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At least 199 records · Page 11Linked to original sources

Galaxy: a platform for interactive large-scale genome analysis.

Accessing and analyzing the exponentially expanding genomic sequence and functional data pose a challenge for biomedical researchers. Here we describe an interactive system, Galaxy, that combines the power of existing genome annotation databases with a simple Web portal to enable users to search remote resources, combine data from independent queries, and visualize the results. The heart of Galaxy is a flexible history system that stores the queries from each user; performs operations such as intersections, unions, and subtractions; and links to other computational tools. Galaxy can be accessed at http://g2.bx.psu.edu.

Biological Evolution↗

Making better babies: public health and race betterment in Indiana, 1920-1935.

In 1920, Indiana's Division of Infant and Child Hygiene inaugurated its first Better Babies Contest at the state fair. For the next 12 years, these contests were the centerpiece of a dynamic infant and maternal welfare program that took shape in Indiana during the decade of the federal Sheppard-Towner act. More than just a lively spectacle for fairgoers, these contests brought public health, "race betterment," and animal breeding together in a unique manner. This article describes one of the most popular expressions of public health and race betterment in rural America. It also raises questions about the intersections between hereditarian and medical conceptions of human improvement during the early 20th century, especially with respect to child breeding and rearing.

Child Welfare↗

Neurogenomics: at the intersection of neurobiology and genome sciences.

Neurogenomics is the study of how the genome as a whole contributes to the evolution, development, structure and function of the nervous system. It includes investigations of how genome products (transcriptomes and proteomes) vary in time and space. Neurogenomics differs markedly from the application of genome sciences to other systems, particularly in the spatial category, because anatomy and connectivity are paramount to our understanding of function in the nervous system. We focus here on some of the influences of genomics and its associated technologies on neuroscience. We discuss comparative genomics, gene expression atlases of the brain, network genetics and applications to behavioral phenotypes, and consider the culture, organization and funding of genome-scale projects.

Animals↗

MarkerMatch: A Proximity-Based Probe-Matching Algorithm for Joint Analysis of Copy-Number Variants from Different Genotyping Arrays.

MOTIVATION: Copy-number variants (CNVs) are a form of genetic structural variation with increasing importance in complex human disorders. Both DNA sequencing and microarray data can be used to call CNVs, which can be used in association tests, such as association between CNV number and disease status. Unlike genotypes, CNV detection in microarrays requires the use of observed intensity signals at each probe, which limits the imputability for analyses that span multiple array types. Thus far, a consensus set of probes (the intersection encompassing the probes that occur in common on all arrays) has been used to circumvent the problem of differing array-specific sensitivities. This has, however, led to excessive reduction in overall sensitivity of CNV calls as arrays can have an undesirably low overlap of probe sets. To overcome this limitation, we developed MarkerMatch, a proximity-based algorithm that matches probes across different genotyping microarrays to maximize the number of probes considered in the CNV calling algorithm, thereby increasing the resolution and sensitivity while preserving precision. RESULTS: By analyzing CNV calls from 4,906 individuals genotyped across three different arrays (Global Screening Array, Omni2.5 array, and Omni Express Exome array), we show that the MarkerMatch approach improves sensitivity by increasing the density of probes available for CNV calling while maintaining precision or improving it relative to the current practice (e.g., use of consensus probes only). We further demonstrate that MarkerMatch exceeds the output from current practice in terms of F1 score, Fowlkes-Mallows index, and Jaccard index. We also optimize MarkerMatch parameters, D MAX and Method, and find an optimal D MAX setting at 10kb, with no clear optimal candidate based on Method, indicating that parameters for this metric should be determined on a use case basis.

Journal Article↗

The pathogenic classification of glaucomas.

On the basis of a pathogenic definition, our classification distinguished for each of the first intersections a main--mostly determinant mechanism and a secondary mechanism, mostly modulating the damages: hydrodynamic alteration and tissue resistance alteration--for the second intersection, outflow block and hypersecretion--for the third. Reflecting the state of present knowledge, from the corresponding forms of the disease, only outflow block glaucoma is completely analysed, the exogenous, trabecular, pretrabecular and mixed glaucomas being described. In order to permit the correct framing of all pretrabecular block glaucomas, the posterior push forms (retrovitreal or parietal) were introduced besides the anterior already described forms (pupillary or angular). As for low tissue resistance glaucomas, genetic, cardiovascular, metabolic, haematologic and ocular influences are mentioned. This classification avoids the theoretical inadvertencies of previous classifications offering the synthetic frame of a coherent system, open to any new developments, all inclusive, terminologically clear and with direct therapeutic references.

Glaucoma↗

Matrix metalloproteinase-9 is required for adequate angiogenic revascularization of ischemic tissues: potential role in capillary branching.

Angiogenesis, an essential component of a variety of physiological and pathological processes, offers attractive opportunities for therapeutic regulation. We hypothesized that matrix metalloproteinase-9 genetic deficiency (MMP-9-/-) will impair angiogenesis triggered by tissue ischemia, induced experimentally by femoral artery ligation in mice. To investigate the role of MMP-9, we performed a series of biochemical and histological analyses, including zymography, simultaneous detection of perfused capillaries, MMP-9 promoter activity, MMP-9 protein, and macrophages in MMP-9-/- and wild-type (WT) mice. We found that ischemia resulted in doubling of capillary density in WT and no change in the MMP-9-/- ischemic tissues, which translated into increased (39%) perfusion capacity only in the WT at 14 days after ligation. We also confirmed that capillaries in the MMP-9-/- presented significantly (P<0.05) less points of capillary intersections, interpreted by us as decreased branching. The combined conclusions from simultaneous localizations of MMP-9 expression, capillaries, and macrophages suggested that macrophage MMP-9 participates in capillary branching. Transplantation of WT bone marrow into the MMP-9-/-, restored capillary branching, further supporting the contribution of bone marrow-derived macrophages in supplying the necessary MMP-9. Our study indicates that angiogenesis triggered by tissue ischemia requires MMP-9, which may be involved in capillary branching, a potential novel role for this MMP that could be exploited to control angiogenesis.

Animals↗

Effects of growth hormone on intestinal morphology of genetically dwarf rats.

Three groups of Lewis rat were studied: dwarf rats, genetically deficient in growth hormone; rehabilitated dwarf rats treated with exogenous growth hormone (GH); and normal wild-type rats. The small intestine of each animal was removed and simple random transverse sections were taken from the proximal and distal regions. The profile areas of villi, crypt and muscle were estimated by point count analysis and combined with intestinal length measurements to obtain absolute volumes. Villus and primary mucosal surface areas were estimated from intersection counts and linear measurements were made of epithelial cell height. Distally, villous volume and surface area were reduced by 42% and 39%, respectively, in the dwarfs compared with controls. These features were significantly smaller (P < 0.01) in dwarfs distally than proximally. Crypt volume and epithelial cell height were decreased equally in both proximal and distal regions of the intestine of dwarf rats. Following GH administration both features increased, crypt volume overshooting control values. These results indicate that GH deficiency has a subtle effect on intestinal morphology and that the intestine is more sensitive distally than proximally. Reconstitution with GH is capable of reversing many of these changes.

Animals↗

Perturbations of the AKT signaling pathway in human cancer.

AKT/PKB (protein kinase B) kinases mediate signaling pathways downstream of activated tyrosine kinases and phosphatidylinositol 3-kinase. AKT kinases regulate diverse cellular processes including cell proliferation and survival, cell size and response to nutrient availability, tissue invasion and angiogenesis. Many oncoproteins and tumor suppressors implicated in cell signaling/metabolic regulation converge within the AKT signal transduction pathway in an equilibrium that is altered in many human cancers by activating and inactivating mechanisms, respectively, targeting these inter-related proteins. We review a burgeoning literature implicating aberrant AKT signaling in many sporadic human cancers as well as in several dominantly inherited cancer syndromes known as phakomatoses. The latter include disorders caused by germline mutations of certain tumor suppressor genes, that is, PTEN, TSC2/TSC1, LKB1, NF1, and VHL, encoding proteins that intersect with the AKT pathway. We also review various pathogenic mechanisms contributing to activation of the AKT pathway in human malignancy as well as current pharmacologic strategies to target therapeutically components of this pathway.

Cell Proliferation↗

High-resolution genomic profiles of human lung cancer.

Lung cancer is the leading cause of cancer mortality worldwide, yet there exists a limited view of the genetic lesions driving this disease. In this study, an integrated high-resolution survey of regional amplifications and deletions, coupled with gene-expression profiling of non-small-cell lung cancer subtypes, adenocarcinoma and squamous-cell carcinoma (SCC), identified 93 focal copy-number alterations, of which 21 span <0.5 megabases and contain a median of five genes. Whereas all known lung cancer genes/loci are contained in the dataset, most of these recurrent copy-number alterations are previously uncharacterized and include high-amplitude amplifications and homozygous deletions. Notably, despite their distinct histopathological phenotypes, adenocarcinoma and SCC genomic profiles showed a nearly complete overlap, with only one clear SCC-specific amplicon. Among the few genes residing within this amplicon and showing consistent overexpression in SCC is p63, a known regulator of squamous-cell differentiation. Furthermore, intersection with the published pancreatic cancer comparative genomic hybridization dataset yielded, among others, two focal amplicons on 8p12 and 20q11 common to both cancer types. Integrated DNA-RNA analyses identified WHSC1L1 and TPX2 as two candidates likely targeted for amplification in both pancreatic ductal adenocarcinoma and non-small-cell lung cancer.

Carcinoma, Non-Small-Cell Lung↗

Pervasive developmental disorders in Prader-Willi syndrome: the Leuven experience in 59 subjects and controls.

In the present study we investigated the co-morbidity of pervasive developmental disorder (PDD) in 59 Prader-Willi syndrome (PWS) individuals and in 59 non-specific mentally retarded controls, matched for IQ, gender, and age. The 'Pervasive Developmental Disorder Mentally Retardation Scale' (PDD-MRScale), a screening questionnaire based on the DSM-III-R criteria for PDD, has been applied in the PWS group and in the control group. Results of the present study revealed a striking autistic-like behavioral phenotype in the majority of the PWS individuals, particularly deficits in the quality of language and communication and of imagination and interests. This intersection with autistic symptomatology is an important addition to the behavioral phenotype in PWS persons. A first approach to delineate subtypes of autistic symptomalogy among PWS persons was performed. Nineteen percent of the PWS group did meet the full diagnostic DSM-III-R criteria for PDD in comparison with 15% in the control group. Results revealed that a higher IQ in PWS does not protect to develop genuine PDD and that uniparental disomy/imprinting mutation as genetic origin seems to be an additional risk factor for developing genuine PDD. The results of the present study suggest the importance of reconsidering the commonly recognized obsessive-compulsive like behavior in PWS persons within the broader spectrum of autism disorders.

Adolescent↗

RNAi and related mechanisms and their potential use for therapy.

Introduction of double-stranded RNAs into cells can suppress gene expression by mechanisms such as mRNA degradation or inhibition of translation. In mammalian cells, these two responses intersect, a feature that was recently used for the development of novel tools for stable and specific gene inactivation. These new tools were successfully applied to inhibit tumorigenicity and viral replication. Future development of appropriate in vivo delivery systems may make this technology useful for disease therapy.

Animals↗

Single mRNAs visualized by ultrastructural in situ hybridization are principally localized at actin filament intersections in fibroblasts.

Considerable evidence indicates that mRNA associates with structural filaments in the cell (cytoskeleton). This relationship would be an important mechanism to effect mRNA sorting since specific mRNAs could be sequestered at sites within the cell. In addition, it can provide a mechanism for spatial regulation of mRNA expression. However, the precise structural interactions between mRNA and the cytoskeleton have yet to be defined. An objective of this work was to visualize "individual" poly(A) mRNA molecules in situ by electron microscopy to identify their relationship to individual filaments. Poly(A) RNA and filaments were identified simultaneously using antibodies to detect hybridized probe and filaments or actin-binding proteins. In human fibroblasts, most of the poly(A) mRNA (72%) was localized within 5 nm of orthogonal networks of F-actin filaments. Poly(A) mRNA also colocalized with vimentin filaments (29%) and microtubules (< 10%). The sites of mRNA localization were predominantly at filament intersections. The majority of poly(A) mRNA and polysomes colocalized with the actin crosslinking proteins, filamin, and alpha-actinin, and the elongation factor, EF-1 alpha (actin-binding protein; ABP-50). Evidence that intersections contained single mRNA molecules was provided by using a labeled oligo dT probe to prime the synthesis of cDNA in situ using reverse transcriptase. Both the poly(A) and cis sequences of the same mRNA molecule could then be visualized independently. We propose that the cytoskeletal intersection is a mRNA receptor and serves as a "microdomain" where mRNA is attached and functionally expressed.

Actins↗

Swarming-coupled expression of the Proteus mirabilis hpmBA haemolysin operon.

The HpmA haemolysin toxin of Proteus mirabilis is encoded by the hpmBA locus and its production is upregulated co-ordinately with the synthesis and assembly of flagella during differentiation into hyperflagellated swarm cells. Primer extension identified a sigma(70) promoter upstream of hpmB that was upregulated during swarming. Northern blotting indicated that this promoter region was also required for concomitant transcription of the immediately distal hpmA gene, and that the unstable hpmBA transcript generated a stable hpmA mRNA and an unstable hpmB mRNA. Transcriptional luxAB fusions to the DNA regions 5' of the hpmB and hpmA genes confirmed that hpmB sigma(70) promoter activity increased in swarm cells, and that there was no independent hpmA promoter. Increased transcription of the hpmBA operon in swarm cells was dependent upon a 125 bp sequence 5' of the sigma(70) promoter -35 hexamer. This sequence spans multiple putative binding sites for the leucine-responsive regulatory protein (Lrp), and band-shift assays with purified Lrp confirmed the presence of at least two such sites. The influence on hpmBA expression of the key swarming positive regulators FlhD(2)C(2) (encoded by the flagellar master operon), Lrp, and the membrane-located upregulator of the master operon, UmoB, was examined. Overexpression of each of these regulators moderately increased hpmBA transcription in wild-type P. mirabilis, and the hpmBA operon was not expressed in any of the flhDC, lrp or umoB mutants. Expression in the mutants was not recovered by cross-complementation, i.e. by overexpression of FlhD(2)C(2), Lrp or UmoB. Expression of the zapA protease virulence gene, which like hpmBA is also upregulated in swarm cells, did not require Lrp, but like flhDC it was upregulated by UmoB. The results indicate intersecting pathways of control linking virulence gene expression and swarm cell differentiation.

Amino Acid Sequence↗

The biological "scrabble" of pulmonary arteriovenous malformations: considerations in the setting of cavopulmonary surgery.

Pulmonary arteriovenous fistulas are vascular malformations, which, by virtue of producing abnormal vascular connections proximal to the units of gas exchange, result in intrapulmonary right-to-left shunting. These malformations or fistulas reflect at least in part disordered angiogenesis, and less commonly recruitment and dilation of pre-existing vascular channels. Pulmonary arteriovenous fistulas occur in a number of diverse clinical settings. Such fistulas are a well-established feature of the Weber-Osler-Rendu complex, or hereditary haemorrhagic telangiectasia, an autosomal dominant vascular dysplasia characterized by mucocutaneous telangiectasis, epistaxis, gastrointestinal haemorrhage, and arteriovenous malformations in the lung, brain, liver and elsewhere. They are also seen in the patient with acute or chronic liver disease, disease that is usually but not invariably severe, or those with non-cirrhotic portal hypertension. They may occur as congenital malformations, single or diffuse, large or small in isolation, and when large or extensive enough may result in hypoxaemia, clinical cyanosis, and heart failure. Cerebral vascular accidents are also a well-known complication of this disorder. An extensive literature has accumulated with regard to the pulmonary arteriovenous fistulas seen in the setting of the Weber-Osler-Rendu complex, and there is considerable information on the genetics, basic biology, clinical findings, complications and therapeutic interventions of these malformations in the setting of this syndrome. These issues, however, are not the primary considerations of this review, although some aspects of this fascinating disorder will be discussed later. Rather the focus will be on pulmonary arteriovenous malformations that develop in the setting of cavopulmonary surgery, and their relationship to the pulmonary arteriovenous fistulas occurring in the hepatopulmonary syndrome. The complex tapestry of these overlapping and intersecting clinical observations will be unfolded in the light of their chronology.

Angiography↗

Multiomics: the intersection of personalized nutrition in cardiometabolic diseases.

BACKGROUND: Cardiometabolic diseases are among the leading causes of increasing morbidity and mortality worldwide. However, current population-based dietary recommendations do not sufficiently account for biological differences between individuals and therefore do not have the same effect on everyone. The multiomic approach, which incorporates genomic, epigenomic, transcriptomic, proteomic, metabolomic, and microbiome data, facilitates more accurate classification of disease risk and selection of appropriate nutritional interventions by mapping food-disease relationships across different biological layers. METHODS: Through a narrative synthesis of the current literature, we focused on evidence from multiomic studies to assess their ability to guide personalized nutrition strategies based on individual genetic, metabolic, and microbiome characteristics in cardiometabolic diseases. RESULTS: Recent evidence indicates that metabolomic markers have been reported to provide predictive value in addition to classic risk indicators and to increase the predictive power of models when combined with genetic data. Microbiome research shows that glycemic and lipemic responses can be predicted using algorithms based on gut microbiota. Recent clinical studies show that personalized nutrition plans, which evaluate the microbiome and clinical characteristics together, improve continuous glucose monitoring-based glycemic control, glycated hemoglobin levels, and triglycerides more than the classic Mediterranean diet. CONCLUSION: This review summarizes the current multiomic evidence, discusses the methodological and practical challenges in this field, and highlights future priorities. The integration of digital biomarkers obtained from wearable technologies with multiomic systems and artificial intelligence-supported models, when developed in accordance with ethical and equitable access principles, has the potential to support the transition from the discovery phase to patient-centered clinical applications.

Humans↗

Brassinosteroid signals control expression of the AXR3/IAA17 gene in the cross-talk point with auxin in root development.

Transgenic plants overexpressing AXR3/IAA17 were impaired in root growth. Specifically, they exhibited severe defects in lateral root and root hair development similar to the root phenotypes of epi-brassinolide (epiBL)-treated wild-type plants. Here, we investigated the involvement of AXR3/IAA17 gene expression in brassinosteroid (BR)-regulated root development. Exogenous epiBL application significantly induced expression of the AXR3/IAA17 gene as well as several Aux/IAA genes, such as AXR2/IAA7, SLR/IAA14, and IAA28. We analyzed the transcription levels of several Aux/IAA genes related to root development in the BR signaling mutant bri1 and the BR biosynthesis mutant det2. AXR3/IAA17 gene expression was significantly decreased in bri1 plants. In det2 plants, expression of AXR3/IAA17 slightly decreased. This in turn suggests that epiBL induced these Aux/IAA genes, and that these induced gene products might function as factors in root development. Furthermore, AXR3/IAA17 might be involved in the BR signaling pathway, suggesting an intersection node of BR-auxin signaling in root development.

Arabidopsis↗

Are phospholipid-binding antibodies implicated in the pathogenesis of diabetic microangiopathy?

Diabetic retinopathy (DR) is a major cause of blindness in the working population of the Western world and there is no doubt that its prevalence is strongly related to the duration of diabetes and the glycemic control. However, although intensive diabetes management, with the goal of achieving near-normal glycemia, has been shown to prevent and/or delay the onset of DR, there is now ample of evidence that the development of this microangiopathy is a multifactorial process in which genetic, metabolic, haemostatic and growth factors play an important role. Moreover, given the suggestions that immunological mechanisms might have a role in the pathogenesis of diabetic microangiopathy via immune complex deposition, it has been hypothesized that antiphospholipid antibodies (A-Ab) directed against endothelial antigens could be responsible for initiating vascular injury. In particular, not only A-Ab production was found to be increased in patients with overt nephropathy or macroangiopathy but also Lupus Anticoagulant positivity, representing an intersection point between immune and haemostatic alterations, has been highlighted as a potential and additional risk factor in the pathogenesis of microangiopathy in type 1 diabetics. Moreover, given the high levels of activated protein C, endothelin-1 and thrombo-modulin that have been observed in normo-albuminuric and uncomplicated patients, it has been concluded that the vascular endothelium shifts pathologically from an antithrombotic to a prothrombotic state even in the early phases of the disease. This condition was found to be more pronounced in subjects with anticardiolipin positivity and/or high circulating immune complexes concentrations, since they possess the ability not only to induce platelet activation and aggregation but also to activate the complement system via the classical pathway. Therefore, a potential synergism between generation of autoantibodies, haemostatic alterations and endothelial stress has been suggested, a stimulating hypothesis that needs further studies to be clarified in its complexity.

Antibodies, Antiphospholipid↗

Lymphoid enhancer factor-1 links two hereditary leukemia syndromes through core-binding factor alpha regulation of ELA2.

Two hereditary human leukemia syndromes are severe congenital neutropenia (SCN), caused by mutations in the gene ELA2, encoding the protease neutrophil elastase, and familial platelet disorder with acute myelogenous leukemia (AML), caused by mutations in the gene AML1, encoding the transcription factor core-binding factor alpha (CBFalpha). In mice, CBFalpha regulates the expression of ELA2, suggesting a common link for both diseases. However, gene-targeted mouse models have failed to reproduce either human disease, thus prohibiting further in vivo studies in mice. Here we investigate CBFalpha regulation of the human ELA2 promoter, taking advantage of bone marrow obtained from patients with either illness. In particular, we have identified novel ELA2 promoter substitutions (-199 C to A) within a potential motif for lymphoid enhancer factor-1 (LEF-1), a transcriptional mediator of Wnt/beta-catenin signaling, in SCN patients. The LEF-1 motif lies adjacent to a potential CBFalpha binding site that is in a different position in human compared with mouse ELA2. We find that LEF-1 and CBFalpha co-activate ELA2 expression. In vitro, the high mobility group domain of LEF-1 interacts with the runt DNA binding and proline-, serine-, threonine-rich activation domains of CBFalpha. ELA2 transcript levels are up-regulated in bone marrow of an SCN patient with the -199 C to A substitution. Conversely, a mutation of the CBFalpha activation domain, found in a patient with familial platelet disorder with AML, fails to stimulate the ELA2 promoter in vitro, and bone marrow correspondingly demonstrates reduced ELA2 transcript. Observations in these complementary patients indicate that LEF-1 cooperates with CBFalpha to activate ELA2 in vivo and also suggest the possibility that up-regulating promoter mutations can contribute to SCN. Two hereditary AML predisposition syndromes may therefore intersect via LEF-1, potentially linking them to more generalized cancer mechanisms.

Animals↗