Structural organization and functional divergence of high isoelectric point α-amylase genes in bread wheat (Triticum aestivum L.) and barley (Hordeum vulgare L.)

Abstract Background High isoelectric point α-amylase genes (Amy1) play major roles during cereal seed germination, and are associated with unacceptable high residual α-amylase activities in ripe wheat grains. However, in wheat and barley, due to extremely high homology of duplicated copies, and large and complex genome background, the knowledge on this multigene family is limited. Results In the present work, we identified a total of 41 Amy1 genes among 13 investigated grasses. By using genomic resources and experimental validation, the exact copy numbers and chromosomal locations in wheat and barley were determined. Phylogenetic and syntenic analyses revealed tandem gene duplication and chromosomal rearrangement leading to separation of Amy1 into two distinct loci, Amy1θ and Amy1λ. The divergence of Amy1λ from Amy1θ was driven by adaptive selection pressures performed on two amino acids, Arg97 and Asn233 (P > 0.95*). The predicted protein structural alteration caused by substitution of Asp233Asn in the conserved starch binding surface site, and significantly expressional differentiation during seed germination and grain development provided evidence of functional divergence between Amy1θ and Amy1λ genes. We screened out candidate copies (TaAmy1-A1/A2 and TaAmy1-D1) associated with high residual α-amylase activities in ripe grains. Furthermore, we proposed an evolutionary model for expansion dynamics of Amy1 genes. Conclusions Our study provides comprehensive analyses of the Amy1 multigene family, and defines the fixation of two spatially structural Amy1 loci in wheat and barley. Potential functional divergence between them is reflected by their sequence features and expressional patterns, and driven by gene duplication, chromosome rearrangement and natural selections during gene family evolution. Furthermore, the discrimination of differentially effective copies during seed germination and/or grain development will provide guidance to manipulation of α-amylase activity in wheat and barley breeding for better yield and processing properties

The impacts of BSMV on vegetative growth and water status in hulless barley (Hordeum vulgare var. nudum) in VIGS study

Barley stripe mosaic virus (BSMV) is an established and extensively used virus-induced gene silencing (VIGS) vector for gene function analysis in monocots. However, the phenotypes generated by targeted gene silencing may be affected or masked by symptoms of BSMV infection. To better understand the potential effects of BSMV-VIGS in hulless barley (Hordeum vulgare var. nudum), the accumulation pattern of BSMV and its impacts on vegetative growth and water status were investigated. The results indicated that the vegetative growth of infected plants was significantly and continuously impacted by BSMV from 10 to 40 days post inoculation (dpi). When the accumulation of BSMV was extremely high (7 to 11 dpi), infected plants displayed twisted leaf tips with an increased water lose rate (WLR) and decreased water content (WC). Virus accumulation declined and stabilized after 25 dpi, at this stage, the WLR and WC were unaffected in the infected plants. The efficiency of VIGS was tested by the silencing of Phytoene desaturase (PDS). RT-qPCR indicated that BSMV-VIGS can be sustained with good efficiency for up to 40 dpi under an altered condition with lower temperature (22 ±1°C) and higher relative humidity (70 ±10%). It was concluded that 25 to 40 dpi was the appropriate time zone for drought-related gene analysis by BSMV-VIGS under such condition

Pathways of lymph node metastasis and prognosis after right hemicolectomy for cecal cancer: results from a retrospective single center

Abstract Background The recommended operation for cecum cancer (CC) is right hemicolectomy (RH) in some Western countries while the principle of D3 lymphadenectomy in Japan recommends resecting approximately 10 cm from the tumor edge. Therefore, the optimal surgical approach for cecum cancer (CC) remains controversial. We conducted this retrospective study to explore the pattern of lymph node metastasis and better surgical procedures for CC. Methods A total of 224 cecum cancer patients from January 1, 2014, to December 31, 2021, were retrospectively included in the final study. The pattern of lymph node metastasis (LNM) was investigated. Results A total of 113 (50.4%, 113/224) patients had pathologically confirmed LNM. The most frequent metastatic site was no. 201 lymph node (46%, 103/224), while 20 (8.9%, 20/224) patients had LNM in no. 202 lymph node, and 8 (3.6%, 8/224) patients had LNM in no. 203 lymph node. Only 1 (0.4%, 1/224) patient had LNM in no. 221 lymph node, four (1.8, 4/224%) patients had LNM in no. 223 lymph node, and no patients had LNM in no. 222 lymph node. LNM in no. 223 lymph node was significantly associated with a poor prognosis. Multivariate analysis indicated that LNM in no. 223 lymph node (HR = 4.59, 95% CI 1.18–17.86, P = 0.028) was the only independent risk factor associated with worse disease-free survival (DFS). Conclusions The LNM in no. 223 lymph node for cecum cancer was rare. Therefore, standard right hemicolectomy excision is too extensive for most CC cases

Dehydration induced transcriptomic responses in two Tibetan hulless barley (Hordeum vulgare var. nudum) accessions distinguished by drought tolerance

Abstract Background The harsh environment on the Qinghai-Tibetan Plateau gives Tibetan hulless barley (Hordeum vulgare var. nudum) great ability to resist adversities such as drought, salinity, and low temperature, and makes it a good subject for the analysis of drought tolerance mechanism. To elucidate the specific gene networks and pathways that contribute to its drought tolerance, and for identifying new candidate genes for breeding purposes, we performed a transcriptomic analysis using two accessions of Tibetan hulless barley, namely Z772 (drought-tolerant) and Z013 (drought-sensitive). Results There were more up-regulated genes of Z772 than Z013 under both mild (5439-VS-2604) and severe (7203-VS-3359) dehydration treatments. Under mild dehydration stress, the pathways exclusively enriched in drought-tolerance genotype Z772 included Protein processing in endoplasmic reticulum, tricarboxylic acid (TCA) cycle, Wax biosynthesis, and Spliceosome. Under severe dehydration stress, the pathways that were mainly enriched in Z772 included Carbon fixation in photosynthetic organisms, Pyruvate metabolism, Porphyrin and chlorophyll metabolism. The main differentially expressed genes (DEGs) in response to dehydration stress and genes whose expression was different between tolerant and sensitive genotypes were presented in this study, respectively. The candidate genes for drought tolerance were selected based on their expression patterns. Conclusions The RNA-Seq data obtained in this study provided an initial overview on global gene expression patterns and networks that related to dehydration shock in Tibetan hulless barley. Furthermore, these data provided pathways and a targeted set of candidate genes that might be essential for deep analyzing the molecular mechanisms of plant tolerance to drought stress

La percepción del aspecto imperfectivo del Pretérito Imperfecto : Estudio de las dificultades en alumnos suecos de español como lengua extranjera en nivel A2

Uno de los aspectos de la gramática española que presenta mayor dificultad para el aprendizaje y uso es la diferenciación entre los distintos tiempos verbales. En nuestro estudio nos hemos centrado en la percepción que alumnos suecos de E/LE en nivel A2 tienen del aspecto imperfectivo del pretérito imperfecto. Para lograr nuestro objetivo se seleccionaron 20 informantes cuya lengua materna es el sueco y cuyo único contacto con el español se da en la escuela, y se les entregaron cinco ejercicios. Los resultados a los que se ha llegado son que los alumnos tienen más dificultades en la comprensión del carácter aspectual del pretérito imperfecto que del pretérito indefinido. Por otra parte, dentro de los distintos usos del imperfecto, el que más errores produce es el uso descriptivo de la acción. Por último, si nos centramos en los tipos de verbos conjugados en el tiempo verbal relativo a nuestro estudio, los que resultan más difíciles de entender son los verbos de estado

Transcriptome Assembly and Analysis of Tibetan Hulless Barley (<i>Hordeum vulgare</i> L. var. <i>nudum</i>) Developing Grains, with Emphasis on Quality Properties

<div><p>Background</p><p>Hulless barley is attracting increasing attention due to its unique nutritional value and potential health benefits. However, the molecular biology of the barley grain development and nutrient storage are not well understood. Furthermore, the genetic potential of hulless barley has not been fully tapped for breeding.</p><p>Methodology/Principal Findings</p><p>In the present study, we investigated the transcriptome features during hulless barley grain development. Using Illumina paired-end RNA-Sequencing, we generated two data sets of the developing grain transcriptomes from two hulless barley landraces. A total of 13.1 and 12.9 million paired-end reads with lengths of 90 bp were generated from the two varieties and were assembled to 48,863 and 45,788 unigenes, respectively. A combined dataset of 46,485 All-Unigenes were generated from two transcriptomes with an average length of 542 bp, and 36,278 among were annotated with gene descriptions, conserved protein domains or gene ontology terms. Furthermore, sequences and expression levels of genes related to the biosynthesis of storage reserve compounds (starch, protein, and β-glucan) were analyzed, and their temporal and spatial patterns were deduced from the transcriptome data of cultivated barley Morex.</p><p>Conclusions/Significance</p><p>We established a sequences and functional annotation integrated database and examined the expression profiles of the developing grains of Tibetan hulless barley. The characterization of genes encoding storage proteins and enzymes of starch synthesis and (1–3;1–4)-β-D-glucan synthesis provided an overview of changes in gene expression associated with grain nutrition and health properties. Furthermore, the characterization of these genes provides a gene reservoir, which helps in quality improvement of hulless barley.</p></div