A compendium of reviews in biochemistry and molecular biology published in the second half of 1991.

A compendium of reviews and mini-reviews in biochemistry and molecular biology published in the second half of 1991 is presented. In all 880 titles are listed from 108 different publications. This compendium presents the references by journal name--the most suitable format for a hardcopy of this information. 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 pre-formatted 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.

     

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.     

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.     

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.     

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.     

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 compendium of reviews in biochemistry and molecular biology published in the first half of 1991.

1. A compendium of reviews and minireviews in Biochemistry and Molecular Biology published in the first half of 1991 is presented. In all there are 380 titles from 81 different publications. The compendium includes the main keywords associated with each review; over 2500 different keywords are used.     

A Key and Compendium to Species of the Heterodera avenae Group (Nematoda: Heteroderidae)

A key based on cyst and juvenile characters is given for identification of 12 valid Heterodera species in the H. avenae group. A compendium providing the most important diagnostic characters for use in identification of species is included as a supplement to the key. Cyst characters are most useful for separating species; these include shape, color, cyst wall pattern, fenestration, vulval slit length, and the posterior cone including presence or absence of bullae and underbridge. Also useful are those of second-stage juvenile characteristics including aspects of the stylet knobs, tail hyaline tail terminus, and lateral field. Photomicrographs of diagnostically important morphological features complement the compendium.     

The craniofacial anomalies archive at St. Louis Children's Hospital: 20 years of craniofacial imaging experience.

This article describes how the Craniofacial Imaging Laboratory at the Cleft Palate and Craniofacial Deformities Institute, St. Louis Children's Hospital, Washington University Medical Center, has developed an electronic archive for the storage of computed tomography image digital data that is independent of scanner hardware and independent of units of storage media (i.e., floppy disks and optical disks). The archive represents one of the largest repositories of high-quality computed tomography data of children with craniofacial deformities in the world. Archiving reconstructed image data is essential for comparative imaging, surgical simulation, quantitative analysis, and use with solid model fabrication (e.g., stereolithography). One tertiary craniofacial center's experience in the establishment and maintenance of such an archive through three generations of storage technology is reported. The current archive is housed on an external 35-GB hard drive attached to a Windows-based desktop server. Data in the archive were categorized by specific demographics into groups of patients, number of scans, and diagnoses. The Craniofacial Imaging Laboratory archive currently contains computed tomography image digital data for 1827 individual scans. The earliest scan was done in 1980; the most recently stored scan for the purposes of this report occurred in May of 2000. The average number of scans archived per complete year was 94, with a range of 59 to 138. Of the 1827 total scans, 74 percent could be classified into specific diagnostic categories. The majority of the archive (55 percent) is composed of the following five diagnoses: sagittal synostosis (17 percent), unilateral coronal synostosis (11 percent), hemifacial microsomia (10 percent), plagiocephaly without synostosis (10 percent), and metopic synostosis (7 percent). Storage of computed tomography image data in a digital archive currently allows for continuous upgrading of image display and analysis and facilitates longitudinal and cross-sectional studies, both intramural and extramural. Internet access for clinical and research purposes is feasible, but contingent on protection of patient confidentiality. The future of digital imaging regarding craniofacial computed tomography scan storage and processing is also discussed.     

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/.     

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’.     

Networking personal computers

Network technology allows more convenient delivery of computer-aided learning programs. Software and peripheral devices such as printers may be shared between all workstations. The network provides an expedient environment for the development of software, and eradicates the logistic problems of software dispersal via floppy discs. The system can easily be tailored for individual courses, and facilitates more rapid updating of course and revision material. Linking computers from departmental research and administrative groups allows the use of electronic mail and sharing of expensive peripherals such as laser printers, plotters and further links to external networks and computer systems.     

Particle-loaded membranes for sample concentration and/or clean-up in bioanalysis

Solid-phase extraction nowadays is a major sample preparation tool. The latest development in this area is the introduction of particle-loaded membranes (membrane-extraction disks). The potential of these extraction membranes in bioanalysis is discussed with respect to recoveries, reproducibility, sensitivity and speed. A comparison is made between liquid-liquid extraction and solid-phase extraction using traditional sorbents and extraction disks, and off-line and on-line techniques. Particle-loaded membranes are available in disks with diameters of 4–90 mm. The 25–90 mm disks are mainly used for off-line extractions of mainly environmental samples, while the 4 mm disks are available in the so-called drug tubes that can be used in the same way as conventional extraction cartridges for the extraction of drugs from biological fluids. The main advantage of using drug tubes is the smaller desorption volume and, therefore, the increased sensitivity. Cutting smaller disks, from the commercially available disks, allows the use of on-line extractions in column-switching systems. The main conclusion is that in many cases particle-loaded membranes are more efficient than packed solid-phase extraction cartridges.     

Precision cell location and relocation techniques. An application for cell image analysis

Two methods for precise cell location and relocation were developed at the Cell Image Analysis Laboratory, NASA, to increase the efficiency of the cell image acquisition process. The first method uses a Zeiss Zonax with a 10 micron scanning stage and automatically records cell coordinates on 5.25-inch floppy disks. The second method uses a Digital Positioning Device with a 10 micron scanning stage, and the cell coordinates displayed on light-emitting diodes (LEDs) are recorded manually. Because of its superior speed and automation, the Zonax was selected as the method of choice. By using a Zonax for off-line cell location and another Zonax for on-line cell relocation, more than three times the number of digitized images were collected in ten months than in the previous three years. Other beneficial applications of the cell location and relocation methods were realized in photomicrography, data base verification and cytopathology.     

Biochemical characterization of individual normal, floppy and rheumatic human mitral valves.

Human mitral valves (32 floppy and 17 rheumatic) obtained at surgery were analysed and compared with 35 normal (autopsy) valves. Total amounts of collagen, proteoglycan and elastin were increased approx. 3-fold in floppy and rheumatic valves. The water content of rheumatic cusps was lower than normal. The most significant changes in floppy valves were the 59% increase in mean value of the proteoglycan content, a large increase in the ease of extractability of proteoglycans from 26.7 to 57.2% of the total and a 62% increase in mean value of the elastin content in the anterior cusps. Normal human mitral valve cusps contained a mean proportion of 29.3 (and chordae 26.6) type III collagen (as % of total types III + I collagen), the values increasing significantly to 33.2 and 36.3% respectively in chronic rheumatic disease. The ratio observed in floppy valves depended on the extent of secondary surface fibrosis, which could be demonstrated histologically; in valve cusps with considerable secondary fibrosis, the percentage of type III increased significantly (to 34.4%), whereas it decreased significantly (to 25.2%) when fibrosis was negligible. It is concluded that the ratio of collagen types in floppy valves reflects the extent of secondary fibrosis rather than the pathogenesis of the disrupted collagen in the central core of the valve.     

Bacterial Infection and Ion Absorption Capacity in Beet Disks

The effect of bacterial contamination on the development ofa salt absorption capacity in disks of beetroot tissue has beeninvestigated. When disks are aged in water with adequate aerationat 25°C they develop a greatly increased capacity for saltabsorption. The development of this capacity is amenable toexperimental control and may be retarded by inhibitory compoundssuch as acriflavine, hibitane, and chlorocholine chloride. Acomparison of the rate of this development in disks aged understerile and non-sterile conditions has shown that non-sterileconditions retard development. Autoclaving the medium was moreeffective than sterilizing the tissue in eliminating the inhibitoryeffect. Attention is drawn to the risk of obtaining misleadingresults from a failure to take account of this factor.