A compendium of reviews in biochemistry and molecular biology published in the first half of 1992.

1. A compendium of reviews and mini-reviews in Biochemistry and Molecular Biology published in the first half of 1992 is presented. In all 499 titles are listed from 95 different publications. 2. This compendium presents the references by Journal Name. Keywords have been included with each reference to increase the value of the collection. Keyword and author cross-reference indexes are not included but are available in the electronic database from which this version was constructed. Should anyone wish to have this information in electronic form it can be distributed on MS-DOS formatted floppy disks in either Reference Manager or Medline format. The author should be contacted for details of the number of preformatted floppy disks required.     

A compendium of reviews in biochemistry and molecular biology published in the first half of 1993

• 1.1. A compendium of reviews and mini-reviews in Biochemistry and Molecular Biology published in the first half of 1993 is presented. In all 554 titles are listed from 103 different publications.
• 2.2. This compendium presents the references by Journal Name. Keywords have been included with each reference to increase the value of the collection. Keyword and author cross-reference indexes are not included but are available in the electronic database from which this version was constructed. Should anyone wish to have this information in electronic form it can be distributed on MS-DOS formatted flopppy disks in either Reference Manager or Medline format. The author should be contacted for details of the number of pre-formatted floppy disks required.

     

A compendium of reviews in biochemistry and molecular biology published in the second half of 1993

• 1.1. A compendium of reviews and mini-reviews in Biochemistry and Molecular Biology published in the second half of 1993 is presented. In all 1063 titles are listed from 127 different publications.
• 2.2. This compendium presents the references Journal by Journal. Keyword and author cross-reference indexes are not included but are available in the computer database that is the companion to this paper version. The electronic form contains details of reviews published since 1990 as listed in this and earlier compendia. Anyone wishing to receive this database should contact the author: it can be distributed either via Internet or on MS-DOS formatted flopppy disks in either Reference Manager or Medline format. Please contact the author for details of the number of pre-formatted floppy disks required.

     

ASTRAL compendium enhancements

The ASTRAL compendium provides several databases and tools to aid in the analysis of protein structures, particularly through the use of their sequences. It is partially derived from the SCOP database of protein domains, and it includes sequences for each domain as well as other resources useful for studying these sequences and domain structures. Several major improvements have been made to the ASTRAL compendium since its initial release 2 years ago. The number of protein domain sequences included has doubled from 15 190 to 30 867, and additional databases have been added. The Rapid Access Format (RAF) database contains manually curated mappings linking the biological amino acid sequences described in the SEQRES records of PDB entries to the amino acid sequences structurally observed (provided in the ATOM records) in a format designed for rapid access by automated tools. This information is used to derive sequences for protein domains in the SCOP database. In cases where a SCOP domain spans several protein chains, all of which can be traced back to a single genetic source, a ‘genetic domain’ sequence is created by concatenating the sequences of each chain in the order found in the original gene sequence. Both the original-style library of SCOP sequences and a new library including genetic domain sequences are available. Selected representative subsets of each of these libraries, based on multiple criteria and degrees of similarity, are also included. ASTRAL may be accessed at http://astral.stanford.edu/.     

A microcomputer-based information storage and retrieval system for the maintenance of records for a culture collection

A microcomputer-based system for the storage and retrieval of information on strains in a culture collection is described. The system was designed around commercially available software packages written for microcomputers. Two additional programs were written using the BASIC language to allow a catalogue of the culture collection to be printed in a specific format. The details of each strain in the collection were stored on a floppy disc. Details of new strains were added to this database and information relating to existing cultures was modified or, where necessary, deleted from the collection. The database can be searched to supply details of a particular culture or to identify those cultures which possess certain attributes. The records for the whole collection were sorted alphabetically by species name, and numerically by accession number, and a word-processing package was used to print a catalogue of the culture collection.     

A microcomputer-based information storage and retrieval system for the maintenance of records for a culture collection

A microcomputer-based system for the storage and retrieval of information on strains in a culture collection is described. The system was designed around commercially available software packages written for microcomputers. Two additional programs were written using the BASIC language to allow a catalogue of the culture collection to be printed in a specific format. The details of each strain in the collection were stored on a floppy disc. Details of new strains were added to this database and information relating to existing cultures was modified or, where necessary, deleted from the collection. The database can be searched to supply details of a particular culture or to identify those cultures which possess certain attributes. The records for the whole collection were sorted alphabetically by species name, and numerically by accession number, and a word-processing package was used to print a catalogue of the culture collection.     

Computerization of a bank of platelets with HLA phenotype and preserved at -196 degrees C

In order to complete the logistics of the unit cytapheresis, we have developed a decision helping system which rests upon the computer management of -196 degrees C cryopreserved HLA type platelets. The hardware used is a micro-computer equipped with two floppy disks and a printer. Two files have been created: namely "Product" and "Patient". Data relating to 800 platelet concentrates may be recorded on a floppy disk. The software which has been developed has several functions: 1 - The input of the parameters of a HLA type concentrate with the possibility of reservation for the given recipient; 2 - The print out of the bank's stock; 3 - The selection and the reservation of HLA matched platelets according to the recipient; 4 - The print out of concentrates allocated to each patient, it is possible to thaw out chosen platelet concentrate and a thawing report is printed out, thus enabling one to locate the concentrate in the bank. Thanks to this "aid in decision making", the management of - 196 degrees C cryopreserved HLA type platelets may be carried out. The proposed software allows an one line answer for any emergency transfusion case. Considering the recipient HLA typing the suitable best match platelet concentrates are instantly transfused or save.     

A compendium of reviews in biochemistry and molecular biology published in the first half of 1990

A compendium of reviews and minireviews in biochemistry and molecular biology published in the first half of 1990 is presented. The 316 titles from 72 different publications are presented sorted by author and sorted by journal.     

Applications of microcomputer technology to cytophotometry.

Lack of appropriate software support for microprocessor program development has previously limited the applications of such technology in the field of microspectrophotometry. This paper describes our use of a Vickers M86 integrating microdensitometer coupled through a custom-designed interface circuit to a Processor Technology SOL III microcomputer. W e have developed a series of interactive, user-oriented programs for DNA-Feulgen cytophotometry with this instrument to allow automatic storage of data in files on floppy disks and instant retrieval of sets of measurements for statistical processing. The same data files can also be used to generate graphic displays in the form of bar histograms or plots of linear regressions on a video monitor and to produce hardcopy output of data files and graphic displays through the use of a high speed DIABLO printer.     

Structural foundations for explaining the physiological roles of murzymes embedded in diverse phospholipid membranes

The advent of improved structural biology protocols and bioinformatics methodologies have provided paradigm-shifting insights on metabolic or physiological processes catalyzed by homo?/hetero- proteins (super)complexes embedded in phospholipid membranes of cells/organelles. In this panoramic review, we succinctly elucidate the structural features of select redox proteins from four systems: hepatocyte/adrenal cortex endoplasmic reticulum (microsomes), inner mitochondrial membrane (cristae), thylakoid membrane (grana), and in the flattened disks of rod/cone cells (in retina). Besides catalyzing fast/crucial (photo)chemical reactions, these proteins utilize the redox-active diatomic gaseous molecule of oxygen, the elixir of aerobic life. Quite contrary to extant perceptions that invoke primarily deterministic affinity-binding or conformation-change based “proton-pump”/“serial electron-relay” type roles, we advocate murzyme functions for the membrane-embedded proteins in these systems. Murzymes are proteins that generate/stabilize/utilize diffusible reactive (oxygen) species (DRS/DROS) based activities. Herein, we present a brief compendium of the recently revealed wealth of structural information and mechanistic concepts on how the membrane proteins use DRS/DROS to aid ‘effective charge separation’ and facilitate trans-membrane dynamics of diverse species in milieu, thereby enabling the cells to function as ‘simple chemical engines’.     

Curation of the Mammalian Palmitoylome Indicates a Pivotal Role for Palmitoylation in Diseases and Disorders of the Nervous System and Cancers

Palmitoylation involves the reversible posttranslational addition of palmitate to cysteines and promotes membrane binding and subcellular localization. Recent advancements in the detection and identification of palmitoylated proteins have led to multiple palmitoylation proteomics studies but these datasets are contained within large supplemental tables, making downstream analysis and data mining time-consuming and difficult. Consequently, we curated the data from 15 palmitoylation proteomics studies into one compendium containing 1,838 genes encoding palmitoylated proteins; representing approximately 10% of the genome. Enrichment analysis revealed highly significant enrichments for Gene Ontology biological processes, pathway maps, and process networks related to the nervous system. Strikingly, 41% of synaptic genes encode a palmitoylated protein in the compendium. The top disease associations included cancers and diseases and disorders of the nervous system, with Schizophrenia, HD, and pancreatic ductal carcinoma among the top five, suggesting that aberrant palmitoylation may play a pivotal role in the balance of cell death and survival. This compendium provides a much-needed resource for cell biologists and the palmitoylation field, providing new perspectives for cancer and neurodegeneration.     

A genome-wide RNA interference screen identifies caspase 4 as a factor required for tumor necrosis factor alpha signaling

Tumor necrosis factor alpha (TNF-α) is a potent inflammatory cytokine secreted upon cellular stress as well as immunological stimuli and is implicated in the pathology of inflammatory diseases and cancer. The therapeutic potential of modifying TNF-α pathway activity has been realized in several diseases, and antagonists of TNF-α have reached clinical applications. While much progress in the understanding of signaling downstream of the TNF-α receptor complex has been made, the compendium of factors required for signal transduction is still not complete. In order to find novel regulators of proinflammatory signaling induced by TNF-α, we conducted a genome-wide small interfering RNA screen in human cells. We identified several new candidate modulators of TNF-α signaling, which were confirmed in independent experiments. Specifically, we show that caspase 4 is required for the induction of NF-κB activity, while it appears to be dispensable for the activation of the Jun N-terminal protein kinase signaling branch. Taken together, our experiments identify caspase 4 as a novel regulator of TNF-α-induced NF-κB signaling that is required for the activation of IκB kinase. We further provide the genome-wide RNA interference data set as a compendium in a format compliant with minimum information about an interfering RNA experiment (MAIRE).     

A microcomputer program for establishing and maintaining a database for laboratory culture collections

A computer program that facilitates the creation of a culture collection database has been written for a microcomputer (Apple He with a Z-80 card) using dBASE II® (Ashton-Tate). The Culture Collection Program accommodates up to 250 individual strain records on one 5 1/4" floppy disk. For each strain, information that can be stored includes the name of the micro-organism, culture collection number, antibiotic resistance markers, plasmids, genetic markers, references, growth medium, growth temperature and additional comments. The last date of subculturing can be ascertained and information about the status of the preserved cultures can also be noted. With a menu-driven format which requires no computer programming expertise, the user can readily create new entries, update old ones and search the database for strains with certain common properties.     

The layered organization of nucleosomes in 30 nm chromatin fibers

We have used electron microscopy and established methods of three-dimensional reconstruction to obtain structural information on the 30 nm chromatin fibers from sea cucumber sperm and chicken erythrocytes. The fibers show a longitudinal periodicity of 10–11 nm. We have interpreted this periodicity as due to a grouping of nucleosomes into disks, each disk containing about 5–6 nucleosomes. These disks are closely stacked to form the chromatin fiber. We have built a detailed model for four fibers and we have determined the approximate coordinates of all the nucleosomes in them. The average distance found between neighboring nucleosomes has a value close to 11 nm. They may be connected either as a regularly distorted helix or as a layered zigzag. The second model appears more appropriate, since in the constrictions of the fibers the nucleosomes can only be connected as a zigzag.     

Email lists in laboratory animal science

Email lists can be invaluable for acquiring information that may not be easily accessible in the published literature. The author discusses the general format and functioning of email lists and describes six lists that can be valuable tools for education, training, and information exchange in the field of laboratory animal science.     

Inexpensive, semi-automated system for measuring mechanical properties of soft tissues.

Stiffness and strength are important properties of many tissues, but standard material-testing equipment is expensive, often ill-suited for testing soft tissues, and rarely accessible to biologists. We describe a system built around a microcomputer and an electronic balance which is particularly well-suited for measuring stress and strain in small samples of soft tissue. We use a discarded floppy disk drive as a linear actuator to strain the sample, while an electronic balance measures the tension (used to calculate stress). We give an algorithm for a program to drive a microcomputer which controls the floppy disk drive via its parallel port and records the balance measurements via its serial port. We used this system to obtain stress-strain curves from a sample of latex rubber and a sample of soft insect cuticle. Three tests of the rubber sample gave nearly identical results, with smooth, J-shaped stress-strain curves. The stress-strain curves gave a modulus elasticity value of 1.72 Mpa over the steep, straight region, well within the range for natural latex rubber. We also tested a sample of abdominal cuticle from a caterpillar (Manduca sexta). The caterpillar cuticle had a J-shaped stress-strain curve with a modulus of elasticity of 2.11 Mpa over the steep part of the curve. J. Exp. Zool. 284:374-378, 1999.     

Reducing Post Analytical Error: Perspectives on New Formats for the Blood Sciences Pathology Report

Little has changed in the way we report pathology results from blood sciences over the last 50 years other than moving to electronic display from paper. In part, this is aspiration to preserve the format of a paper report in electronic format. It is also due to the limitations of electronic media to display the data. The advancement of web-based technologies and functionality of hand-held devices together with wireless and other technologies afford the opportunity to rethink data presentation with the aim of emphasising the message in the data, thereby modifying clinical behaviours and potentially reducing post-analytical error. This article takes the form of a commentary which explores new developments in the field of infographics and, together with examples, suggests some new approaches to communicating what is currently just data into information. The combination of graphics and a new approach to provocative interpretative commenting offers a powerful tool in improving pathology utilisation. An additional challenge is the requirement to consider how pathology reports may be issued directly to patients.     

An ensemble biclustering approach for querying gene expression compendia with experimental lists

MOTIVATION: Query-based biclustering techniques allow interrogating a gene expression compendium with a given gene or gene list. They do so by searching for genes in the compendium that have a profile close to the average expression profile of the genes in this query-list. As it can often not be guaranteed that the genes in a long query-list will all be mutually coexpressed, it is advisable to use each gene separately as a query. This approach, however, leaves the user with a tedious post-processing of partially redundant biclustering results. The fact that for each query-gene multiple parameter settings need to be tested in order to detect the 'most optimal bicluster size' adds to the redundancy problem. RESULTS: To aid with this post-processing, we developed an ensemble approach to be used in combination with query-based biclustering. The method relies on a specifically designed consensus matrix in which the biclustering outcomes for multiple query-genes and for different possible parameter settings are merged in a statistically robust way. Clustering of this matrix results in distinct, non-redundant consensus biclusters that maximally reflect the information contained within the original query-based biclustering results. The usefulness of the developed approach is illustrated on a biological case study in Escherichia coli. Availability and implementation: Compiled Matlab code is available from http://homes.esat.kuleuven.be/~kmarchal/Supplementary_Information_DeSmet_2011/.     

Molecular and structural analysis of C4-specific PEPC isoform from Pennisetum glaucum plays a role in stress adaptation

As an activator of adenylate cyclase, the neuropeptide Pituitary Adenylate Cyclase Activating Peptide (PACAP) impacts levels of cyclic AMP, a key second messenger available in brain cells. PACAP is involved in certain adult behaviors. To elucidate PACAP interactions, a compendium of microarrays representing mRNA expression in the adult mouse whole brain was pooled from the Phenogen database for analysis. A regulatory network was computed based on mutual information between gene pairs using gene expression data across the compendium. Clusters among genes directly linked to PACAP, and probable interactions between corresponding proteins were computed. Database “experts” affirmed some of the inferred relationships. The findings suggest ADCY7 is probably the adenylate cyclase isoform most relevant to PACAP's action. They also support intervening roles for kinases including GSK3B, PI 3-kinase, SGK3 and AMPK. Other high-confidence interactions are hypothesized for future testing. This new information has implications for certain behavioral and other disorders.