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PubMed2002

Combinatorial informatics in the post-genomics ERA.

The multitude of potential drug targets emerging from genome sequencing demands new approaches to drug discovery. A chemogenomics strategy, which involves the generation of small-molecule compounds that can be used both as tools to probe biological mechanisms and as leads for drug-property optimization, provides a highly parallel, industrialized solution. Key to the success of this strategy is an integrated suite of chemi-informatics applications that can allow the rapid and directed optimization of chemical compounds with drug-like properties using 'just-in-time' combinatorial chemical synthesis. An effective embodiment of this process requires new computational and data-mining tools that cover all aspects of library generation, compound selection and experimental design, and work effectively on a massive scale.

Combinatorial Chemistry Techniques↗

PubMed2026

Uniform processing and analysis of IGVF massively parallel reporter assay data with MPRAsnakeflow.

As researchers and clinicians seek to identify human genomic alterations relevant to traits and disorders, identifying and aggregating evidence providing mechanistic support for associations between alterations and phenotypes remains challenging. In particular, the study of noncoding genomic variation remains a major challenge because of the lack of accurate functional annotation for activity in a given context and across alleles. Experimental evidence is critical for prioritizing and interpreting functional effects of genetic alterations. Massively parallel reporter assays (MPRAs) have emerged as a powerful high-throughput approach, enabling quantification of regulatory element activity and allelic effects, as well as systematic dissection of gene regulatory logic and variant effects across different contexts. However, the diversity of MPRA designs, lack of standardized formats, and many potential processing parameters hamper data integration, reproducibility, and meta-analyses across studies. To address these challenges, the Impact of Genomic Variation on Function (IGVF) Consortium established an MPRA focus group to develop community standards, including harmonized file formats, and robust analysis pipelines for a wide range of library types and experimental designs. Here, we present these formats and comprehensive computational tools, MPRAlib and MPRAsnakeflow, for uniform processing from raw sequencing reads to counts, processing, and visualization. Using diverse MPRA data sets, we investigated technical variability sources including barcode sequence bias, outlier barcodes, and delivery method (episomal vs. lentiviral). Our results establish best practices for MPRA data generation and analysis, facilitating robust, reproducible research and large-scale integration. The presented tools and standards are publicly available, providing a foundation for future collaborative efforts in regulatory genomics.

Humans↗

PubMed2003

Structural properties of Gerstmann-Straussler-Scheinker disease amyloid protein.

Prion protein (PrP) amyloid formation is a central feature of genetic and acquired forms of prion disease such as Gerstmann-Sträussler-Scheinker disease (GSS) and variant Creutzfeldt-Jakob disease. The major component of GSS amyloid is a PrP fragment spanning residues approximately 82-146. To investigate the determinants of the physicochemical properties of this fragment, we synthesized PrP-(82-146) and variants thereof, including entirely and partially scrambled peptides. PrP-(82-146) readily formed aggregates that were partially resistant to protease digestion. Peptide assemblies consisted of 9.8-nm-diameter fibrils having a parallel cross-beta-structure. Second derivative of infrared spectra indicated that PrP-(82-146) aggregates are primarily composed of beta-sheet (54%) and turn (24%) which is consistent with their amyloid-like properties. The peptide induced a remarkable increase in plasma membrane microviscosity of primary neurons. Modification of the amino acid sequence 106-126 caused a striking increase in aggregation rate, with formation of large amount of protease-resistant amorphous material and relatively few amyloid fibrils. Alteration of the 127-146 region had even more profound effects, with the inability to generate amyloid fibrils. These data indicate that the intrinsic properties of PrP-(82-146) are dependent upon the integrity of the C-terminal region and account for the massive deposition of PrP amyloid in GSS.

Amino Acid Sequence↗

PubMed2006

Structural differentiation of the HIV-1 polyA signals.

The Human Immunodeficiency Virus Type 1 (HIV-1) encodes the polyadenylation (polyA) signal (AAUAAA) within the highly conserved untranslated region (UTR) at both 5' and 3' terminals of the viral transcript. In polyadenylation, an RNA transcript is cleaved and then elongated with adenine nucleotides while repression of the 5' signal and utilization of the 3' signal occurs. Because experimental studies have yet to analyze the structures of both 5' and 3' signals from a global perspective, other structural conformations involving these signals may exist and could be pivotal to understanding key functional processes. To distinguish the differential regulation of the 5' and 3' polyA signals, we studied the structural tendencies of both the 5' and 3' UTR in HIV-1. Through computational folding predictions of multiple HIV-1 strains using the Massively Parallel Genetic Algorithm (MPGAfold) capable of dynamically elucidating key alternative conformations, the 5' polyA signal was found to be dominantly occluded in a hairpin loop while the 3' polyA signal showed variability between hairpin and linear conformations with a propensity for the linear structure with an asymmetric internal loop. Furthermore, the energies and predictions of these structures indicate that the polyA signals have some metastable characteristics indicating an ability to switch into different conformations that can regulate viral function.

3' Untranslated Regions↗

PubMed1999

Hunting with traps: genome-wide strategies for gene discovery and functional analysis.

With sequence analysis of the human genome well underway, there is an increasingly urgent challenge to understand the fundamental function and interplay of genes that build and maintain an organism. Several approaches will be critical for interpreting gene function, including random cDNA sequencing, expression profiling in different tissues, genetic analysis of human or model organism phenotypes, and creation of transgenic or "knockout" animals. Traditional gene-trapping approaches, in which genes are randomly disrupted with DNA elements inserted throughout the genome, have been used to generate large numbers of mutant organisms for genetic analysis. Recent modifications of gene-trapping methods and their increased use in mammalian systems are likely to result in a wealth of new information on gene function. Various trapping strategies allow genes to be segregated based on criteria like the specific subcellular location of an encoded protein, the tissue expression profile, or responsiveness to specific stimuli. Genome-wide gene-trapping strategies, which integrate gene discovery and expression profiling, can be applied in a massively parallel format to produce living assays for drug discovery.

Genes↗

PubMed2000

Discovering patterns in microarray data.

The human genome is a complex system characterized by gene interactions and nonlinear behaviors. Complex systems cannot be viewed as the aggregate of their isolated pieces but must be studied as an integrated whole. Microarray technologies offer the opportunity to see the entire biological system as it existed at one moment in time. It is tempting to try to analyze the entire microarray at once to immediately discover the pattern being sought, for example, the pattern of a breast cancer. However, such an analysis would be a mistake because microarrays provide massively parallel information, the analysis of which is a nondeterministic polynomial time (NP)-hard problem. Current statistical methods are not sufficiently powerful to solve this NP-hard problem. The best approach to microarray analysis is to begin with a small number of the elements in the microarray known to be a pattern and ask questions of the other elements in the microarray; i.e., perform instantaneous scientific experiments regarding whether each of the other elements in the microarray are related to the known pattern.

Algorithms↗

PubMed2003

[Progress in molecular biology study of DNA computer].

DNA (deoxyribonucleotide acids) computer is an emerging new study area that basically combines molecular biology study of DNA molecules and computational study on how to employ these specific molecules to calculate. In 1994 Adleman described his pioneering research on DNA computing in Science. This is the first experimental report on DNA computer study. In 2001 Benenson et al published a paper in Nature regarding a programmable and autonomous DNA computing device. Because of its Turing-like functions, the device is regarded as another milestone progress for DNA computer study. The main features of DNA computer are massively parallel computing ability and potential enormous data storage capacity. Comparing with conventional electronic computers, DNA molecules provide conceptually a revolution in computing, and more and more implications have been found in various disciplines. DNA computer studies have brought great progress not only in its own computing mechanisms, but also in DNA manipulation technologies especially nano-technology. This article presents the basic principles of DNA computer, its applications, its important relationship with genomic research and our comments on all above issues.

Computers, Molecular↗

PubMed2001

Genomic approaches to elucidating the pathophysiology of renal diseases.

The physiological and pathological processes of the kidney as a whole can now be analyzed with a molecular precision at a genomic-scale. Using massively parallel cDNA microarray technology, the mRNA expression of thousands of genes can be quantified simultaneously. The advantages of microarray analyses include the ability to examine the interaction of several genes or the entire genome in a single experiment. Bioinformatics approaches such as data mining through mathematical condensation of the massive gene expression profiles are essential for elucidating molecular and biological logic underlying gene expression programs. Genes that encode similar protein components are often coordinately regulated. Recent application of gene expression profiling to the normal human renal cortical tissue, experimental in vitro and in vivo models has shown that cellular activation is accompanied by changes of hundreds of genes in parallel. The databases of gene expression emerging from these studies will be used to interpret the pathological changes in gene expression that accompany a variety of human renal diseases.

Gene Expression Profiling↗

PubMed2002

Programs of gene expression during the laying down of memory formation as revealed by DNA microarrays.

Many experiments in the past have demonstrated the requirement of de novo gene expression during memory formation. In contrast to the initial reductionistic view that genes relevant to learning and memory would be easily found and would provide a simple key to understand this brain function, it is becoming apparent that the genetic contribution to memory is complex. Previous approaches have been focused on individual genes or genetic pathways and failed to address the massively parallel nature of genome activities and collective behavior of the genes that ultimately control the molecular mechanisms underlying brain function. In view of the broad variety of genes and the cross talk of genetic pathways involved in this regulation, only gene expression profiles may reflect the complete behavior of regulatory pathways. In this review we illustrate how DNA microarray-based gene expression profiling may help to dissect and analyze the complex mechanisms involved in gene regulation during the acquisition and storage of memory in the mammalian brain.

Animals↗

PubMed2006

Transcriptome profiling uncovers metabolic and regulatory processes occurring during the transition from desiccation-sensitive to desiccation-tolerant stages in Medicago truncatula seeds.

To investigate regulatory processes and protective mechanisms leading to desiccation tolerance (DT) in seeds, 16086-element microarrays were used to monitor changes in the transcriptome of desiccation-sensitive 3-mm-long radicles of Medicago truncatula seeds at different time points during incubation in a polyethylene glycol (PEG) solution at -1.7 MPa, resulting in a gradual re-establishment of DT. Gene profiling was also performed on embryos before and after the acquisition of DT during maturation. More than 1300 genes were differentially expressed during the PEG incubation. A large number of genes involved in C metabolism are expressed during the re-establishment of DT. Quantification of C reserves confirms that lipids, starch and oligosaccharides were mobilised, coinciding with the production of sucrose during the early osmotic adjustment. Several clusters of gene profiles were identified with different time-scales. Genes expressed early during the PEG incubation belonged to classes involved in early stress and adaptation responses. Interestingly, several regulatory genes typically expressed during abiotic/drought stresses were also upregulated during maturation, arguing for the partial overlap of ABA-dependent and -independent regulatory pathways involved in both drought and DT. At later time points, in parallel to the re-establishment of DT, upregulated genes are comparable with those involved in late seed maturation. Concomitantly, a massive repression of genes belonging to numerous classes occurred, including cell cycle, biogenesis, primary and energy metabolism. The re-establishment of DT in the germinated radicles appears to concur with a partial return to the quiescent state prior to germination.

Abscisic Acid↗

PubMed1992

A rat model of human T lymphocyte virus type I (HTLV-I) infection. 1. Humoral antibody response, provirus integration, and HTLV-I-associated myelopathy/tropical spastic paraparesis-like myelopathy in seronegative HTLV-I carrier rats.

Human T lymphocyte virus type I (HTLV-I) can be transmitted into several inbred strains of newborn and adult rats by inoculating newly established HTLV-I-immortalized rat T cell lines or the human T cell line MT-2. The transmission efficiency exceeds 80%, regardless of strain differences or the age at transmission. The production of anti-HTLV-I antibodies significantly differs among the strains and depends on the age at the time of transmission. Rats neonatally inoculated with HTLV-I-positive rat or human cells generally become seronegative HTLV-I carriers throughout their lives, whereas adult rats inoculated with HTLV-I-positive cells at 16 wk of age become seropositive HTLV-I carriers. The HTLV-I provirus genome is present in almost all organs, regardless of whether the carriers are seronegative or seropositive. According to antibody titers to HTLV-I, there are three groups of inbred rat strains: ACI, F344, and SDJ (high responders); WKA, BUF, and LEJ (intermediate responders); and LEW (low responder). Three of three 16-mo-old seronegative HTLV-I carrier rats of the WKA strain developed spastic paraparesis of the hind legs. Neuropathological examinations revealed that the lesions were confined primarily to the lateral and anterior funiculi of the spinal cord. Both myelin and axons were extensively damaged in a symmetrical fashion, and infiltration with massive foamy macrophages was evident. The most severe lesions were at levels of the thoracic cord and continued from the cervical to the lumbar area. These histopathological features as well as clinical symptoms largely parallel findings in humans with HTLV-I-associated myelopathy/tropical spastic paraparesis (HAM/TSP). These HTLV-I carrier rats, in particular the WKA rats described above, can serve as a useful animal model for investigating virus-host interactions in the etiopathogenesis of HTLV-I-related immunological diseases, particularly HAM/TSP.

Aging↗

PubMed2003

[Genetic testing].

The first genetic tests started to be developed about twenty years ago. Their initial applications were limited to genetic counselling and prenatal diagnosis of a few hereditary diseases. Technological progress and the identification of genes responsible for many hereditary diseases have led to their development and diffusion. They have become a nearly irreplaceable tool for the diagnosis of hereditary diseases. In the future, their indications should increase when genes implicated in multifactorial diseases are progressively identified. The impact will probably be particularly important in cardiology because most cardiovascular diseases are multifactorial. The first predisposing factors (factor V. prothrombin...) for a predisposition to thrombosis are now daily genetic investigations. In parallel, the progress in pharmacogenetics should enable everyone to have appropriate qualitative and quantitative treatment according to their genetic makeups, which should improve both efficacy and safety. In order to face up to the exponential increase in demand for the genetic tests which will result from these advances, the laboratories should have new high speed, powerful and economic equipment. DNA microchips, which are currently under development could, at least initially, provide a solution to this problem. It is now certain that genetic testing will become routine and, in time, it will be used massively in both hospital and community medicine.

Adult↗

PubMed2025

Unequally Abundant Chromosomes and Unusual Collections of Transferred Sequences Characterize Mitochondrial Genomes of Gastrodia (Orchidaceae), One of the Largest Mycoheterotrophic Plant Genera.

The mystery of genomic alternations in heterotrophic plants is among the most intriguing in evolutionary biology. Compared to plastid genomes (plastomes) with parallel size reduction and gene loss, mitochondrial genome (mitogenome) variation in heterotrophic plants remains underexplored in many aspects. To further unravel the evolutionary outcomes of heterotrophy, we present a comparative mitogenomic study with 13 de novo assemblies of Gastrodia (Orchidaceae), one of the largest fully mycoheterotrophic plant genera, and its relatives. Analyzed Gastrodia mitogenomes range from 0.56 to 2.1 Mb, each consisting of numerous, unequally abundant chromosomes or contigs. Size variation might have evolved through chromosome rearrangements followed by stochastic loss of "dispensable" chromosomes, with deletion-biased mutations. The discovery of a hyper-abundant (∼15 times intragenomic average) chromosome in two assemblies represents the hitherto most extreme copy number variation in any mitogenomes, with similar architectures discovered in two metazoan lineages. Transferred sequence contents highlight asymmetric evolutionary consequences of heterotrophy: despite drastically reduced intracellular plastome transfers convergent across heterotrophic plants, their rarity of horizontally acquired sequences sharply contrasts parasitic plants, where massive transfers from their hosts prevail. Rates of sequence evolution are markedly elevated but not explained by copy number variation, extending prior findings of accelerated molecular evolution from parasitic to heterotrophic plants. Putative evolutionary scenarios for these mitogenomic convergence and divergence fit well with the common (e.g. plastome contraction) and specific (e.g. host identity) aspects of the two heterotrophic types. These idiosyncratic mycoheterotrophs expand known architectural variability of plant mitogenomes and provide mechanistic insights into their content and size variation.

Genome, Mitochondrial↗

PubMed2004

A microfluidic system for large DNA molecule arrays.

Single molecule approaches offer the promise of large, exquisitely miniature ensembles for the generation of equally large data sets. Although microfluidic devices have previously been designed to manipulate single DNA molecules, many of the functionalities they embody are not applicable to very large DNA molecules, normally extracted from cells. Importantly, such microfluidic devices must work within an integrated system to enable high-throughput biological or biochemical analysis-a key measure of any device aimed at the chemical/biological interface and required if large data sets are to be created for subsequent analysis. The challenge here was to design an integrated microfluidic device to control the deposition or elongation of large DNA molecules (up to millimeters in length), which would serve as a general platform for biological/biochemical analysis to function within an integrated system that included massively parallel data collection and analysis. The approach we took was to use replica molding to construct silastic devices to consistently deposit oriented, elongated DNA molecules onto charged surfaces, creating massive single molecule arrays, which we analyzed for both physical and biochemical insights within an integrated environment that created large data sets. The overall efficacy of this approach was demonstrated by the restriction enzyme mapping and identification of single human genomic DNA molecules.

DNA↗

PubMed2005

Large scale molecular dynamics simulation of native and mutant dihydropteroate synthase-sulphanilamide complexes suggests the molecular basis for dihydropteroate synthase drug resistance.

Antibiotic resistance is hampering the efficacy of drugs in the treatment of several pathological infections. Dihydropteroate synthase (DHPS) has been targeted by sulphonamide inhibitors for the past 60 years and has developed different amino acid mutations to survive sulpha drug action. We couple homology modelling techniques and massively parallel molecular dynamics simulations to study both the drug-bound and apo forms of native and mutant DHPS. Simulations of the complex between sulphanilamide and Streptomyces pneumoniae, DHPS shows how sulphanilamide is able to position itself close to 6-hydroxymethyl-7, 8-dihydropteridine-phosphate in a suitable position for the enzymatic transformation whereas in the mutant complex the sulpha drug is expelled from the catalytic site. Our simulations, therefore, provide insight into the molecular basis for drug resistance with S. pneumoniae DHPS.

Anti-Bacterial Agents↗

PubMed2003

Sizing the holin lesion with an endolysin-beta-galactosidase fusion.

Double-stranded DNA phages require two proteins for efficient host lysis: the endolysin, a muralytic enzyme, and the holin, a small membrane protein. In an event that defines the end of the vegetative cycle, the lambda holin S acts suddenly to permeabilize the membrane. This permeabilization enables the R endolysin to attack the cell wall, after which cell lysis occurs within seconds. A C-terminal fusion of the R endolysin with full-length beta-galactosidase (beta-Gal) was tested for lytic competence in the context of the late-gene expression system of an induced lambda lysogen. Under these conditions, the hybrid R-beta-Gal product, an active tetrameric beta-Gal greater than 480 kDa in mass, was fully functional in lysis mediated by the S holin. Western blot analysis demonstrated that the lytic competence was not due to the proteolytic release of the endolysin domain of the R-beta-Gal fusion protein. The ability of this massive complex to be released by the S holin suggests that S causes a generalized membrane disruption rather than a regular oligomeric membrane pore. Similar results were obtained with an early lysis variant of the S holin and also in parallel experiments with the T4 holin, T, in an identical lambda context. However, premature holin lesions triggered by depolarization of the membrane were nonpermissive for the hybrid endolysin, indicating that these premature lesions constituted less-profound damage to the membrane. Finally, a truncated T holin functional in lysis with the endolysin is completely incompetent for lysis with the hybrid endolysin. A model for the formation of the membrane lesion within homo-oligomeric rafts of holin proteins is discussed.

Amino Acid Sequence↗

PubMed1997

Peroxynitrite modulates tyrosine-dependent signal transduction pathway of human erythrocyte band 3.

Peroxynitrite, the product of the reaction between nitric oxide and superoxide anion, is able to nitrate protein tyrosines. If this modification occurs on phosphotyrosine kinase substrates, it can down-regulate cell signaling. We investigated the effects of peroxynitrite on band 3-mediated signal transduction of human erythrocytes. Peroxynitrite treatment induced two different responses. At low concentrations (10-100 microM) it stimulated a metabolic response, leading to 1) a reversible inhibition of phosphotyrosine phosphatase activity, 2) a rise of tyrosine phosphorylation in the 22K cytoplasmic domain of band 3, 3) the release of glyceraldehyde 3-phosphate dehydrogenase from the membrane, and 4) the enhancement of lactate production. At high concentrations (200-1000 microM), peroxynitrite induced 1) cross-linking of membrane proteins, 2) inhibition of band 3 tyrosine phosphorylation, 3) nitration of tyrosines in the 22K cytoplasmic domain of band 3, 4) binding of hemoglobin to the membrane, 5) irreversible inhibition of phosphotyrosine kinase activity, 6) massive methemoglobin production, and 7) irreversible inhibition of lactate production. Our results demonstrate that at concentrations that could conceivably be achieved in vivo (10-100 microM), peroxynitrite behaves like other oxidants, i.e., it stimulates band 3 tyrosine phosphorylation and increases glucose metabolism. Thus, one plausible physiologic effect of peroxynitrite is the up-regulation of signaling through the reversible inhibition of phosphotyrosine phosphatase activity. At high concentrations of peroxynitrite, the tyrosine phosphorylation ceases in parallel with the nitration of band 3 tyrosines, but at these concentrations phosphotyrosine kinase activity and glycolysis are also irreversibly inhibited. Thus, at least in red blood cells, the postulated down-regulation of signaling by peroxynitrite cannot merely be ascribed to the nitration of tyrosine kinase targets.

Amino Acid Sequence↗

PubMed1998

Parallel thermodynamic analysis of duplexes on oligodeoxyribonucleotide microchips.

A microchip method has been developed for massive and parallel thermodynamic analyses of DNA duplexes. Fluorescently labeled oligonucleotides were hybridized with oligonucleotides immobilized in the 100 x 100 x 20 mum gel pads of the microchips. The equilibrium melting curves for all microchip duplexes were measured in real time in parallel for all microchip duplexes. Thermodynamic data for perfect and mismatched duplexes that were obtained using the microchip method directly correlated with data obtained in solution. Fluorescent labels or longer linkers between the gel and the oligonucleotides appeared to have no significant effect on duplex stability. Extending the immobilized oligonucleotides with a four-base mixture from the 3'-end or one or two universal bases (5-nitroindole) from the 3'- and/or 5'-end increased the stabilities of their duplexes. These extensions were applied to increase the stabilities of the duplexes formed with short oligonucleotides in microchips, to significantly lessen the differences in melting curves of the AT- and GC-rich duplexes, and to improve discrimination of perfect duplexes from those containing poorly recognized terminal mismatches. This study explored a way to increase the efficiency of sequencing by hybridization on oligonucleotide microchips.

Acrylic Resins↗