Pan-chloroplast genomes for accession-specific marker development in Hibiscus syriacus

Hibiscus syriacus L. is a renowned ornamental plant. We constructed 95 chloroplast genomes of H. syriacus L. cultivars using a short-read sequencing platform (Illumina) and a long-read sequencing platform (Oxford Nanopore Technology). The following genome assembly, we delineate quadripartite structures encompassing large single-copy, small single-copy, and inverted repeat (IRa and IRb) regions, from 160,231 bp to 161,041 bp. Our comprehensive analyses confirmed the presence of 79 protein-coding genes, 30 tRNA genes, and 4 rRNA genes in the pan-chloroplast genome, consistent with prior research on the H. syriacus chloroplast genome. Subsequent pangenome analysis unveiled widespread genome sequence conservation alongside unique cultivar-specific variant patterns consisting of 193 single-nucleotide polymorphisms and 61 insertions or deletions. The region containing intra-species variant patterns, as identified in this study, has the potential to develop accession-specific molecular markers, enhancing precision in cultivar classification. These findings are anticipated to drive advancements in breeding strategies, augment biodiversity, and unlock the agricultural potential inherent in H. syriacus.

Admixture of divergent genomes facilitates hybridization across species in the family Brassicaceae

Hybridization and polyploidization are pivotal to plant evolution. Genetic crosses between distantly related species are rare in nature due to reproductive barriers but how such hurdles can be overcome is largely unknown. Here we report the hybrid genome structure of xBrassicoraphanus, a synthetic allotetraploid of Brassica rapa and Raphanus sativus. We performed cytogenetic analysis and de novo genome assembly to examine chromosome behaviors and genome integrity in the hybrid. Transcriptome analysis was conducted to investigate expression of duplicated genes in conjunction with epigenome analysis to address whether genome admixture entails epigenetic reconfiguration. Allotetraploid xBrassicoraphanus retains both parental chromosomes without genome rearrangement. Meiotic synapsis formation and chromosome exchange are avoided between nonhomologous progenitor chromosomes. Reconfiguration of transcription network occurs, and less divergent cis-elements of duplicated genes are associated with convergent expression. Genome-wide DNA methylation asymmetry between progenitors is largely maintained but, notably, B. rapa-originated transposable elements are transcriptionally silenced in xBrassicoraphanus through gain of DNA methylation. Our results demonstrate that hybrid genome stabilization and transcription compatibility necessitate epigenome landscape adjustment and rewiring of cis-trans interactions. Overall, this study suggests that a certain extent of genome divergence facilitates hybridization across species, which may explain the great diversification and expansion of angiosperms during evolution.

AB0446 IMPROVEMENT OF BELIMUMAB ON QUALITY OF LIFE IN PATIENTS WITH SYSTEMIC LUPUS ERYTHEMATOSUS

Background

Accumulating evidence supports an impaired quality of life in patients with systemic lupus erythematosus (SLE). A study reported the patients concerns centred on fatigue[1].

Objectives

We investigated the effect of belimumab on quality of life in patients with SLE.

Methods

SLE patients from Guangdong Second Provincial General Hospital treated with belimumab (n=19) or control group (n=22) were included. Patients in control group were in traditional treatment without belimumab. Data were collected prospectively at treatment initiation and now, including Systemic Lupus Erythematosus Disease Activity Index (SLEDAI), Pittsburgh Sleep Quality Index (PSQI) and the SF-36 (Table 1).

Table 1.SLEDAIPPSQIPSF-36PGroupPre-treatmentPost-treatment-Pre-treatmentPost-treatment-Pre-treatmentPost-treatment-Belimumab group11±4.676.11±3.550.0016±3.833.58±2.010.02519.47±187.79685.62±141.780.004Control group8.82±5.693.55±2.110.0006.5±3.525.86±3.240.536541.73±185.22700.42±123.900.002P0.1990.007-0.6650.011-0.7050.723-

Results

Belimumab group showed improvement in SLEDAI, PSQI and the SF-36 (P＜0.05). Control group was improvement in SLEDAI and the SF-36 (P＜0.05), no changes in PSQI (P=0.536). However, the improvement of belimumab group in SLEDAI and PSQI observably outperformed the improvement of control group.

Conclusion

Belimumab effectively improve quality of life in patients with SLE. Further study of pediatric patients with SLE is still warranted.

References

[1]Golder V, Ooi J, Antony A S, et al. Discordance of patient and physician health status concerns in systemic lupus erythematosus. Lupus,2018,27(3):501-506.

Disclosure of Interests

None declared

Expanded transcriptomic view of strawberry fruit ripening through meta-analysis

Strawberry is an important fruit crop and a model for studying non-climacteric fruit ripening. Fruit ripening and senescence influence strawberry fruit quality and postharvest storability, and have been intensively studied. However, genetic and physiological differences among cultivars preclude consensus understanding of these processes. We therefore performed a meta-analysis by mapping existing transcriptome data to the newly published and improved strawberry reference genome and extracted meta-differentially expressed genes (meta-DEGs) from six cultivars to provide an expanded transcriptomic view of strawberry ripening. We identified cultivar-specific transcriptome changes in anthocyanin biosynthesis-related genes and common changes in cell wall degradation, chlorophyll degradation, and starch metabolism-related genes during ripening. We also identified 483 meta-DEGs enriched in gene ontology categories related to photosynthesis and amino acid and fatty acid biosynthesis that had not been revealed in previous studies. We conclude that meta-analysis of existing transcriptome studies can effectively address fundamental questions in plant sciences.

Reduced fertility caused by meiotic defects and micronuclei formation during microsporogenesis in xBrassicoraphanus

Background

Hybridization and polyploidization events are important driving forces in plant evolution. Allopolyploids formed between different species can be naturally or artificially created but often suffer from genetic instability and infertility in successive generations. xBrassicoraphanus is an intergeneric allopolyploid obtained from a cross between Brassica rapa and Raphanus sativus, providing a useful resource for genetic and genomic study in hybrid species.

Objective

The current study aims to understand the cause of hybrid sterility and pollen abnormality in different lines of synthetic xBrassicoraphanus from the cytogenetic perspective.

Methods

Alexander staining was used to assess the pollen viability. Cytogenetic analysis was employed to monitor meiotic chromosome behaviors in pollen mother cells (PMCs). Origins of parental chromosomes in xBrassicoraphanus meiocytes were determined by genome in situ hybridization analysis.

Results

The xBrassicoraphanus lines BB#4 and BB#6 showed high rates of seed abortion and pollen deformation. Abnormal chromosome behaviors were observed in their PMCs, frequently forming univalents and inter-chromosomal bridges during meiosis. A positive correlation also exists between meiotic defects and the formation of micronuclei, which is conceivably responsible for unbalanced gamete production and pollen sterility.

Conclusion

These results suggest that unequal segregation of meiotic chromosomes, due in part to non-homologous interactions, is responsible for micronuclei and unbalanced gamete formation, eventually leading to pollen degeneration and inferior fertility in unstable xBrassicoraphanus lines.

Analyses of targeted/untargeted metabolites and reactive oxygen species of pepper fruits provide insights into seed browning induced by chilling

Hot peppers are sensitive to low temperature, and seed browning significantly reduces the fruit quality. This study aims to clarify the mechanisms of seed browning in terms of metabolite changes. Metabolites were analysed during a 30-day-storage period at 2 °C and 10 °C. Gamma-aminobutyric acid, tyrosine, phenylalanine, and isoleucine concentrations were significantly higher at 2 °C storage than at 10 °C. Reactive oxygen species (ROS) generation was associated with seed browning. Transcription of jasmonic acid synthesis and ROS scavenging genes were higher in hot peppers stored at 2 °C than those stored at 10 °C. This study elucidated the mechanisms underlying seed browning and chill damage in hot peppers during storage at low temperatures and our findings may help improve hot peppers' quality following harvesting.

Jasmonic acid and ERF family genes are involved in chilling sensitivity and seed browning of pepper fruit after harvest

Pepper (Capsicum annuum L.) fruit is sensitive to temperatures below 10 °C, which severely diminish fruit quality during cold chain distribution. Seed browning was a major chilling symptom in 36 genotypes of C. annuum fruit screened after storage at 2 °C for 3 weeks. Among them, pepper fruits of chilling-insensitive 'UZB-GJG-1999-51' and -sensitive 'C00562' were treated at 2 °C for 0 or 24 h, respectively. Analyses of integrated transcriptome-metabolome and relative gene expression in seeds obtained from the two genotypes were conducted to identify key factors involved in the seed browning induced by chilling. The relative contents of branched-chain amino acids such as leucine, isoleucine, and valine were significantly increased after chilling. Transcriptome identification showed 3,140 differentially expressed genes (log twofold change > 1.0 and FDR-corrected p value < 0.05) affected by chilling between the two genotypes. Particularly, genes related to jasmonic acid synthesis and signaling were differentially expressed. A regulatory network of jasmonic acid synthesis and signaling, and regulation of ERF family genes might contribute to chilling response in pepper fruit. The results of this study may help facilitate further studies to develop chilling-insensitive peppers and could be a basis for improving postharvest fruit quality.

The thick aleurone1 Gene Encodes a NOT1 Subunit of the CCR4-NOT Complex and Regulates Cell Patterning in Endosperm

Maize (Zea mays) thick aleurone1 (thk1-R) mutants form multiple aleurone layers in the endosperm and have arrested embryogenesis. Prior studies suggest that thk1 functions downstream of defective kernel1 (dek1) in a regulatory pathway that controls aleurone cell fate and other endosperm traits. The original thk1-R mutant contained an ∼2-Mb multigene deletion, which precluded identification of the causal gene. Here, ethyl methanesulfonate mutagenesis produced additional alleles, and RNA sequencing from developing endosperm was used to identify a candidate gene based on differential expression compared with the wild-type progenitor. Gene editing confirmed the gene identity by producing mutant alleles that failed to complement existing thk1 mutants and that produced multiple-aleurone homozygous phenotypes. Thk1 encodes a homolog of NEGATIVE ON TATA-LESS1, a protein that acts as a scaffold for the CARBON CATABOLITE REPRESSION4-NEGATIVE ON TATA-LESS complex. This complex is highly conserved and essential in all eukaryotes for regulating a wide array of gene expression and cellular activities. Maize also harbors a duplicate locus, thick aleurone-like1, which likely accounts for the ability of thk1 mutants to form viable cells. Transcriptomic analysis indicated that THK1 regulates activities involving cell division, signaling, differentiation, and metabolism. Identification of thk1 provides an important new component of the DEK1 regulatory system that patterns cell fate in endosperm.

Timing and Pattern of Anthocyanin Accumulation during Grain Filling in Purple Waxy Corn (Zea mays L.) Suggest Optimal Harvest Dates

Purple-corn kernels contain anthocyanins, a group of antioxidants proposed to be beneficial to human health. This study investigated the concentrations of anthocyanins and amino acids and the composition of fatty acids in the kernels of purple waxy corn (Zea mays L.) "Heukjinjuchal" during grain filling to determine when the grain nutritional value is at its highest. During grain filling, anthocyanin contents increased as the kernel color darkened. Among the anthocyanins measured, cyanidin-3-β-O-glucoside reached the highest contents, 57.0-409.1 mg kg-1 fresh weight in raw kernels and 1027.6 mg kg-1 in dry seeds. Pelargonidin-3-β-O-glucoside and malvidin-3-β-O-glucoside became detectable at 21 days after silking; they occurred in the second- and third-highest amounts, respectively, among anthocyanins in the purple-corn cultivars tested. The anthocyanin accumulation pattern was strongly associated with physicochemical properties and partly associated with amino acid content. Anthocyanin contents increased in a stepwise rather than linear fashion. This study showed that kernels undergo dramatic changes that affect the nutritional value of fresh corn.

Meiotic Chromosome Stability and Suppression of Crossover Between Non-homologous Chromosomes in xBrassicoraphanus, an Intergeneric Allotetraploid Derived From a Cross Between Brassica rapa and Raphanus sativus

Hybridization and polyploidization are major driving forces in plant evolution. Allopolyploids can be occasionally formed from a cross between distantly related species but often suffer from chromosome instability and infertility. xBrassicoraphanus is an intergeneric allotetraploid (AARR; 2n = 38) derived from a cross between Brassica rapa (AA; 2n = 20) and Raphanus sativus (RR; 2n = 18). xBrassicoraphanus is fertile and genetically stable, while retaining complete sets of both B. rapa and R. sativus chromosomes. Precise control of meiotic recombination is essential for the production of balanced gametes, and crossovers (COs) must occur exclusively between homologous chromosomes. Many interspecific hybrids have problems with meiotic division at early generations, in which interactions between non-homologous chromosomes often bring about aneuploidy and unbalanced gamete formation. We analyzed meiotic chromosome behaviors in pollen mother cells (PMCs) of allotetraploid and allodiploid F1 individuals of newly synthesized xBrassicoraphanus. Allotetraploid xBrassicoraphanus PMCs showed a normal diploid-like meiotic behavior. By contrast, allodiploid xBrassicoraphanus PMCs displayed abnormal segregation of chromosomes mainly due to the absence of homologous pairs. Notably, during early stages of meiosis I many of allodiploid xBrassicoraphanus chromosomes behave independently with few interactions between B. rapa and R. sativus chromosomes, forming many univalent chromosomes before segregation. Chromosomes were randomly assorted at later stages of meiosis, and tetrads with unequal numbers of chromosomes were formed at completion of meiosis. Immunolocalization of HEI10 protein mediating meiotic recombination revealed that COs were more frequent in synthetic allotetraploid xBrassicoraphanus than in allodiploid, but less than in the stabilized line. These findings suggest that structural dissimilarity between B. rapa and R. sativus chromosomes prevents non-homologous interactions between the parental chromosomes in allotetraploid xBrassicoraphanus, allowing normal diploid-like meiosis when homologous pairing partners are present. This study also suggests that CO suppression between non-homologous chromosomes is required for correct meiotic progression in newly synthesized allopolyploids, which is important for the formation of viable gametes and reproductive success in the hybrid progeny.

Revealing biomass heterosis in the allodiploid xBrassicoraphanus, a hybrid between Brassica rapa and Raphanus sativus, through integrated transcriptome and metabolites analysis

BACKGROUND

Heterosis is biologically important but the molecular basis of the phenomenon is poorly understood. We characterized intergeneric hybrids between B. rapa cv. Chiifu and R. sativus cv. WK10039 as an extreme example of heterosis. Taking advantage of clear heterosis phenotypes and the genetic distance between parents, we performed transcriptome and metabolite analysis to decipher the molecular basis of heterosis.

RESULTS

The heterosis was expressed as fresh weight in the field and as inflorescence stem length in the glass house. Flowering time, distributed as a normal segregating population, ranged from the early flowering of one parent to the late flowering of the other, in contrast to the homogeneous flowering time in a typical F1 population, indicating unstable allelic interactions. The transcriptome and metabolome both indicated that sugar metabolism was altered, suggesting that the change in metabolism was linked to the heterosis. Because alleles were not shared between the hybridized genomes, classic models only partly explain this heterosis, indicating that other mechanisms are involved.

CONCLUSION

The differential expression of genes for primary and secondary metabolism, along with the altered metabolite profiles, suggests that heterosis could involve a change in balance between primary and secondary metabolism.

MiR-744 mediates the Oxaliplatin chemoresistance in colorectal cancer through inhibiting BIN1

Colorectal cancer (CRC) is one of the most common malignant cancers worldwide. However, lacking of novel and sensitive chemotherapy revealed the major challenge to improve the survival of CRC patients. The aim of this study was to explore the effect and mechanism of miR-744 on the oxaliplatin chemoresistance in CRC. Firstly, the levels of miR-744 were elevated significantly in CRC tissues from patients with oxaliplatin administration before surgery and in oxaliplatin-resistant HCT116 cells. Then, the oxaliplatin chemoresistance was enhanced by miR-744 overexpression, while was attenuated by miR-744 inhibition in HCT116 and T84 cells. Additionally, the level of BIN1 protein was found to be regulated negatively by miR-744, and BIN1 overexpression blocked the oxaliplatin chemoresistance induced by miR-744. Furthermore, BIN1 was proved to be a direct target of miR-744 by luciferase reporter assay. Taken together, these findings demonstrated that miR-744 might positively mediate the oxaliplatin chemoresistance through suppressing BIN1 expression in CRC cells, thus suggested a rationale target for the developing more effective strategies to reverse oxaliplatin resistance in CRC treatment.

MYB1 transcription factor is a candidate responsible for red root skin in radish (Raphanus sativus L.)

Root skin color is one of the economically important traits in radish (Raphanus sativus), and the pigmentation in red skin varieties is largely attributable to anthocyanin accumulation. Pelargonidin was found as a major anthocyanin pigment accumulated in the sub-epidermal layer of red radish roots. In the 20 F₂ population generated from the F₁ with red root skins, root skins with red and white colors segregated in a 3:1 ratio. Additionally, a test cross between a red F₃ individual and a white skin individual gave rise to 1:1 segregation of red and white, indicating that the root skin color of radish is determined by a single locus and red color is dominant over white. We performed association mapping for root skin color using SNPs obtained from RNA-seq analysis. Segregation analysis on the 152 F₃ test-cross population revealed an RsMyb1 transcription factor as a candidate gene to determine root skin color. A PCR marker based on the polymorphism within 2 kb of RsMyb1 was developed and tested on 12 and 152 individuals from F₂ and F₃ test cross populations, respectively, and red and white root skin colors were completely distinguished corresponding to the genotypes. Expression levels of RsMyb1 in red or purple root cultivars were significantly higher than in white root cultivars. These findings suggest that RsMyb1 is a crucial determinant for anthocyanin biosynthesis in radish roots, and the molecular marker developed in this study will be useful for marker-assisted selection for red skin individuals at early seedling stages.

MGIS: managing banana (Musa spp.) genetic resources information and high-throughput genotyping data

Unraveling the genetic diversity held in genebanks on a large scale is underway, due to advances in Next-generation sequence (NGS) based technologies that produce high-density genetic markers for a large number of samples at low cost. Genebank users should be in a position to identify and select germplasm from the global genepool based on a combination of passport, genotypic and phenotypic data. To facilitate this, a new generation of information systems is being designed to efficiently handle data and link it with other external resources such as genome or breeding databases. The Musa Germplasm Information System (MGIS), the database for global ex situ-held banana genetic resources, has been developed to address those needs in a user-friendly way. In developing MGIS, we selected a generic database schema (Chado), the robust content management system Drupal for the user interface, and Tripal, a set of Drupal modules which links the Chado schema to Drupal. MGIS allows germplasm collection examination, accession browsing, advanced search functions, and germplasm orders. Additionally, we developed unique graphical interfaces to compare accessions and to explore them based on their taxonomic information. Accession-based data has been enriched with publications, genotyping studies and associated genotyping datasets reporting on germplasm use. Finally, an interoperability layer has been implemented to facilitate the link with complementary databases like the Banana Genome Hub and the MusaBase breeding database.

Database URL:https://www.crop-diversity.org/mgis/

Chemical composition and antifungal activity of Carica papaya Linn. seed essential oil against Candida spp

In recent years, the incidence of clinical yeast infections has increased dramatically. Due to the extensive use of broad-spectrum antifungal agents, there has been a notable increase in drug resistance among infections yeast species. As one of the most popular natural antimicrobial agents, essential oils (EOs) have attracted a lot of attention from the scientific community. The aim of this study was to analyse the chemical composition and examine the antifungal activity of the EO extracted from the seeds of Carica papaya Linn. The papaya seed EO was analysed by gas chromatography-mass spectrometry. The major constituent is benzyl isothiocyanate (99·36%). The filter paper disc diffusion method and broth dilution method were employed. The EO showed inhibitory effect against all the tested Candida strains including C. albicans, C. glabrata, C. krusei, C. parapsilosis and C. tropical with inhibition zone diameters in the range of 14·2-33·2 mm, the minimal inhibitory concentrations (MICs) in the range of 4·0-16·0 μg ml^-1 and the minimum fungicidal concentrations (MFCs) in the range of 16·0-64·0 μg ml^-1 . Here, we found that the papaya seed EO has promising anticandida activity and identify C. papaya L. as a potential natural source of antifungal agents.

SIGNIFICANCE AND IMPACT OF THE STUDY

The chemical composition and antifungal activity of essential oil of Carica papaya seeds were studied. The oil of papaya seeds could inhibit the growth of Candida spp. for the first report. Carica Papaya may be recognized as a possible new source of natural antifungal agents.

Root Glucosinolate Profiles for Screening of Radish (Raphanus sativus L.) Genetic Resources

Radish (Raphanus sativus L.), a root vegetable, is rich in glucosinolates (GLs), which are beneficial secondary metabolites for human health. To investigate the genetic variations in GL content in radish roots and the relationship with other root phenotypes, we analyzed 71 accessions from 23 different countries for GLs using HPLC. The most abundant GL in radish roots was glucoraphasatin, a GL with four-carbon aliphatic side chain. The content of glucoraphasatin represented at least 84.5% of the total GL content. Indolyl GL represented only 3.1% of the total GL at its maximum. The principal component analysis of GL profiles with various root phenotypes showed that four different genotypes exist in the 71 accessions. Although no strong correlation with GL content and root phenotype was observed, the varied GL content levels demonstrate the genetic diversity of GL content, and the amount that GLs could be potentially improved by breeding in radishes.

Blocking proteinase-activated receptor 2 alleviated neuropathic pain evoked by spinal cord injury

Spinal cord injury (SCI) is an extremely serious type of physical trauma observed in clinics. Especially, neuropathic pain resulting from SCI has a lasting and significant impact on most aspects of daily life. Thus, a better understanding of the molecular pathways responsible for the cause of neuropathic pain observed in SCI is important to develop effectively therapeutic agents and treatment strategies. Proteinase-activated receptors (PARs) are a family member of G-protein-coupled receptors and are activated by a proteolytic mechanism. One of its subtypes PAR2 has been reported to be engaged in mechanical and thermal hyperalgesia. Thus, in this study we specifically examined the underlying mechanisms responsible for SCI evoked-neuropathic pain in a rat model. Overall, we demonstrated that SCI increases PAR2 and its downstream pathways TRPV1 and TRPA1 expression in the superficial dorsal horn of the spinal cord. Also, we showed that blocking spinal PAR2 by intrathecal injection of FSLLRY-NH2 significantly inhibits neuropathic pain responses induced by mechanical and thermal stimulation whereas FSLLRY-NH2 decreases the protein expression of TRPV1 and TRPA1 as well as the levels of substance P and calcitonin gene-related peptide. Results of this study have important implications, i.e. targeting one or more of these signaling molecules involved in activation of PAR2 and TRPV1/TRPA1 evoked by SCI may present new opportunities for treatment and management of neuropathic pain often observed in patients with SCI.

A putative plant organelle RNA recognition protein gene is essential for maize kernel development

Basal endosperm transfer layer (BETL) cells are responsible for transferring apoplastic solutes from the maternal pedicel into the endosperm, supplying the grain with compounds required for embryo development and storage reserve accumulation. Here, we analyze the maize (Zea mays L.) empty pericarp6 (emp6) mutant, which causes early arrest in grain development. The Emp6+gene function is required independently in both the embryo and endosperm. The emp6 mutant causes a notable effect on the differentiation of BETL cells; the extensive cell wall ingrowths that distinguish BETL cells are diminished and BETL marker gene expression is compromised in mutant kernels. Transposon tagging identified the emp6 locus as encoding a putative plant organelle RNA recognition (PORR) protein, 1 of 15 PORR family members in maize. The emp6 transcript is widely detected in plant tissues with highest levels in embryos and developing kernels. EMP6-green fluorescent protein (GFP) fusion proteins transiently expressed in Nicotiana benthamiana leaves were targeted specifically to mitochondria. These results suggest that BETL cell differentiation might be particularly energy intensive, or alternatively, that mitochondria might confer a developmental function.

Genome-wide copy number profiling using high-density SNP array in chickens

Phenotypic diversity is a direct consequence resulting mainly from the impact of underlying genetic variation, and recent studies have shown that copy number variation (CNV) is emerging as an important contributor to both phenotypic variability and disease susceptibility. Herein, we performed a genome-wide CNV scan in 96 chickens from 12 diversified breeds, benefiting from the high-density Affymetrix 600 K SNP arrays. We identified a total of 231 autosomal CNV regions (CNVRs) encompassing 5.41 Mb of the chicken genome and corresponding to 0.59% of the autosomal sequence. The length of these CNVRs ranged from 2.6 to 586.2 kb with an average of 23.4 kb, including 130 gain, 93 loss and eight both gain and loss events. These CNVRs, especially deletions, had lower GC content and were located particularly in gene deserts. In particular, 102 CNVRs harbored 128 chicken genes, most of which were enriched in immune responses. We obtained 221 autosomal CNVRs after converting probe coordinates to Galgal3, and comparative analysis with previous studies illustrated that 153 of these CNVRs were regarded as novel events. Furthermore, qPCR assays were designed for 11 novel CNVRs, and eight (72.73%) were validated successfully. In this study, we demonstrated that the high-density 600 K SNP array can capture CNVs with higher efficiency and accuracy and highlighted the necessity of integrating multiple technologies and algorithms. Our findings provide a pioneering exploration of chicken CNVs based on a high-density SNP array, which contributes to a more comprehensive understanding of genetic variation in the chicken genome and is beneficial to unearthing potential CNVs underlying important traits of chickens.

The naked endosperm genes encode duplicate INDETERMINATE domain transcription factors required for maize endosperm cell patterning and differentiation

The aleurone is the outermost layer of cereal endosperm and functions to digest storage products accumulated in starchy endosperm cells as well as to confer important dietary health benefits. Whereas normal maize (Zea mays [Zm]) has a single aleurone layer, naked endosperm (nkd) mutants produce multiple outer cell layers of partially differentiated cells that show sporadic expression of aleurone identity markers such as a viviparous1 promoter-β-glucuronidase transgene. The 15:1 F2 segregation ratio suggested that two recessive genes were involved, and map-based cloning identified two homologous genes in duplicated regions of the genome. The nkd1 and nkd2 genes encode the INDETERMINATE1 domain (IDD) containing transcription factors ZmIDDveg9 and ZmIDD9 on chromosomes 2 and 10, respectively. Independent mutant alleles of nkd1 and nkd2, as well as nkd2-RNA interference lines in which both nkd genes were knocked down, also showed the nkd mutant phenotype, confirming the gene identities. In wild-type kernels, the nkd transcripts were most abundant around 11 to 16 d after pollination. The NKD proteins have putative nuclear localization signals, and green fluorescent protein fusion proteins showed nuclear localization. The mutant phenotype and gene identities suggest that NKD controls a gene regulatory network involved in aleurone cell fate specification and cell differentiation.

The thick aleurone1 mutant defines a negative regulation of maize aleurone cell fate that functions downstream of defective kernel1

The maize (Zea mays) aleurone layer occupies the single outermost layer of the endosperm. The defective kernel1 (dek1) gene is a central regulator required for aleurone cell fate specification. dek1 mutants have pleiotropic phenotypes including lack of aleurone cells, aborted embryos, carotenoid deficiency, and a soft, floury endosperm deficient in zeins. Here we describe the thick aleurone1 (thk1) mutant that defines a novel negative function in the regulation of aleurone differentiation. Mutants possess multiple layers of aleurone cells as well as aborted embryos. Clonal sectors of thk1 mutant tissue in otherwise normal endosperm showed localized expression of the phenotype with sharp boundaries, indicating a localized cellular function for the gene. Sectors in leaves showed expanded epidermal cell morphology but the mutant epidermis generally remained in a single cell layer. Double mutant analysis indicated that the thk1 mutant is epistatic to dek1 for several aspects of the pleiotropic dek1 phenotype. dek1 mutant endosperm that was mosaic for thk1 mutant sectors showed localized patches of multilayered aleurone. Localized sectors were surrounded by halos of carotenoid pigments and double mutant kernels had restored zein profiles. In sum, loss of thk1 function restored the ability of dek1 mutant endosperm to accumulate carotenoids and zeins and to differentiate aleurone. Therefore the thk1 mutation defines a negative regulator that functions downstream of dek1 in the signaling system that controls aleurone specification and other aspects of endosperm development. The thk1 mutation was found to be caused by a deletion of approximately 2 megabases.

Maize opaque5 encodes monogalactosyldiacylglycerol synthase and specifically affects galactolipids necessary for amyloplast and chloroplast function

The maize (Zea mays) opaque5 (o5) locus was shown to encode the monogalactosyldiacylglycerol synthase MGD1. Null and point mutations of o5 that affect the vitreous nature of mature endosperm engendered an allelic series of lines with stepwise reductions in gene function. C(18:3)/C(18:2) galactolipid abundance in seedling leaves was reduced proportionally, without significant effects on total galactolipid content. This alteration in polar lipid composition disrupted the organization of thylakoid membranes into granal stacks. Total galactolipid abundance in endosperm was strongly reduced in o5(-) mutants, causing developmental defects and changes in starch production such that the normal simple granules were replaced with compound granules separated by amyloplast membrane. Complete loss of MGD1 function in a null mutant caused kernel lethality owing to failure in both endosperm and embryo development. The data demonstrate that low-abundance galactolipids with five double bonds serve functions in plastid membranes that are not replaced by the predominant species with six double bonds. Furthermore, the data identify a function of amyloplast membranes in the development of starch granules. Finally, the specific changes in lipid composition suggest that MGD1 can distinguish the constituency of acyl groups on its diacylglycerol substrate based upon the degree of desaturation.

Penalized gaussian process regression and classification for high-dimensional nonlinear data

The model based on Gaussian process (GP) prior and a kernel covariance function can be used to fit nonlinear data with multidimensional covariates. It has been used as a flexible nonparametric approach for curve fitting, classification, clustering, and other statistical problems, and has been widely applied to deal with complex nonlinear systems in many different areas particularly in machine learning. However, it is a challenging problem when the model is used for the large-scale data sets and high-dimensional data, for example, for the meat data discussed in this article that have 100 highly correlated covariates. For such data, it suffers from large variance of parameter estimation and high predictive errors, and numerically, it suffers from unstable computation. In this article, penalized likelihood framework will be applied to the model based on GPs. Different penalties will be investigated, and their ability in application given to suit the characteristics of GP models will be discussed. The asymptotic properties will also be discussed with the relevant proofs. Several applications to real biomechanical and bioinformatics data sets will be reported.

Regulation of aleurone development in cereal grains

The aleurone layer of cereal grains is important biologically as well as nutritionally and economically. Here, current knowledge on the regulation of aleurone development is reviewed. Recent reports suggest that the control of aleurone development is more complex than earlier models portrayed. Multiple levels of genetic regulation control aleurone cell fate, differentiation, and organization. The hormones auxin and cytokinin can also influence aleurone development. New technical advances promise to facilitate future progress.

Measuring Fatigue in PZT Thin Films

Small signal dielectric response is reported for a variety of PZT thin film samples. Small and large signal responses, recorded simultaneously during the fatiguing of PZT thin films, are used to identify distinct fatigue mechanisms. Microcracking or electrode delamination less than 100 Å is sufficient to explain the high correlation between the dielectric permittivity and remanent polarization during fatigue.

Descriptive study of enzootic nasal adenocarcinoma in goats in southwestern China

This is the first report on enzootic nasal adenocarcinoma (ENA) in goats (Nanjiang Yellow goats and Jianyang Big-ear Black goats) in southwestern China. The clinical, histological and ultrastructural features of ENA in goats were described. From July 2007 to May 2009, 21 cases of ENA in goats, from 6 months to 8 years old, were diagnosed solely in one big herd. Clinically, the affected goats showed nasal discharge, facial swelling, sneezing, stertorous breathing and weight loss. Tumours that originated from the ethmoid area of the nasal cavity were unilateral (18/21) or bilateral (3/21). All tumours were classified as low grade adenocarcinomas by histopathological examination and were displayed a combination of tubular and papillary growth. No metastases were detected in regional lymph nodes, brain or other organs. Ultrastructurally, virus-like particles with an average diameter between 80 and 110 nm were observed in 5/7 examined tumours.

High-throughput linkage analysis of Mutator insertion sites in maize

Insertional mutagenesis is a cornerstone of functional genomics. High-copy transposable element systems such as Mutator (Mu) in maize (Zea mays) afford the advantage of high forward mutation rates but pose a challenge for identifying the particular element responsible for a given mutation. Several large mutant collections have been generated in Mu-active genetic stocks, but current methods limit the ability to rapidly identify the causal Mu insertions. Here we present a method to rapidly assay Mu insertions that are genetically linked to a mutation of interest. The method combines elements of MuTAIL (thermal asymmetrically interlaced) and amplification of insertion mutagenized sites (AIMS) protocols and is applicable to the analysis of single mutants or to high-throughput analyses of mutant collections. Briefly, genomic DNA is digested with a restriction enzyme and adapters are ligated. Polymerase chain reaction is performed with TAIL cycling parameters, using a fluorescently labeled Mu primer, which results in the preferential amplification and labeling of Mu-containing genomic fragments. Products from a segregating line are analyzed on a capillary sequencer. To recover a fragment of interest, PCR products are cloned and sequenced. Sequences with lengths matching the size of a band that co-segregates with the mutant phenotype represent candidate linked insertion sites, which are then confirmed by PCR. We demonstrate the utility of the method by identifying Mu insertion sites linked to seed-lethal mutations with a preliminary success rate of nearly 50%.

Relation of ventricular repolarization to cardiac cycle length in normal subjects, hypertrophic cardiomyopathy, and patients with myocardial infarction

BACKGROUND

Prolonged QT interval and QT dispersion have been reported to reflect an increased inhomogeneity of ventricular repolarization, which is believed to be responsible for the development of arrhythmic events in patients with long QT syndrome, coronary heart disease, and myocardial infarction, congestive heart failure, and hypertrophic cardiomyopathy (HC).

HYPOTHESIS

This study was undertaken to determine whether an abnormal QT/RR dynamicity may reflect autonomic imbalance and may contribute to arrhythmogenesis in patients with heart disease.

METHODS

The relation between QT, QTpeak (QTp), Tpeak-Tend (TpTe) intervals and cardiac cycle length was assessed in 70 normal subjects, 37 patients with HC, and 48 survivors of myocardial infarction (MI). A set of 10 consecutive electrocardiograms was evaluated automatically in each subject using QT Guard software (Marquette Medical Systems, Milwaukee, Wisc.).

RESULTS

In patients with HC, all intervals were significantly prolonged compared with normals (p < 0.001 for QT and QTp; p < 0.04 for TpTc); in survivors of MI, this was true for the maximum QT and QTp intervals (p < 0.05). A strong linear correlation between QT, QTp, and RR intervals was observed in normals and in patients with MI and HC (r = 0.65-0.59, 0.82-0.77, 0.79-0.74, respectively, p < 0.0001). TpTe interval only showed a weak correlation with heart rate in normals (r = 0.24, p < 0.05) and was rate-independent in both patient groups (p = NS). Compared with normals, the slopes of QT/RR and QTp/RR regression lines were significantly steeper in patients with MI and HC (0.0990-0.0883, 0.1597-0.1551, 0.1653-0.1486, respectively). Regression lines were neither parallel nor identical between normals and patients (T > 1.96, Z > 3.07). There was no difference in steepness for TpTeR/RR lines between groups (0.0110, 0.0076, 0.0163, respectively). TpTe/QTp ratio was similar in normals and in patients with MI and HC (0.30 +/- 0.03, 0.31 +/- 0.07, 0.30 +/- 0.04, respectively), in the absence of any correlation between QTp and TpTe intervals, suggesting disproportional prolongation of both components of QT interval.

CONCLUSION

Compared with normals, a progressive increase in QT and QTp intervals at slower heart rates in patients with MI and HC may indicate an enhanced variability of the early ventricular repolarization and may be one of the mechanisms of arrhythmogenesis.

Effects of subchronic methyl tert-butyl ether ether exposure on male Sprague-Dawley rats

Methyl tert-butyl ether (MTBE) is an additive used to oxygenate gasoline to improve air quality by reducing tailpipe emissions of carbon monoxide and ozone precursors. Although several toxicity studies in rats have been conducted to examine the acute, subchronic, and chronic toxicities by employing various routes of exposure to MTBE, few data were available on the effects of MTBE exposure on blood. In this study, MTBE was administered to rats at dose levels of 0, 400, 800, and 1600 mg/kg/day, respectively. After 2- or 4-weeks treatment period, rats were euthanized and blood was collected for the assay of hematological indicators and blood biochemistry indicators. Some organs, including brain, heart, liver, spleen, lung, kidneys, testes, epididymis, thymus, and prostate, were immediately removed and weighed. Possible subchronic health effects of MTBE exposure by gavage were evaluated on mortality, body weight, relative organ weight, hematology, and blood biochemistry indicators in male Sprague-Dawley rats. The results indicated that MTBE did not disrupt the growth rate of rats. Relative organ weight showed change in heart, liver, kidney, testes, thymus, and prostate. In the 2-week treatment, MTBE exerted toxicity on white blood cell count, including lymphocyte, granulocyte, and eosinophil. This finding was especially strong at 1600 mg/kg/day MTBE. In the 4-week treatment, hemoglobin at high dose MTBE significantly increased. The results of the assay for the biochemistry indicators and relative organ weight indicated that MTBE could impair liver and kidney functions and also have adverse effects on lipid metabolism and immune system. It was conducted that subchronic MTBE exposure induced the adverse effects occurring in the relative organ weight, the hematological indicators, and the biochemistry indicators under high MTBE dose.

Production of herbicide-resistant sweet potato plants transformed with the bar gene

Herbicide-resistant sweet potato plants were produced through biolistics of embryogenic calli derived from shoot apical meristems. Plant materials were bombarded with the vectors containing the beta-glucuronidase gene (gusA) and the herbicide-resistant gene (bar). Selection was carried out using phosphinothricin (PPT). Transformants were screened by the histochemical GUS and Chlorophenol Red assays. PCR and Southern-blot analyses indicated the presence of introduced bar gene in the genomic DNA of the transgenic plants. When sprayed with Basta, the transgenic sweet potato plants was tolerant to the herbicide. Hence, we report successful transformation of the bar gene conferring herbicide resistance to sweet potato.

Exploitation of pepper EST-SSRs and an SSR-based linkage map

As genome and cDNA sequencing projects progress, a tremendous amount of sequence information is becoming publicly available. These sequence resources can be exploited for gene discovery and marker development. Simple sequence repeat (SSR) markers are among the most useful because of their great variability, abundance, and ease of analysis. By in silico analysis of 10,232 non-redundant expressed sequence tags (ESTs) in pepper as a source of SSR markers, 1,201 SSRs were found, corresponding to one SSR in every 3.8 kb of the ESTs. Eighteen percent of the SSR-ESTs were dinucleotide repeats, 66.0% were trinucleotide, 7.7% tetranucleotide, and 8.2% pentanucleotide; AAG (14%) and AG (12.4%) motifs were the most abundant repeat types. Based on the flanking sequences of these 1,201 SSRs, 812 primer pairs that satisfied melting temperature conditions and PCR product sizes were designed. 513 SSRs (63.1%) were successfully amplified and 150 of them (29.2%) showed polymorphism between Capsicum annuum 'TF68' and C. chinense 'Habanero'. Dinucleotide SSRs and EST-SSR markers containing AC-motifs were the most polymorphic. Polymorphism increased with repeat length and repeat number. The polymorphic EST-SSRs were mapped onto the previously generated pepper linkage map, using 107 F(2) individuals from an interspecific cross of TF68 x Habanero. One-hundred and thirtynine EST-SSRs were located on the linkage map in addition to 41 previous SSRs and 63 RFLP markers, forming 14 linkage groups (LGs) and spanning 2,201.5 cM. The EST-SSR markers were distributed over all the LGs. This SSR-based map will be useful as a reference map in Capsicum and should facilitate the use of molecular markers in pepper breeding.

Is QT dispersion associated with sudden cardiac death in patients with hypertrophic cardiomyopathy?

QT dispersion is significantly greater in patients with hypertrophic cardiomyopathy (HCM) than that in healthy subjects. Few data exist regarding the prognostic value of QT dispersion in HCM. In this study, we retrospectively investigated the association between QT dispersion and sudden cardiac death in 46 patients with HCM (mean 33.1 +/- 15.5 years, 32 men). The case group consisted of 23 HCM patients who died suddenly, and the control group consisted of 23 HCM patients who survived uneventfully during follow-up. Study patients were pair-matched for age, gender, and maximum left ventricular wall thickness. QT dispersion (maximum minus minimum QT interval) was manually measured on early 12-lead ECGs using a digitizing board. An in-house program was used for calculating QT interval, QT dispersion, JT interval, and JT dispersion (maximum minus minimum J point to T end interval). Patients in the case group tended to have shorter RR intervals than those in the control group (777 +/- 171 vs 856 +/- 192 ms, P = 0.08). Maximum corrected QT and JT intervals did not discriminate the case group from controls (489 +/- 29 vs 479 +/- 27 ms, P = NS; 375 +/- 36 vs 366 +/- 22 ms, P = NS, respectively). Greater QT dispersion and JT dispersion were found in the case group compared with controls (74 +/- 28 vs 59 +/- 21 ms, P = 0.02 and 76 +/- 32 vs 59 +/- 26 ms, P = 0.03, respectively). The measurements of maximum QT, JT, and T peak to T end intervals, precordial QT and JT dispersion, and T peak and T end dispersion were all comparable between the two groups (P = NS for all). No systematic changes in ECG measurements were found from late ECGs of the case group compared to those from early ECGs (P = NS). No correlation between maximum left ventricular wall thickness and QT dispersion, JT dispersion, maximum QTc or JTc intervals was observed (r < 0.29, P > 0.05 for all). Our results show that increased QT dispersion and JT dispersion is weakly associated with sudden cardiac death in the selected patients with HCM.

Use of Pi5(t) markers in marker-assisted selection to screen for cultivars with resistance to Magnaporthe grisea

Identification of the PCR markers tightly linked to genes that encode important agronomic traits is useful for marker-assisted selection (MAS). The rice Pi5(t) locus confers broad-spectrum resistance to Magnaporthe grisea, the causal agent of rice blast disease. It has been hypothesized that the Pi5(t) locus carries the same gene as that encoded by the Pi3(t) and Pii(t) loci. We developed three PCR-based dominant markers (JJ80-T3, JJ81-T3, and JJ113-T3) from three previously identified BIBAC clones-JJ80, JJ81, and JJ113-that are linked to the Pi5(t) locus. PCR analysis of 24 monogenic lines revealed that these markers are present only in lines that carry Pi5(t), Pi3(t), and Pii(t). PCR and DNA gel-blot analysis of candidate resistance lines using JJ80-T3, JJ81-T3, and JJ113-T3 indicated that Tetep is the likely donor of Pi5(t). Of the 184 rice varieties tested, 34 carried the JJ80-T3-, JJ81-T3-, and JJ113-T3-specific bands. Disease evaluation of those 34 varieties revealed that all conferred resistance to PO6-6. The genomic structure of three of these resistant varieties (i.e., IR72, Taebaeg, Jahyangdo) is most similar to that of Pi5(t). Our results demonstrate the usefulness of the JJ80-T3, JJ81-T3, and JJ113-T3 markers for MAS for M. grisea resistance.

A new design of specimen stage for in situ magnetising experiments in the transmission electron microscope

A new stage for carrying out in situ magnetising experiments in the transmission electron microscope has been designed, constructed and tested. The principal advantages of the stage are that it delivers horizontal fields with negligible perturbation to the illumination and is suitable for operation in pulsed or continuous field mode. Details of its performance, including field calibration, are given. The paper concludes with a description of where the stage is likely to be of most use.

Microminiaturized immunoassays using quantum dots as fluorescent label by laser confocal scanning fluorescence detection

An immunoassay readout method based on fluorescent imaging analysis with laser confocal scanning is described. The ZnS-coated CdSe quantum dots (ZnS/CdSe QDs) were linked to a detection antibody. Immunoassay was carried out on a glass chip using a sandwich assay approach, where antibody covalently bound to a glass chip was allowed to capture antigen specially. Afterwards, the detection antibody labeled with QD was allowed to bind selectively to the captured antigen. The fluorescent signals of the sandwich conjugate were detected by a laser confocal scanner. A diode laser was used to excite efficiently the fluorescent signals while bovine serum albumin was used to eliminate nonspecific binding sites. The detection limit of this approach was up to 10(-9) M under current experimental conditions. The specificity of the QDs-labeled immunoglobulin (IgG) was tested by an experiment using goat IgG and human IgG samples. The result was consistent with the binding specificity in a sandwich-type assay. The potential of this method to function as a simple and efficient readout strategy for immunoassay in biochip is discussed.

[Raman spectra of the serums from cancerous persons]

The serums of different categories, those who are normal people and those who are patient suffering from nasopharyngeal cancer, liver cancer and chronic leukaemia, were determined by laser Raman spectra at the range of 0-2,000 cm-1. The results demonstrated that the serums of those who are suffering from the same disease show different characteristic peak height, but their Raman spectrogram characteristics are almost the same. There exists great difference in the laser Raman spectrogram for the serums of the different kinds of cancerous patients. Near the characteristic peaks of laser Raman spectrograms of serums from the cancerous patients, the normal person's serum has no Raman spectrogram characteristic peak.

Can the assessment of dynamic QT dispersion on exercise electrocardiogram predict sudden cardiac death in hypertrophic cardiomyopathy?

Premature sudden cardiac death (SD) is a critical event in the natural history of hypertrophic cardiomyopathy (HCM), and occurs during or just after physical exertion in approximately 60% of instances. Abnormalities in ventricular repolarization may not be present at rest in some patients but may become apparent under certain conditions. This study was performed to examine whether dynamic QT dispersion during exercise is associated with SD in HCM. Twenty-four HCM patients with catastrophic events (group I; 18 SD, 6 ventricular fibrillation) and 24 event-free survivors (group II) were studied. The two groups were pair-matched for age, gender, and maximum left ventricular wall thickness. QT intervals were manually measured from 12-lead exercise electrocardiogram (ECG) with a digitizing board. A custom-developed program was used to calculate QT and JT dispersion. The QT/RR relationship was evaluated by the slope of linear regression analysis. Before exercise, significant differences in heart rate and JT dispersion were found between group I and II. During exercise, heart rate increased and QT decreased significantly in both groups. QT and JT dispersion decreased in both groups, though the magnitude of reduction was greater in group I than in group II. No significant differences in QTc interval and QT or JT dispersion were found between the groups at any stages. At 3 minutes of recovery, heart rate had decreased but remained higher than before exercise, and all measurements of QT components remained shorter compared with those made before exercise in both groups. There was a strong correlation between QT and RR interval during exercise in all study patients (r = 0.95). No difference in the slope of QT against RR intervals was found between the groups (0.317 vs 0.319). In conclusion, exercise reduced QT dispersion in patients with HCM. The dynamic changes in QT dispersion examined by this method on exercise ECG did not make additional contributions in their risk stratification.

Predictive value of wavelet decomposition of the signal-averaged electrocardiogram in idiopathic dilated cardiomyopathy

BACKGROUND

Wavelet decomposition of the signal-averaged electrocardiogram has been proposed as a method of detecting small and transient irregularities hidden within the QRS complex and of overcoming some of the limitations of time domain analysis of the signal-averaged electrocardiogram.

AIM

This study evaluated the potential utility of wavelet decomposition analysis in the risk stratification of patients with idiopathic dilated cardiomyopathy.

METHODS AND RESULTS

Both wavelet decomposition and time domain analysis were applied to the signal-averaged electrocardiogram recordings of 82 patients with idiopathic dilated cardiomyopathy (mean age 43 +/- 14 years, 60 men) and 72 normal controls (mean age 44 +/- 15 years, 48 men). Three conventional time domain indices and four wavelet decomposition analysis parameters (QRS length, maximum count, surface area, and relative length) were derived from each recording using a Del Mar CEWS system and an in-house software package, respectively. The results showed that (1) more patients with idiopathic dilated cardiomyopathy than without had late potentials, and that the filtered QRS duration was significantly longer in patients than in controls (P<0.001). Similarly, abnormal wavelet decomposition analysis was more common in patients and wavelet decomposition measurements were significantly different between patients and controls (P<0.01); (2) conventional time domain analysis did not distinguish between clinically stable patients and patients who developed progressive heart failure, or between patients with and without arrhythmic events; (3) wavelet decomposition analysis identified patients who went on to develop progressive heart failure but failed to distinguish patients with arrhythmic events from those without; (4) survival analyses of a mean follow-up of 23 months showed that patients with late potentials tended to develop progressive heart failure more frequently than others (P=0.06). Patients with an abnormal wavelet decomposition result more frequently developed progressive heart failure than those with a normal wavelet decomposition result (P=0.027); (5) in a univariate analysis (Cox model), wavelet decomposition measurements but not time domain indices significantly correlated with the development of progressive heart failure (P=0.01). Multivariate analysis showed that only left ventricular end-diastolic dimension and peak oxygen consumption during exercise remained significant predictors of progressive heart failure.

CONCLUSION

Wavelet decomposition analysis of the signal-averaged electrocardiogram is superior to conventional time domain analysis for identifying patients with idiopathic dilated cardiomyopathy at increased risk of clinical deterioration. Wavelet decomposition analysis, however, is unlikely to prospectively distinguish patients at a high risk of arrhythmic events in idiopathic dilated cardiomyopathy in its present form.