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PubMed2002

Sequences of elongation factors-1 alpha and -1 gamma and stimulation by juvenile hormone in Locusta migratoria.

Two cDNAs encoding the alpha and gamma subunits of translation elongation factor-1 (EF-1) have been cloned and sequenced from the African migratory locust, Locusta migratoria. Southern blotting and real-time PCR analyses indicated that these sequences represent single copy genes. Comparison with sequences from other species indicated greater conservation for EF-1 alpha than for EF-1 gamma. The developmental profiles for EF-1 alpha and -1 gamma mRNA expression in the fat body paralleled reported changes in the hemolymph juvenile hormone (JH) titer in the fifth instar and were elevated during early reproductive maturation in the female adult. In maturing adults, there was a greater accumulation of EF-1 alpha and -1 gamma transcripts in females than in males. The levels of both transcripts were greatly increased by an enriched diet, previously shown to elevate JH titers and accelerate vitellogenin production. Treating JH-deprived adult females with the JH analog, methoprene, resulted in more than doubling of transcript levels of both genes, supporting the hypothesis that JH could stimulate the accumulation of LmEF-1 alpha and -1 gamma transcripts. We suggest that production of elongation factors, increased by JH, may contribute to the massive protein synthesis required for egg production.

Amino Acid Sequence↗
PubMed2003

Influence of zinc deficiency on the mRNA expression of zinc transporters in adult rats.

The accumulation of zinc in the cell is a sum of influx and efflux processes via transporter proteins, like the four Zn transporters (ZnT1-4), the divalent cation transporter 1 (DCT1) and of storage processes mainly bound to metallothionein (MT). To study the effect of Zn deficiency on mRNA expression levels, adult rats were used as an animal model. Food intake was restricted to 8 g/day containing 2 microg Zn/g fortified with pure phytate in Zn deficiency rats and 58 microg Zn/g in controls (n = 7). At day 1, 2, 4, 7, 11, 16, 22, and 29 of Zn deficiency, 3 animals were sacrificed, respectively (n = 24). Zn deficiency was evident from reduced plasma Zn, plasma alkaline phosphatase activity and severe mobilization of Zn from tissue stores (mainly skeleton), while food intake and body weight remained unaffected. Tissues representing Zn absorption (jejunum, colon), Zn storage and utilization (muscle, liver), and Zn excretion (kidney) were retrieved. Total RNA contents increased in colon (p = 0.003) and trend to decrease in liver (p = 0.086). Zn deficiency was without effect on tissue total RNA concentrations in muscle tissue and kidney. Real-time reverse transcription (RT) polymerase chain reaction (PCR) assays were developed and a relative quantification on the basis of GAPDH was applied. Assays allowed a relative and accurate quantification of mRNA molecules with a sufficiently high sensitivity and repeatability. All known Zn transporter subtypes were found in the tissues. ZnT3 was newly elucidated and sequenced in rat tissues. Expression patterns and reactions to Zn deficiency were specific for the tissue analysed. Expression results imply that some transporters are expressed constitutively, whereas others are highly regulated in tissues responsible for Zn homeostasis. The most distinct changes of expression levels were shown in colon which can therefore be postulated as a highly Zn sensitive tissue. MT was down-regulated in all tissues, massively in liver (p < 0.001) and in colon (p = 0.002) and in tendency also in the jejunum and kidney. In parallel with intracellular Zn status it is a potent candidate gene for Zn deficiency. ZnT1 and ZnT2 showed a significant up-regulation of mRNA expression in colon (p = 0.032 and p = 0.026) and for ZnT2 a trend of down regulation in jejunum (p = 0.098). This study provides the first comparative view of regulation of gene expression and fully quantitative expression analysis of all known Zn transporters in a non growing adult rat model on a constant platform and therefore allows a direct comparison.

Animals↗
PubMedDate not supplied

Prominent white matter cavitation in an infant with Alexander's disease.

The clinical history and autopsy findings are reported on a case of infantile Alexander's disease (AD). The patient, a white baby girl, developed seizures at age 4 months accompanied by internal hydrocephalus. She died at age 11 months following a progressive, downhill course of profound psychomotor retardation, recurrent seizures and cachexia. The general autopsy was remarkable for cachexia. The formalin fixed brain and spinal cord were studied by light and electron microscopy (EM). The brain was normal in weight for age but showed diffuse pallor of white matter and marked cavitation involving the cerebral and cerebellar subcortical white matter, most profound in the frontal lobes. Microscopically the CNS showed classic features of AD with diffuse paucity of myelin and massive proliferation of astrocytes bearing Rosenthal fibers (RF). The latter appeared as granular osmiophilic deposits associated with 8-10 nm filaments within astrocytic processes and cell bodies by EM. This case of AD is remarkable for the extreme degree of cavitation. Cavitary changes affect up to one third of typical cases of AD and are invariably present in the frontal white matter. Affected patients are generally much younger and have a shorter clinical course than AD patients without brain cavitation. The dysmyelination of AD inversely parallels the temporal sequence of normal myelination and suggests a relative resistance of early myelinated structures to the presumed astrocytic defect causing AD. Adults with de novo formation of RF's in the CNS have a varied clinical and pathological appearance, rarely show brain cavitation and should probably be distinguished from classic AD in children.

Astrocytes↗
PubMed2003

Chromatin remodeling as a guide to transcriptional regulatory networks in mammals.

An important challenge of genome biology is a dissection of transcriptional regulatory networks that operate inside the nucleus during ontogeny and disease (Wyrick and Young [2002] Curr. Opin. Genet. Dev. 12:130). Limitations of existing experimental tools greatly complicate such analysis in the human genome: for example, genome-wide expression profiling of cells responding to a stimulus fails to reveal a majority of the genes involved in the functional network of responding to that stimulus [Giaver et al., 2002; Birrell et al., 2002]. This article discusses recent advances in analyzing mammalian transcriptional regulatory circuits [Nikiforov et al., 2002; Weinmann et al., 2002; Ren et al., 2000]. As evidenced by these and other data, paucity of information about the location of regulatory DNA elements in the human genome presents an obstacle to comprehensive transcription network analysis. It has been known since the late 1970s that chromatin over active regulatory DNA stretches is stably remodeled into "nuclease hypersensitive sites" [Elgin, 1988; Gross and Garrard 1988]. Massively parallel analysis of such remodeling in cell nuclei identifies regulatory DNA that is difficult to map comprehensively using other approaches, reveals genes poised for rapid activation, and offers a novel perspective on the "epigenome"--the regulatory program being executed by the genome in a given cell type.

Animals↗
PubMed2005

Structural polymorphism of the HIV-1 leader region explored by computational methods.

Experimental studies revealed that the elements of the human immunodeficiency virus type 1 (HIV-1) 5'-untranslated leader region (5'-UTR) can fold in vitro into two alternative conformations, branched (BMH) and 'linearized' (LDI) and switch between them to achieve different functionality. In this study we computationally explored in detail, with our massively parallel genetic algorithm (MPGAfold), the propensity of 13 HIV-1 5'-UTRs to fold into the BMH and the LDI conformation types. Besides the BMH conformations these results predict the existence of two functionally equivalent types of LDI conformations. One is similar to what has been shown in vitro to exist in HIV-1 LAI, the other is a novel conformation exemplified by HIV-1 MAL long-distance interactions. These novel MPGAfold results are further corroborated by a consensus probability matrix algorithm applied to a set of 155 HIV-1 sequences. We also have determined in detail the impact of various strain mutations, domain sizes and folds of elongating sequences simulating folding during transcription on HIV-1 RNA secondary structure folding dynamics.

5' Untranslated Regions↗
PubMed1992

Regulation and light-harvesting complex II association of a Dunaliella protein homologous to early light-induced proteins in higher plants.

The unicellular green alga Dunaliella bardawil responds to high light, nutrient deprivation, and several other types of stress by massive accumulation of beta-carotene. We have previously cloned a nuclear gene, cbr, that is co-induced with accelerated carotenogenesis. The predicted product of cbr is closely related to early light-induced proteins (Elips) of higher plants, and also shows resemblance to chlorophyll a/b-binding proteins. In the present study, the determination of the cbr transcription start site supported the previously proposed site of translation initiation. Antibodies raised against a synthetic oligopeptide matching the predicted sequence of Cbr recognized two polypeptides of apparently 17 and 19 kDa that were induced in parallel to cbr transcript accumulation in highly illuminated or sulfate-starved D. bardawil cells. The antibodies also cross-reacted with an approximately 20-kDa polypeptide in sulfate-starved Dunaliella salina. In both D. bardawil and D. salina, Cbr was found exclusively in the thylakoid membranes. After mild solubilization, Cbr co-fractionated with light-harvesting complex II (LHCII) in sucrose gradient centrifugation and gel electrophoresis and was specifically associated with a minor LHCII complex. An occasionally observed, faster mobility Cbr form, free of LHCII, was probably released from the larger complex. These results support the conclusion that Cbr belongs to a class of stress-induced proteins transiently associated with antennae complexes.

Amino Acid Sequence↗
PubMed2007

Stage-specific alterations of the genome, transcriptome, and proteome during colorectal carcinogenesis.

To identify sequential alterations of the genome, transcriptome, and proteome during colorectal cancer progression, we have analyzed tissue samples from 36 patients, including the complete mucosa-adenoma-carcinoma sequence from 8 patients. Comparative genomic hybridization (CGH) revealed patterns of stage specific, recurrent genomic imbalances. Gene expression analysis on 9K cDNA arrays identified 58 genes differentially expressed between normal mucosa and adenoma, 116 genes between adenoma and carcinoma, and 158 genes between primary carcinoma and liver metastasis (P < 0.001). Parallel analysis of our samples by CGH and expression profiling revealed a direct correlation of chromosomal copy number changes with chromosome-specific average gene expression levels. Protein expression was analyzed by two-dimensional gel electrophoresis and subsequent mass spectrometry. Although there was no direct match of differentially expressed proteins and genes, the majority of them belonged to identical pathways or networks. In conclusion, increasing genomic instability and a recurrent pattern of chromosomal imbalances as well as specific gene and protein expression changes correlate with distinct stages of colorectal cancer progression. Chromosomal aneuploidies directly affect average resident gene expression levels, thereby contributing to a massive deregulation of the cellular transcriptome. The identification of novel genes and proteins might deliver molecular targets for diagnostic and therapeutic interventions.

Adult↗
PubMed2002

An assessment of Motorola CodeLink microarray performance for gene expression profiling applications.

DNA microarrays enable users to obtain information on differences in transcript abundance on a massively parallel scale. Recently, however, data analyses have revealed potential pitfalls related to image acquisition, variability and misclassifications in replicate measurements, cross-hybridization and sensitivity limitations. We have generated a series of analytical tools to address the manufacturing, detection and data analysis components of a microarray experiment. Together, we have used these tools to optimize performance in an expression profiling study. We demonstrate three significant advantages of the Motorola CodeLink platform: sensitivity of one copy per cell, coefficients of variation of 10% in the hybridization signals across slides and across target preparations, and specificity in distinguishing highly homologous sequences. Slides where oligonucleotide probes are spotted in 6-fold redundancy were used to demonstrate the effect of replication on data quality. Lastly, the differential expression ratios obtained with the CodeLink expression platform were validated against those obtained with quantitative reverse transcription-PCR assays for 54 genes.

Gene Expression Profiling↗
PubMed2004

A case study of high-throughput biological data processing on parallel platforms.

MOTIVATION: Analysis of large biological data sets using a variety of parallel processor computer architectures is a common task in bioinformatics. The efficiency of the analysis can be significantly improved by properly handling redundancy present in these data combined with taking advantage of the unique features of these compute architectures. RESULTS: We describe a generalized approach to this analysis, but present specific results using the program CEPAR, an efficient implementation of the Combinatorial Extension algorithm in a massively parallel (PAR) mode for finding pairwise protein structure similarities and aligning protein structures from the Protein Data Bank. CEPAR design and implementation are described and results provided for the efficiency of the algorithm when run on a large number of processors. AVAILABILITY: Source code is available by contacting one of the authors.

Algorithms↗
PubMed2003

Massive parallelism, randomness and genomic advances.

In reviewing the past decade, it is clear that genomics was, and still is, driven by innovative technologies, perhaps more so than any other scientific area in recent memory. From the outset, computing, mathematics and new automated laboratory techniques have been key components in allowing the field to move forward rapidly. We highlight some key innovations that have come together to nurture the explosive growth that makes a new era of genomics a reality. We also document how these new approaches have fueled further innovations and discoveries.

Animals↗
PubMed2006

Screening the receptorome yields validated molecular targets for drug discovery.

With the recently completed sequencing and annotation of the human genome, it has become clear that a significant portion of the genome encodes signal-transducing molecules including receptors, protein kinases, ion channels, transporters and coupling proteins. This review focuses on membrane-localized receptors, which represent the largest single group of signal-transducing molecules. Indeed, one can estimate that nearly 10% of the human genome encodes membrane-localized receptors (e.g. G-protein coupled receptors, ligand-gated ion channels and transporters). We have defined that portion of the human genome that encodes 'receptors' the receptorome. In this article, we will demonstrate how the massively parallel screening of the receptorome provides a facile and under-utilized screening platform for drug discovery. Using case studies, we will show how receptorome-based screening elucidates the mechanisms responsible for serious side-effects of both approved and investigational medications. Additionally, we will provide evidence that receptorome-based screening provides insights into novel therapeutic indications of approved medications and serves to validate targets for therapeutic drug discovery.

Antipsychotic Agents↗
PubMed2004

Genomics and the Human Genome Project: implications for psychiatry.

In the past decade the Human Genome Project has made extraordinary strides in understanding of fundamental human genetics. The complete human genetic sequence has been determined, and the chromosomal location of almost all human genes identified. Presently, a large international consortium, the HapMap Project, is working to identify a large portion of genetic variation in different human populations and the structure and relationship of these variants to each other. The Human Genome Project has approached human genetics on a scale not previously seen in biology. This has been made possible by dramatic advances in high throughput technology and bio-informatics. Tools such as gene chips and micro-arrays have spawned an entirely new strategy to examine the function and expression of genes in a massively parallel fashion. Together these tools have dramatically advanced our knowledge about the human genome. They promise powerful new approaches to complex genetic traits such as psychiatric illness. The goals and progress of the Human Genome Project and the technology involved are reviewed. The implications of this science for psychiatric genetics are discussed.

Computational Biology↗
PubMed1999

Genome-scale Gene Expression Analysis and Pathway Reconstruction in KEGG.

The massively parallel hybridization technologies by DNA chips and microarrays make it possible to monitor expression patterns of the whole set of genes in a genome under various conditions. The vast amount of data generated by such technologies necessitates the development of a new database management system that integrates expression data with other molecular biology databases and various analysis tools. We report here an extension of our KEGG (Kyoto Encyclopedia of Genes and Genomes) and DBGET/LinkDB systems for analyzing gene expression data in conjunction with pathway information and genomic information. It is now possible to make use of expression data for the reconstruction of pathways from the complete genome sequences.

Journal Article↗
PubMed2006

Graphical exploratory data analysis of RNA secondary structure dynamics predicted by the massively parallel genetic algorithm.

Studies indicate that RNA may enter intermediate and multiple conformational states, which may impact gene expression and molecular function. It is known that the biologically functional states of RNA molecules may not correspond to their minimum energy conformations, that kinetic barriers may trap the molecule in a local minimum, that folding often occurs during transcription, and that cases exist in which a molecule will transition between one or more functional conformations. Thus, methods for simulating the folding pathway and dynamic behavior of an RNA molecule are important for the prediction of RNA structure and its associated functions. We have developed several data mining techniques guided by interactive visualization tools associated with our massively parallel genetic algorithm for RNA/DNA secondary structure prediction, MPGAfold, and StructureLab analysis workbench. Most of the methods and tools are also applicable to dynamic programming algorithm (DPA) folding data analysis. When applied to MPGAfold results these methodologies are used to determine the significant intermediate and final structures associated with co-transcriptional and full length RNA folding. Since the genetic algorithm is essentially stochastic, multiple runs are required to develop a consensus understanding of an RNA structure. The interactive visualizations facilitate interpretation of results from sequential or full length individual MPGAfold runs, final results of multiple folding runs, including multiple population sizes, and the results from multiple RNA sequences of one family. This paper describes several of these techniques and shows how they are used to help solve this highly combinatoric problem.

Algorithms↗
PubMedDate not supplied

p53 gene mutations and protein nuclear accumulation are early events in intestinal type gastric cancer but late events in diffuse type.

We screened for p53 alterations in 71 early gastric cancers of differing histological types and growth patterns, 18 advanced cancers of diffuse type, 19 dysplastic lesions, and 12 extensive intestinal metaplasia cases. Tumors were investigated for gene mutations (exons 5-8) with PCR-based denaturing gradient gel electrophoresis and sequencing techniques, and for protein accumulation with immunohistochemical methods. Nontumor samples were studied with immunohistochemistry alone. Of the early cancers, intestinal tumors showed a much higher p53 mutation frequency (41%) than did diffuse cancers (4%). When comparing early and advanced tumors of the same type, we observed a similarity in mutation frequency (41 versus about 50%) for intestinal tumors, and a significant increase for diffuse tumors (from 4 to 33%). Immunopositive case distribution between tumor types and stages paralleled that of mutated cases. Immunohistochemical and genetic analysis gave concordant results for all samples with gene mutations. Eighteen of the 65 (28%) nonmutated tumors displayed significant immunoreactivity. Early tumors that massively penetrated the submucosa, i.e., the early tumors for which prognosis is worst, showed the highest frequency both of p53 gene mutation and of nonmutated protein accumulation. Twelve of 19 dysplastic lesions showed significant immunoreactivity, whereas intestinal metaplasias proved unreactive in all but a few cells. Our results yield two implications: that p53 alterations have a crucial and early role in gastric carcinogenesis of intestinal type, likely acting at the transition step between metaplasia and dysplasia; and that the alterations are mainly associated with tumor progression in cancer of diffuse type.

Adenocarcinoma↗
PubMed1990

Acid helix-turn activator motif.

A common sequence/structural motif pattern has been identified within the steroid/thyroid hormone receptors and other transcriptional activators using a new massively parallel symbolic learning assistant computer system. The pattern appears nearly diagnostic of transcription activation, including relative activation strength, among nuclear and DNA-binding prokaryotic proteins. In cases where mutation/deletion/chimeric studies have identified the activation domain, the pattern matches within that domain. These facts and the nature of the pattern itself strongly support the idea that the patterned domain is directly involved in a protein-protein transcription activation interaction.

Amino Acid Sequence↗
PubMed1989

Macrophage infiltration precedes and is a prerequisite for lymphocytic insulitis in pancreatic islets of pre-diabetic BB rats.

We have analysed whether infiltration of macrophages and lymphocyte subtypes into pancreatic islets of diabetes prone BB rats occurs at random or whether insulitis requires a specific sequence of events. Serial sections from more than 700 islets of diabetes prone BB rats (70-150 days of age) were analysed for infiltrating immunocytes and expression of major histocompatibility complex antigens by 4-11 different monoclonal antibodies. In parallel, electron microscopy was performed in a fraction of islets. Part of the animals had been treated with macrophage toxic silica particles. A specific non-random sequence of events was identified and 4 stages of islet inflammation were recognised. Stages 1a and 1b are defined by macrophage (ED1+, W3/25+. Ox3/6/17+, ED2-) infiltration and concomitant enhanced major histocompatibility complex class I antigen expression initially at one pole or at the periphery of islets. T-, NK- and B-lymphocytes are absent (less than 1 cell per mean islet section). In stage 2, more macrophages are infiltrating and concomitantly Ox19+-T-lymphocytes and Ox8+-granular (NK-) lymphocytes are observed. In stage 3, additional massive infiltration of Ox12+-B-lymphocytes is noted. Silica treatment of BB rats largely prevented macrophage infiltration. Concomitantly islets were free of lymphocytes. Thus, macrophage infiltration clearly precedes T- and NK-lymphocyte and later B-lymphocyte infiltration. Lymphocytes do not infiltrate islets in the absence of prior macrophage invasion.

Animals↗
PubMed1999

The gospel of the fossil brain: Tilly Edinger and the science of paleoneurology.

Tilly Edinger (1897-1967) was a vertebrate paleontologist interested in the evolution of the central nervous system. By combining methods and insights gained from comparative neuroanatomy and paleontology, she almost single-handedly founded modern paleoneurology in the 1920s while working at the Senckenberg Museum in Frankfurt am Main. Edinger's early research was mostly descriptive and conducted within the theoretical framework of brain evolution formulated by O. C. Marsh in the late 19th century. Nevertheless, she became immediately known in 1929 after publishing an extensive review on "fossil brains." Reconstructing evolutionary history from the fossil record instead of from the comparative analysis of living forms allowed her to identify the sequence of neural innovations within several mammalian lineages. Anti-Jewish terrorism forced Edinger to leave Nazi Germany in 1939. After finding refuge first in England, she continued her career at Harvard's Museum of Comparative Zoology. There she documented the occurrence of gross neural correlates of specialized behavior in several vertebrate lineages, and identified parallel evolution in mammalian sulcation patterns. Her insight that neural innovations need not be "correlated" with either nonneural innovations or with evolutionary "success" led her to reject Marsh's theory of progressive increase in brain size over time and other "anthropocentric" understandings of brain evolution. Edinger's research, her insistence on a stratigraphic and evolutionary framework for interpretation, and her massive compilations of paleoneurological literature established her as the leading definer, practitioner, and chronicler of her field.

Brain↗