Biomass recovery through secondary succession in the Cordillera Central de los Andes, Colombia

Estimations on biomass recovery rates by secondary tropical forests are needed to understand the complex tropical succession, and their importance on CO2 capture, to offset the warming of the planet. We conducted the study in the Porce River Canyon between 550 and 1 700m.a.s.l. covering tropical and premontane moist belts. We established 33 temporary plots of 50m x 20m in secondary forests, including fallows to succesional forests, and ranging between 3 and 36 years old; we measured the diameter at breast height (D) of all woody plants with D > or = 5cm. In each one of these plots we established five 10m x 10m subplots, in which we measured the diameter betweem 1cm < or = D < 5cm of all woody plants. We estimated the biomass of pastures by harvesting 54 plots of 2m x 2m, and of shrubs in the fallows by harvesting the biomass in 18 plots of 5m x 2m. We modeled Bav (above ground live biomass of woody plants) and Brg (coarse root biomass) as a function of succesional age (t) with the growth model of von Bertalanffy, using 247t/ha and 66t/ha as asymptote, respectively. Besides, we modeled the ratios brg/bav = f(D) and Brg/Bav = f(t). The model estimated that 87 years are required to recover the existing Bav of primary forests through secondary succession, and 217 years for the Brg of the primary forest. The maximum instantaneous growth rate of the Bav was 6.95 t/ha/yr at age 10. The maximum average growth rate of the Bav was 6.26 t/ha/yr at age 17. The weighted average of the absolute growth rate of the Bav reached 4.57t/ha/yr and the relative growth rate 10% annually. The ratio brg/bav decreases with increasing D. The ratio Brg/Bav initially increases very rapidly until age 5 (25%), then decreases to reach 25 years (18%) and increases afterwards until the ratio reaches the asymptote (26.7%).     

Plant neighbor identity influences plant biochemistry and physiology related to defense

Background  

Chemical and biological processes dictate an individual organism's ability to recognize and respond to other organisms. A small but growing body of evidence suggests that plants may be capable of recognizing and responding to neighboring plants in a species specific fashion. Here we tested whether or not individuals of the invasive exotic weed, Centaurea maculosa, would modulate their defensive strategy in response to different plant neighbors.     

Native Variants of the MRB1 Complex Exhibit Specialized Functions in Kinetoplastid RNA Editing

Adaptation and survival of Trypanosoma brucei requires editing of mitochondrial mRNA by uridylate (U) insertion and deletion. Hundreds of small guide RNAs (gRNAs) direct the mRNA editing at over 3,000 sites. RNA editing is controlled during the life cycle but the regulation of substrate and stage specificity remains unknown. Editing progresses in the 3’ to 5’ direction along the pre-mRNA in blocks, each targeted by a unique gRNA. A critical editing factor is the mitochondrial RNA binding complex 1 (MRB1) that binds gRNA and transiently interacts with the catalytic RNA editing core complex (RECC). MRB1 is a large and dynamic complex that appears to be comprised of distinct but related subcomplexes (termed here MRBs). MRBs seem to share a ‘core’ complex of proteins but differ in the composition of the ‘variable’ proteins. Since some proteins associate transiently the MRBs remain imprecisely defined. MRB1 controls editing by unknown mechanisms, and the functional relevance of the different MRBs is unclear. We previously identified two distinct MRBs, and showed that they carry mRNAs that undergo editing. We proposed that editing takes place in the MRBs because MRBs stably associate with mRNA and gRNA but only transiently interact with RECC, which is RNA free. Here, we identify the first specialized functions in MRBs: 1) 3010-MRB is a major scaffold for RNA editing, and 2) REH2-MRB contains a critical trans-acting RNA helicase (REH2) that affects multiple steps of editing function in 3010-MRB. These trans effects of the REH2 include loading of unedited mRNA and editing in the first block and in subsequent blocks as editing progresses. REH2 binds its own MRB via RNA, and conserved domains in REH2 were critical for REH2 to associate with the RNA and protein components of its MRB. Importantly, REH2 associates with a ~30 kDa RNA-binding protein in a novel ~15S subcomplex in RNA-depleted mitochondria. We use these new results to update our model of MRB function and organization.     

Efficient construction of a highly useful phage-displayed human antibody repertoire

We have constructed a highly useful phage-displayed human antibody repertoire with limited cloning efforts. Our strategy was to maximize diversity during the first steps of library construction through the use of various lymphoid sources from several donors, inclusion of different immunoglobulin isotypes, and performance of multiple separate amplification reactions with all possible combinations within a complex primer set. The resulting variable region collections were cloned to form a moderate size library, composed by 4.25x10(8) single chain antibody fragments. This repertoire was successfully used to retrieve binders to seven model antigens: six proteins and one 12 aa peptide. Binding affinities reached nanomolar and even subnanomolar range. Sequence diversity and V-gene usage variability among binders were proven. Our approach was not focused on absolute library size, but on a high quality sampling of variable regions from the human antibody repertoire.     

Affinity adsorption of lysozyme on a macroligand prepared with Cibacron Blue 3GA attached to yeast cells

The objective of this study was the development of affinity adsorbent particles with the appropriate characteristics to be applied in protein purification using the affinity ultrafiltration method. To prepare affinity macroligands Cibacron Blue 3GA, as a ligand molecule, was immobilized by covalent bonding onto yeast cell walls, the support material or matrix. The maximum attachment of the ligand to the matrix was 212 μmol/g (ligand dry weight/yeast dry weight). Lysozyme was selected as the protein model for the adsorption studies. Its adsorption onto the matrix without ligand and matrix with attached ligand were investigated batch-wise. The adsorption equilibrium isotherms appeared to follow a typical Langmuir isotherm. The maximum adsorption capacity (q(m)) of the Cell-Cibacron macroligand for lysozyme was 110 mg/ml of wet macroligand. The adsorbent was also employed for the separation of lysozyme from hen egg white. High purity lysozyme was obtained.     

Next generation sequencing provides rapid access to the genome of Puccinia striiformis f. sp. tritici, the causal agent of wheat stripe rust

Background

The wheat stripe rust fungus (Puccinia striiformis f. sp. tritici, PST) is responsible for significant yield losses in wheat production worldwide. In spite of its economic importance, the PST genomic sequence is not currently available. Fortunately Next Generation Sequencing (NGS) has radically improved sequencing speed and efficiency with a great reduction in costs compared to traditional sequencing technologies. We used Illumina sequencing to rapidly access the genomic sequence of the highly virulent PST race 130 (PST-130).

Methodology/Principal Findings

We obtained nearly 80 million high quality paired-end reads (>50x coverage) that were assembled into 29,178 contigs (64.8 Mb), which provide an estimated coverage of at least 88% of the PST genes and are available through GenBank. Extensive micro-synteny with the Puccinia graminis f. sp. tritici (PGTG) genome and high sequence similarity with annotated PGTG genes support the quality of the PST-130 contigs. We characterized the transposable elements present in the PST-130 contigs and using an ab initio gene prediction program we identified and tentatively annotated 22,815 putative coding sequences. We provide examples on the use of comparative approaches to improve gene annotation for both PST and PGTG and to identify candidate effectors. Finally, the assembled contigs provided an inventory of PST repetitive elements, which were annotated and deposited in Repbase.

Conclusions/Significance

The assembly of the PST-130 genome and the predicted proteins provide useful resources to rapidly identify and clone PST genes and their regulatory regions. Although the automatic gene prediction has limitations, we show that a comparative genomics approach using multiple rust species can greatly improve the quality of gene annotation in these species. The PST-130 sequence will also be useful for comparative studies within PST as more races are sequenced. This study illustrates the power of NGS for rapid and efficient access to genomic sequence in non-model organisms.     

Oral rehabilitation of severely worn dentition using an overlay for immediate re-establishment of occlusal vertical dimension

The aim of this study was to describe the treatment used in an elderly patient presenting with bruxism and dental erosion, with good gingival health and bone support, but with decreased occlusal vertical dimension (OVD). The oral rehabilitation of elderly patients presenting with bruxism in association with tooth erosion has been a great challenge for dentists. The loss of OVD, the presence of occlusal instability and the absence of an effective anterior guide due excessive dental wear, can damage stomatognathic system (SS) biology, the function and the aesthetics. In the first treatment stage, an overlay removable partial denture (ORPD) was fabricated for the immediate re-establishment of function and aesthetics. After a 2-month follow up, with the patient presenting no symptoms, a second rehabilitation stage was accomplished, with fixed and removable prostheses. Oral rehabilitation with an ORPD was able to re-establish the SS biology, but a correct diagnosis and treatment plan are essential for success. The ORPD is a non-invasive and reversible restoring modality for general dentists that allow the re-establishment of the patient's immediate aesthetics and function at low cost.     

The missing link in coenzyme A biosynthesis: PanM (formerly YhhK), a yeast GCN5 acetyltransferase homologue triggers aspartate decarboxylase (PanD) maturation in Salmonella enterica

Coenzyme A (CoA) is an essential cofactor for all forms of life. The biochemistry underpinning the assembly of CoA in Escherichia coli and other enterobacteria is well understood, except for the events leading to maturation of the L-aspartate-α-decarboxylase (PanD) enzyme that converts pantothenate to β-alanine. PanD is synthesized as pro-PanD, which undergoes an auto-proteolytic cleavage at residue Ser25 to yield the catalytic pyruvoyl moiety of the enzyme. Since 1990, it has been known that E. coli yhhK strains are pantothenate auxotrophs, but the role of YhhK in pantothenate biosynthesis remained an enigma. Here we show that Salmonella enterica yhhK strains are also pantothenate auxotrophs. In vivo and in vitro evidence shows that YhhK interacts directly with PanD, and that such interactions accelerate pro-PanD maturation. We also show that S. enterica yhhK strains accumulate pro-PanD, and that not all pro-PanD proteins require YhhK for maturation. For example, the Corynebacterium glutamicum panD(+) gene corrected the pantothenate auxotrophy of a S. enterica yhhK strain, supporting in vitro evidence obtained by others that some pro-PanD proteins autocleave at faster rates. We propose the name PanM for YhhK to reflect its role as a trigger of pro-PanD maturation by stabilizing pro-PanD in an autocleavage-prone conformation.     

Inferring parameters shaping amino acid usage in prokaryotic genomes via Bayesian MCMC methods

Molar content of guanine plus cytosine (G + C) and optimal growth temperature (OGT) are main factors characterizing the frequency distribution of amino acids in prokaryotes. Previous work, using multivariate exploratory methods, has emphasized ascertainment of biological factors underlying variability between genomes, but the strength of each identified factor on amino acid content has not been quantified. We combine the flexibility of the phylogenetic mixed model (PMM) with the power of Bayesian inference via Markov Chain Monte Carlo (MCMC) methods, to obtain a novel evolutionary picture of amino acid usage in prokaryotic genomes. We implement a Bayesian PMM which incorporates the feature that evolutionary history makes observed data interdependent. As in previous studies with PMM, we present a variance partition; however, attention is also given to the posterior distribution of "systematic effects" that may shed light about the relative importance of and relationships between evolutionary forces acting at the genomic level. In particular, we analyzed influences of G + C, OGT, and respiratory metabolism. Estimates of G + C effects were significant for amino acids coded by G + C or molar content of adenine plus thymine (A + T) in first and second bases. OGT had an important effect on 12 amino acids, probably reflecting complex patterns of protein modifications, to cope with varying environments. The effect of respiratory metabolism was less clear, probably due to the already reported association of G + C with aerobic metabolism. A "heritability" parameter was always high and significant, reinforcing the importance of accommodating phylogenetic relationships in these analyses. "Heritable" component correlations displayed a pattern that tended to cluster "pure" G + C (A + T) in first and second codon positions, suggesting an inherited departure from linear regression on G + C.