Phylogenetic analysis of Codium species from Brazil, with the description of the new species C. pernambucensis (Bryopsidales, Chlorophyta)

The genus Codium comprises c. 125 species widely distributed in marine coastal environments throughout the world. Due to morphological plasticity, the taxonomic delimitation of Codium species can be difficult. Sequences of the first exon of the large subunit of RUBISCO (rbcL) have been used in the molecular delimitation of species and for phylogenetic purposes. In the present study, we complement previous morphological work on Brazilian Codium species with molecular systematics. Based on the partial rbcL sequences, seven species are recognized along the Brazilian coast: C. decorticatum, C. intertextum, C. isthmocladum, C. profundum, C. spongiosum, C. taylorii and the new species Codium pernambucensis. Ten unique sequences were obtained among the samples examined, which we used in combination with previously published sequences to infer molecular phylogenies using various methods. The resulting trees showed three principal monophyletic groupings: Clade A with species having a prostrate habit, not branched, and mostly with small, grouped utricles; Clade B primarily consisting of upright species with cylindrical branches and large individual utricles; and Clade C composed of upright species with cylindrical branches that are slightly flattened, and have intermediate-sized individual utricles. The Brazilian species grouped with morphologically similar taxa from other geographic localities, and are present in all three main clades. A new sprawling species, Codium pernambucensis is described based on morphology and molecular analyses.

RNA extraction from ten year old formalin-fixed paraffin-embedded breast cancer samples: a comparison of column purification and magnetic bead-based technologies

Abstract Background The development of protocols for RNA extraction from paraffin-embedded samples facilitates gene expression studies on archival samples with known clinical outcome. Older samples are particularly valuable because they are associated with longer clinical follow up. RNA extracted from formalin-fixed paraffin-embedded (FFPE) tissue is problematic due to chemical modifications and continued degradation over time. We compared quantity and quality of RNA extracted by four different protocols from 14 ten year old and 14 recently archived (three to ten months old) FFPE breast cancer tissues. Using three spin column purification-based protocols and one magnetic bead-based protocol, total RNA was extracted in triplicate, generating 336 RNA extraction experiments. RNA fragment size was assayed by reverse transcription-polymerase chain reaction (RT-PCR) for the housekeeping gene glucose-6-phosphate dehydrogenase (G6PD), testing primer sets designed to target RNA fragment sizes of 67 bp, 151 bp, and 242 bp. Results Biologically useful RNA (minimum RNA integrity number, RIN, 1.4) was extracted in at least one of three attempts of each protocol in 86–100% of older and 100% of recently archived ("months old") samples. Short RNA fragments up to 151 bp were assayable by RT-PCR for G6PD in all ten year old and months old tissues tested, but none of the ten year old and only 43% of months old samples showed amplification if the targeted fragment was 242 bp. Conclusion All protocols extracted RNA from ten year old FFPE samples with a minimum RIN of 1.4. Gene expression of G6PD could be measured in all samples, old and recent, using RT-PCR primers designed for RNA fragments up to 151 bp. RNA quality from ten year old FFPE samples was similar to that extracted from months old samples, but quantity and success rate were generally higher for the months old group. We preferred the magnetic bead-based protocol because of its speed and higher quantity of extracted RNA, although it produced similar quality RNA to other protocols. If a chosen protocol fails to extract biologically useful RNA from a given sample in a first attempt, another attempt and then another protocol should be tried before excluding the case from molecular analysis.

A systematic review with procedural assessments and meta-analysis of Low Level Laser Therapy in lateral elbow tendinopathy (tennis elbow)

Abstract Background Recent reviews have indicated that low level level laser therapy (LLLT) is ineffective in lateral elbow tendinopathy (LET) without assessing validity of treatment procedures and doses or the influence of prior steroid injections. Methods Systematic review with meta-analysis, with primary outcome measures of pain relief and/or global improvement and subgroup analyses of methodological quality, wavelengths and treatment procedures. Results 18 randomised placebo-controlled trials (RCTs) were identified with 13 RCTs (730 patients) meeting the criteria for meta-analysis. 12 RCTs satisfied half or more of the methodological criteria. Publication bias was detected by Egger's graphical test, which showed a negative direction of bias. Ten of the trials included patients with poor prognosis caused by failed steroid injections or other treatment failures, or long symptom duration or severe baseline pain. The weighted mean difference (WMD) for pain relief was 10.2 mm [95% CI: 3.0 to 17.5] and the RR for global improvement was 1.36 [1.16 to 1.60]. Trials which targeted acupuncture points reported negative results, as did trials with wavelengths 820, 830 and 1064 nm. In a subgroup of five trials with 904 nm lasers and one trial with 632 nm wavelength where the lateral elbow tendon insertions were directly irradiated, WMD for pain relief was 17.2 mm [95% CI: 8.5 to 25.9] and 14.0 mm [95% CI: 7.4 to 20.6] respectively, while RR for global pain improvement was only reported for 904 nm at 1.53 [95% CI: 1.28 to 1.83]. LLLT doses in this subgroup ranged between 0.5 and 7.2 Joules. Secondary outcome measures of painfree grip strength, pain pressure threshold, sick leave and follow-up data from 3 to 8 weeks after the end of treatment, showed consistently significant results in favour of the same LLLT subgroup (p < 0.02). No serious side-effects were reported. Conclusion LLLT administered with optimal doses of 904 nm and possibly 632 nm wavelengths directly to the lateral elbow tendon insertions, seem to offer short-term pain relief and less disability in LET, both alone and in conjunction with an exercise regimen. This finding contradicts the conclusions of previous reviews which failed to assess treatment procedures, wavelengths and optimal doses.

cDNA-AFLP analysis of Psidium guajava L. cultivars under water stress and mechanical injury: methodological implications

Studies involving amplified fragment length polymorphism (cDNA-AFLP) have often used polyacrylamide gels with radiolabeled primers in order to establish best primer combinations, to analyze, and to recover transcript-derived fragments. Use of automatic sequencer to establish best primer combinations is convenient, because it saves time, reduces costs and risks of contamination with radioactive material and acrylamide, and allows objective band-matching and more precise evaluation of transcript-derived fragments intensities. This study aimed at examining the gene expression of commercial cultivars of P. guajava subjected to water and mechanical injury stresses, combining analyses by automatic sequencer and fluorescent kits for polyacrylamide gel electrophoresis. Firstly, 64 combinations of EcoRI and MseI primers were tested. Ten combinations with higher number of polymorphic fragments were then selected for transcript-derived fragments recovering and cluster analysis, involving 45 saplings of P. guajava. Two groups were obtained, one composed by the control samplings, and another formed by samplings undergoing stress, with no clear distinction between stress treatments. The results revealed the convenience of using a combination of automatic sequencer and fluorescent kits for polyacrylamide gel electrophoreses to examine gene expression profiles. The Unweighted Pair Group Method with Arithmetic Mean analysis using Euclidean distances points out a similar induced response mechanism of P. guajava undergoing water stress and mechanical injury.

Long-term effects of oil pollution in mangrove forests (Baixada Santista, Southeast Brazil) detected using a GIS-based multitemporal analysis of aerial photographs

Oil spills are potential threats to the integrity of highly productive coastal wetlands, such as mangrove forests. In October 1983, a mangrove area of nearly 300 ha located on the southeastern coast of Brazil was impacted by a 3.5 million liter crude oil spill released by a broken pipeline. In order to assess the long-term effects of oil pollution on mangrove vegetation, we carried out a GIS-based multitemporal analysis of aerial photographs of the years 1962, 1994, 2000 and 2003. Photointerpretation, visual classification, class quantification, ground-truth and vegetation structure data were combined to evaluate the oil impact. Before the spill, the mangroves exhibited a homogeneous canopy and well-developed stands. More than ten years after the spill, the mangrove vegetation exhibited three distinct zones reflecting the long-term effects of the oil pollution. The most impacted zone (10.5 ha) presented dead trees, exposed substrate and recovering stands with reduced structural development. We suggest that the distinct impact and recovery zones reflect the spatial variability of oil removal rates in the mangrove forest. This study identifies the multitemporal analysis of aerial photographs as a useful tool for assessing a system's capacity for recovery and monitoring the long-term residual effects of pollutants on vegetation dynamics, thus giving support to mangrove forest management and conservation.

Evidence on the best chlorhexidine concentration to perform oral hygiene: meta-analysis

Although scientific literature has demonstrated the relevance of oral hygiene with chlorhexidine in preventing ventilation-associated pneumonia, there is a wide variation of concentrations, frequency and techniques when using the antiseptic. The aim of this research was to assessthe best chlorhexidine concentration used to perform oral hygiene to prevent ventilation-associated pneumonia. A systematic review followed by four meta-analysis using chlorhexidine concentration as criterion was carried out. Articles in English, Spanish or Portuguese indexed in the Cochrane, Embase, Lilacs, PubMed/Medline and Ovid electronic databases were selected. The research was carried out from May to June 2011. The primary outcome measure of interest was ventilation-associated pneumonia. Ten primary studies were divided in four groups (Gl-4), based on chlorhexidine concentration criterion. Gl (5 primary studies, chlorhexidine 0.12%) showed homogeneity among studies and the use of chlorhexidine represented a protective factor. G2 (3 primary studies, chlorhexidine 0.20%) showed heterogeneity among studies and chlorhexidine did not represent a protective factor. G3 (2 primary studies, chlorhexidine 2,00%) showed homogeneity among studies and the use of chlorhexidine was significant. G4 (10 primary studies with different chlorhexidine concentrations) showed homogeneity among studies and the common Relative Risk was significant. Statistic analyses showed a protective effect of oral hygiene with chlorhexidine in preventing ventilation-associated pneumonia. However, it was not possible to identity a standard to establish optimal chlorhexidine concentration.