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At least 865 records · Page 48Linked to original sources

Structures and dynamics of Drosophila Tpr inconsistent with a static, filamentous structure.

Here we report immunofluorescence localizations of the Drosophila Tpr protein which are inconsistent with a filament-forming protein statically associated with nuclear pore complex-associated intranuclear filaments. Using tissues from throughout the Drosophila life cycle, we observe that Tpr is often localized to discontinuous, likely granular or particulate structures in the deep nuclear interior. These apparent granules have no obvious connectivity to pore complexes in the nuclear periphery, and are often localized on the surfaces of chromosomes and to the perinucleolar region. Most strikingly, after 1 h of heat shock, the great majority of the Tpr in the deep nuclear interior accumulates at a single heat shock puff, while Tpr in the nuclear periphery appears unchanged. This heat shock puff, 93D, is a known repository for many components of pre-mRNA metabolism during heat shock. Although we do not observe Tpr at sites of transcription under normal conditions, the 93D heat shock result leads us to favor a role for Tpr in mRNA metabolism, such as the transport of mRNA through the nuclear interior to nuclear pore complexes. Consistent with this, we observe networks of Tpr containing granules spanning between the nucleolus and the nuclear periphery which are also decorated by an anti-SR protein antibody. Since we also observe Drosophila Tpr in reticular or fibrous structures in other nuclei, such as salivary gland polytene nuclei, these results indicate that Tpr can exist in at least two structural forms, and suggest that Tpr may relocalize or even change structural forms in response to cellular needs.

Active Transport, Cell Nucleus↗

Leptomonas seymouri, Trypanosoma brucei: a method for isolating trypanosomatid nuclear factors which bind T. brucei single-stranded g-rich telomere sequence.

Sequential expression of variant surface glycoproteins (VSG) in Trypanosoma brucei is the basis of antigenic variation which is essential for parasite survival. Telomere distal copies of VSG genes, so-called basic copies, provide a repository of VSG sequence information for variability, but actively expressed copies are found only at subtelomeric regions of chromosomes. Of eight or so expression sites (ES) in the T. brucei genome, only one is active at one time. Movement of a basic copy VSG gene to an ES requires a recombination event of unknown mechanism. The properties of telomeres have been speculated to be important for control of VSG expression or basic copy mobilization, prompting us to begin to investigate telomere-binding proteins in trypanosomatids. The T. brucei telomere sequence is known, facilitating design of synthetic telomeric DNAs. Here we describe a method for preparation of active trypanosomatid nuclear extracts. We show that in T. brucei and Leptomonas seymouri, factors can be detected which bind a g-rich single-strand telomere sequence based on the T. brucei telomere. The L. seymouri telomere-binding factor, LST-1, dissociates in the presence of high salt to produce a core factor, LST-2, migrating similarly to the T. brucei telomere-binding factor TBT-1. The affinity of LST-2 and TBT-1 for DNA under high salt conditions is characteristic of telomere proteins.

Animals↗

NIGMS human/rodent somatic cell hybrid mapping panels 1 and 2.

The NIGMS Human Genetic Mutant Cell Repository is currently distributing two well-characterized human/rodent somatic cell hybrid mapping panels. Mapping Panel 1 consists of DNA isolated from 18 hybrid cell cultures retaining from 1 to 19 human chromosomes. Mapping Panel 2 contains DNA from hybrids retaining 1 or 2 human chromosomes. All but 2 of the hybrids retain a single intact human chromosome. Mapping Panel 2 is also available as cell cultures. These resources should prove valuable to the Human Genome Project initiative. This article describes the sources of the hybrid cell cultures and the procedures utilized to prepare and characterize the panels.

Animals↗

Unique genetic variation revealed by a microsatellite polymorphism survey in ten wild-derived inbred strains.

Here we report on a genome polymorphism survey using 254 microsatellite markers in ten recently wild-derived inbred strains. Allele size analysis showed that the rate of polymorphism of these wild-derived mouse strains when compared with any of the common laboratory strains is on average 79.8%. We found 632 wild-derived alleles that were not present in the common laboratory strains, representing a 61% increase over the genetic variation observed in the laboratory strains. We also found that on average 14.5% of the microsatellite alleles of any given wild-derived inbred strain were unique. Our results indicate that the recently wild-derived mouse strains represent repositories of unique naturally occurring genetic variability and may prove invaluable for the study of complex phenotypes and in the construction of new mouse models of human disease.

Alleles↗

Sorption Mechanisms of Eu(3+) on CSH Phases of Hydrated Cements.

The sorption mechanisms of Eu(3+) on calcium silicate hydrate (CSH) phases of hydrated cement were investigated as a tool for the prediction of the behavior of trivalent radionuclides with aged/degraded cements in radioactive waste repositories. Four techniques were used: site-selective and time-resolved luminescence spectroscopy, XPS, high-resolution SEM coupled with EDX, and XRD. Results showed that europium is not precipitated in the solution despite its low solubility limit. It is strongly retained on CSH, resulting in a more than 99.8% sorption rate. Two main sorption sites were characterized by luminescence spectroscopy. One site, with a long lifetime, can be interpreted as Eu included in the framework of CSH. Another one, with a shorter lifetime, can be interpreted as a site with a hydrated environment that is high but is less than that of europium hydroxide. It corresponds to superficial complexation or precipitation. Copyright 2001 Academic Press.

Journal Article↗

Study of the catalytic behavior of montmorillonite/iron(III) and Mn(III) cationic porphyrins.

Two samples of montmorillonite (one of Brazilian origin, BNC1 clay, and the other STX-1, supplied by the Clay Mineral Society Repository (University of Missouri, USA) were allowed to react with biomimetic metalloporphyrins of Fe(III) and Mn(III) in cationic form. The compounds were characterized by several techniques, showing that the metalloporphyrins molecules were adsorbed at the surface of the clay platelet crystals. The catalytic activities of the intercalated complexes for the oxidation of alkane were dependent upon the concentration of the porphyrin immobilized in the clay and factors such as the metal ion species in the porphyrins, choice of solvent, and concentration of the iodosylbenzene oxidant. Good selectivity to cyclohexanol instead of cyclohexanone was observed for the catalytic oxidation of cyclohexane by iodosylbenzene.

Aluminum Silicates↗

Gene structure prediction by spliced alignment of genomic DNA with protein sequences: increased accuracy by differential splice site scoring.

Gene identification in genomic DNA from eukaryotes is complicated by the vast combinatorial possibilities of potential exon assemblies. If the gene encodes a protein that is closely related to known proteins, gene identification is aided by matching similarity of potential translation products to those target proteins. The genomic DNA and protein sequences can be aligned directly by scoring the implied residues of in-frame nucleotide triplets against the protein residues in conventional ways, while allowing for long gaps in the alignment corresponding to introns in the genomic DNA. We describe a novel method for such spliced alignment. The method derives an optimal alignment based on scoring for both sequence similarity of the predicted gene product to the protein sequence and intrinsic splice site strength of the predicted introns. Application of the method to a representative set of 50 known genes from Arabidopsis thaliana showed significant improvement in prediction accuracy compared to previous spliced alignment methods. The method is also more accurate than ab initio gene prediction methods, provided sufficiently close target proteins are available. In view of the fast growth of public sequence repositories, we argue that close targets will be available for the majority of novel genes, making spliced alignment an excellent practical tool for high-throughput automated genome annotation.

Algorithms↗

Database challenges and solutions in neuroscientific applications.

In the scientific community, the quality and progress of various endeavors depend in part on the ability of researchers to share and exchange large quantities of heterogeneous data with one another efficiently. This requires controlled sharing and exchange of information among autonomous, distributed, and heterogeneous databases. In this paper, we focus on a neuroscience application, Neuroanatomical Rat Brain Viewer (NeuART Viewer) to demonstrate alternative database concepts that allow neuroscientists to manage and exchange data. Requirements for the NeuART application, in combination with an underlying network-aware database, are described at a conceptual level. Emphasis is placed on functionality from the user's perspective and on requirements that the database must fulfill. The most important functionality required by neuroscientists is the ability to construct brain models using information from different repositories. To accomplish such a task, users need to browse remote and local sources and summaries of data and capture relevant information to be used in building and extending the brain models. Other functionalities are also required, including posing queries related to brain models, augmenting and customizing brain models, and sharing brain models in a collaborative environment. An extensible object-oriented data model is presented to capture the many data types expected in this application. After presenting conceptual level design issues, we describe several known database solutions that support these requirements and discuss requirements that demand further research. Data integration for heterogeneous databases is discussed in terms of reducing or eliminating semantic heterogeneity when translations are made from one system to another. Performance enhancement mechanisms such as materialized views and spatial indexing for three-dimensional objects are explained and evaluated in the context of browsing, incorporating, and sharing. Policies for providing the system with fault tolerance and avoiding possible intellectual property abuses are presented. Finally, two existing systems are evaluated and compared using the identified requirements.

Animals↗

Functional localization of a "Time Keeper" function separate from attentional resources and task strategy.

The functional neuroanatomy of time estimation has not been well-documented. This research investigated the fMRI measured brain response to an explicit, prospective time interval production (TIP) task. The study tested for the presence of brain activity reflecting a primary time keeper function, distinct from the brain systems involved either in conscious strategies to monitor time or attentional resource and other cognitive processes to accomplish the task. In the TIP task participants were given a time interval and asked to indicate when it elapsed. Two control tasks (counting forwards, backwards) were administered, in addition to a dual task format of the TIP task. Whole brain images were collected at 1.5 Tesla. Analyses (n = 6) yielded a statistical parametric map (SPM ¿z¿) reflecting time keeping and not strategy (counting, number manipulation) or attention resource utilization. Additional SPM ¿z¿s involving activation associated with the accuracy and magnitude the of time estimation response are presented. Results revealed lateral cerebellar and inferior temporal lobe activation were associated with primary time keeping. Behavioral data provided evidence that the procedures for the explicit time judgements did not occur automatically and utilized controlled processes. Activation sites associated with accuracy, magnitude, and the dual task provided indications of the other structures involved in time estimation that implemented task components related to controlled processing. The data are consistent with prior proposals that the cerebellum is a repository of codes for time processing, but also implicate temporal lobe structures for this type of time estimation task.

Adult↗

Magnetic resonance image tissue classification using a partial volume model.

We describe a sequence of low-level operations to isolate and classify brain tissue within T1-weighted magnetic resonance images (MRI). Our method first removes nonbrain tissue using a combination of anisotropic diffusion filtering, edge detection, and mathematical morphology. We compensate for image nonuniformities due to magnetic field inhomogeneities by fitting a tricubic B-spline gain field to local estimates of the image nonuniformity spaced throughout the MRI volume. The local estimates are computed by fitting a partial volume tissue measurement model to histograms of neighborhoods about each estimate point. The measurement model uses mean tissue intensity and noise variance values computed from the global image and a multiplicative bias parameter that is estimated for each region during the histogram fit. Voxels in the intensity-normalized image are then classified into six tissue types using a maximum a posteriori classifier. This classifier combines the partial volume tissue measurement model with a Gibbs prior that models the spatial properties of the brain. We validate each stage of our algorithm on real and phantom data. Using data from the 20 normal MRI brain data sets of the Internet Brain Segmentation Repository, our method achieved average kappa indices of kappa = 0.746 +/- 0.114 for gray matter (GM) and kappa = 0.798 +/- 0.089 for white matter (WM) compared to expert labeled data. Our method achieved average kappa indices kappa = 0.893 +/- 0.041 for GM and kappa = 0.928 +/- 0.039 for WM compared to the ground truth labeling on 12 volumes from the Montreal Neurological Institute's BrainWeb phantom.

Adult↗

Automated histogram-based brain segmentation in T1-weighted three-dimensional magnetic resonance head images.

Current semiautomated magnetic resonance (MR)-based brain segmentation and volume measurement methods are complex and not sufficiently accurate for certain applications. We have developed a simpler, more accurate automated algorithm for whole-brain segmentation and volume measurement in T(1)-weighted, three-dimensional MR images. This histogram-based brain segmentation (HBRS) algorithm is based on histograms and simple morphological operations. The algorithm's three steps are foreground/background thresholding, disconnection of brain from skull, and removal of residue fragments (sinus, cerebrospinal fluid, dura, and marrow). Brain volume was measured by counting the number of brain voxels. Accuracy was determined by applying HBRS to both simulated and real MR data. Comparing the brain volume rendered by HBRS with the volume on which the simulation is based, the average error was 1.38%. By applying HBRS to 20 normal MR data sets downloaded from the Internet Brain Segmentation Repository and comparing them with expert segmented data, the average Jaccard similarity was 0.963 and the kappa index was 0.981. The reproducibility of brain volume measurements was assessed by comparing data from two sessions (four total data sets) with human volunteers. Intrasession variability of brain volumes for sessions 1 and 2 was 0.55 +/- 0.56 and 0.74 +/- 0.56%, respectively; the mean difference between the two sessions was 0.60 +/- 0.46%. These results show that the HBRS algorithm is a simple, fast, and accurate method to determine brain volume with high reproducibility. This algorithm may be applied to various research and clinical investigations in which brain segmentation and volume measurement involving MRI data are needed.

Adult↗

Mechanisms of chlorophyllin anticarcinogenesis: dose-responsive inhibition of aflatoxin uptake and biodistribution following oral co-administration in rainbow trout.

Chlorophyllin (CHL) is a potent blocking agent against aflatoxin B(1) DNA adduction and tumorigenesis in the trout model, but mechanisms responsible for this chemoprotection in vivo are not well established. This study employed aflatoxin B(2) (AFB(2)), a structural analogue of AFB(1) that cannot be metabolized directly to the 8,9-exo-epoxide electrophile, to investigate CHL effects on carcinogen uptake and distribution kinetics following oral exposure in trout. CHL was shown to form an AFB(2) complex in vitro with a dissociation constant (K(d) = 1.92 +/- 0.13 microM) comparable to that with AFB(1). Following gavage, [(3)H]AFB(2) equivalents distributed rapidly from the stomach to other organs including blood, liver, and eventually to bile as a major repository. Bile was found to contain almost entirely parent AFB(2) 1 h after gavage, with a single metabolite dominating 3-24 h and an additional metabolite prominent by 48 h after gavage. Addition of sufficient CHL (>/=13.9 mM) to assure >99% complexation of AFB(2) (0.906 microM) in the gavage mix resulted in 80-90% reduction in AFB(2) equivalents in liver and bile 3 h after gavage. In three separate kinetic studies of up to 120 h postgavage, addition of >/=13.9 mM CHL to the gavage mix reproducibly and markedly delayed the rate of AFB(2) loss from stomach, retarded its appearance in blood, liver, and bile, and reduced peak AFB(2) concentrations in those tissues by up to 60%. Introduction of a food bolus immediately after gavage prolonged AFB(2) residence in stomach and intestine but did not abrogate the inhibitory effects of CHL on AFB(2) uptake and distribution. These results demonstrate that oral co-treatment with CHL under conditions where complex formation is initially assured, substantially reduces AFB(2) systemic uptake and target organ bioavailability in the trout.

Aflatoxins↗

A new strategy in design of +RNA virus infectious clones enabling their stable propagation in E. coli.

Infectious clone methodology is a valuable tool of modern experimental virology. However, its use is often constrained by the instability of infectious clone constructs during propagation in E. coli. To circumvent this problem, we have devised a strategy that could be suitable for design of +RNA virus molecular clones in general. An infectious clone is assembled as "infectious DNA," and expression of problem regions present in the viral cDNA is prevented during propagation in E. coli by insertion of short introns. To demonstrate the feasibility of this approach, a highly unstable Japanese encephalitis flavivirus infectious clone has been successfully converted into a remarkably stable infectious DNA construct with the specific infectivity of 10(6) pfu/microg in cell culture. The proposed strategy may be useful in the design of self-amplifying gene therapy vectors and development of new immunization methodologies, and could facilitate creation of molecular repositories of existing viral vaccines.

Base Sequence↗

Development of biotechnology in India.

India has embarked upon a very ambitious program in biotechnology with a view to harnessing its available human and unlimited biodiversity resources. It has mainly been a government sponsored effort with very little private industry participation in investment. The Department of Biotechnology (DBT) established under the Ministry of Science and Technology in 1986 was the major instrument of action to bring together most talents, material resources, and budgetary provisions. It began sponsoring research in molecular biology, agricultural and medical sciences, plant and animal tissue culture, biofertilizers and biopesticides, environment, human genetics, microbial technology, and bioprocess engineering, etc. The establishment of a number of world class bioscience research institutes and provision of large research grants to some existing universities helped in developing specialized centres of biotechnology. Besides DBT, the Department of Science & Technology (DST), also under the Ministry of S&T, sponsors research at universities working in the basic areas of life sciences. Ministry of Education's most pioneering effort was instrumental in the creation of Biochemical Engineering Research Centre at IIT Delhi with substantial assistance from the Swiss Federal Institute of Technology, Zurich, Switzerland to make available state-of-the-art infrastructure for education, training, and research in biochemical engineering and biotechnology in 1974. This initiative catalysed biotechnology training and research at many institutions a few years later. With a brief introduction, the major thrust areas of biotechnology development in India have been reviewed in this India Paper which include education and training, agricultural biotechnology, biofertilizers and biopesticides, tissue culture for tree and woody species, medicinal and aromatic plants, biodiversity conservation and environment, vaccine development, animal, aquaculture, seri and food biotechnology, microbial technology, industrial biotechnology, biochemical engineering and associated activities such as creation of biotechnology information system and national repositories. Current status of intellectual property rights has also been discussed. Contribution to the India's advances in biotechnology by the industry, excepting a limited few, has been far below expectations. The review concludes with some cautious notes.

Agriculture↗

Orthopoxvirus Genome Sequencing, Assembly, and Analysis.

Poxviruses have exceptionally large genomes compared to most other viruses, which represent unique challenges to sequencing and assembly due to complex features such as repeat elements and low complexity sequences. The 2022 global mpox outbreak led to an unprecedented level of poxvirus sequencing as public health and research institutions faced with large sample numbers and demand for fast turnaround, merged NGS protocols designed for small RNA viruses with poxvirus expertise. Traditional manual assembly, checking, and editing of genomes was not feasible. Here, we present a protocol for metagenomic sequencing and orthopoxvirus genome assembly directly from DNA extracted from a patient lesion swab with no viral enrichment or host depletion. This sequencing approach is cost effective when using high throughput sequencing instruments and allows for detection of genomic insertions, deletions, and large rearrangement with confidence. We describe usage of two publicly available bioinformatic pipelines for genome assembly, quality control, annotation, and submission to sequence repositories.

Orthopoxvirus↗

Mechanisms to stimulate research on assay systems to detect aneuploidy.

The present database on the induction of aneuploidy is inadequate to make comparisons between effects on lower eukaryotic and higher eukaryotic organisms. There is also an urgent need to develop new assays to detect the induction of aneuploidy in animals, as well as assays in lower eukaryotic organisms which can be used in mass-screening programs. The development of chemical and data repositories of chemicals that induce aneuploidy with known activity is proposed as a mechanism to stimulate research in this area. An efficient mechanism to develop a comprehensive database on particular assay systems and a defined set of chemicals is an international Collaborative Trial developed under and sponsored by the International Program on Chemical Safety at the World Health Organization. IPCS is sponsored by voluntary contributions from those member countries who consider such collaborative studies of importance for the development of methodology that can be used to evaluate the mutagenic and carcinogenic potential of environmental chemicals. Exposure to natural and manmade chemicals can be unique, and member countries cannot necessarily assume that chemicals to which native populations will be exposed will be tested elsewhere. The development of an International Collaborative Trial on chemicals that induce aneuploidy and a wide range of eukaryotic assay systems provide an excellent mechanism for the development of a comprehensive database. Within 2-3 years these new data could help to resolve some of the numerous questions that have arisen during the course of the research presented in this Volume.

Aneuploidy↗

New cancer biomarkers deriving from NCI early detection research.

Cancer is not a single disease but an accumulation of several events, genetic and epigenetic, arising in a single cell over a long time interval. A high priority in the cancer field is to identify these events. This can be achieved by characterizing cancer-associated genes and their protein products. Identifying the molecular alterations that distinguish any particular cancer cell from a normal cell will ultimately help to define the nature and predict the pathologic behavior of that cancer cell. It will also indicate the responsiveness to treatment of that particular tumor. Understanding the profile of molecular changes in any particular cancer will be extremely useful as it will become possible to correlate the resulting phenotype of that cancer with molecular events. Achieving these goals and knowledge will provide an opportunity for discovering new biomarkers for early cancer detection and developing prevention approaches. This will also help us identify new targets for therapeutic development. Advancement in technology includes methods and tools that enable research including, but not limited to, instrumentation, techniques, devices, and analysis tools (e.g., computer software). Resources such as databases, reagents, and tissue repositories are different than technologies. The identification and definition of the molecular profiles of cancer will require the development and dissemination of high-throughput molecular analysis technologies, as well as elucidation of all of the molecular species embedded in the genome of cancer and normal cells. The main challenge in cancer control and prevention is to detect the cancer early. This could then enable effective interventions and therapies contributing to reduction in mortality and morbidity. At a specific time, biomarkers serve as molecular signposts of the physiologic state of a cell. These signposts are the result of genes, their products (proteins) and other organic chemicals made by the cell. Biomarkers could prove to be vital for the identification of early cancer and subjects at risk of developing cancer as a normal cell progresses through the complex process of transformation to a cancerous state. This chapter discusses ongoing research in genetic and proteomic approaches to identify molecular signatures such as protein profiles, microsatellite instability, hypermethylation, and single nucleotide polymorphisms. Other topics covered here include the use of genomics and proteomics as high-throughput technology platforms to facilitate biomarker-aided detection of early cancer. Other areas covered include issues surrounding the analysis, validation, and predictive value of biomarkers using such technologies. Recent advances in noninvasive techniques, such as buccal cell isolates serving as viable sources of biomarkers, complementary to traditional sources such as serum or plasma, are also presented. The review also brings attention to the efforts of the Early Detection Research Network (EDRN) at the National Cancer Institute (NCI), in bringing together scientific expertise from leading national and international institutions, to identify and validate biomarkers for the detection of precancerous and cancerous cells in determining risk for developing cancer. The network's serious determined efforts in linking discovery to process development, resulting in early detection tests and clinical assessment, are also discussed.

Biomarkers, Tumor↗

Study on established lymphoid cells in maple syrup urine disease. Correlation with clinical heterogeneity.

Branched-chain keto acid dehydrogenase complex (BCKAD) was measured in lymphoid cells established from five patients with maple syrup urine disease (MSUD) and six control subjects. Two other MSUD lymphoid cell lines obtained from The Human Genetic Mutant Cell Repository were used as references. One day after subculture, the cells grew logarithmically up to 4-5 days. With this cell growth, BCKAD activity increased greatly in controls, but not in MSUD cells. The maximum BCKAD activity of MSUD cells was less than 7% and 13%-16% of the control in classic and variant types, respectively. Leucine added to culture medium at the concentration of 10-20 mM significantly inhibited cell growth in MSUD cells alone, and with increasing concentration and impaired enzyme activity in a cell line, the effect became more prominent. The effects of isoleucine and valine were mild and did not differ between control and MSUD cells.

3-Methyl-2-Oxobutanoate Dehydrogenase (Lipoamide)↗