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PubMed1994

Progression of glomerular diseases.

The nature and slope of progression of glomerular diseases is the subject of considerable discussion. The use of renal biopsies has been accompanied by considerable improvement in the classification of glomerular disease. However, the clinical and histological tools available to assess prognosis in individual patients lack accuracy, especially in slowly progressive glomerular diseases such as diabetes mellitus. The development of molecular biology tools provides a new approach to the analysis of glomerulosclerosis. The accumulation of extracellular matrix in the glomerulus results from an exaggerated synthesis of collagens and other molecules forming the basement membranes, and is accompanied by an increase in the corresponding mRNAs. The measure of local glomerular gene activation can therefore provide a dynamic view of glomerular scarring. Utilizing a method combining microdissection of the glomeruli, reverse transcription in situ and a competitive polymerase-chain-reaction assay we were able to measure minute amounts of mRNAs in single mouse and human glomeruli. Both in mouse models and in human glomerulosclerosis we found upregulation of basement membrane collagen genes in the glomeruli. The increase appeared to be parallel to the slope of progression of glomerulosclerosis in experimental animals. This new approach may therefore provide a quantitative and sensitive method to define the propensity to sclerosis in human disease.

Animals↗

PubMed2006

Interpreter of maladies: redescription mining applied to biomedical data analysis.

Comprehensive, systematic and integrated data-centric statistical approaches to disease modeling can provide powerful frameworks for understanding disease etiology. Here, one such computational framework based on redescription mining in both its incarnations, static and dynamic, is discussed. The static framework provides bioinformatic tools applicable to multifaceted datasets, containing genetic, transcriptomic, proteomic, and clinical data for diseased patients and normal subjects. The dynamic redescription framework provides systems biology tools to model complex sets of regulatory, metabolic and signaling pathways in the initiation and progression of a disease. As an example, the case of chronic fatigue syndrome (CFS) is considered, which has so far remained intractable and unpredictable in its etiology and nosology. The redescription mining approaches can be applied to the Centers for Disease Control and Prevention's Wichita (KS, USA) dataset, integrating transcriptomic, epidemiological and clinical data, and can also be used to study how pathways in the hypothalamic-pituitary-adrenal axis affect CFS patients.

Algorithms↗

PubMed2003

Heritable syndromes with hypothalamic hamartoma and seizures: using rare syndromes to understand more common disorders.

Manifestations of non-syndromic hypothalamic hamartomas are different from those of the syndromic hamartomas, and the syndromic ones are rare. In spite of the rarity of the syndromic hamartomas, they can be a powerful biological tool to help us understand the pathophysiology of these heritable disorders. Several disorders that include hypothalamic hamartomas are reviewed here and the current understanding of the biology of the lesions is summarized.

Abnormalities, Multiple↗

PubMed2000

Site-specific administration of antisense oligonucleotides using biodegradable polymer microspheres provides sustained delivery and improved subcellular biodistribution in the neostriatum of the rat brain.

Antisense oligonucleotides (ODNs) are being increasingly used in the central nervous system as biological tools, as drug-target validation agents and as potential therapeutic agents. Although the local delivery of naked ODNs to the brain can result in the desired biological effects, the duration of efficacy is relatively short lived due to the combined effects of rapid ODN degradation and elimination half-lives in vivo. In this study, we have examined the use of biodegradable polymer microspheres as a site-specific delivery system for targeting ODNs to the neostriatum of the rat brain. Model phosphorothioate backbone-modified ODNs were entrapped within poly(D,L-lactide-co-glycolide) (PLAGA) microspheres using a double emulsion-deposition method and the formulations characterised in terms of particle size, surface morphology, percent encapsulation efficiency, ODN loading and in vitro release profiles. For in vivo evaluation, PLAGA microspheres containing fluorescently-labelled ODNs were stereo-taxically administered to the neostriatum of the rat brain and biodistribution of ODNs monitored after 48 h. Administration of free fluorescently-labelled ODNs to the neostriatum resulted in a punctate cellular distribution of ODNs after 24 h with little or no ODN remaining in the neostriatum after 48 h. In comparison, fluorescently-labelled ODNs delivered using polymer microspheres were intensely visible in cells after 48 h post-administration and the fluorescence appeared to be diffuse covering both cytosolic and nuclear regions. Dual-label immunohistochemical analyses suggested that ODNs were mainly distributed to neuronal cells. These data indicate that site-specific administration of ODNs using biodegradable polymer microspheres will not only provide sustained delivery of nucleic acids but can also improve the cellular distribution of ODNs to brain cells. Sustained or controlled-release biodegradable polymer formulations, therefore, represent an attractive strategy for improved local delivery of ODNs to the CNS.

Animals↗

PubMed2006

Mammalian genome targeting using site-specific recombinases.

Nowadays, a wide array of procedures in mouse technology has been made available to researchers in order to establish valuable models for the study of gene function. The efficiency of gene transfer and gene targeting as methods for producing genetic changes in mice, in addition to continuous advances in molecular biology tools, has converted the mouse into the major experimental model for the study of mammalian physiology. In recent years, the emergence of site-specific recombinases as tools to engineer mammalian genomes has opened new avenues into the design of genetically modified mouse models. The original Cre and FLP recombinases have demonstrated their utility in developing conditional gene targeting, and now other analogous recombinases are also ready to be used, in the same way or in combined strategies, to achieve more sophisticated experimental schemes for addressing complex biological questions. The properties of site-specific recombinases in combination with other biotechnological tools (tet on/off system, siRNA mediated gene silencing, fluorescent proteins, et al.) make them useful instruments to induce precise mutations in specific cells or tissues in a time-controlled manner. This ability can be applied in functional genomics in several ways: from conditional and inducible gene targeting to controlled expression of transgenes and recombination-mediated cassette exchange in mouse models for the study of development or disease phenotypes. This review focuses on the use of site-specific recombinases for mouse genome manipulation. A historical perspective of site-specific recombinases is considered and a number of strategies for achieving inducible or conditional genomic manipulations are contemplated in the context of current techniques for producing genetically modified mice. Finally, several model generation approaches from recent examples in the literature are revised.

Alleles↗

PubMed2001

Biochemical engineering of natural product biosynthesis pathways.

Metabolic engineering of natural products is a science that has been built on the goals of traditional strain improvement with the availability of modern molecular biological technologies. In the past 15 years, the state of the art in metabolic engineering of natural products has advanced from the first proof-of-principle experiment based on minimal known genetics to a commonplace event using highly specific and sophisticated gene manipulation methods. With the availability of genes, host organisms, vector systems, and standard molecular biological tools, it is expected that metabolic engineering will be translated into industrial reality.

Bacteria↗

PubMed2001

Oncogenic potential of human neurotropic virus: laboratory and clinical observations.

Cancer is a multi-step disease involving a series of genetic alterations that result in the loss of control of cell proliferation and differentiation. Such genetic alterations could emerge from the activation of oncogenes and the loss or malfunctioning of tumor suppressor gene activity. Our understanding of cancer has greatly increased through the use of DNA tumor viruses and their transforming proteins as a biological tool to decipher a cascade of events that lead to deregulation of cell proliferation and subsequent tumor formation. For the past ten years our laboratory has focused on the molecular biology of the human neurotropic papovavirus, JCV. This virus causes progressive multifocal leukoencephalopathy, a fatal neurodegenerative disease of the central nervous system in immunocompromised patients. JCV is a common human virus that infects more than 80% of humans but does not induce any obvious clinical symptoms. The increased incidence of acquired immune deficiency syndrome and the use of immunosuppressive chemotherapy have dramatically raised the incidence of PML. The coincidental occurrence of malignant astrocytes and oligodendrocytes in PML patients, coupled with the induction of glioblastoma in JCV-infected nonhuman primates, provides intriguing speculation on the association between JCV and CNS malignancies. In this report we discuss clinical data and laboratory observations pointing to the direct involvement of JCV in cancer.

Animals↗

PubMed1997

Skin biopsy as a nondestructive tool for the toxicological assessment of endangered populations of pinnipeds: preliminary results on mixed function oxidase in Otaria flavescens.

The aim of this study was to develop and validate a method for assessing the toxicological risk of endangered populations of pinnipeds based on a nondestructive biological tool, the skin biopsy specimen. Skin biopsies can be obtained from pinnipeds by anaesthetising the animals and taking a small amount of skin in the anterior flipper area, or by shooting a biopsy dart with a crossbow. Skin biopsy material is suitable for a wide range of chemical and biomarker analysis. Organochlorines and polycyclic aromatic hydrocarbons can be analysed in subcutaneous fat and MFO activity (BPMO), Cyt.P450 isoforms, and DNA damage can be detected in epidermis.

Animals↗

PubMed2003

Baculovirus display strategies: Emerging tools for eukaryotic libraries and gene delivery.

Recombinant baculoviruses have been extensively used as vectors for abundant expression of a large variety of foreign proteins in insect cell cultures. The appeal of the system lies essentially in easy cloning techniques and virus propagation combined with the eukaryotic post-translational modification machinery of the insect cell. Recently, a novel molecular biology tool was established by the development of baculovirus surface display, using different strategies for presentation of foreign peptides and proteins on the surface of budded virions. This eukaryotic display system enables presentation of large complex proteins on the surface of baculovirus particles and has thereby become a versatile system in molecular biology. Surface display strategies play an important role, as they may be used to enhance the efficiency and specificity of viral binding and entry to mammalian cells. In addition, baculovirus surface display vectors have been engineered to contain mammalian promoter elements designed for gene delivery both in vitro and in vivo. Moreover, baculovirus capsid display has recently been developed; this holds promise for intracellular targeting of the viral capsid and subsequent cytosolic delivery of desired protein moieties. Finally, the viruses can accommodate large insertions of foreign DNA and replicate only in insect cells. Together, these are attributes that are very likely to make them important tools in functional genomics and proteomics.

Animals↗

PubMed2003

Monoclonal antibodies inducing conformational changes on the antigen molecule.

Monoclonal antibodies (MoAbs) are extensively used as biological tools because of their invariable specificity. However, the interpretation of results can be misled by the behaviour of MoAb displaying allosteric effects, i.e. long-range conformational changes on the antigen (Ag). It has been shown that some MoAbs are able to modify the spatial structure of the corresponding protein Ag, affecting in this way its biological activity as well as its binding to a second MoAb. Thus, a researcher using a MoAb as a tool to investigate some features of an antigenic molecule must be aware of the possible positive or negative allosteric properties of the antibody.

Antibodies, Monoclonal↗

PubMed2000

Identification of an Arg403Gln beta myosin heavy chain gene mutation in a Portuguese family with hypertrophic cardiomyopathy.

INTRODUCTION: The etiology of Familial Hypertrophic Cardiomyopathy (HCM) is attributed to the mutation of genes that encode sarcomeric proteins in the heart. Until now no gene mutations had been identified in Portuguese families with HCM. OBJECTIVE: The main objective of this study is to describe a Portuguese family with HCM carrying an Arg403Gln mutation in the beta myosin heavy chain gene. METHODS: With the help of several Molecular Biology tools, 40 families with HCM were studied. In all these families, one member was identified as carrying an Arg403Gln mutation in the beta myosin heavy chain gene. All family members were submitted to a physical exam, EKG and echocardiography. Those carrying a gene mutation were also submitted to Holter monitoring and to magnetic ressonance imaging. RESULTS: Molecular biology techniques are extremely important for the diagnosis of HCM, particularly in healthy carriers. CONCLUSION: The use of molecular diagnostic tools in HCM is very useful because it allows us to identify the healthy carriers and establish earlier clinical and prevention programs for these individuals.

Amino Acid Substitution↗

PubMed1998

Screening blood donations for viral genomes: multicenter study of real-time simulation using pooled samples on the model of hepatitis C virus RNA detection.

BACKGROUND: The systematic screening for several blood-borne viral genomes in blood donations is a complementary safety measure planned or discussed by the national authorities of several countries. STUDY DESIGN AND METHODS: To appreciate the feasibility of such screening using pooled samples, a multicenter study of real-time simulation has been performed on the model of hepatitis C virus (HCV) infection. Four blood transfusion center laboratories and two research and diagnosis laboratories simultaneously screened, by several HCV RNA polymerase chain reaction assays, a panel of plasma sample pools of different sizes (500, 100, and 10 samples), collected from HCV-infected or HCV-uninfected blood donors. One viremic plasma was introduced in each pool. HCV RNA was detected by in-house polymerase chain reaction procedures or by standardized manual or semi-automated polymerase chain reaction assays. RESULTS: The results indicate the feasibility of sample pooling, which renders the screening for viral genomes by molecular biology techniques applicable in the short term and the importance of the experience of laboratory personnel in the use of molecular biology tools. CONCLUSION: The improvement of standardized assays needs to be continued, and training of laboratory staff members appears to be a crucial step before systematic screening of blood donations for viral genomes by molecular biology techniques can occur.

Blood Donors↗

PubMedDate not supplied

[Antiphospholipid antibodies: clinical significance and biological diagnosis].

The term "antiphospholipids" (aPLs) refers to an heterogeneous family of antibodies diagnosed either by clotting tests: the lupus anticoagulants or by Elisa: anticardiolipin (aCL) and anti-beta2-glycoprotein I (anti-beta2GP1) especially. aPLS recognize phospholipids, alone or bound to plasma protein cofactor(s), or the cofactors themselves. aPLs have long been described in autoimmune diseases such as SLE, but may also be found in other clinical settings including infections, malignancies and drug administration. Their persistent presence can be associated with venous and/or arterial thrombotic complications and/or recurrent miscarriage, thus defining the "antiphospholipid syndrome" (APS). The heterogeneity of aPLs makes a comprehensive approach to laboratory investigation essential. Detection of lupus anticoagulants relies on increased clotting times in phospholipid-dependent tests. Their 4 step diagnosis includes: 1) screening (by at least two different tests); 2) demonstration of an inhibitory activity; 3) evidence of its phospholipid dependence; 4) exclusion of an associated coagulopathy. Among the aPLs detected by Elisa, IgG aCL are the most frequently investigated. However, other antibodies may represent useful biological tools. Among them, anti-beta2GP1 are thought to be more closely associated with a history of thrombosis than aCL and testing for anti-beta2 GP1 should now be systematically included in the biological diagnosis of APS. The Elisa used for aCL and anti-beta2GP1 are not fully standardized, and a number of methodological parameters may account for the interlaboratory discrepancies often observed. The clinical importance of other antibodies such as antiphosphatidylethanolamine, antiprothrombin or antiannexin V is being evaluated. An appropriate laboratory investigation of APS should, in all cases, combine the use of clotting and immunological assays, and assess the persistence of autoantibodies over time.

Adult↗

PubMed1992

On genetic components in autoimmunity: a critical review based on evolutionarily oriented rationality.

The immune system furnishes the organism with the utmost effective defence mechanisms against "foreign" and changes in "self" without doing self-harm. However, optimized efficacy in the defence against the immense variety of "foreign" antigens generates a higher risk for inadvertent self challenge. Such inherent short-comings are the inevitable burden traded for the benefits of an optimally organized defence system. The central molecules involved in specific immune reactions include antigen receptors of B and T lymphocytes, and antigen-presenting proteins encoded by the major histocompatibility complex (MHC; in man HLA). The genetics and evolution of these multigene families is discussed here with respect to their potential contributions to disturbances of "self" recognition. Simple molecular biological tools and procedures for efficiently screening the immunologically relevant genes are described.

Amino Acid Sequence↗

PubMed1989

Biology of large bowel cancer.

The progression of large bowel cancer from the colon crypt cell involves a series of sequential stages of altered growth regulation. An increase in the proliferative compartment of the colonic crypt characterizes the earliest stage. This is followed by loss of normal maturation and gain of more autonomous growth. Ultimately, cells that acquire the capability to migrate and grow at a distant site appear as metastases. Clinical and pathologic observations have been used to identify these stages of large bowel cancer progression, but only with the recent application of molecular and biologic tools are we beginning to identify potential mechanisms responsible for the altered growth. The development of laboratory models that reflect the key clinical and pathologic stages of progression should prove particularly valuable in sorting out the biology of large bowel tumor progression. The challenge then will be to use this knowledge for the design of preventive and therapeutic strategies.

Animals↗

PubMed2005

The function of the extracellular regions in opioid receptor binding: insights from computational biology.

Pain management using opioid analgesics strives to achieve three goals: maximum efficacy, minimal risk of tolerance and physical dependence, and negligible side effects. Following the cloning of opioid and nociceptin receptors, novel ligands can be designed to target specific residues of these membrane proteins with the goal of improving efficacy and reducing side effects through selectivity. For the most part, ligand design has focused on binding sites located in the transmembrane region of the receptors, and has ignored the extracellular domains. In this review, we discuss the evidence for the interaction of the extracellular regions with opioids and show how computational biology tools can be used to model these domains for use in drug discovery. A computational model of the kappa-opioid receptor which includes the loop regions is presented. The model combines knowledge-based information, bioinformatics and computational tools to identify regions of the extracellular loop domains that can be targeted by drug design.

Analgesics, Opioid↗

PubMed2001

ASTM lights the way for tissue engineered medical products standards: jump start for combination medical products that restore biological function of human tissues.

Everybody hopes for better health and restoration of impaired bodily function, and now that hope is illuminated by the promise of powerful biological tools that make human cells grow and replace human tissue. ASTM Committee F04 on Medical and Surgical Materials and Devices is taking the lead by defining some of those tools as standards that can be used for the development, production, testing, and regulatory approval of medical products.

Artificial Organs↗

PubMed2002

The uptake machinery of clostridial actin ADP-ribosylating toxins--a cell delivery system for fusion proteins and polypeptide drugs.

Several bacterial protein toxins, including Clostridium botulinum C2 toxin, Clostridum perfringens iota toxin, Clostridium difficile ADP-ribosyltransferase, and the Bacillus-produced vegetative insecticidal proteins, target the cytoskeleton by ADP-ribosylation of actin. All these toxins are binary in structure and consist of an enzyme component, possessing ADP-ribosyltransferase activity and a separated binding and translocation component, which is involved in the delivery of the enzyme component into the cell. The toxins are not only important virulence factors but also cell biological tools to study the function of the actin cytoskeleton. Moreover, the binary toxins turned out to be effective transporter systems for the delivery of specific fusion toxins (e.g., Rho-ADP-ribosylating C3 exoenzyme) into cells. The present review describes the biological functions of the toxins, focuses on recent studies on the uptake and delivery mechanism and discusses the usage as a drug delivery system.

ADP Ribose Transferases↗