255 increased and 1,653 decreased). The observed changes were highly concordant with published literature on hypoxic stress but showed relatively little overlap (12-22%) with changes in gene expression that have been reported to occur after heat stress in other systems. Of note, of these 2,908 sequences, only 387 (213 increased and 174 decreased) both exhibited changes in expression of twofold or greater and were highly expressed in at least three of the five experiments. We conclude that the effect of hypoxia on gene expression by HepG2 cells is broad, has a significant component of downregulation, and includes a relatively small number of genes whose response is truly independent of cell and stress type.

Carcinoma, Hepatocellular↗

Genetic Basis of Pancreatic Steatosis: A Systematic Review of Comparison between African and Non-African Populations.

This systematic review compared genetic evidence of pancreatic steatosis across African and non-African populations to illuminate ancestry-specific mechanisms and precision-prevention opportunities. Following PRISMA guidelines for reporting, a search was conducted across PubMed, Scopus, Web of Science, and NHGRI-EBI GWAS Catalog for studies spanning 2011 to 31st March 2026. Eligible studies included genome-wide association studies (GWAS), polygenic risk score (PRS), and Mendelian randomization (MR) analyses that reported genetic associations with pancreatic fat phenotypes and had explicit ancestry stratification or comparison. Narrative thematic synthesis was performed due to methodological heterogeneity. Six core genetic studies (N > 120,000 participants) were included. The only multi-ethnic GWAS found a strong protective variant of African ancestry, rs73449607 (near PDX1/PLUTO), which reduced pancreatic fat (&#x3b2; = -0.67, P = 4.50 &#xd7; 10&#x207b;&#x2078;) and explained 14.3% of the variance in African Americans (versus 5.3% overall). UK Biobank race-stratified PRS analyses confirmed the lowest pancreatic fat fraction in Black participants, with the strongest HbA1c PRS-fat association in this group (&#x3c1; = 0.23, P < 0.0001). European-dominant GWAS highlighted risk loci, including FUT2 rs601338 (higher fat and chronic pancreatitis risk, OR 1.26). MR studies demonstrated causal links between genetically predicted intra-pancreatic fat deposition (IPFD) and pancreatic ductal adenocarcinoma (PDAC) (OR 2.46 per SD) but not diabetes. African-ancestry genomes confer substantial protection against pancreatic steatosis, whereas non-African genomes are enriched for risk alleles that amplify the non-alcoholic fatty pancreas disease (NAFPD)-to-PDAC cascade. These ancestry-differentiated mechanisms position NAFPD as a precision medicine target.

Africa↗

Mapping cis-acting regulatory variation in recombinant congenic strains.

We present an integrated approach for the enriched detection of genes subject to cis-acting variation in the mouse genome. Gene expression profiling was performed with lung tissue from a panel of recombinant congenic strains (RCS) derived from A/J and C57BL/6J inbred mouse strains. A multiple-regression model measuring the association between gene expression level, donor strain of origin (DSO), and predominant strain background identified over 1,500 genes (P < 0.05) whose expression profiles differed according to the DSO. This model also identified over 1,200 genes whose expression showed dependence on background (P < 0.05), indicating the influence of background genetic context on transcription levels. Sequences obtained from 1-kb segments of 3'-untranslated regions identified single nucleotide polymorphisms in 64% of genes whose expression levels correlated with DSO status, compared with 29% of genes that displayed no association (P < 0.01, Fisher exact test). Allelic imbalance was identified in 50% of genes positive for expression-DSO association, compared with 22% of negative genes (P < 0.05, Fisher exact test). Together, these results demonstrate the utility of RCS mice for identifying the roles of proximal genetic determinants and background genetic context in determining gene expression levels. We propose the use of this integrated experimental approach in multiple tissues from this and other RCS panels as a means for genome-wide cataloging of genetic regulatory mechanisms in laboratory strains of mice.

Allelic Imbalance↗

Molecular profiling of murine sensory neurons in the nodose and dorsal root ganglia labeled from the peritoneal cavity.

Vagal afferent neurons are thought to convey primarily physiological information, whereas spinal afferents transmit noxious signals from the viscera to the central nervous system. To elucidate molecular identities for these different properties, we compared gene expression profiles of neurons located in nodose ganglia (NG) and dorsal root ganglia (DRG) in mice. Intraperitoneal administration of Alexa Fluor-488-conjugated cholera toxin B allowed enrichment for neurons projecting to the viscera. Fluorescent neurons in DRG (from T10 to T13) and NG were isolated using laser-capture microdissection. Gene expression profiles of these afferent neurons, obtained by microarray hybridization, were analyzed using multivariate spectral map analysis, significance analysis of microarrays (SAM) algorithm, and fold-difference filtering. A total of 1,996 genes were differentially expressed in DRG vs. NG, including 41 G protein-coupled receptors and 60 ion channels. Expression profiles obtained on laser-captured neurons were contrasted to those obtained on whole ganglia, demonstrating striking differences and the need for microdissection when studying visceral sensory neurons because of dilution of the signal by somatic sensory neurons. Furthermore, we provide a detailed catalog of all adrenergic and cholinergic, GABA, glutamate, serotonin, and dopamine receptors; voltage-gated potassium, sodium, and calcium channels; and transient receptor potential cation channels present in afferents projecting to the peritoneal cavity. Our genome-wide expression profiling data provide novel insight into molecular signatures that underlie both functional differences and similarities between NG and DRG sensory neurons. Moreover, these findings will offer novel insight into mode of action of pharmacological agents modulating visceral sensation.

Animals↗