Molecular taxonomic identification in the absence of a ‘barcoding gap’: a test with the endemic flora of the Canarian oceanic hotspot

We use a comprehensive subset of Canarian angiosperms corresponding to 23 families, 35 genera and 60 Canarian endemic taxa to test whether this flora is suitable to taxonomic identification with the two proposed plant DNA barcode sequences and whether these sequences may reveal the existence of cryptic species overlooked by morphology. The rate of discrimination success between the insular congeneric samples using the rbcL+matK combination and a ‘character‐based’ approach (where we use only the combination of nucleotide positions in an alignment that allows unambiguous species identification) is higher (82.29%) than that obtained with the ‘distance‐based’ approach (80.20%) used by the CBOL Plant Working Group in 2009 and also when compared with tests conducted in other floras. This suggests that the molecular identification of the Canarian endemic flora can be achieved as successfully as in other floras where the incidence of radiation is not as relevant. The facts that (i) a distance‐based criterion was unable to discriminate between congeneric and conspecific comparisons and (ii) only the character‐based discrimination criterion resolved cases that the distance‐based criterion did not, further support the use of a character discrimination approach for a more efficient DNA barcoding of floras from oceanic islands like the Canaries. Thus, a barcoding gap seems not to be necessary for the correct molecular characterization of the Canarian flora. DNA barcodes also suggest the possible existence of cryptic taxa to be further investigated by morphology and that the current taxonomic status of some of the taxa analysed may need revision.     

The Effect of Different Types of Musculoskeletal Injuries on Blood Concentration of Serum Amyloid A in Thoroughbred Racehorses

BackgroundTraining-induced muscle, skeletal and joint trauma may result in acute phase response reflected by the changes in the blood concentration of serum amyloid A (SAA) in racehorses. It remains yet unclear if such systemic reaction could be triggered by sport injuries and what is the impact of different types of musculoskeletal trauma on SAA concentrations in racehorses. This study aimed to determine changes in the SAA blood concentration in racehorses with different types of injuries of musculoskeletal system.ResultsMean SAA concentration within the first 4 days of the injury of muscle and tendon was significantly higher than in bone fractures, dorsal metacarpal disease, joint trauma or in the healthy horses (p<0,001). There were no significant differences between the other groups.ConclusionsStrain injuries of muscle and tendons can cause a moderate increase in SAA blood concentration in racehorses, reflecting the occurrence of the acute phase response. Similar reaction is not observed in the stress-related bone injuries.     

Expression of DNA Damage Response Molecules PARP1, γH2AX,BRCA1, and BRCA2 Predicts Poor Survival of Breast Carcinoma Patients

BACKGROUND: Poly(ADP-ribose) polymerase 1 (PARP1), γH2AX, BRCA1, and BRCA2 are conventional molecular indicators of DNA damage in cells and are often overexpressed in various cancers. In this study, we aimed, using immunohistochemical detection, whether the co-expression of PARP1, γH2AX, BRCA1, and BRCA2 in breast carcinoma (BCA) tissue can provide more reliable prediction of survival of BCA patients. MATERIALS AND METHODS: We investigated immunohistochemical expression and prognostic significance of the expression of PARP1, γH2AX, BRCA1, and BRCA2 in 192 cases of BCAs. RESULTS: The expression of these four molecules predicted earlier distant metastatic relapse, shorter overall survival (OS), and relapse-free survival (RFS) by univariate analysis. Multivariate analysis revealed the expression of PARP1, γH2AX, and BRCA2 as independent poor prognostic indicators of OS and RFS. In addition, the combined expressional pattern of BRCA1, BRCA2, PARP1, and γH2AX (CSbbph) was an additional independent prognostic predictor for OS (P < .001) and RFS (P < .001). The 10-year OS rate was 95% in the CSbbph-low (CSbbph scores 0 and 1) subgroup, but that was only 35% in the CSbbph-high (CSbbph score 4) subgroup. CONCLUSION: This study has demonstrated that the individual and combined expression patterns of PARP1, γH2AX, BRCA1, and BRCA2 could be helpful in determining an accurate prognosis for BCA patients and for the selection of BCA patients who could potentially benefit from anti-PARP1 therapy with a combination of genotoxic chemotherapeutic agents.     

Silicon improves salinity tolerance and affects ammonia assimilation in maize roots

The present study was conducted to evaluate the effect of different salt concentrations (50 and 200 mM NaCl) on growth, permeability properties (electrolyte leakage, cell viability) and activity of glutamine synthetase (GS) and glutamate dehydrogenase (GDH) in roots of maize seedlings. Both salt concentrations significantly affected growth and permeability properties of maize seedling roots and this negative effect increased with concentration of salt and duration of experiments. On the other hand salinity induced only small changes in the activities of GS and GDH, usually small increase in the activity was observed. To characterise the possible protective effect of silicon (Si) on maize roots exposed to saline stress, different concentrations of Si were simultaneously applied to both, low (50 mM) and high (200 mM) salt concentrations. Possible protective effects of Si on studied parameters were analysed in time range of 3 days treatment with the most positive effect on salt-induced root growth inhibition at high salt concentration and electrolyte leakage. The results show significant increase in GDH activity under all the tested conditions, although the mechanisms underlying this increase have not been elucidated. The results indicate that silicon may ameliorate the salt-induced root growth inhibition and increase the plant vigour at stressful conditions.     

BBR induces apoptosis in HepG2 cell through an Akt‐ASK1‐ROS‐p38MAPKs‐linked cascade

Berberine (BBR) has indicated significant antimicrobial activity against a variety of organisms including bacteria, viruses, and fungi. The mechanism by which BBR initiates apoptosis remains poorly understood. In the present study, we demonstrated that BBR exhibited significant cytotoxicity in human hepatoma HepG2 cells. Herein, we investigated cytotoxicity mechanism of BBR in HepG2 cells. The results showed that the induction of apoptosis in HepG2 cells by BBR was characterized by DNA fragmentation, an increased percentage of annexin V, and the activation of caspase‐3. The expressions of Bcl‐2 protein and pro‐caspase‐3 were reduced by BBR in HepG2 cells. However, Bax protein was increased in the cells. BBR‐induced apoptosis was preceded by increased generation of reactive oxygen species (ROS). NAC treatment, a scavenger of ROS, reversed BBR‐induced apoptosis effects via inhibition of Bax activation and Bcl‐2 inactivation. BBR‐induced, dose‐dependent induction of apoptosis was accompanied by sustained phosphorylation of MAP Kinases (JNK and p38 MAPK), ASK1, Akt, and p53. Furthermore, SB203580, p38 inhibitor, reduced the apoptotic effect of BBR, and blocks the generation of ROS and NO as well as activation of Bax. We found that the treatment of HepG2 cells with BBR triggers generation of ROS through Akt phosphorylation, resulting in dissociation of the ASK1‐mediated activation of JNK and p38 pathways. J. Cell. Biochem. 109: 329–338, 2010. © 2009 Wiley‐Liss, Inc.     

tsORFdb: Theoretical Small Open Reading Frames (ORFs) database and massProphet: Peptide Mass Fingerprinting (PMF) tool for unknown small functional ORFs

Peptide mass fingerprinting (PMF) has become one of the most widely used methods for rapid identification of proteins in proteomics research. Many peaks, however, remain unassigned after PMF analysis, partly because of post-translational modification and the limited scope of protein sequences. Almost all PMF tools employ only known or predicted protein sequences and do not include open reading frames (ORFs) in the genome, which eliminates the chance of finding novel functional peptides. Unlike most tools that search protein sequences from known coding sequences, the tool we developed uses a database for theoretical small ORFs (tsORFs) and a PMF application using a tsORFs database (tsORFdb). The tsORFdb is a database for ORFeome that encompasses all potential tsORFs derived from whole genome sequences as well as the predicted ones. The massProphet system tries to extend the search scope to include the ORFeome using the tsORFdb. The tsORFdb and massProphet should be useful for proteomics research to give information about unknown small ORFs as well as predicted and registered proteins.     

Molecular cloning and expression profiles of calreticulin gene from the diamondback moth,Plutella xylostella

Calreticulin (CRT) plays pivotal roles in Ca²⁺ homeostasis, molecular chaperoning, infection, inflammation and innate immunity. In an attempt to study the involvement of CRT in innate immunity, the full-length cDNA of calreticulin (PxCRT) was cloned from the diamondback moth, Plutella xylostella. It consists of 1674 bp (excluding poly-A tail) with a longest open reading frame (ORF) of 1197 bp encoding 398 amino acids. In silico analysis of PxCRT ORF reveals that it has various repeat motifs and endoplasmic reticulum retention signal found in all the calreticulin proteins. As expected, high amino acid sequence identities were found from other CRTs identified from Bombyx mori (87%), Galleria mellonella (87%), Apis mellifera (74%), Anopheles gambiae (74%), Tribolium castaneum (73%), Culex quinquefasciatus (73%), Rhodnius prolixus (72%), Nasonia vitripennis (71%), Drosophila melanogaster (71%) and Haemaphysalis qinghaiensis (68%). During development, P. xylostella expressed PxCRT predominantly in the pupal stage. In addition, spatial expression pattern analysis indicates that PxCRT was highly expressed in the silk gland. PxCRT mRNA, furthermore, was strongly induced 3 to 6 h after laminarin treatment, suggesting that PxCRT appears to be involved in immune responses and also plays an important role in the silk gland.