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At least 253 records · Page 14Linked to original sources

PubMed2005

Global synthetic-lethality analysis and yeast functional profiling.

The Saccharomyces genome-deletion project created >5900 'molecularly barcoded' yeast knockout mutants (YKO mutants). The YKO mutant collections have facilitated large-scale analyses of a multitude of mutant phenotypes. For example, both synthetic genetic array (SGA) and synthetic-lethality analysis by microarray (SLAM) methods have been used for synthetic-lethality screens. Global analysis of synthetic lethality promises to identify cellular pathways that 'buffer' each other biologically. The combination of global synthetic-lethality analysis, together with global protein-protein interaction analyses, mRNA expression profiling and functional profiling will, in principle, enable construction of a cellular 'wiring diagram' that will help frame a deeper understanding of human biology and disease.

Chromosome Mapping↗

PubMed2004

Hemosoft: a new software for blood bank and apheresis management.

BACKGROUND: Blood banks (BB) generate large volumes of information relating to patients and blood products sometimes stored indefinitely. Today computers are the main keys used to manage this task. BB information systems are developed mainly to assist BB specialists. MATERIALS AND METHODS: We developed a new software, Hemosoft, in our blood bank. We have carried out a great deal of research into BB programs around the world in terms of program features. Using the latest technology, Hemosoft has been designed to run on a multi-user platform on the basis of a modular structure, and high security levels. RESULTS: Hemosoft's structural advantages are: (1) its modular structure and client/server architecture reduce initial hardware costs. (2) Relational database structure provides consistent and secure data access, (3) user-friendly graphical interface, (4) according to operational needs, Hemosoft can be expanded and transferred on to different platforms. As a MS Windows based program with graphical user interfacing, Hemosoft has all the functions and advantages of windows based applications. Barcode printing is available to ISBT 128 standard. Hemosoft's integrated modules are: blood donation, transfusion, product management, administrative follow-up, apheresis, stock management, staff-management, inter-center communication, statistics, archive, internet and video-conferencing systems, accounts, integration and security. CONCLUSION: It fulfills international transfusion medicine requirements, legislative measures and guidelines. We believe that Hemosoft is a high quality, competitive program developed to meet international standards. It is our hope that it will enforce transfusion medicine and blood banking nationwide.

Blood Banks↗

PubMed2005

Pattern specificity of human visual motion processing.

Visual motion processing is strongly susceptible to adaptation. A variety of patterns have been used as stimuli in previous studies. Three of these, namely random dots, barcode-like gratings, and sinusoidal gratings, were compared in the present study using motion-onset visual evoked potentials (VEPs). We assessed the effects of the adaptation pattern and the test pattern to which the VEP is recorded. Furthermore, we evaluated the interaction between both, i.e. whether differences between adaptation and test pattern affect the response. Isodirectional and antidirectional adaptation were used to differentiate between the actual motion adaptation and associated flicker adaptation. Motion adaptation was almost 2.5-fold stronger (p < 0.01) if the same rather than different pattern types were used for both adaptation and test. This implies that separate neural populations are involved, suggesting the presence of pattern-tuned motion mechanisms.

Adaptation, Ocular↗

PubMed2024

Mudskipper detects combinatorial RNA binding protein interactions in multiplexed CLIP data.

The uncovering of protein-RNA interactions enables a deeper understanding of RNA processing. Recent multiplexed crosslinking and immunoprecipitation (CLIP) technologies such as antibody-barcoded eCLIP (ABC) dramatically increase the throughput of mapping RNA binding protein (RBP) binding sites. However, multiplex CLIP datasets are multivariate, and each RBP suffers non-uniform signal-to-noise ratio. To address this, we developed Mudskipper, a versatile computational suite comprising two components: a Dirichlet multinomial mixture model to account for the multivariate nature of ABC datasets and a softmasking approach that identifies and removes non-specific protein-RNA interactions in RBPs with low signal-to-noise ratio. Mudskipper demonstrates superior precision and recall over existing tools on multiplex datasets and supports analysis of repetitive elements and small non-coding RNAs. Our findings unravel splicing outcomes and variant-associated disruptions, enabling higher-throughput investigations into diseases and regulation mediated by RBPs.

RNA-Binding Proteins↗

PubMed2024

Whole-genome sequences reveal zygotic composition in chimeric twins.

While most dizygotic twins have a dichorionic placenta, rare cases of dizygotic twins with a monochorionic placenta have been reported. The monochorionic placenta in dizygotic twins allows in utero exchange of embryonic cells, resulting in chimerism in the twins. In practice, this chimerism is incidentally identified in mixed ABO blood types or in the presence of cells with a discordant sex chromosome. Here, we applied whole-genome sequencing to one triplet and one twin family to precisely understand their zygotic compositions, using millions of genomic variants as barcodes of zygotic origins. Peripheral blood showed asymmetrical contributions from two sister zygotes, where one of the zygotes was the major clone in both twins. Single-cell RNA sequencing of peripheral blood tissues further showed differential contributions from the two sister zygotes across blood cell types. In contrast, buccal tissues were pure in genetic composition, suggesting that in utero cellular exchanges were confined to the blood tissues. Our study illustrates the cellular history of twinning during human development, which is critical for managing the health of chimeric individuals in the era of genomic medicine.

Humans↗

PubMed2007

dSLAM analysis of genome-wide genetic interactions in Saccharomyces cerevisiae.

Analysis of genetic interactions has been extensively exploited to study gene functions and to dissect pathway structures. One such genetic interaction is synthetic lethality, in which the combination of two non-lethal mutations leads to loss of organism viability. We have developed a dSLAM (heterozygote diploid-based synthetic lethality analysis with microarrays) technology that effectively studies synthetic lethality interactions on a genome-wide scale in the budding yeast Saccharomyces cerevisiae. Typically, a query mutation is introduced en masse into a population of approximately 6000 haploid-convertible heterozygote diploid Yeast Knockout (YKO) mutants via integrative transformation. Haploid pools of single and double mutants are freshly generated from the resultant heterozygote diploid double mutant pool after meiosis and haploid selection and studied for potential growth defects of each double mutant combination by microarray analysis of the "molecular barcodes" representing each YKO. This technology has been effectively adapted to study other types of genome-wide genetic interactions including gene-compound synthetic lethality, secondary mutation suppression, dosage-dependent synthetic lethality and suppression.

Base Sequence↗

PubMed2006

Phylogeny of venus clams (Bivalvia: Venerinae) as inferred from nuclear and mitochondrial gene sequences.

Venerinae (Heterodonta: Veneridae) is a diverse, commercially important, and cosmopolitan marine bivalve subfamily. Recent workers synonymized it with the subfamily Chioninae, due to their overall morphological similarity. The use of traditional shell-based characters alone, however, is questionable for resolving phylogenetic relationships of this group. A phylogenetic study was carried out, based on nucleotide sequences of the mitochondrial large ribosomal subunit (16S), cytochrome oxidase subunit I (COI), and the nuclear protein-coding gene histone 3, to investigate the relationships and circumscription of Venerinae and the phylogenetic pattern of characters in this group. This study consists of a total of 55 taxa: 13 venerine genera, 24 chionine taxa, and 18 taxa of other venerid subfamilies. We analyzed the alignments using a Bayesian approach using Markov Chain Monte Carlo tree sampling and maximum parsimony methods. The resulting phylogenetic hypothesis suggests that Chioninae and Venerinae are actually discrete taxa, but that the circumscription suffered from misplacement of some genera. Our analysis showed that the former chionine genera Chamelea and Clausinella should be placed in Venerinae, as sister taxa to Venus. We re-analyzed morphological and anatomical features in light of the molecular data to describe monophyletic entities. Features of the hinge and internal shell as well as the degree of siphonal fusion are identified as characters to morphologically distinguish the two subfamilies. Of the three genes used in this study, only COI (commonly used as "barcoding" gene) posed substantial problems in obtaining sequence data from older museum material.

Animals↗

PubMed2006

Relationship between morphological taxonomy and molecular divergence within Crustacea: proposal of a molecular threshold to help species delimitation.

With today's technology for production of molecular sequences, DNA taxonomy and barcoding arose as a new tool for evolutionary biology and ecology. However, their validities still need to be empirically evaluated. Of most importance is the strength of the correlation between morphological taxonomy and molecular divergence and the possibility to define some molecular thresholds. Here, we report measurements of this correlation for two mitochondrial genes (COI and 16S rRNA) within the sub-phylum Crustacea. Perl scripts were developed to ensure objectivity, reproducibility, and exhaustiveness of our tests. Our analysis reveals a general correlation between molecular divergence and taxonomy. This correlation is particularly high for shallow taxonomic levels allowing us to propose a COI universal crustacean threshold to help species delimitation. At higher taxonomic levels this correlation decreases, particularly when comparing different families. Those results plead for DNA use in taxonomy and suggest an operational method to help crustacean species delimitation that is linked to the phylogenetic species definition. This pragmatic tool is expected to fine tune the present classification, and not, as some would have believed, to tear it apart.

Amino Acids↗

PubMed2006

A molecular phylogeny of Anopheles annulipes (Diptera: Culicidae) sensu lato: the most species-rich anopheline complex.

The Australasian Annulipes Complex is the most species-rich among Anopheles mosquitoes, with at least 15 sibling species suspected. Members of this complex are the most likely vectors of malaria in the past in southern Australia and are involved in the spread of myxomatosis among rabbits. In this, the first comprehensive molecular study of the Annulipes Complex, 23 ITS2 rDNA variants were detected from collections throughout Australia and Papua New Guinea, including diagnostic variants for the previously identified An. annulipes species A-G. Specimens of each ITS2 variant were sequenced for portions of the mitochondrial COI, COII and nuclear EF-1alpha genes. Partitioned Bayesian and Maximum Parsimony analyses confirmed the monophyly of the Annulipes Complex and revealed at least 17 clades that we designate species A-Q. These species belong to two major clades, one in the north and one mainly in the south, suggesting that climate was a driver of species radiation. We found that 65% (11) of the 17 sibling species recorded here had unique COI sequences, suggesting that DNA barcoding will be useful for diagnosing species within the Annulipes Complex. A comparison of the taxa revealed morphological characters that may be diagnostic for some species. Our results substantially increase the size of the subgenus Cellia in Australasia, and will assist species-level studies of the Annulipes Complex.

Animals↗

PubMed2006

Molecular phylogenetics and delimitation of species in Cortinarius section Calochroi (Basidiomycota, Agaricales) in Europe.

Cortinarius is the most species rich genus of mushroom forming fungi with an estimated 2000 spp. worldwide. However, species delimitation within the genus is often controversial. This is particularly true in the section Calochroi (incl. section Fulvi), where the number of accepted taxa in Europe ranges between c.60 and c.170 according to different taxonomic schools. Here, we evaluated species delimitation within this taxonomically difficult group of species and estimated their phylogenetic relationships. Species were delimited by phylogenetic inference and by comparison of ITS sequence data in combination with morphological characters. A total of 421 ITS sequences were analyzed, including data from 53 type specimens. The phylogenetic relationships of the identified species were estimated by analyzing ITS data in combination with sequence data from the two largest subunits of RNA polymerase II (RPB1 and RPB2). Seventy-nine species were identified, which are believed to constitute the bulk of the diversity of this group in Europe. The delimitation of species based on ITS sequences is more consistent with a conservative morphological species concept for most groups. ITS sequence data from 30 of the 53 types were identical to other taxa, and most of these can be readily treated as synonyms. This emphasizes the importance of critical analysis of collections before describing new taxa. The phylogenetic separation of species was, in general, unambiguous and there is considerable potential for using ITS sequence data as a barcode for the group. A high level of homoplasy and phenotypic plasticity was observed for morphological and ecological characters. Whereas most species and several minor lineages can be recognized by morphological and ecological character states, these same states are poor indicators at higher levels.

Agaricales↗

PubMed2001

To err is human nature. Can transfusion errors due to human factors ever be eliminated?

BACKGROUND: Fatal hemolytic transfusion reaction due to ABO incompatibility occurs mainly as a result of clerical errors. Blood sample drawn from the wrong patient and labeled as another patient's specimen will not be detected by the blood bank unless there is a previous ABO grouping result. METHODS: In Hong Kong, we had designed a transfusion wristband system--portable barcode scanner system to detect such clerical errors. The system was well accepted by the house staff and had prevented two BO mismatched transfusion. Other current system of patient's identification may have similar results, but the wristband system has the advantages of being simple, inexpensive and easy to implement. The Hong Kong Government is planning to replace the personal identity card for all citizens with an electronic smart card by 2003. If the new card contains the person's detailed red cell phenotypes in digital code, then the phenotypes of all blood donors and admitted patients will be readily available. It is feasible to issue phenotype-matched blood to patients without any need of pre-transfusion testing, therefore eliminating mismatched transfusions for most patients. RESULTS: Our pilot study of 474 patients showed that the system was safe and up to 98% of admitted patients could be transfused without delays. CONCLUSIONS: Patients with rare phenotypes, visitors or illegal immigrants may still need pre-transfusion antibody screen, but if most patients can be issued blood units without testings, the potential savings in health care amount to US$14 million/year.

ABO Blood-Group System↗

PubMed2003

A chemical genomics approach to understanding drug action.

The complete collection of yeast deletion strains represents a unique, living biological computer for understanding gene function. The molecular 'barcodes' present in each of the deletion strains allow a quantitative ranking of the importance of any gene under any experimental condition of choice. In this article, some of the recent results generated from experiments that exploit the yeast deletion collection to understand mechanisms of drug action are discussed.

Drug Evaluation, Preclinical↗

PubMed2000

Cryptography with DNA binary strands.

Biotechnological methods can be used for cryptography. Here two different cryptographic approaches based on DNA binary strands are shown. The first approach shows how DNA binary strands can be used for steganography, a technique of encryption by information hiding, to provide rapid encryption and decryption. It is shown that DNA steganography based on DNA binary strands is secure under the assumption that an interceptor has the same technological capabilities as sender and receiver of encrypted messages. The second approach shown here is based on steganography and a method of graphical subtraction of binary gel-images. It can be used to constitute a molecular checksum and can be combined with the first approach to support encryption. DNA cryptography might become of practical relevance in the context of labelling organic and inorganic materials with DNA 'barcodes'.

Computer Communication Networks↗

PubMedDate not supplied

[Direct collection of information during blood donation in blood mobiles].

Direct data storage, in the presence of the donor, ensures a realistic reliability and erases any deferred interpretation of the essential information for a good donation identification. Computers can help relieve this restraint. Indeed the evolution of microcomputers (increased capacity and power, decreased weight and volume, and good performance in any use makes them more and more accurate. Associated use of barcodes and microcomputers gives a nonmanual non-human line of words: donor-donation-analysis-blood products-patient. We found, working that way, the following advantages: Information secured. No deferred inputs. Instart comparison of the information on the donor's past history. Accurate donation-donor connection. Such a system represents one more step towards a continuous line of treatment from Donor to Patient in regard of Blood Transfusion Safety.

Blood Donors↗

PubMed1996

Development of computer-assisted patient control for use in the hospital setting during mass casualty incidents.

Hospital resolution of mass casualty incidents can have difficulties involving "command and control" and information management, ineffective use of triage classes, and missed diagnostic procedures, leading to lower quality of care. A computer system has been developed to supply continuously updated group and patient data. The system uses barcoded identifiers to represent patients, injuries, facilities, and locations, in order to minimize errors and make exchange of data possible. The system communicates with the permanent hospital information system. This article reports the use of this technology during several experiments and real incidents. Computer registration based on bar codes, despite the greater number of items entered, still showed 25% fewer inaccuracies when compared with handwritten medical charts. Extensive training was shown to be unnecessary. Paramedical personnel judged the automated procedures to be an improvement during the admission of 143 evacuated patients.

Attitude of Health Personnel↗

PubMed1997

Benchmarking the perioperative process. I. Patient routing systems: a method for continual improvement of patient flow and resource utilization.

The article presents an overview of the design and application of a real-time patient routing system, based on barcode and local area network technology, that was designed to track the progress of patients during the perioperative process. We present data on all patients undergoing ambulatory surgery. Patients' progress during their surgical stay was recorded at 17 strategic events using this real-time patient tracking technology. These times were used to identify inefficiencies in the perioperative process by identifying bottlenecks and areas of high variation. We found that both raw and actual operating room (OR) utilization efficiency was less than 50%. Points of high variation in a patient's progress occurred during the time from admit to the hospital until the patient was ready for the OR; the time from when a patient was ready for the OR until they were called for; and the time a patient spends in the OR preoperative holding room. Causes for variation were identified and traced back to individual procedures, activities, and work processes. Multidisciplinary improvement teams were created to improve the pinpointed problem areas. The real-time patient routing system is a process that has proven to be highly valuable to all participants in the surgical process in bringing about rational, data driven efficiencies in perioperative services. This process has the potential to facilitate multidisciplinary cooperation in efforts to contain and reduce costs of perioperative services.

Appointments and Schedules↗

PubMed2003

Biological sample collection and processing for molecular epidemiological studies.

Molecular epidemiology uses biomarkers and advanced technology to refine the investigation of the relationship between environmental exposures and diseases in humans. It requires careful handling and storage of precious biological samples with the goals of obtaining a large amount of information from limited samples, and minimizing future research costs by use of banked samples. Many factors, such as tissue type, time of collection, containers used, preservatives and other additives, transport means and length of transit time, affect the quality of the samples and the stability of biomarkers and must be considered at the initial collection stage. An efficient study design includes provisions for further processing of the original samples, such as cryopreservation of isolated cells, purification of DNA and RNA, and preparation of specimens for cytogenetic, immunological and biochemical analyses. Given the multiple uses of the samples in molecular epidemiology studies, appropriate informed consent must be obtained from the study subjects prior to sample collection. Use of barcoding and electronic databases allow more efficient management of large sample banks. Development of standard operating procedures and quality control plans is a safeguard of the samples' quality and of the validity of the analyses results. Finally, specific state, federal and international regulations are in place regarding research with human samples, governing areas including custody, safety of handling, and transport of human samples, as well as communication of study results.Here, we focus on the factors affecting the quality and the potential future use of biological samples and some of the provisions that must be made during collection, processing, and storage of samples, based on our experience in the Superfund Basic Research Program and Children's Environmental Health Center, at the University of California, Berkeley.

Humans↗

PubMed1986

The NCI Drug Information System. 4. Inventory and Shipping Modules.

The Inventory/Shipping package of the NCI Drug Information System (DIS) is designed to support all inventory and shipping operations associated with the testing by the NCI of large numbers of chemicals for anticancer activity. Two major databases, an Inventory database and a Shipping History database, contain all of the data associated with these operations. Software that supports the operations in an online interactive manner also provides for the accessing and updating of these databases as necessary. Special hardware in the form of barcode reader/printers and digital balances is also interfaced to the system to improve the efficiency of the operations.

Antineoplastic Agents↗