Comparative protein population investigation of the Alnus serrulatarugosa complex

The data from electrophoretic and serological studies with proteins extracted from pollen from: eight populations of the Alnus serrulata-rugosa complex indicate that some bands of the protein pattern (Type A bands) were consistently present in all the samples collected from various populations. The Type A band pattern was not influenced by individual genotypes or environmental differences. Attempts to use bands other than those of Type A in the characterization of populations within the complex did not prove valuable. The importance of using a sample size large enough to cope with the problem of variability within a population was revealed. The data obtained by the use of qualitative serological techniques (Ouchterlony method) agreed with those obtained by the quantitative turbidimetric procedure (Boyden procedure). Serology differences among populations within the complex were not detected. However, marked differences were detected when compared to Betula populifolia, another genus in the same family. All but one sample of seeds of the complex studied revealed 95% sterility because of abnormal embryo development. Viability pollen tests of the 14 samples from the eight populations revealed 94–99% viability. We believe that a taxonomic treatment which designates this complex as one species with varieties or subspecies is the best interpretation of the data available from diverse disciplines and several independent studies.     

Disc-electrophoresis of albumin and globulin fractions from dormant achenes of Lasthenia

Albumin and globulin fractions were extracted from dormant seeds of all 20 taxa of Lasthenia. After disc-electrophoresis on basic 7% acrylamide gels, mean R_p values, coefficients of variation and 95% confidence intervals were computed for both types of protein bands. Dendrograms were produced using similarity coefficients, indicating interspecific affinities among the taxa which differ from the sectional taxonomy of the genus. Protein data concerning certain problematical relationships are compared with published taxonomical and chemical data.     

The role of a putative peroxisomal-targeted epoxide hydrolase of Nicotiana benthamiana in interactions with Colletotrichum destructivum, C. orbiculare or Pseudomonas syringae pv. tabaci

Motif analysis among 30 EH1 and EH2 epoxide hydrolases from Solanaceaeous plants showed differences primarily in the lid region around the catalytic site. Based on in silico models of 3D structures, EH1 proteins lack a catalytic triad because of the orientation of one of the conserved lid tyrosines, while the orientation of that tyrosine in EH2 proteins fomed a catalytic triad inside a hydrophobic tunnel. Two similar EH2 protein genes from Nicotiana benthamiana, NbEH2.1 and NbEH2.2, have a predicted peroxisomal targeting sequence, catalytic triad, and structural similarities to a potato cutin monomer-synthesizing epoxide hydrolase. NbEH2.1 expression increased with infections by the hemibiotrophs, Colletotrichum destructivum, Colletotrichum orbiculare or Pseudomonas syringae pv. tabaci only during their biotrophic phases, while there was only a slight increase during the hypersensitive response to P. syringae pv. tabaci (avrPto). In contrast, among the four pathogens, NbEH2.2 expression increased only in response to P. syringae pv. tabaci. Virus-induced gene silencing of NbEH2.1 significantly affected only the interaction with C. destructivum, resulting in a delay in the appearance of necrosis that may be related to its biotrophic phase being restricted to single epidermal cells, which is unique among these pathogens. These results differed from that of a previously reported EH1 gene of N. benthamiana for these interactions, demonstrating specialization among EH genes in basal resistance.     

Proteomic analysis of wild type and arsenite-resistant Leishmania donovani

Leishmania donovani, causative organism for visceral leishmaniasis, is responsible for considerable mortality and morbidity worldwide. Generation of drug-resistant variants continue to challenge the chemotherapy, the mainstay to fight the disease. The aim of current study was proteomic profiling of wild type (Ld-Wt) and arsenite-resistant (Ld-As20) L. donovani. Significant differences in protein profiles were observed between Ld-As20 and its parent Ld-Wt strain. Proteomic analysis of 158 spots from Ld-Wt and 144 spots from, Ld-As20 identified 77 and 74 protein entries, respectively, through MALDI-TOF/TOF based mass spectrometry and database search. A shift in the isoelectric point of few proteins was observed both in Ld-Wt and Ld-As20, which raises the possibility of continuous arsenite stress, resulting in the differences in the protein profiles of drug-resistant strain from its parent wild type strain. The comparative proteomic data holds the key for elucidation of the multifactorial and complex drug resistance mechanism, like arsenite resistance, in the parasite.     

Comparative bioluminescence dynamics among multiple Armillaria gallica, A. mellea, and A. tabescens genets

Bioluminescence is well known among white-spored species of Basidiomycota including several species of the white-rot wood decay genus Armillaria. Previous work demonstrated consistent differences among A. gallica, A. mellea, and A. tabescens in luminescence magnitude and in luminescence expression relative to environmental stimuli. In the present studies, temporal fluctuations in mycelial luminescence were quantitatively characterized using genets matched for geographical location. All genets derived from rhizomorphs or basdiomata were constitutively luminescent while six of 13 genets originating from mycelial fans were inconsistently luminescent. Using time series of 1000 consecutive measurements over 800 ms intervals, fluctuation patterns had significantly quantifiable structure and were not simply ‘white noise’. Fluctuation patterns were qualitatively similar with alternating periods of rapid fluctuation and relative stability, regardless of luminescence magnitude. Anomalous spikes or shifts in luminescence were recorded for several genets suggesting further work to identify the transient stimuli which elicited these altered luminescence patterns.     

Taxonomic serology of Amoeba proteus

The serological distances among six and eight strains of Amoeba proteus were determined. Quantitative immunological precipitation methods have the sensitivity and accuracy to detect the small differences in taxonomic relationships within this species. The data suggest that the _ShP strain might not belong to the proteus species and support the hypothesis that Amoeba indica is a strain of A. proteus. The invasion of a strain of A. proteus by infectious rod-shaped bacteria caused a diversion in taxonomic relationships with the original strain. Present serological findings are compared to previous data.     

Infection of Locusta migratoria with entomopoxviruses from Arphia conspersa and Melanoplus sanguinipes grasshoppers

Entomopoxvirus (EPV) occlusion bodies isolated from Arphia conspersa and Melanoplus sanguinipes grasshoppers were fed to 3rd and 4th instar Locusta migratoria nymphs. Locus mortality induced by A. conspersa EPV was first detected 18 days after addition of virus to the diet, and reached a level of approximately 68% of the colony population by 60 days after virus inoculation. In a similar population of L. migratoria nymphs, mortality induced by M. sanguinipes virus reached 90% 60 days after virus inoculation. Entomopoxvirus was isolated from M. sanguinipes EPV infected locust nymphs and the viral DNA was cleaved with several restriction endonucleases. The DNA fragment patterns obtained after agarose gel electrophoresis were compared with the fragment patterns from the original sample of M. sanguinipes EPV DNA cleaved with the same restriction endonucleases. No differences in the cleavage patterns were detected between the two virus DNA samples. Virus structural proteins of M. sanguinipes EPV purified from infected locust nymphs were compared by polyacrylamide gel electrophoresis with virus proteins isolated from the original sample of M. sanguinipes EPV. A total of six different virus protein bands were detected between the two poxvirus preparations.     

Molecular characterization and expression analysis of Acmago and AcY14 in Antrodia cinnamomea

Mago nashi (Mago) and Y14 proteins, highly conserved among eukaryotes, participate in mRNA localization and splicing, and as such play important roles in oogenesis, embryogenesis and germ-line sex determination during animal development. Here we identified mago (Acmago) and Y14 (AcY14) homologues derived from Antrodia cinnamomea. Acmago encodes 149 amino acids and AcY14 encodes 168 amino acids. Multiple amino acid sequence alignment as well as secondary and tertiary structure prediction showed that AcMago and AcY14 have similar protein structure to the reported crystal structures of other Mago and Y14 proteins. During fungal development both Acmago and AcY14 genes were abundantly expressed in natural basidiomes. This is the first report of the molecular characterization and expression analysis of the mago and Y14 genes from fungi.     

Genome-wide identification and analysis of the aldehyde dehydrogenase (ALDH) gene superfamily of Gossypium raimondii

Background

Aldehyde dehydrogenases (ALDHs) are members of the NAD(P)⁺-dependent protein superfamily which catalyzes aliphatic and aromatic aldehyde oxidation to non-toxic carboxylic acids. ALDH genes may offer promise for improving plant adaptation to environmental stress. Recently, elucidated genome sequences of Gossypium raimondii provide a foundation for systematic identification and analysis of ALDH genes. To date, this has been accomplished for many plant species except G. raimondii.

Results

In this study, thirty unique ALDH sequences that code for 10 ALDH families were identified in the G. raimondii genome. Phylogenetic analysis revealed that ALDHs were split into six clades in G. raimondii, and ALDH proteins from the same families were clustered together. Phylogenetic relationships of ALDHs from 11 plant species suggest that ALDHs in G. raimondii shared the highest protein homology with ALDHs from poplar. Members within ALDH families possessed homologous exon–intron structures. Chromosomal distribution of ALDH did not occur evenly in the G. raimondii genome and many ALDH genes were involved in the syntenic region as documented by identification of physical locations among single chromosomes. In addition, syntenic analysis revealed that homologues of many G. raimondii ALDHs appeared in corresponding Arabidopsis and poplar syntenic blocks, indicating that these genes arose prior to G. raimondii, Arabidopsis and poplar speciation. Finally, based on gene expression analysis of microarray and RNA-seq, we can speculate that some G. raimondii ALDH genes might respond to drought or waterlogging stresses.

Conclusion

Genome-wide identification and analysis of the evolution and expression of ALDH genes in G. raimondii laid a foundation for studying this gene superfamily and offers new insights into the evolution history and speculated roles in Gossypium. These data can be used to inform functional genomic studies and molecular breeding in cotton.     

Electrophoretic studies on blood proteins of Arvicanthis niloticus

Electrophoretic patterns of blood proteins were compared among groups of Arvicanthis niloticus from widely distant origin: Senegal, Haute-Volta, Egypt. Four blood proteins/enzymes were studied: albumin, transferrin, esterase and 6-phosphogluconate dehydrogenase. The results demonstrate two levels of difference: (a) inter-population differences; and (b) intra-species genetic polymorphism. The latter was not observed for all populations nor for all loci. The differences between populations suggest that some process of specification could be under way among Arvicanthis.     

Variation in levels of lipid components and protein in ecogeographic races of Sorghum bicolor

Sorghum bicolor (L.) Moench is a widespread grass of the African savanna. It contains wild and cultivated subspecies which have morphologically distinct ecogeographic races. Measurements of the amount of oil and protein in sorghum grains revealed significant differences in protein levels between wild and cultivated subspecies. Measurements of the relative percentages of fatty acid components of oil also revealed significant differences in levels of oleic and linoleic acid among wild and cultivated races. We conclude that morphological differences acquired in the course of differentiation of ecogeographic races have been paralleled by differentiation in levels of lipid components and grain protein levels.     

Production of Agaricus bisporus on substrates pre-colonized by Scytalidium thermophilum and supplemented at casing with protein-rich supplements

The objective of this study was to evaluate performance of Agaricus bisporus (Ab) on substrates pre-colonized by Scytalidiumthermophilum (St), a thermophilic fungus known to enhance yields of Ab and increase selectivity of the substrate. The radial extension rate (RER) of the mycelium of three strains of St and their influence on the growth of a brown strain of Ab were evaluated. We also determined the time required for colonization of pangola grass by St in a compost pile and the influence of three protein-rich supplements on yield of Ab on pangola grass (Digitaria decumbens) colonized by St. RER of St ranged from 10.1 mm/d on grass to 18.9 mm/d on potato dextrose yeast extract agar, with significant differences among substrates and among strains. Ab grew faster on substrate colonized for 1, 2, or 3 days by St (RER of 3.31, 3.29, 3.23 mm/d, respectively) compared to non-colonized substrate (1.85 mm/d). Ab was cultivated on substrate samples selected daily from the St-inoculated pile, with biological efficiencies (BE) ranging from 4% (day 0) to 73.9% (day 2). Protein-rich supplements (soybean, black beans and cowpeas) added at casing significantly stimulated mushroom yield on St-colonized substrate compared to the non-supplemented control. BE varied from 26.1% on substrate non-supplemented to 73.1% on compost supplemented with ground soybean. There were no significant differences in mushroom yield observed among supplements evaluated.     

Foliar flavonoids of North American Solanum section Solanum

A total of ten flavonoids, all flavonols, were isolated from leaves of eleven species of Solanum sect. Solanum. Most species had relatively few compounds, primarily quercetin 3-O-glycosides. Little intraspecific variation in flavonoids was observed, except in S. americanum were it correlated with previously recognized races. Flavonoid data are of little help in determining ancestries of polyploid species, but do rule out S. sarrachoides as a progenitor of S. villosum and S. nigrum. Solanum sarrachoides is unique among species examined in having free flavonoid aglycones as well as extensive 3-O-methoxylation.     

Molecular phylogeny of the Pycnonotus sinensis and Pycnonotus taivanus in Taiwan based on sequence variations of nuclear CHD and mitochondrial cytochrome b genes

Sequences of the partial 293-bp nuclear Z-chromosome-linked chromo-helicase binding protein (CHD-Z) and 729-bp mitochondrial cytochrome b (cyt b) genes were obtained from two species of the same family Pycnonotidae of Pycnonotus sinensis (P. sinensis, Chinese Bulbul) and Pycnonotus taivanus (P. taivanus, Taiwan Bulbul) distributed in Taiwan. A panel of 10 individuals (n = 5 for each) with unknown relationship was used to characterize single nucleotide polymorphisms (SNPs) of these genes. We identified 2 and 10 SNPs in CHD-Z and cyt b loci, respectively. Frequency of SNPs was 10 per every 1465- and 729-bp on average. Pairwise nucleotide divergences of CHD-Z and cyt b genes among 10 specimens ranged from 0 to 0.0034 and 0 to 0.0055, respectively. Phylogenetic analysis suggested that the P. taivanus group assignment based on the CHD-Z and cyt b sequences is obviously very similar to P. sinensis.     

Proteomic analysis of two Trypanosoma cruzi zymodeme 3 strains

Two Trypanosoma cruzi Z3 strains, designated as 3663 and 4167, were previously isolated from insect vectors captured in the Brazilian Amazon region. These strains exhibited different infection patterns in Vero, C6/36, RAW 264.7 and HEp-2 cell lineages, in which 3663 trypomastigote form was much less infective than 4167 ones. A proteomic approach was applied to investigate the differences in the global patterns of protein expression in these two Z3 strains. Two-dimensional (2D) protein maps were generated and certain spots were identified by mass spectrometry (MS). Our analyses revealed a significant difference in the expression profile of different proteins between strains 3663 and 4167. Among them, cruzipain, an important regulator of infectivity. This data was corroborated by flow cytometry analysis using anti-cruzipain antibody. This difference could contribute to the infectivity profiles observed for each strain by in vitro assay using different cell lines.     

Sterol-binding polysaccharides of Rhizopus arrhizus, Penicillium roquefortii and Saccharomyces carlsbergensis

Polysaccharides that bind with sterols and render them water-soluble were isolated from two mycelial fungi, Rhizopus arrhizus and Penicillium roquefortii and a yeast Saccharomyces carlsbergensis. The polysaccharides from R. arrhizus and S. carlsbergensis were accompanied by small quantities of phosphorus, protein and lipid, none of which significantly influenced the binding of sterol to polysaccharide. The chemical composition and sterol-binding properties of the polysaccharides from the filamentous species were almost identical, but differed significantly from those of the yeast polysaccharide. The principal sterol-binding polysaccharide of S. carlsbergensis was identified as a mannan and that of the filamentous fungi as a glucan(s). The binding capacity of the purified yeast polysaccharide was almost two-fold greater than that of R. arrhizus and P. roquefortii.     

Differential expression of boule and dazl in adult germ cells of the Asian seabass

Fertility genes boule and dazl constitute the evolutionarily conserved DAZ (Deleted in AZoospermia) family of RNA binding proteins essential for germline development across animal phyla. Here we report the cloning and expression analysis of boule and dazl from the Asian seabass (Lates calcarifer), a marine fish that undergoes sequential male-to-female sex reversal. Molecular cloning and sequence comparison led to the identification of boule and dazl cDNAs. RT-PCR analysis showed that both boule and dazl RNAs were restricted to the gonads among adult organs examined. Chromogenic in situ hybridization revealed germ cell-specific expression for both boule and dazl in female and male adults. Importantly, distinct differences were found between boule and dazl in terms of temporospatial expression and subcellular distribution. The boule RNA was abundant in late gametogenic cells except sperm. Interestingly, dazl expression increases in early oocytes and concentrates in a perinuclear speckle that appears to develop ultimately into the Balbiani body in advanced oocytes. The dazl RNA was found to be abundant in spermatocytes but hardly detectable in sperm. These data demonstrate that boule and dazl are germ cell markers in the adult Asian seabass, and that bisexual germline-specific expression has been conserved for boule and dazl in fish.     

Effects of seston variability on the clearance rate and absorption efficiency of the mussels Aulacomya maoriana, Mytilus galloprovincialis and Perna canaliculus from New Zealand

The clearance rates (CR in l g⁻¹ h⁻¹) and net absorption efficiencies (AE) of three co-occurring mytilid species were estimated to determine the effects of variation in ambient seston quantity (total particulate matter, TPM, mg l⁻¹) and quality (particulate organic matter, POM, mg l⁻¹; percent organic matter, PCOM=POM/TPM) on these physiological functions. CR_S estimates were significantly different among the species (Mytilus galloprovincialis>Perna canaliculus=Aulacomya maoriana), but were not correlated with differences in species-dependent mean body size (P. canaliculus>M. galloprovincialis>A. maoriana). AE estimates were independent of mean body weight, and did not differ among the species. For all three species, CR responded in a simple linear manner to seston organic content, either in terms of POM (for A. maoriana and M. galloprovincialis), or PCOM (for P. canaliculus). The AE response, although also of a simple linear type, was species-dependent and involved interactions of two or three seston components: TPM, POM and PCOM for A. maoriana; POM and PCOM for M. galloprovincialis; and TPM and PCOM for P. canaliculus. For all three species, seston variation explained 15-20% of the variation in CR and 52-59% of the variation in AE. Comparisons among the species indicated that two very different responses to variation in seston quantity and quality exist. First, significant differences in CR result from species-dependent differences in the magnitude of the response to seston variation. Second, species-dependent responses to variation in seston variation resulted in the similarity of the AE responses. Thus, the three species appear to have evolved different strategies for dealing with seston variation, but with the end result that their AE responses do not differ. Finally, no evidence was found of a negative association between CR and AE for any of the three species, suggesting that under the seston conditions experienced in this work, these species do not have the physiological compensatory capacity to reduce CR in order to increase AE. The importance of a comparative (i.e., multi-species) approach utilising ambient seston is emphasised by the findings of this research if we are to understand better the feeding and digestive physiologies of suspension-feeding organisms such as mussels.     

SDS-PAGE comparative studies on the polyhedral and viral polypeptides of the nuclear polyhedrosis viruses of Mamestra brassicae, Autographa californica, and Lymantria dispar

After solubilization of polyhedra of Autographa californica, Lymantria dispar, and Mamestra brassicae nuclear polyhedrosis viruses, PAGE showed at least eight distinct polyhedral polypeptide bands. Whereas the molecular weights of the major polypeptide were similar for the three NPVs (28.0–30.0 kdalton), characteristic differences between the species were found for the minor polypeptides having molecular weights in the range from 12.4 to 62.0 kdalton. It is assumed that these polypeptides are not generated by polyhedral alkaline protease since they are detected after protease inactivation. The data demonstrate that different baculoviruses can be distinguished from each other by SDS-PAGE of their polyhedral polypeptides.