Application of a bioinformatics training delivery method for reaching dispersed and distant trainees

Many initiatives have addressed the global need to upskill biologists in bioinformatics tools and techniques. Australia is not unique in its requirement for such training, but due to its large size and relatively small and geographically dispersed population, Australia faces specific challenges. A combined training approach was implemented by the authors to overcome these challenges. The “hybrid” method combines guidance from experienced trainers with the benefits of both webinar-style delivery and concurrent face-to-face hands-on practical exercises in classrooms. Since 2017, the hybrid method has been used to conduct 9 hands-on bioinformatics training sessions at international scale in which over 800 researchers have been trained in diverse topics on a range of software platforms. The method has become a key tool to ensure scalable and more equitable delivery of short-course bioinformatics training across Australia and can be easily adapted to other locations, topics, or settings.     

Tyrosinases of motile Azospirillum strains

A number of motile strains of Azospirillum brasilense, A. lipoferum, and A. irakense, were found to possess tyrosinase activity both on the surface of and inside the cells. A. brasilense Sp245, Sp7, and A. irakense KBC-1 each possessed two forms of tyrosinase of different molecular masses; A. lipoferum 43, A. lipoferum 59b, and A. irakense KA-3 each had a single tyrosinase form of approximately the same molecular mass; and A. brasilense Sp107 possessed a single form of tyrosinase different from all the other forms.     

Electrophoretic analysis of endonuclease-generated fragments of k-DNA, of esterase isoenzymes, and of surface proteins as aids for species identification of insect trypanosomatids

In order to verify the applicability of biochemical methods for species identification of Trypanosomatidae, 13 species of monoxenic trypanosomatids plus the heteroxenous Trypanosoma cruzi were comparatively analyzed by three different biochemical methods. Insect trypanosomatids examined were: Crithidia acanthocephali, C. fasciculata (three varieties), C. luciliae luciliae, C. luciliae thermophila, C. deanei, C. oncopelti, Herpetomonas muscarum muscarum, H. megaseliae, H. samuelpessoai, H. mariadeanei, Leptomonas seymouri, L. collosoma, L. samueli, and Blastocrithidia culicis. Also included in the survey were aposymbiotic strains of C. deanei and C. oncopelti. Methods used were: electrophoretic profiling of endonuclease-generated fragments of k-DNA, esterase isoenzymes profiling, and polyacrylamide-gel electrophoresis (SDS-PAGE) of radioiodinated cell surface proteins. Interspecific but not intraspecific differences were detected by all three methods among the 13 monoxenic species examined. Thus, it is concluded that these methods can be successfully used, in addition to classical criteria, for species identification of insect trypanosomatids.     

A Unified Rapid PCR Method for Detection of Normal and Expanded Trinucleotide Alleles of CAG Repeats in Huntington Chorea and CGG Repeats in Fragile X Syndrome

We report on a unified rapid betaine-based-PCR protocol for amplification of the (CAG)n region in Huntington disease (HD) and the (CGG)n region in Fragile X syndrome (FXS), followed by an electrophoretic separation on automated sequencer for precise determination of the triplet numbers. The high betaine concentration (2.5 M betaine) permits precise amplification of the CAG and CGG repeats. Ten HD affected patients and 10 healthy individuals from HD families were re-evaluated. For FXS the CGG region in normal individuals and premutations of about 100 repeats were precisely amplified by this protocol. Ten unrelated FXS premutation carriers and 24 mentally retarded non-FXS affected boys were re-examined by this method. The results totally coincided with the previous ones. This protocol is a good choice as a fast screening test. Within 24 h we can have preliminary information on the patient’s genetic status. Normal individuals, CGG premutation carriers up to 100 repeats, as well as HD patients carrying an expansion up to 50 CAG repeats can be easily clarified. This accounts for a relatively large proportion (about 90%) of the suspected HD and FXS patients, referred to our laboratory for genetic analysis. The calculation of the repeat’s number is more accurate for the correct interpretation of the results, screening tests and genetic counselling.     

Estimating Population Size and Density Using Line Transect Sampling

ANDERSON and POSPAHALA (1970) investigated the estimation of wildlife population size using the belt or line transect sampling method and devised a correction for bias, thus leading to a class of estimators with desirable characteristics. This work was given a basic and rigorous mathematica framework by BURNHAM and ANDERSON (1976). In the present article we use this mathematical framework to develop an estimator of population size and density using weighted least squares. The approach is a two-stage Method.     

An in-depth look at pressure sores using monolithic silicon pressure sensors

Three-dimensional scalar pressure distributions were measured in solid tissue near bony prominences in vitro in meat and in vivo in pigs using silicon pressure sensors. Data are in accord with previous theoretical models and indicate that pressure is three to five times higher internally near a bony prominence than it is at the skin over the prominence. Pressure sores are thus thought to begin internally; by the time they are evident at the skin, the sore has worked its way completely from bone to skin. This conclusion is in accord with previous clinical data. Future measurement of local vector forces is needed to fully characterize the force distribution in vivo.     

Lipid-dependent recovery of alpha-bungarotoxin and monoclonal antibody binding to the purified alpha-subunit from Torpedo marmorata acetylcholine receptor. Enhancement by noncompetitive channel blockers

Recently the purified alpha-subunit from Torpedo marmorata acetylcholine receptor was shown to bind alpha-bungarotoxin with a KD approximately 3 nM in the presence of sodium dodecyl sulfate (Tzartos, S.J., and Changeux, J.P. (1983) EMBO J. 2, 381-387). Here we describe a further significant step toward renaturation of the alpha-subunit as judged by toxin and monoclonal antibody binding. Purified T. marmorata receptor subunits were diluted with 1% lipids (asolectin) plus 0.5% Na+ cholate. An anion-exchange resin eliminated most of the detergents, leaving approximately 0.1% Na+ cholate and the lipids. After this treatment, about 20% of the alpha-subunit recovered (but not the beta-, gamma-, or delta-subunit) exhibited a high affinity for radioiodinated alpha-bungarotoxin with a KD approximately 0.5 nM. The 34,000- and 27,000-dalton proteolytic peptides of the alpha-subunit conserved this lipid-dependent toxin binding. Unlabeled alpha-toxins, hexamethonium, and carbamylcholine competed with alpha-bungarotoxin for the renatured alpha-subunit. Noncompetitive channel blockers doubled the lipid-dependent toxin-binding capacity of the alpha-subunit but had no effect on the 27,000-dalton peptide. The binding of several monoclonal antibodies to the main immunogenic region (which is particularly sensitive to denaturation) significantly increased. In particular, binding of antibody 16 changed from 1% to denatured to 100% to the lipid-renaturated alpha-subunit. The binding of these antibodies was lost with the lipid-renatured 34,000- and 27,000-dalton peptides.     

Isoelectric point determination of human and camel beta-endorphin, alpha-endorphin and enkephalins

The isoelectric point of the camel and the human β-endorphin, of the α-endorphin and the enkephalins were determined by analytical isoelectric focusing on 1 mm thin polyacrylamide gel slab. The difficulty of staining peptides as short as β-endorphin or smaller was overcomed using a modification of Bibring and Baxandall's or Faupel and Von Arx's staining method. The camel β-endorphin gives two bands having isoelectric point of 10.3 and 10.4, the human β-endorphin focus at pH 9.9, while α-endorphin, leu and met-enkephalin at pH 5.9, 5.5 and 5.45 respectively. The staining method described coupled with the isoelectric focusing seems to be fit for discriminating β-endorphin in a crude rat pituitary extract.     

Ultrastructure of the developing pigment strand of rice (Oryza sativa L.) in relation to its role in solute transport

Summary The developing pigment strand of rice (Oryza sativa L.) was studied by conventional electron microscopy and also by use of thick sections post-fixed with zinc iodide and osmium (ZIO).When the rice caryopsis achieves maximum length, a suberised adcrusting wall layer is laid down over the original primary walls of the pigment strand. Concomitant with suberin deposition a proliferation of tubular endoplasmic reticulum occurs in the cytoplasm giving rise to numerous interconnected vesicles which bear ribosomes. The vesicles in the general cytoplasm retain their ribosomes while those close to the wall become smooth and contain an electron-opaque granular material which is eventually deposited to the outside of the plasmalemma. This granular material may be the precursor(s) from which suberin is polymerised. The suberised wall attains about six times the width of the original primary wall and plasmodesmata, which traverse both primary wall and suberised wall layers, become greatly elongated.Lipid bodies increase in both size and frequency during development, eventually coalescing to form a complete plug across the pigment strand and occluding the symplast of this tissue. The significance of these ultrastructural observations is discussed in relation to the previously demonstrated role of the pigment strand as a translocation pathway for water and assimilates during grain filling.Abbreviations ER endoplasmic reticulum - ZIO zinc iodide-osmium fixation     

Pulmonary clearance of inhaled 99mTc-DTPA: effects of surfactant depletion by lung lavage

The influence of surfactant depletion on clearance from the lungs of inhaled technetium-99m-labeled diethylenetriamine pentaacetate (99mTc-DTPA) was studied in rabbits. Surfactant was removed by repeated lung lavage with isotone saline. To minimize structural damage to the lungs, pressure generated insufflation with short expiration was utilized. Aerosolized 99mTc-DTPA was administered via a bag-in-bottle system. Radioactivity was measured with a gamma camera and time-activity curves were obtained over the base of the right lung. Six nonlavaged rabbits served as controls. In six lavaged rabbits clearance of 99mTc-DTPA was significantly faster than in controls. In three rabbits given natural surfactant into the trachea after lung lavage, 99mTc-DTPA was eliminated faster than in controls but slower than in surfactant-depleted animals. The results indicate a role of surfactant on clearance rate of 99mTc-DTPA from rabbit lungs. Measurements of 99mTc-DTPA clearance may be useful in studying the function of the surfactant system in different lung disorders.