Simple, fast and inexpensive hot sodium hydroxide and tris DNA extraction method for genotyping tomato and melon seeds

Seed commerce is a highly profitable global market. Most commercialized seeds are hybrid seeds originating from a controlled cross between two selected parental lines. The market value of hybrid seeds depends on their hybrid genetic purity. DNA molecular markers are a reliable and widespread tool to genotype plant materials; however, DNA extraction from seeds is challenging, often laborious and expensive. With the ultimate goal of creating a tomato and melon hybrid seeds purity test, various challenges arise. To overcome these problems and with the purpose of crude DNA extraction, a simple, fast, inexpensive and easily scalable adaptation of the hot sodium hydroxide and tris method coupled to a competitive allele-specific PCR genotyping method is proposed.

Determination of policyclic aromatic compounds, (PAH, nitro-PAH and oxy-PAH) in soot collected from a diesel engine operating with different fuels

A qualitative and quantitative analysis of polycyclic aromatic compounds (PACs; polycyclic aromatic hydrocarbons (PAHs), oxygenated and nitrated polycyclic aromatic hydrocarbons (OPAHs and NPAHs)) present in the soluble organic fraction (SOF) of different soot samples has been carried out to determine the effect of soot-generation conditions on their composition and health effects. The soot samples were generated using a diesel engine bench powered by diesel (DS) and biodiesel (BS) fuels under different combustion conditions. To optimize the procedure, a surrogate soot (Printex-U) and a certified reference material (SRM1650b) were also tested. Different extraction methods were used to extract the PAHs, OPAHs and NPAHs, and the Soxhlet technique using pyridine:acetic acid 1 % was found to be the most suitable procedure to extract the highest concentration (ng mg-1) and more types of PAHs and OPAHs from the soot. The results show that the PACs identified, and their concentrations, depend on the formation and collection conditions. The predominant compounds in all soot samples studied were fluorene (Flo), phenanthrene (Phe), fluoranthene (Fla), pyrene (Pyr), 9-fluorenone (9Flo) and 9,10-anthraquinone (9,10Anq). As such, the presence of these PACs in the atmosphere of urban and rural areas can mainly be attributed to the emissions from diesel vehicles. The percentage of OPAHs with respect to total PACs was highest in the soot generated from a biofuel. These oxidized compounds favor regeneration of the diesel particulate filter (DPF). The results also indicate that the carcinogenicity of the soot depends on the combustion conditions and type of fuel.

The degradation of performance of a state-of-the-art skin image classifier when applied to patient-driven internet search

Model Dermatology ( https://modelderm.com ; Build2021) is a publicly testable neural network that can classify 184 skin disorders. We aimed to investigate whether our algorithm can classify clinical images of an Internet community along with tertiary care center datasets. Consecutive images from an Internet skin cancer community ('RD' dataset, 1,282 images posted between 25 January 2020 to 30 July 2021; https://reddit.com/r/melanoma ) were analyzed retrospectively, along with hospital datasets (Edinburgh dataset, 1,300 images; SNU dataset, 2,101 images; TeleDerm dataset, 340 consecutive images). The algorithm's performance was equivalent to that of dermatologists in the curated clinical datasets (Edinburgh and SNU datasets). However, its performance deteriorated in the RD and TeleDerm datasets because of insufficient image quality and the presence of out-of-distribution disorders, respectively. For the RD dataset, the algorithm's Top-1/3 accuracy (39.2%/67.2%) and AUC (0.800) were equivalent to that of general physicians (36.8%/52.9%). It was more accurate than that of the laypersons using random Internet searches (19.2%/24.4%). The Top-1/3 accuracy was affected by inadequate image quality (adequate = 43.2%/71.3% versus inadequate = 32.9%/60.8%), whereas participant performance did not deteriorate (adequate = 35.8%/52.7% vs. inadequate = 38.4%/53.3%). In this report, the algorithm performance was significantly affected by the change of the intended settings, which implies that AI algorithms at dermatologist-level, in-distribution setting, may not be able to show the same level of performance in with out-of-distribution settings.

A Molecular Stratification of Chilean Gastric Cancer Patients with Potential Clinical Applicability

Gastric cancer (GC) is a complex and heterogeneous disease. In recent decades, The Cancer Genome Atlas (TCGA) and the Asian Cancer Research Group (ACRG) defined GC molecular subtypes. Unfortunately, these systems require high-cost and complex techniques and consequently their impact in the clinic has remained limited. Additionally, most of these studies are based on European, Asian, or North American GC cohorts. Herein, we report a molecular classification of Chilean GC patients into five subtypes, based on immunohistochemical (IHC) and in situ hybridization (ISH) methods. These were Epstein-Barr virus positive (EBV+), mismatch repair-deficient (MMR-D), epithelial to mesenchymal transition (EMT)-like, and accumulated (p53+) or undetected p53 (p53-). Given its lower costs this system has the potential for clinical applicability. Our results confirm relevant molecular alterations previously reported by TCGA and ACRG. We confirm EBV+ and MMR-D patients had the best prognosis and could be candidates for immunotherapy. Conversely, EMT-like displayed the poorest prognosis; our data suggest FGFR2 or KRAS could serve as potential actionable targets for these patients. Finally, we propose a low-cost step-by-step stratification system for GC patients. To the best of our knowledge, this is the first Latin American report on a molecular classification for GC. Pending further validation, this stratification system could be implemented into the routine clinic.

Glucocorticoids Decrease Longitudinal Bone Growth in Pediatric Kidney Transplant Recipients by Stimulating the FGF23/FGFR3 Signaling Pathway

Renal transplantation (RTx) is an effective therapy to improve clinical outcomes in pediatric patients with terminal chronic kidney disease. However, chronic immunosuppression with glucocorticoids (GCs) reduces bone growth and BMD. The mechanisms causing GC-induced growth impairment have not been fully clarified. Fibroblast growth factor 23 (FGF23) is a peptide hormone that regulates phosphate homeostasis and bone growth. In pathological conditions, FGF23 excess or abnormal FGF receptors (FGFR) activity leads to bone growth impairment. Experimental data indicate that FGF23 expression is induced by chronic GC exposure. Therefore, we hypothesize that GCs impair bone growth by increasing FGF23 expression, which has direct effects on bone growth plate. In a post hoc analysis of a multicentric randomized clinical trial of prepubertal RTx children treated with early GC withdrawal or chronic GC treatment, we observed that GC withdrawal was associated with improvement in longitudinal growth and BMD, and lower plasma FGF23 levels as compared with a chronic GC group. In prepubertal rats, GC-induced bone growth retardation correlated with increased plasma FGF23 and bone FGF23 expression. Additionally, GC treatment decreased FGFR1 expression whereas it increased FGFR3 expression in mouse tibia explants. The GC-induced bone growth impairment in tibiae explants was prevented by blockade of FGF23 receptors using either a pan-FGFR antagonist (PD173074), a C-terminal FGF23 peptide (FGF23180-205) which blocks the binding of FGF23 to the FGFR-Klotho complex or a specific FGFR3 antagonist (P3). Finally, local administration of PD173074 into the tibia growth plate ameliorated cartilage growth impairment in GC-treated rats. These results show that GC treatment partially reduces longitudinal bone growth via upregulation of FGF23 and FGFR3 expression, thus suggesting that the FGF23/Klotho/FGFR3 axis at the growth plate could be a potential therapeutic target for the management of GC-induced growth impairment in children.

Integrated single-base resolution maps of transcriptome, sRNAome and methylome of Tomato yellow leaf curl virus (TYLCV) in tomato

Geminiviruses are plant ssDNA viruses that replicate through dsDNA intermediates and form minichromosomes which carry the same epigenetic marks as the host chromatin. During the infection, geminiviruses are targets of the post-transcriptional and transcriptional gene silencing machinery. To obtain insights into the connection between virus-derived small RNAs (vsRNAs), viral genome methylation and gene expression, we obtained the transcriptome, sRNAome and methylome from the geminivirus Tomato yellow leaf curl virus-infected tomato plants. The results showed accumulation of transcripts just at the viral ORFs, while vsRNAs spanned the entire genome, showing a prevalent accumulation at regions where the viral ORFs overlapped. The viral genome was not homogenously methylated showing two highly methylated regions located in the C1 ORF and around the intergenic region (IR). The compilation of those results showed a partial correlation between vsRNA accumulation, gene expression and DNA methylation. We could distinguish different epigenetic scenarios along the viral genome, suggesting that in addition to its function as a plant defence mechanism, DNA methylation could have a role in viral gene regulation. To our knowledge, this is the first report that shows integrative single-nucleotide maps of DNA methylation, vsRNA accumulation and gene expression from a plant virus.

The cancer-related transcription factor RUNX2 modulates expression and secretion of the matricellular protein osteopontin in osteosarcoma cells to promote adhesion to endothelial pulmonary cells and lung metastasis

Osteosarcomas are bone tumors that frequently metastasize to the lung. Aberrant expression of the transcription factor, runt-related transcription factor 2 (RUNX2), is a key pathological feature in osteosarcoma and associated with loss of p53 and miR-34 expression. Elevated RUNX2 may transcriptionally activate genes mediating tumor progression and metastasis, including the RUNX2 target gene osteopontin (OPN/SPP1). This gene encodes a secreted matricellular protein produced by osteoblasts to regulate bone matrix remodeling and tissue calcification. Here we investigated whether and how the RUNX2/OPN axis regulates lung metastasis of osteosarcoma. Importantly, RUNX2 depletion attenuates lung metastasis of osteosarcoma cells in vivo. Using next-generation RNA-sequencing, protein-based assays, as well as the loss- and gain-of-function approaches in selected osteosarcoma cell lines, we show that osteopontin messenger RNA levels closely correlate with RUNX2 expression and that RUNX2 controls the levels of secreted osteopontin. Elevated osteopontin levels promote heterotypic cell-cell adhesion of osteosarcoma cells to human pulmonary microvascular endothelial cells, but not in the presence of neutralizing antibodies. Collectively, these findings indicate that the RUNX2/OPN axis regulates the ability of osteosarcoma cells to attach to pulmonary endothelial cells as a key step in metastasis of osteosarcoma cells to the lung.

First Report of Pepper vein yellows virus Infecting Sweet Pepper in Spain

In November 2012, unusual symptoms were observed in plants of sweet pepper (Capsicum annuum L.) grown in commercial greenhouses of Almería Province, southeastern Spain. Symptoms included interveinal yellowing, upward leaf curling, and internode shortening, and were more evident in the upper part of the plant. Abnormal ripening of fruits was observed in symptomatic plants, with fruits remaining orange in the red varieties and yellow in the orange varieties, thus reducing their marketability. During December 2012 and January 2013, severe outbreaks of this disease syndrome occurred, with many greenhouses exhibiting almost 100% incidence. The symptoms observed were similar to those reported for isolates of Pepper vein yellows virus (PeVYV, genus Polerovirus, family Luteoviridae) (previously also named Pepper yellow leaf curl virus [PYLCV] and Pepper yellows virus [PYV]) (2,4). Twenty five symptomatic leaf and/or fruit samples (some of them supplied by Zeraim Ibérica, S.A.), each from a different greenhouse, were analyzed and all reacted positively in double-antibody sandwich-ELISA with an antiserum against the polerovirus Cucurbit aphid-borne yellows virus (CABYV) (Sediag, Longvic, France), known to cross-react with PeVYV (2). Total RNA was extracted by TRIsure reagent (Bioline, London, United Kingdom) from symptomatic leaves and analyzed by reverse transcription (RT)-PCR with primers Pol-G-F (5'-GAYTGCTCYGGYTTYGACTGGAG-3') and Pol-G-R (5'-GATYTTATAYTCATGGTAGGCCTTGAG-3') designed for universal detection of poleroviruses by amplifying the RNA-dependent RNA polymerase (RdRp) and coat protein (CP) partial genes (3). DNA fragments of the expected size (1.1 kbp) were amplified supporting a polerovirus infection in all the analyzed samples. The PCR product obtained from one sample (Almería-1) was extracted from agarose gel with a QIAquick gel extraction kit (Qiagen, Hilden, Germany), cloned in pGEM-T Easy vector (Promega, Madison, WI), and one clone was sequenced (Macrogen Inc., Seoul, South Korea). The PCR products amplified from three other samples (2-13, 7-13, and 8-13) were directly sequenced. The nucleotide identity between the amplified fragments (GenBank Accession Nos. KC769487, KC839992 to 94), calculated after alignment with ClustalW, was 99.7 to 100%. The highest nucleotide identity of the Spanish sequences was with a PeVYV isolate from Turkey (FN600344, named as PYV) (98.5 to 98.7%). The spread of PeVYV in Spain is additional evidence of the emergence of this virus as a global threat for pepper crops after its first detection in Japan in 1995 and recent reports from the Mediterranean Basin (1,2). References: (1) N. Buzkan et al. Arch. Virol. 158:881, 2013. (2) A. Dombrovsky et al. Phytoparasitica 38:477, 2010. (3) D. Knierim et al. Plant Pathol. 59:991, 2010. (4) R. Murakami et al. Arch. Virol. 156:921, 2011.

Application of cluster analysis to surface ozone, NO₂ and SO₂ daily patterns in an industrial area in Central-Southern Spain measured with a DOAS system

The daily variations of surface ozone, NO₂ and SO₂ have been investigated in a heavily industrialised area in the centre of the Iberian Peninsula (Puertollano) using hourly values recorded during two years (2008-2009) with an active LP-DOAS system. The meteorological conditions and air masses have been studied using the HYSPLIT model. The maximum hourly levels of these air pollutants exceeded 100 ppb for ozone, 150 ppb for SO₂ and 210 ppb for NO₂. However, mean values for ozone, NO₂ and SO₂ were of 49, 10 and 3 ppb respectively. Daily-monthly evolutions (defined as daily evolutions for different months) have been analysed in order to know the general daily behaviour of these species. Air pollution problems have been identified using the thresholds defined in the European Directive 2008. The limits to protect human health (human health protection limitations) have been exceeded during the study period. In order to find a set of representative daily cycles for each pollutant at different air quality regimes, a K-mean cluster technique has been applied. Five and four optimal cluster numbers have been obtained for the daily patterns of ozone and SO₂ respectively. In addition, we studied the daily variation of the temperature, relative and specific humidity and wind speed associated with each air pollutant daily pattern. Ozone daily patterns showed typical daily variations with one exception of a cluster which presents a peak in the early morning. For SO₂, the first two clusters present a low mixing ratio, however cluster 3 and 4 are less frequent but with higher levels. The more frequent air pollutant daily patterns do not exceed the threshold defined in the Directive. Nevertheless, clusters with lower frequency (representing between 5 and 7% of days) exceed the thresholds and could be considered as air pollution events.

Spondylodiscitis in patients under haemodyalisis

PURPOSE

The purpose of this study was to reach conclusions about the diagnosis and treatment of a series of patients with spondylodiscitis under haemodialysis treatment.

METHODS

We collected and studied 23 patients included in a prospective database from two neighbouring hospitals. Descriptive statistical analysis was performed.

RESULTS

The diagnosis was frequently made very late and early negative cultures were not uncommon; magnetic resonance images allowed for an early diagnosis with accurate anatomical information. Empirical antibiotic treatment with prompt surgery produced good results in patients under risk of, or having neurological problems. Surgical approaches did not differ from pyogenic or tuberculous spondylodiscitis. Age in our series was not a predictive issue.

CONCLUSIONS

Whenever a patient under haemodialysis has symptoms of spinal disease, particularly back pain with fever, they should undergo an MRI. If diagnosis of spondylodiscitis is made prompt empirical antibiotherapy should be instituted. Blood cultures should be performed and tissue samples taken for cultures; however, culture outcome must not delay therapy. Early surgical decompression leads to good results.

Night-time atmospheric fate of acrolein and crotonaldehyde

The absolute rate coefficients for the gas-phase reaction of the NO3 radical with acrolein and crotonaldehyde have been measured overthe temperature range 249-330 K, using a discharge flow system and monitoring the NO3 radical by laser induced fluorescence (LIF). The obtained rate coefficients at 298 K for NO3 reactions with acrolein and crotonaldehyde were (3.30 +/- 0.39) x 10(-15) cm3 molecule(-1) s(-1) for acrolein and (1.35 +/- 0.04) x 10(-14) cm3 molecule(-1) s(-1) for crotonaldehyde, and the proposed Arrhenius expressions are k(T) = (1.72 +/- 0.5) x 10(-13) exp[(-1190 +/- 43)/T] and k(T) = (5.02 +/- 0.7) x 10(-13) exp[(-1076 +/- 47)/T], respectively, in units of cm3 molecule(-1) s(-1). In addition, the products and mechanisms were investigated using an environmental chamber/FTIR absorption system. Formaldehyde, CO, and acryloylperoxy nitrate were identified as the main products for the acrolein reaction with molar yields of 31.6 +/- 2.0, 20.9 +/- 1.9, and 47 +/- 3, respectively. In the crotonaldehyde reaction the main products detected were crotonylperoxy nitrate and CO with yields of 93.6 +/- 4.3 and 8.3 +/- 1.1, respectively. On the basis of the rate constant measured, the activation energy calculated, and the identified products, abstraction of the aldehydic H seems to be the main degradation pathway at room temperature for the reaction of acrolein with NO3. For crotonaldehyde, the mechanism is unclear on the basis of the experimental results. The atmospheric implications of the reactions in question are also discussed.

[Epilepsy equivalents: a term in disuse?]

The term 'epileptic equivalent' has had different meanings in recent years, for both doctors and lawyers (who have copied their reports). Our interest is due to finding that in the jurisprudence of the Supreme Court that we have reviewed, these terms are still taken into consideration when passing judgement or declaring a defendant immune from prosecution. This might mean a complete or partial defence, according to the grade of psychological illness of the person who commits the punishable act. Thus, there are still references to dysthymia, residual or larvate epilepsy, etcetera, and medical experts relate them directly to epileptic disorders, to judge from the references made in many of the sentences reviewed. This has influenced penal classification in one way or another. People who have never had an epileptic crisis have been considered to be epileptics. The same may also be said of the well-known epileptic character or epileptic personality. Therefore this paper considers the importance of language in this disorder. It invites relevant persons or institutions to unify opinions and modernize the terminology in accordance with modern scientific knowledge [REV NEUROL 1999; 28: 524-8].

[Civil and criminal responsibility of epileptics]

Since the new Penal Code has come into force, certain sections have been altered, such as those dealing with exculpatory circumstances, and as specialists treating patients with possible mental changes, we should be aware that section 20 now takes the place of the former section 8. The situation of the epileptic with regard to civil and criminal responsibility, has hardly changed. This is not surprising in view of current clinico-therapeutic knowledge. Epileptic patients are legally able to testify, inherit etc. and also have the obligation to compensate for damage they have caused. An attempt is made to define the immunity from prosecution of epileptics in accordance with non-static criteria, and to use a mixed biological-mental formula, which would make it possible to discover whether there was an alteration or anomaly of mental state at the time of the criminal offence, which would mean that the patient was unable to understand the unlawfulness of his action, or to act in accordance with such understanding. The deed itself is considered, without labelling illnesses or persons, seeking a simple definition of immunity from prosecution. The epileptic is immune from prosecution during a full attack, whilst during the rest of the time each case has to be decided individually. We emphasize the necessity of 'declassifying' epilepsy as a typical endogenous psychosis, which puts these patients into the group of the insane, although this term is no longer included in the new legal code.