JColorGrid: software for the visualization of biological measurements

Background  

Two-dimensional data colourings are an effective medium by which to represent three-dimensional data in two dimensions. Such "color-grid" representations have found increasing use in the biological sciences (e.g. microarray 'heat maps' and bioactivity data) as they are particularly suited to complex data sets and offer an alternative to the graphical representations included in traditional statistical software packages. The effectiveness of color-grids lies in their graphical design, which introduces a standard for customizable data representation. Currently, software applications capable of generating limited color-grid representations can be found only in advanced statistical packages or custom programs (e.g. micro-array analysis tools), often associated with steep learning curves and requiring expert knowledge.     

Effect of salinity on tomato (Lycopersicon esculentum Mill.) during seed germination stage

A study was conducted using ten genetically diverse genotypes along with their 45F₁ (generated by diallel mating) under normal and salt stress conditions. Although, tomato (Lycopersicon esculentum Mill.) is moderately sensitive to salinity but more attention to salinity is yet to be required in the production of tomato. In present study, germination rate, speed of germination, dry weight ratio and Na⁺/K⁺ ratio in root and shoot, were the parameters assayed on three salinity levels; control, 1.0 % NaCl and 3.0 % NaCl with Hoagland’s solution. Increasing salt stress negatively affected growth and development of tomato. When salt concentration increased, germination of tomato seed was reduced and the time needed to complete germination lengthened, root/shoot dry weight ratio was higher and Na⁺ content increased but K⁺ content decreased. Among the varieties, Sel-7 followed by Arka Vikas and crosses involving them as a parent were found to be the more tolerant genotypes in the present study on the basis of studied parameters.     

Joint Report of the First International Comparison Test on Swine Lymphocyte Alloantigens (SLA)

The first international comparison test on swine lymphocyte alloantigens (SLA) was held in Helsinki, Finland in July 1986. The results reported were based on a comparison of 157 alloantisera originating from six laboratories. The antisera were tested against a selected panel of 264 lymphocyte samples belonging to four laboratories. The most common breeds in Europe were chosen for this first comparison test (Landrace and Large White). Eighteen of the 31 previously known specificities were confirmed and a new nomenclature was established.     

Preparation of o-palmitoyl alkyl lactates through lipase atalysis

Preparation of o-palmitoyl alkyl lactates with methyl, ethyl, propyl, isopropyl and butyl lactates were attempted in a complex esterification reaction using lipases as catalysts. Compared to lactic acid, alkyl lactates were found to be less inhibitory in nature as they resulted in slightly better yields at shake-flask level. Of the alkyl lactates tested, butyl lactate showed better esterification. Porcine pancreas lipase gave higher yields of esters than Rhizomucor miehei lipase (Lipozyme IM20).     

Expression of endogenous proteins in maize hybrids in a multi-location field trial in India

Genetically modified (GM) crops undergo large scale multi-location field trials to characterize agronomics, composition, and the concentration of newly expressed protein(s) [herein referred to as transgenic protein(s)]. The concentration of transgenic proteins in different plant tissues and across the developmental stages of the plant is considered in the safety assessment of GM crops. Reference or housekeeping proteins are expected to maintain a relatively stable expression pattern in healthy plants given their role in cellular functions. Understanding the effects of genotype, growth stage and location on the concentration of endogenous housekeeping proteins may provide insight into the contribution these factors could have on transgenic protein concentrations in GM crops. The concentrations of three endogenous proteins (actin, elongation factor 1-alpha, and glyceraldehyde 3-phosphate dehydrogenase) were measured in several different maize hybrids grown across multiple field locations over 2 years. Leaf samples were collected from healthy plants at three developmental stages across the growing seasons, and protein concentrations were quantified by indirect enzyme-linked immunosorbent assay (ELISA) for each protein. In general, the concentrations of these three endogenous proteins were relatively consistent across hybrid backgrounds, when compared within one growth stage and location (2–26%CV), whereas the concentrations of proteins in the same hybrid and growth stage across different locations were more variable (12–64%CV). In general, the protein concentrations in 2013 and 2014 show similar trends in variability. Some degree of variability in protein concentrations should be expected for both transgenic and endogenous plant-expressed proteins. In the case of GM crops, the potential variation in protein concentrations due to location effects is captured in the current model of multi-location field testing.     

Intron open reading frames as mobile elements and evolution of a group I intron

Group I introns are proposed to have become mobile following the acquisition of open reading frames (ORFs) that encode highly specific DNA endonucleases. This proposal implies that intron ORFs could behave as autonomously mobile entities. This was supported by abundant circumstantial evidence but no experiment of ORF transfer from an ORF- containing intron to its ORF-less counterpart has been described. In this paper we present such experiments, which demonstrate the efficient mobility of the mitochondrial nad1-i4-orf1 between two Podospora strains. The homing of this mobile ORF was accompanied by a bidirectional co-conversion that did not systematically involve the whole intron sequence. Orf1 acquisition would be the most recent step in the evolution of the nad1-i4 intron, which has resulted in many strains of Podospora having an intron with two ORFs (biorfic) and four splicing pathways. We show that two of the splicing events that operate in this biorfic intron, as evidenced by PCR experiments, are generated by a 5'-alternative splice site, which is most probably a remnant of the monoorfic ancestral form of the intron. We propose a sequential evolution model that is consistent with the four organizations of the corresponding nad1 locus that we found among various species of the Pyrenomycete family; these organizations consist of no intron, an intron alone, a monoorfic intron, and a biorfic intron.      

Marmoset phylogenetics, conservation perspectives, and evolution of the mtDNA control region

Marmosets (genus Callithrix) are a diverse group of platyrrhine primates with 13-15 purported taxa, many of them considered endangered. Morphological analyses constitute most of the basis for recognition of these forms as distinct taxa. The purpose of this study was to provide a molecular view, based on mitochondrial control region sequences, of the evolutionary history of the marmosets, concomitant with a molecular phylogenetic perspective on species diversity within the group. An additional purpose was to provide the first comparative examination of a complete New World monkey control region sequence with those of other mammals. The phylogenetic analyses provide convincing support for a split between the Atlantic forest and Amazonian marmosets, with the inclusion of the pygmy marmoset (Cebuella pygmaea) at the base of the Amazonian clade. The earliest branch of the Atlantic forest group was C. aurita. In the Amazonian group, the analyses do not support the recognition of C. humeralifer and the recently described C mauesi as distinct taxa. They do, however, support a clear distinction between C. argentata and a strongly supported mixed clade of C. humeralifer and C. mauesi. In the Atlantic forest group, the phylogenetic tree suggests mixing between C. penicillata, C. kuhli, and possibly C. jacchus. Most of the sequence features characteristic of other mammal control regions were also evident in marmosets, with the exception that conserved sequence blocks (CSBs) 2 and 3 were not clearly identifiable. Tandem repeat units often associated with heteroplasmy in a variety of other mammals were not evident in the marmoset sequences.      

A field study of the effects of elevated CO2 and plant species diversity on ecosystem-level gas exchange in a planted calcareous grassland

The relationship between plant species diversity and ecosystem CO₂ and water vapour fluxes was investigated for planted calcareous grassland communities composed of 5, 12, or 32 species assembled from the native plant species pool. These diversity manipulations were done in factorial combination with a CO₂ enrichment experiment in order to investigate the degree to which ecosystem responses to elevated CO₂ are altered by a loss of plant diversity. Ecosystem CO₂ and H₂O fluxes were measured over several 24-h periods during the 1994 and 1995 growing seasons. Ecosystem CO₂ assimilation on a ground area basis decreased with decreasing plant diversity in the first year and this was related to a decline in above-ground plant biomass. In the second year, however, CO₂ assimilation was not affected by diversity, and this corresponded to the disappearance of a diversity effect on above-ground biomass. Irrespective of diversity treatment, CO₂ assimilation on a ground area basis was linearly related to peak above-ground biomass in both years. Elevated CO₂ significantly increased ecosystem CO₂ assimilation in both years with no interaction between diversity and CO₂ treatment, and no corresponding increase in above-ground biomass. There were no significant effects of diversity on water vapour flux, which was measured only in the second year. There were indications of a small CO₂ effect on water vapour flux (3–9% lower at elevated CO₂ depending on the light level). Our findings suggest that decreasing plant species diversity may substantially decrease ecosystem CO₂ assimilation during the establishment of such planted calcareous grassland communities, but also suggest that this effect may not persist. In addition, we find no evidence that plant species diversity alters the response of ecosystem CO₂ assimilation to elevated CO₂.     

Correlation between the number of adult male Pectinophora gossypiella (Saund.) (Lep., Gelechidae) catches on pheromone traps and the rate of infestation in fruiting bodies of cotton plants by young larvae in three regions of central Greece

In order to evaluate the influence of the number of catches in pheromone-baited traps on the percentage of larval infestation, six delta traps equipped with sex attractant were placed in each of three regions in Central Greece (Farkadona, Farsala, Almyros) in cotton fields from 20 June until 30 September 1995. The collection of fruiting bodies took place weekly and the counting of adults in the traps was carried out each day. The population fluctuation in all three regions was similar with their peak during the first weeks of August. In Farkadona the infestation level was low (1% at the first sampling of August) with a maximum of 9% in the last sampling of September. In Farsala and Almyros, the infestation level was already high (10% and above) in early August. There was a significant positive linear correlation between the number of moth catches and the infestation percentage from first- and second-stage larvae on the first (R = 0694) and second (R = 0.7399) boll-feeding generations.