Effect of Soil Type and In Vitro Proliferation Conditions on Acclimation and Growth of Willow Shoots Micropropagated in Continuous Immersion Bioreactors.

Salix viminalis L. is a species with high capacity for micropropagation and acclimation and could therefore be used to evaluate emergent techniques in the field of plant propagation. The aims of this study were to propagate willow in liquid medium with a continuous immersion system, to explore the application of photoautotrophic conditions and to investigate the adaptation of willow plantlets to different soils that could be used as alternatives to commercial peat. For proliferation, we used 3% sucrose or sugar-free medium, and as substrates, we used commercial peat, a soil from an oak forest with high organic matter content and a crop soil with low organic matter content. The effect of sugar supplementation during proliferation and the soil characteristics during acclimation and growth were evaluated on the basis of aerial and root growth and the hydrolytic and dehydrogenase enzymatic activities of the soils. The results indicate that under photoautotrophic conditions, the supplementation of sucrose during micropropagation did not affect the subsequent growth of the plantlets. All plants acclimated without loss, but the type of soil influenced the height and vigor. Plants produced the highest shoots in peat, whereas the most root development occurred in crop soil. Soil enzyme activities were more influenced by the type of soil than by the presence of plants.

Genomic Alterations in Head and Neck Squamous Cell Carcinoma: Level of Evidence According to ESMO Scale for Clinical Actionability of Molecular Targets (ESCAT).

Development of high-throughput technologies helped to decipher tumor genomic landscapes revealing actionable molecular alterations. We aimed to rank the level of evidence of recurrent actionable molecular alterations in head and neck squamous cell carcinoma (HNSCC) on the basis of the European Society for Medical Oncology (ESMO) Scale for Clinical Actionability of Molecular Targets (ESCAT) to help the clinicians prioritize treatment. We identified actionable alterations in 33 genes. HRAS-activating mutations were ranked in tier IB because of the efficacy of tipifarnib (farnesyltransferase inhibitor) in HRAS-mutated patients with HNSCC (nonrandomized clinical trial). Microsatellite instability (MSI), high tumor mutational burden (TMB), and NTRK fusions were ranked in tier IC because of PD-1 and TRK tyrosine kinase inhibitors tissue-agnostic approvals. CDKN2A-inactivating alterations and EGFR amplification were ranked in tier IIA because of the efficacy of palbociclib (CDK4/6 inhibitor) and afatinib (tyrosine kinase inhibitor) in these respective molecular subgroups in retrospective analyses of clinical trials. Molecular alterations in several genes, including PIK3CA gene, were ranked in tier IIIA because of clinical benefit in other tumor types, whereas molecular alterations in IGF1R and TP53 genes were ranked in tier IVA and tier V, respectively. The most compelling actionable molecular alterations in HNSCC according to ESCAT include HRAS-activating mutations, MSI, high TMB, NTRK fusions, CDKN2A-inactivating alterations, and EGFR amplification.

Fine-needle aspiration as an alternative to core needle biopsy for tumour molecular profiling in precision oncology: prospective comparative study of next-generation sequencing in cancer patients included in the SHIVA02 trial.

High-throughput molecular profiling of solid tumours using core needle biopsies (CNB) allows the identification of actionable molecular alterations, with around 70% success rate. Although several studies have demonstrated the utility of small biopsy specimens for molecular testing, there remains debate as to the sensitivity of the less invasive fine-needle aspiration (FNA) compared to CNB to detect molecular alterations. We aimed to prospectively evaluate the potential of FNA to detect such alterations in various tumour types as compared to CNB in cancer patients included in the SHIVA02 trial. An in-house amplicon-based targeted sequencing panel (Illumina TSCA 99.3 kb panel covering 87 genes) was used to identify pathogenic variants and gene copy number variations (CNV) in concomitant CNB and FNA samples obtained from 61 patients enrolled in the SHIVA02 trial (NCT03084757). The main tumour types analysed were breast (38%), colon (15%), pancreas (11%), followed by cervix and stomach (7% each). We report 123 molecular alterations (85 variants, 23 amplifications and 15 homozygous deletions) among which 98 (80%) were concordant between CNB and FNA. The remaining discordances were mainly related to deletions status, yet undetected alterations were not exclusively specific to FNA. Comparative analysis of molecular alterations in CNB and FNA showed high concordance in terms of variants as well as CNVs identified. We conclude FNA could therefore be used in routine diagnostics workflow and clinical trials for tumour molecular profiling with the advantages of being minimally invasive and preserve tissue material needed for diagnostic, prognostic or theranostic purposes.

Extraction and quantification of chlorophenolate molecules in soils spiked with 2,4-dichlorophenol and 2,4,5-trichlorophenol.

The compounds 2,4-dichlorophenol (2,4-DCP) and 2,4,5-trichlorophenol (2,4,5-TCP) are classified as priority pollutants, with potentially hazardous impacts on the environment. In soil, dissociation of the phenol group occurs, resulting in the simultaneous presence of neutral phenol and anionic phenolate. Although the toxicity of 2,4-DCP and 2,4,5-TCP to soil microbiota has been suggested to be mainly due to the phenolate anion, this hypothesis cannot be tested due to the lack of appropriate methods of extracting and quantifying the anionic form of these compounds (unlike the neutral form, which can be easily quantified). In this study, we developed a method that enables extraction and quantification of phenolate ions. The method could therefore be used to elucidate the processes that regulate the behaviour of chlorophenolic molecules in soil and to clarify the distribution and toxicity of these compounds in the edaphic environment. The proposed method uses saline solutions (CaCl2, KCl and K2SO4) of low ionic strength to extract the chlorophenolate anion from soil, followed by sequential transformation of the anion from the aqueous solution to an organic solvent that enables subsequent identification and quantification of the molecule by gas chromatography. Two soils of contrasting pH were used to test whether the proposed method was practicable. The method enabled analysis of the distribution of the neutral and anionic forms of the chlorophenols in both types of soil considered and revealed the influence of soil pH in this distribution.

Relationships among bulk soil physicochemical, biochemical, and microbiological parameters in an organic alfalfa-rice rotation system.

The microbial communities of bulk soil of rice paddy fields under an ancient organic agriculture regimen, consisting on an alfalfa-rice rotation system, were characterized. The drained soil of two adjacent paddies at different stages of the rotation was compared before rice seeding and after harvesting. The relationships among the soil microbial, physicochemical, and biochemical parameters were investigated using multivariate analyses. In the first year of rice cropping, aerobic cultivable heterotrophic populations correlated with lineages of presumably aerobic bacteria (e.g., Sphingobacteriales, Sphingomonadales). In the second year of rice cropping, the total C content correlated with presumable anaerobic bacteria (e.g., Anaerolineae). Independently of the year of rice cropping, before rice seeding, proteolytic activity correlated positively with the cultivable aerobic heterotrophic and ammonifier populations, the soil catabolic profile and with presumable aerobes (e.g., Sphingobacteriales, Rhizobiales) and anaerobes (e.g., Bacteroidales, Anaerolineae). After harvesting, strongest correlations were observed between cultivable diazotrophic populations and bacterial groups described as comprising N2 fixing members (e.g., Chloroflexi-Ellin6529, Betaproteobacteria, Alphaproteobacteria). It was demonstrated that chemical parameters and microbial functions were correlated with variations on the total bacterial community composition and structure occurring during rice cropping. A better understanding of these correlations and of their implications on soil productivity may be valid contributors for sustainable agriculture practices, based on ancient processes.

Uso de biocidas y mecanismos de respuesta bacteriana / Use of biocides and bacterial response mechanisms

La constante aparición de microorganismos que incrementan su tolerancia a sustancias utilizadas para su control como los biocidas está generando atención en salud pública y debe ser estudiado, teniendo en cuenta los diversos riesgos que se pueden enfrentar principalmente en pacientes con alta susceptibilidad a las infecciones asociadas a la atención en salud, dado que estos biocidas son utilizados cotidianamente lo que ha generado mecanismos bacterianos como lo son la formación de biopelículas y aquellos que incrementan su tolerancia como la generación de bombas de flujo. Esta respuesta bacteriana a la presión de los biocidas se potencia por la aparición de microorganismos resistentes a los antimicrobianos de uso en el tratamiento y control de las infecciones lo que hace difícil el control de estos. Se realizó una revisión de literatura disponible en las bases de datos Proquest, ovid, Science direct, PubMed, donde se encontraron un total de 103 artículos y se seleccionaron 73, de acuerdo con el año de publicación en los idiomas español e inglés, que incluyeron estudios descriptivos y de revisión. El objetivo de este artículo fue realizar una revisión acerca de los principales mecanismos de acción de biocidas y la respuesta de tolerancia que presentan los microorganismos frente a estos; lo que conlleva a la reflexión sobre las implicaciones del uso de estas sustancias sobre la salud humana.

The constant appearance of microorganisms that increase their tolerance to substances used for their control such as biocides is generating attention in public health and should be studied, taking into account the various risks that can be faced mainly in patients with high susceptibility to infections associated with health care, given that these biocides are used on a daily basis, which has generated bacterial mechanisms such as the formation of biofilms and those that increase their tolerance, such as the generation of flow pumps. This bacterial response to the pressure of the biocides is enhanced by the appearance of microorganism's resistant to the antimicrobials used in the treatment and control of infections, which makes their control difficult. A literature review was made available in the databases Proquest, ovid, Science direct, PubMed, where a total of 103 articles were found and 73 were selected, according to the year of publication in the Spanish and English languages, which included Descriptive and review studies. The objective of this article is to carry out a review about the main action mechanisms of biocides and the tolerance response presented by microorganisms against them; which leads to reflection on the implications of the use of these substances on human health.

HIV-1 transmitted drug resistance in Latin America and the Caribbean: what do we know?

Latin America and the Caribbean countries have increased the scaling-up of antiretroviral treatment in the last years. The increase of transmitted drug resistance has been feared due to the worrisome indicators associated with the emergence of drug resistance and monitored by the World Health Organization (WHO). Consequently, our aim was to review all relevant studies on transmitted drug resistance in Latin America and the Caribbean countries, to analyze its levels, to identify the frequency of transmitted drug resistance mutations, and to put these results in the context of the local Latin American and Caribbean countries settings. A systematic search of Spanish, Portuguese, and English literature was performed in databases and international conferences for the period June 1999 to May 2011. In addition, sequences were downloaded from the Los Alamos and Stanford databases and the transmitted drug resistance was reanalyzed according to the WHO Surveillance Drug Resistance Mutation list 2009. In total, 50 articles, 27 abstracts, and 1,922 patients were included. The resistance varied geographically, but most of the countries have reached the WHO threshold of 5% of resistance. According to the sequences available in public databases, the overall prevalence in Latin America and the Caribbean countries for the period 1996-2009 was 7.7% and by region it was 4.3% for the Caribbean, 3.9% for Mexico, 9.4% for Brazil, 10.5% for the Andean region and 4.9% for the Southern Cone. For the last four investigated years (2006-2009), the information was restricted to Brazilian and Venezuelan studies and revealed an overall transmitted drug resistance of 10%. Throughout the study period, limited information was available for the Caribbean and Central American countries. These findings support the need for developing comprehensive surveys of transmitted drug resistance in these regions.