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At least 307 records · Page 17Linked to original sources
PubMed1995

Isolation and functional characterization of the human gene encoding the myeloid zinc finger protein MZF-1.

The expression of the human myeloid zinc finger gene (MZF-1) by human bone marrow cells is necessary for granulopoiesis. We have analyzed the structure and function of the MZF-1 gene by diagnostic polymerase chain reaction, genomic cloning, and promoter analysis. Comparison of human promyelocytic HL-60 cell cDNA with isolated MZF-1 genomic clones indicated that the human MZF-1 gene is without introns and spans approximately 3 kb. Restriction enzyme mapping and Southern analysis indicated further that the human MZF-1 gene is a single-copy gene. Primer extension studies identified the major transcription start site as a thymidine residue located 1102 bp upstream of the ATG translation start codon. A putative TATA box sequence (TAAAAA) was found at -66 bp and a CCAAT box at -130 bp relative to the transcription initiation site. In HL-60 cells, MZF-1 mRNA levels are increased by granulopoietic inducers including retinoic acid and GM-CSF. DNA upstream of the transcription start site contains tandem-repeated consensus retinoic acid response elements at -666 through -696 bp and paired putative GM-CSF-responsive sequences centered at -50 and -100 bp. CAT reporter gene constructs containing these DNA regions promoted transcription and conferred transcriptional responsiveness to retinoic acid and GM-CSF when transfected into HL-60 cells. Additional putative regulatory binding sites included conserved MZF-1 zinc finger binding sequences, the importance of which was suggested by the enhanced expression of the endogenous MZF-1 gene following vector-driven expression of MZF-1 constructs in K562 myeloblastic leukemia cells. These findings provide a clearer basis for understanding the role of MZF-1 gene expression in myeloid cell growth and differentiation.

Base Sequence↗
PubMed2000

A major susceptibility locus for atopic dermatitis maps to chromosome 3q21.

Atopic dermatitis (eczema) is a chronic inflammatory skin disease with onset mainly in early childhood It is commonly the initial clinical manifestation of allergic disease, often preceding the onset of respiratory allergies. Along with asthma and allergic rhinitis, atopic dermatitis is an important manifestation of atopy that is characterized by the formation of allergy antibodies (IgE) to environmental allergens. In the developed countries, the prevalence of atopic dermatitis is approximately 15%, with a steady increase over the past decades. Genetic and environmental factors interact to determine disease susceptibility and expression, and twin studies indicate that the genetic contribution is substantial. To identify susceptibility loci for atopic dermatitis, we ascertained 199 families with at least two affected siblings based on established diagnostic criteria. A genome-wide linkage study revealed highly significant evidence for linkage on chromosome 3q21 (Zall=4.31, P= 8.42 10(-6)). Moreover, this locus provided significant evidence for linkage of allergic sensitization under the assumption of paternal imprinting (hlod=3.71,alpha=44%), further supporting the presence of an atopy gene in this region. Our findings indicate that distinct genetic factors contribute to susceptibility to atopic dermatitis and that the study of this disease opens new avenues to dissect the genetics of atopy.

Adolescent↗
PubMed2001

Macrovascular disease in diabetes: current status.

Clearly, macrovascular complications are the prognosis limiting problem of diabetes patients which consecutively account for the majority of socio-economic burden of the disease. The overall morbidity and mortality development does not indicate improvement hallmarking better or at least adequate care for these patients. Possible explanations address the late detection problem of a clinically silent disease onset as well as unrecognised multiple comorbid conditions all of which end-up with endothelial dysfunction as representation of the so called "functional atherosclerosis" and blood hyperresponsiveness. Here, we describe new experimental aspects of the early atherosclerosis development focussing inflammation as one driving pathogenetic force for the evolution of the complicated lesion type in diabetes. However, emphasis is put on the view that inflammation, atherogenesis and thrombogenesis are severely crosslinked by soluble and cellular adhesion molecules. From a diagnostic point of view genomic detection of risk associated genes opens both the vision of early identification of high risk individuals and the targeting of drug intervention based on conditioned responsiveness. By using available drugs and evidence based risk factor intervention strategies a plea is made for a multimodal therapeutic approach fitted to the individual patient's needs aiming at endpoint reduction. This corresponds to the recent releases of guidelines from nearly all vascular medicine related scientific societies. Diabetes is a vascular disease!

Diabetic Angiopathies↗
PubMed2003

Diagnostic testing in hepatitis C virus infection: viral kinetics and genomics.

Virological tools play a major role in the diagnosis of hepatitis C virus (HCV) infection and in ongoing decision-making based on the patient's virological response to therapy. Virological tools used to assess viral kinetics and viral genomics can also be applied to clinical and translational research, especially in studies aimed at understanding the mechanisms underlying HCV treatment failure. Viral kinetics studies are based on quantification of HCV RNA at prescribed intervals during treatment and mathematical modeling of HCV RNA dynamics. These studies require sensitive and specific HCV RNA assays with an extended dynamic range of quantification. Viral genomics methods are useful to correlate viral kinetics with the intrinsic genomic characteristics of the HCV infecting strain. The interpretation of results utilizing various viral genomics tools is difficult, however, and must include predictive structural and functional genomic analyses. These approaches will be particularly useful in studying the mechanisms of HCV treatment failure with new HCV inhibitors currently under development.

Algorithms↗
PubMed2025

HTSinfer: inferring metadata from bulk Illumina RNA-Seq libraries.

SUMMARY: The Sequencing Read Archive is one of the largest and fastest-growing repositories of sequencing data, containing tens of petabytes of sequenced reads. Its data is used by a wide scientific community, often beyond the primary study that generated them. Such analyses rely on accurate metadata concerning the type of experiment and library, as well as the organism from which the sequenced reads were derived. These metadata are typically entered manually by contributors in an error-prone process, and are frequently incomplete. In addition, easy-to-use computational tools that verify the consistency and completeness of metadata describing the libraries to facilitate data reuse, are largely unavailable. Here, we introduce HTSinfer, a Python-based tool to infer metadata directly and solely from bulk RNA-sequencing data generated on Illumina platforms. HTSinfer leverages genome sequence information and diagnostic genes to rapidly and accurately infer the library source and library type, as well as the relative read orientation, 3' adapter sequence and read length statistics. HTSinfer is written in a modular manner, published under a permissible free and open-source license and encourages contributions by the community, enabling easy addition of new functionalities, e.g. for the inference of additional metrics, or the support of different experiment types or sequencing platforms. AVAILABILITY AND IMPLEMENTATION: HTSinfer is released under the Apache License 2.0. Latest code is available via GitHub at https://github.com/zavolanlab/htsinfer, while releases are published on Bioconda. A snapshot of the HTSinfer version described in this article was deposited at Zenodo at 10.5281/zenodo.13985958.

Metadata↗
PubMed1998

Spermatids as gametes: indications and limitations.

The feasibility of achieving viable embryos, developing to term after transfer into the uterus, by fertilizing oocytes with spermatids has been demonstrated both in animal studies and in preliminary human clinical trials. Here we review the current clinical indications of spermatid conception and discuss the predictable success rates associated with each of these indications. Potential health hazards relating to the use of spermatids for conception are updated taking into account the risk of abnormal or incomplete epigenetic modifications of newly discovered human imprinted genes. We also add new experimental data showing the occurrence of spermatids in patients lacking spermatozoa and demonstrating that round spermatids recovered from patients with complete spermiogenesis failure (no elongated spermatids or spermatozoa ever detected in the patient's history) are often deficient in the factor(s) responsible for oocyte activation. The possible consequences of this deficiency for the occurrence of abnormal fertilization patterns and for the impairment of further preimplantation and post-implantation development are discussed. It is concluded that the development of diagnostic tests to assess the intrinsic quality of spermatids, with regard to their ability to act as gametes, is urgently needed as part of pre-treatment diagnosis before infertile couples are included in a spermatid conception programme. Centres wishing to use spermatids in human assisted reproduction should also be prepared to offer adequate diagnostic methods to control genomic imprinting abnormalities in the progeny.

Female↗
PubMed2002

Biomarkers in cancer screening: a public health perspective.

The last three decades have witnessed a rapid advancement and diffusion of technology in health services. Technological innovations have given health service providers the means to diagnose and treat an increasing number of illnesses, including cancer. In this effort, research on biomarkers for cancer detection and risk assessment has taken a center stage in our effort to reduce cancer deaths. For the first time, scientists have the technologies to decipher and understand these biomarkers and to apply them to earlier cancer detection. By identifying people at high risk of developing cancer, it would be possible to develop intervention efforts on prevention rather than treatment. Once fully developed and validated, then the regular clinical use of biomarkers in early detection and risk assessment will meet nationally recognized health care needs: detection of cancer at its earliest stage. The dramatic rise in health care costs in the past three decades is partly related to the proliferation of new technologies. More recent analysis indicates that technological change, such as new procedures, products and capabilities, is the primary explanation of the historical increase in expenditure. Biomarkers are the new entrants in this competing environment. Biomarkers are considered as a competing, halfway or add-on technology. Technology such as laboratory tests of biomarkers will cost less compared with computed tomography (CT) scans and other radiographs. However, biomarkers for earlier detection and risk assessment have not achieved the level of confidence required for clinical applications. This paper discusses some issues related to biomarker development, validation and quality assurance. Some data on the trends of diagnostic technologies, proteomics and genomics are presented and discussed in terms of the market share. Eventually, the use of biomarkers in health care could reduce cost by providing noninvasive, sensitive and reliable assays at a fraction of the cost of definitive technology, such as CT scan. The National Cancer Institute's Early Detection Research Network (EDRN) has begun an innovative, investigator-initiated project to improve methods for detecting the biomarkers of cancer cells. The EDRN is a consortium of more than 32 institutions to link discovery of biomarkers to the next steps in the process of developing early detection tests. These discoveries will lead to early clinical validation of tests with improved accuracy and reliability.

Biomarkers↗
PubMed2003

Analysis and accurate quantification of CpG methylation by MALDI mass spectrometry.

As the DNA sequence of the human genome is now nearly finished, the main task of genome research is to elucidate gene function and regulation. DNA methylation is of particular importance for gene regulation and is strongly implicated in the development of cancer. Even minor changes in the degree of methylation can have severe consequences. An accurate quantification of the methylation status at any given position of the genome is a powerful diagnostic indicator. Here we present the first assay for the analysis and precise quantification of methylation on CpG positions in simplex and multiplex reactions based on matrix-assisted laser desorption/ ionisation mass spectrometry detection. Calibration curves for CpGs in two genes were established and an algorithm was developed to account for systematic fluctuations. Regression analysis gave R(2) >or= 0.99 and standard deviation around 2% for the different positions. The limit of detection was approximately 5% for the minor isomer. Calibrations showed no significant differences when carried out as simplex or multiplex analyses. All variable parameters were thoroughly investigated, several paraffin-embedded tissue biopsies were analysed and results were verified by established methods like analysis of cloned material. Mass spectrometric results were also compared to chip hybridisation.

Base Sequence↗
PubMed2003

Recognition of mycobacterial epitopes by T cells across mammalian species and use of a program that predicts human HLA-DR binding peptides to predict bovine epitopes.

Bioinformatics tools have the potential to accelerate research into the design of vaccines and diagnostic tests by exploiting genome sequences. The aim of this study was to assess whether in silico analysis could be combined with in vitro screening methods to rapidly identify peptides that are immunogenic during Mycobacterium bovis infection of cattle. In the first instance the M. bovis-derived protein ESAT-6 was used as a model antigen to describe peptides containing T-cell epitopes that were frequently recognized across mammalian species, including natural hosts for tuberculosis (humans and cattle) and small-animal models of tuberculosis (mice and guinea pigs). Having demonstrated that some peptides could be recognized by T cells from a number of M. bovis-infected hosts, we tested whether a virtual-matrix-based human prediction program (ProPred) could identify peptides that were recognized by T cells from M. bovis-infected cattle. In this study, 73% of the experimentally defined peptides from 10 M. bovis antigens that were recognized by bovine T cells contained motifs predicted by ProPred. Finally, in validating this observation, we showed that three of five peptides from the mycobacterial antigen Rv3019c that were predicted to contain HLA-DR-restricted epitopes were recognized by T cells from M. bovis-infected cattle. The results obtained in this study support the approach of using bioinformatics to increase the efficiency of epitope screening and selection.

Animals↗
PubMed1994

In vivo replicative status and envelope heterogeneity of equine infectious anemia virus in an inapparent carrier.

The distribution and replicative status of equine infectious anemia virus (EIAV) DNA in the tissues of a well-characterized inapparent carrier horse were established by using the PCR technique. The EIAV pol region could be amplified in all of the tissues tested, including the cerebellum and periventricular tissue, at concentrations approximately 10(5)-fold less than in the same tissue from an acutely infected horse. Further analysis of the EIAV genome, with primer pairs diagnostic for sequential stages of reverse transcription, suggests that EIAV DNA in the brain, liver, and lymph nodes was incompletely synthesized. The products of reverse transcription were found to diminish progressively during first-strand synthesis, while products indicative of second-strand synthesis were observed only in kidney and spleen DNA samples. Sequences specific for different regions of the envelope could not be amplified from any of the tissues of the inapparent carrier, suggesting that the envelope is highly variable and may be subject to extensive drift. Together, the data suggest that low levels of EIAV replication persist without causing clinical disease in an inapparent carrier.

Animals↗
PubMed2004

Information management and informatics: need for a modern pathology service.

Requirements for information technology in pathology now extend well beyond the provision of purely analytical data. With the aim of achieving seamless integration of laboratory data into the total clinical pathway, "informatics"--the art and science of turning data into useful information--is becoming increasingly important in laboratory medicine. Informatics is a powerful tool in pathology--whether in implementing processes for pathology modernization, introducing new diagnostic modalities (e.g. proteomics, genomics), providing timely and evidence-based disease management, or enabling best use of limited and often costly resources. Providing appropriate information to empowered and interested patients--which requires critical assessment of the ever-increasing volume of information available--can also benefit greatly from appropriate use of informatics. General trends in medical informatics are reflected in current priorities for laboratory medicine, including the need for unified electronic records, computerized order entry, data security and recovery, and audit. The increasing demands placed on pathology information systems in the context of wider developmental change in healthcare delivery are explored in this paper.

Data Collection↗
PubMed2025

Integrating AlphaFold2 models and clinical data to improve the assessment of Short Linear Motifs (SLiMs) and their variants' pathogenicity.

Short Linear Motifs (SLiMs) are protein functionally relevant regions that mediate reversible protein-protein interactions. Variants that disrupt SLiMs can lead to numerous Mendelian diseases. Although various bioinformatic tools have been developed to identify SLiMs, most suffer from low specificity. In our previous work, we demonstrated that integrating sequence variant information with structural analysis can enhance the prediction of true functional SLiMs while simultaneously generating tolerance matrices that indicate whether each of the 19 possible single amino acid substitutions (SASs) is tolerated. However, the scarcity of representative crystallographic structures of SLiM-receptor complexes posed a significant limitation. In this study, we demonstrate that these interactions can be modeled using AlphaFold2 (AF2) to generate high-quality structures that serve as input for our MotSASi method. These AF2-derived structures show robust performance, both in reproducing known structures deposited in the Protein Data Bank (PDB) and in reflecting the deleterious effects of known sequence variants. This updated version of MotSASi expands the repertoire of high-confidence predicted SLiMs and provides a comprehensive catalog of variants located within SLiMs, along with their respective deleteriousness assessments. When compared to AlphaMissense, MotSASi demonstrates superior performance in predicting variant deleteriousness. By contributing to the accurate identification and interpretation of variants, this work aligns with ACMG/AMP standards and aims to improve diagnostic rates in clinical genomics.

Humans↗
PubMed1999

Structure and possible mechanisms of TEL-AML1 gene fusions in childhood acute lymphoblastic leukemia.

TEL-AML1 gene fusion derived by chromosomal translocation is a common acquired genetic lesion in pediatric cancer that is present in approximately 25% of B-cell precursor acute lymphoblastic leukemias, and recent evidence suggests that this recombination event may initiate leukemogenesis prenatally during fetal hemopoiesis. Analysis of the DNA sequence and structure surrounding the breakpoints may reveal clues to their formation. A long-distance inverse PCR strategy was used to amplify TEL-AML1 genomic fusion sequences from diagnostic DNA from nine patients. Breakpoints were scattered within the 14 kb of intronic DNA between exons 5 and 6 of TEL and in two putative cluster regions within AML1 intron 1. Fusion sequences exhibited characteristic signs of nonhomologous end joining, including microhomologies at the end points, and small deletions and duplications. DNA sequences near the breakpoints did not reveal any consistent characteristic signal sequences of the V(D)J recombinase, topoisomerase II consensus sites, or other sequence motifs associated with recombination. However, several translocations occurred near a repeat region of TEL that was found to be highly polymorphic. This region was cloned and found in nuclease sensitivity assays to exhibit paranemic structures, which may have contributed to DNA breakage or illegitimate recombination. The data are compatible with the possibility that TEL-AML1 translocations occur by nonhomologous recombination involving imprecise, constitutive repair processes following DNA double-strand breaks.

Base Sequence↗
PubMed2003

Diagnostic markers that distinguish colon and ovarian adenocarcinomas: identification by genomic, proteomic, and tissue array profiling.

Colon and ovarian cancers can be difficult to distinguish in the abdomen, and the distinction is important because it determines which drugs will be used for therapy. To identify molecular markers for that differential diagnosis, we developed a multistep protocol starting with the 60 human cancer cell lines used by the National Cancer Institute to screen for new anticancer agents. The steps included: (a) identification of candidate markers using cDNA microarrays; (b) verification of clone identities by resequencing; (c) corroboration of transcript levels using Affymetrix oligonucleotide chips; (d) quantitation of protein expression by "reverse-phase" protein microarray; and (e) prospective validation of candidate markers on clinical tumor sections in tissue microarrays. The two best candidates identified were villin for colon cancer cells and moesin for ovarian cancer cells. Because moesin stained stromal elements in both types of cancer, it would probably not have been identified as a marker if we had started with mRNA or protein profiling of bulk tumors. Villin appears at least as useful as the currently used colon cancer marker cytokeratin 20, and moesin also appears to have utility. The multistep process introduced here has the potential to produce additional markers for cancer diagnosis, prognosis, and therapy.

Adenocarcinoma↗
PubMed2005

Toward resolution of cardiovascular health disparities in African Americans: design and methods of the Jackson Heart Study.

OBJECTIVE: The design, overall methods, and major phenotypes for the all-African-American Jackson Heart Study (JHS) are detailed. METHODS: Participants were enrolled from the three counties that make up the Jackson, Mississippi metropolitan area. Relatives of selected participants were recruited to develop a large, nested family cohort. Participants provided extensive medical and social history, had an array of physical and biochemical measurements and diagnostic procedures, and provided genomic DNA. RESULTS: Data and biologic materials have been collected from 5302 adult African Americans, including 1499 members of 291 families. Participants have a high prevalence of diabetes, hypertension, obesity, and related disorders. DISCUSSION: The JHS dataset and biologic materials (serum, DNA, and cryopreserved cells) offer a valuable resource for the study of diseases that are of particular importance to African Americans.

Adult↗