Eukaryotic protein production in designed storage organelles

Background  

Protein bodies (PBs) are natural endoplasmic reticulum (ER) or vacuole plant-derived organelles that stably accumulate large amounts of storage proteins in seeds. The proline-rich N-terminal domain derived from the maize storage protein γ zein (Zera) is sufficient to induce PBs in non-seed tissues of Arabidopsis and tobacco. This Zera property opens up new routes for high-level accumulation of recombinant proteins by fusion of Zera with proteins of interest. In this work we extend the advantageous properties of plant seed PBs to recombinant protein production in useful non-plant eukaryotic hosts including cultured fungal, mammalian and insect cells.     

DNA methylation profile in chronic myelomonocytic leukemia associates with distinct clinical,biological and genetic features

Chromosomal abnormalities are detected in 20–30% of patients with chronic myelomonocytic leukemia (CMML) and correlate with prognosis. On the mutation level, disruptive alterations are particularly frequent in chromatin regulatory genes. However, little is known about the consequential alterations in the epigenetic marking of the genome. Here, we report the analysis of genomic DNA methylation patterns of 64 CMML patients and 10 healthy controls, using a DNA methylation microarray focused on promoter regions. Differential methylation analysis between patients and controls allowed us to identify abnormalities in DNA methylation, including hypermethylation of specific genes and large genome regions with aberrant DNA methylation. Unsupervised hierarchical cluster analysis identified two main clusters that associated with the clinical, biological, and genetic features of patients. Group 1 was enriched in patients with adverse clinical and biological characteristics and poorer overall and progression-free survival. In addition, significant differences in DNA methylation were observed between patients with low risk and intermediate/high risk karyotypes and between TET2 mutant and wild type patients. Taken together, our results demonstrate that altered DNA methylation patterns reflect the CMML disease state and allow to identify patient groups with distinct clinical features.     

A comparison of soil carbon pools and profiles in wetlands in Costa Rica and Ohio

Wetlands are large carbon pools and play important roles in global carbon cycles as natural carbon sinks. This study analyzes the variation of total soil carbon with depth in two temperate (Ohio) and three tropical (humid and dry) wetlands in Costa Rica and compares their total soil C pool to determine C accumulation in wetland soils. The temperate wetlands had significantly greater (P < 0.01) C pools (17.6 kg C m⁻²) than did the wetlands located in tropical climates (9.7 kg C m⁻²) in the top 24 cm of soil. Carbon profiles showed a rapid decrease of concentrations with soil depth in the tropical sites, whereas in the temperate wetlands they tended to increase with depth, up to a maximum at 18–24 cm, after which they started decreasing. The two wetlands in Ohio had about ten times the mean total C concentration of adjacent upland soils (e.g., 161 g C kg⁻¹ were measured in a central Ohio isolated forested wetland, and 17 g C kg⁻¹ in an adjacent upland site), and their soil C pools were significantly higher (P < 0.01). Among the five wetland study sites, three main wetland types were identified – isolated forested, riverine flow-through, and slow-flow slough. In the top 24 cm of soil, isolated forested wetlands had the greatest pool (10.8 kg C m⁻²), significantly higher (P < 0.05) than the other two types (7.9 kg C m⁻² in the riverine flow-though wetlands and 8.0 kg C m⁻² in a slowly flowing slough), indicating that the type of organic matter entering into the system and the type of wetland may be key factors in defining its soil C pool. A riverine flow-through wetland in Ohio showed a significantly higher C pool (P < 0.05) in the permanently flooded location (18.5 kg C m⁻²) than in the edge location with fluctuating hydrology, where the soil is intermittently flooded (14.6 kg C m⁻²).     

Satellite-DNA evolutionary patterns under a complex evolutionary scenario: the case of Acrolophus subgroup (Centaurea L., Compositae) from the western Mediterranean

Within the genus Centaurea (subtribe Centaureinae, tribe Cardueae, Compositae) hybridizations and reticulate-evolution phenomena have widely been recognized. This is especially true in the taxa included in the subgroup Acrolophus from the western Mediterranean area, in which recurrent hybridizations of parapatric ("microallopatric") lineages within the geographical range of a primary radiation have been suggested. The subgroup Acrolophus includes taxa from three sections (i.e. Acrolophus, Phalolepis and Willkommia), and, together with other subgroups, forms the named Jacea group (one of the three main groups into which Centaurea is divided). In this paper, we have studied the influence that the complex evolutionary scenario described for the Acrolophus subgroup from the western Mediterranean exerts on the evolutionary pattern of a satellite-DNA family, the HinfI family, which exists within the genomes of these taxa. To this end, we have analyzed the evolution of this satellite-DNA family in taxa from different taxonomic comparative levels: i) seven subspecies of the C. boissieri complex (one of which with two varieties) of the sect. Willkommia; ii) species of the sections Willkommia (10 species, 19 taxa), Acrolophus (two species), and Phalolepis (two species), all in the Acrolophus subgroup; iii) one external species to the Jacea group, C. granatensis from the group Acrocentron; iv) and species from other related genera from the Centaureinae subtribe (Phonus and Carthamus, both belonging to the Carthamus group). The influence of the suggested model for the origin and diversification of the Acrolophus subgroup is evidenced by the existence of three different HinfI satellite-DNA subfamilies coexisting in some genomes, and by the analysis that we have made by comparing site-by-site the transition stages in the process of concerted evolution between the sequences of the each subfamily. From this analysis, we can deduce that the HinfI repeated subfamilies evolved in a gradual manner, and that the different stages of concerted evolution fit quite well with the combined nuclear-chloroplast-DNA-deduced divergences and phylogeny of the subtribe Centaureinae. The HinfI satellite-DNA from the Carthamus species group (genera Carthamus and Phonus) and from the Acrocentron group (Centaurea granatensis) shows a high intraspecific conservation of the repeats, suggesting that the mechanisms producing concerted evolution have been efficient in these taxa. In addition, the comparison of individual nucleotide positions between related species shows a paucity in the spreading of variants in each subfamily with satellite-DNA divergence, an indication of a constant rate of homogenization of the repeated cluster. On the contrary, this trend is absent in the comparisons of the HinfI sequences from taxa of the subgroup Acrolophus. In this subgroup, we have found in this repetitive family similar representative average sequences for each taxon analyzed, polymorphic sites in each taxon being scant, most of them autapomorphic, representing early stages of genetic differentiation between taxa in the process of concerted evolution. The absence of concerted evolution was visualized by similar levels of intraspecific variation and interspecific divergence and by the lack of fixed species-diagnostic nucleotide sites. These facts might reflect the reticulate mode of evolution of Acrolophus.     

Association of the I148M/PNPLA3 variant with elevated alanine transaminase levels in normal-weight and overweight/obese Mexican children

Background and aims

Non-alcoholic fatty liver disease (NAFLD) and elevated alanine transaminase (ALT) levels are common in obese Hispanic adults and children. Recently, a PNPLA3 gene variant (I148M) was strongly associated with NAFLD and higher ALT levels in obese adults, including Hispanics. The aims of this study were to estimate the frequency of elevated ALT levels, and to address the influence of obesity and PNPLA3/I148M on ALT levels in a general population sample of Mexican school-aged children.

Methods

A total of 1037 non-related Mexican children aged 6 to 12 years were genotyped for the I148M variant. Anthropometric, clinical and metabolic parameters were collected from all participants.

Results

Elevated ALT levels (> 35 U/L) were more frequent in obese (26.9%) and overweight (9.3%) than in normal weight children (2.2%). The M148M genotype was significantly associated with elevated ALT levels in this population (OR = 3.7, 95% CI 2.3–5.9; P = 3.7 × 10^− 8), and children carrying the M148M genotype showed significantly lower HDL cholesterol levels and BMI z-core (P = 0.036 and 0.015, respectively). On stratifying by BMI percentile, this genotype conferred a much greater risk of elevated ALT levels in normal weight (OR = 19.9, 95% CI 2.5–157.7; P = 0.005) than overweight and obese children (OR = 3.4, 95% CI 1.3–8.9; P = 0.014 and OR = 3.1, 95% CI 1.7–5.5; P = 1.4 x10^− 4, respectively).

Conclusions

The I148M PNPLA3 variant is strongly associated with elevated ALT levels in normal weight and overweight/obese Mexican children. Thus, the M148M genotype may be considered as an important risk factor for liver damage in this population.     

Mutagenesis of human DNA polymerase lambda: essential roles of Tyr505 and Phe506 for both DNA polymerase and terminal transferase activities

DNA polymerase (pol) λ is homologous to pol β and has intrinsic polymerase and terminal transferase activities. However, nothing is known about the amino acid residues involved in these activites. In order to precisely define the nucleotide-binding site of human pol λ, we have mutagenised two amino acids, Tyr505 and the neighbouring Phe506, which were predicted by structural homology modelling to correspond to the Tyr271 and Phe272 residues of pol β, which are involved in nucleotide binding. Our analysis demonstrated that pol λ Phe506Arg/Gly mutants possess very low polymerase and terminal transferase activities as well as greatly reduced abilities for processive DNA synthesis and for carrying on translesion synthesis past an abasic site. The Tyr505Ala mutant, on the other hand, showed an altered nucleotide binding selectivity to perform the terminal transferase activity. Our results suggest the existence of a common nucleotide-binding site for the polymerase and terminal transferase activities of pol λ, as well as distinct roles of the amino acids Tyr505 and Phe506 in these two catalytic functions.     

Isolation and characterization of a potato cDNA corresponding to a 1-aminocyclopropane-1-carboxylate (ACC) oxidase gene differentially activated by stress

1-Aminocyclopropane-1-carboxylate (ACC) oxidase enzyme catalyses the final step in ethylene biosynthesis, converting 1-aminocyclopropane-1-carboxylic acid to ethylene. A cDNA clone encoding an ACC oxidase, ST-ACO3, was isolated from potato (Solanum tuberosum L.) by differential screening of a Fusarium eumartii infected-tuber cDNA library. The deduced amino acid sequence exhibited similarity to other ACC oxidase proteins from several plants species. Northern blot analysis revealed that the ST-ACO3 mRNA level increased in potato tubers upon inoculation with F. eumartii, as well as after treatment with salicylic acid and indole-3-acetic acid, suggesting a cross-talk between different signalling pathways involved in the defence response of potato tubers against F. eumartii attack.     

Metabolic Characterization of Acutely Isolated Hippocampal and Cerebral Cortical Slices Using [U-<Superscript>13</Superscript>C]Glucose and [1,2-<Superscript>13</Superscript>C]Acetate as Substrates

Brain slice preparations from rats, mice and guinea pigs have served as important tools for studies of neurotransmission and metabolism. While hippocampal slices routinely have been used for electrophysiology studies, metabolic processes have mostly been studied in cerebral cortical slices. Few comparative characterization studies exist for acute hippocampal and cerebral cortical slices, hence, the aim of the current study was to characterize and compare glucose and acetate metabolism in these slice preparations in a newly established incubation design. Cerebral cortical and hippocampal slices prepared from 16 to 18-week-old mice were incubated for 15–90 min with unlabeled glucose in combination with [U-¹³C]glucose or [1,2-¹³C]acetate. Our newly developed incubation apparatus allows accurate control of temperature and is designed to avoid evaporation of the incubation medium. Subsequent to incubation, slices were extracted and extracts analyzed for ¹³C-labeling (%) and total amino acid contents (µmol/mg protein) using gas chromatography–mass spectrometry and high performance liquid chromatography, respectively. Release of lactate from the slices was quantified by analysis of the incubation media. Based on the measured ¹³C-labeling (%), total amino acid contents and relative activity of metabolic enzymes/pathways, we conclude that the slice preparations in the current incubation apparatus exhibited a high degree of metabolic integrity. Comparison of ¹³C-labeling observed with [U-¹³C]glucose in slices from cerebral cortex and hippocampus revealed no significant regional differences regarding glycolytic or total TCA cycle activities. On the contrary, results from the incubations with [1,2-¹³C]acetate suggest a higher capacity of the astrocytic TCA cycle in hippocampus compared to cerebral cortex. Finally, we propose a new approach for assessing compartmentation of metabolite pools between astrocytes and neurons using ¹³C-labeling (%) data obtained from mass spectrometry. Based on this approach we suggest that cellular metabolic compartmentation in hippocampus and cerebral cortex is very similar.     

Shoot regeneration and determination of iridoid levels in the medicinal plant <Emphasis Type="Italic">Castilleja tenuiflora</Emphasis> Benth.

Castilleja tenuiflora is a medicinal plant that grows in pine–oak woods primarily in southern and central Mexico. It is highly valued for its medicinal properties, which have been attributed to aucubin-like iridoids. In the present study, we developed an efficient protocol for in vitro shoot proliferation and ex vitro rooting of C. tenuiflora. Using a colorimetric method, we determined total iridoid contents of various different tissues of propagated plants. The shoots were induced from nodal explants cultured on Murashige and Skoog (MS) (1962) medium supplemented with indole-3-butyric acid (IBA) (0 and 0.5 μM) and different concentrations of thidiazuron (TDZ), 6-benzyladenine (BA), or kinetin (KIN) (0–20 μM). Of the cytokinins tested, KIN was more effective for shoot induction than TDZ or BA, and the highest shoot proliferation rate was achieved with 5 μM KIN (4 shoots per explant). Plantlets were rooted on MS medium, nutrient solution, or potting mix, alone or in combination with auxins. The best responses (100% rooting efficiency) were obtained by dipping shoots in half-strength MS medium containing 7.5 μM IBA before transfer to potting mix. On average, each shoot formed 9 roots of 39.3 ± 3.8 mm in length after 21 days. These roots appeared to be more functional than those that developed in nutrient solution, and were associated with a high survival rate (95%) during acclimatization and cultivation in a greenhouse, where flowering occurred after 4 months. Propagated plants accumulated iridoids, thus representing a potential source of pharmacologically useful compounds.     

Studies on plating efficiency and estimation of viability of suspensions of Paracoccidioides brasiliensis yeast cells

Mild sonication was used to obtain single cell suspensions of Paracoccidioides brasiliensis. These cells were intact by microscopic criteria. Direct cell counts in a given inoculum and colony formation on various media were used to determine plating efficiency. Sonicated and nonsonicated cell suspensions were used to study plating efficiency and to estimate viability by means of vital dyes. Methylene blue, Erythrosin B, and Janus green were unreliable when used with P. brasiliensis, but vital dyes were accurate when tested with Candida albicans.Acridine orange gave more meaningful results of viability. Estimates of viability, however, changed significantly as a result of relatively minor alterations in the composition of the suspending medium.In initial experiments, the plating efficiency of P. brasiliensis was dismally low. It descended abruptly with increasing dilution of inoculum. Efficiency was much improved if horse serum was added to brain heart infusion plates or if glucose glycine yeast extract (GGY) plates were incubated at room temperature and mycelial colonies were counted. With the technique we report, current plating efficiency of sonicated suspensions is of the order of 25 %. Our results and procedures have an important bearing upon those studies concerned with in vitro killing of P. brasiliensis in suspensions or with isolating this fungus from clinical or environmental specimens.