Developing an SNP dataset for efficiently evaluating soybean germplasm resources using the genome sequencing data of 3,661 soybean accessions

BACKGROUND

Single nucleotide polymorphism (SNP) markers play significant roles in accelerating breeding and basic crop research. Several soybean SNP panels have been developed. However, there is still a lack of SNP panels for differentiating between wild and cultivated populations, as well as for detecting polymorphisms within both wild and cultivated populations.

RESULTS

This study utilized publicly available resequencing data from over 3,000 soybean accessions to identify differentiating and highly conserved SNP and insertion/deletion (InDel) markers between wild and cultivated soybean populations. Additionally, a naturally occurring mutant gene library was constructed by analyzing large-effect SNPs and InDels in the population.

CONCLUSION

The markers obtained in this study are associated with numerous genes governing agronomic traits, thus facilitating the evaluation of soybean germplasms and the efficient differentiation between wild and cultivated soybeans. The natural mutant gene library permits the quick identification of individuals with natural mutations in functional genes, providing convenience for accelerating soybean breeding using reverse genetics.

MicroRNA 4407 modulates nodulation in soybean by repressing a root-specific ISOPENTENYLTRANSFERASE (GmIPT3)

MicroRNAs (miRNAs) are important regulators of plant biological processes, including soybean nodulation. One miRNA, miR4407, was identified in soybean roots and nodules. However, the function of miR4407 in soybean is still unknown. MiR4407, unique to soybean, positively regulates lateral root emergence and root structures and represses a root-specific ISOPENTENYLTRANSFERASE (GmIPT3). By altering the expression of miR4407 and GmIPT3, we investigated the role of miR4407 in lateral root and nodule development. Both miR4407 and GmIPT3 are expressed in the inner root cortex and nodule primordia. Upon rhizobial inoculation, miR4407 was downregulated while GmIPT3 was upregulated. Overexpressing miR4407 reduced the number of nodules in transgenic soybean hairy roots while overexpressing the wild-type GmIPT3 or a miR4407-resistant GmIPT3 mutant (mGmIPT3) significantly increased the nodule number. The mechanism of miR4407 and GmIPT3 functions was also linked to autoregulation of nodulation (AON), where miR4407 overexpression repressed miR172c and activated its target, GmNNC1, turning on AON. Exogenous CK mimicked the effects of GmIPT3 overexpression on miR172c, supporting the notion that GmIPT3 regulates nodulation by enhancing root-derived CK. Overall, our data revealed a new miRNA-mediated regulatory mechanism of nodulation in soybean. MiR4407 showed a dual role in lateral root and nodule development.

A natural non-synonymous single nucleotide polymorphism (SNP) in GmbHLH113 negates its inhibitory effect on root hair elongation in soybean

Root hair length (RHL) is an important character that affects nutrient acquisition in plants. The regulatory network in soybean controlling RHL is yet to be fully understood. In this study, we identified a quantitative trait locus (QTL) regulating RHL. One candidate causal gene in this QTL (GmbHLH113), preferentially expressed in root hairs, was annotated as encoding a basic Helix-Loop-Helix (bHLH) transcription factor. In wild soybeans, the allelic type of GmbHLH113 with a glycine in the 13^th residue, which was associated with a reduction in RHL, was shown to localize in the nucleus and activate gene transcription. Another allelic type with a single nucleotide polymorphism (SNP) that resulted in a glutamate in the 13^th residue is fixed in cultivated soybeans, and it lost the ability to localize to the nucleus or negatively regulate RHL. The ectopic expression of GmbHLH113 from W05 in Arabidopsis root hairs resulted in shorter RHL and reduced phosphorus (P) accumulation in shoots. Hence a loss-of-function allele in cultivated soybeans might have been selected during domestication due to its association with a longer RHL and improved nutrient acquisition.

QTL analyses of soybean root system architecture revealed genetic relationships with shoot-related traits

The genetic basis of soybean root system architecture (RSA) and the genetic relationship between shoot and RSA were revealed by integrating data from recombinant inbred population grafting and QTL mapping. Variations in root system architecture (RSA) affect the functions of roots and thus play vital roles in plant adaptations and agricultural productivity. The aim of this study was to unravel the genetic relationship between RSA traits and shoot-related traits in soybean. This study characterized RSA variability at seedling stage in a recombinant inbred population, derived from a cross between cultivated soybean C08 and wild soybean W05, and performed high-resolution quantitative trait locus (QTL) mapping. In total, 34 and 41 QTLs were detected for RSA-related and shoot-related traits, respectively, constituting eight QTL clusters. Significant QTL correspondence was found between shoot biomass and RSA-related traits, consistent with significant correlations between these phenotypes. RSA-related QTLs also overlapped with selection regions in the genome, suggesting the cultivar RSA could be a partial consequence of domestication. Using reciprocal grafting, we confirmed that shoot-derived signals affected root development and the effects were controlled by multiple loci. Meanwhile, RSA-related QTLs were found to co-localize with four soybean flowering-time loci. Consistent with the phenotypes of the parental lines of our RI population, diminishing the function of flowering controlling E1 family through RNA interference (RNAi) led to reduced root growth. This implies that the flowering time-related genes within the RSA-related QTLs are actually contributing to RSA. To conclude, this study identified the QTLs that determine RSA through controlling root growth indirectly via regulating shoot functions, and discovered superior alleles from wild soybean that could be used to improve the root structure in existing soybean cultivars.

Priming-induced alterations in histone modifications modulate transcriptional responses in soybean under salt stress

Plants that have experienced certain abiotic stress may gain tolerance to a similar stress in subsequent exposure. This phenomenon, called priming, was observed here in soybean (Glycine max) seedlings exposed to salt stress. Time-course transcriptomic profiles revealed distinctively different transcriptional responses in the primed seedlings from those in the non-primed seedlings under high salinity stress, indicating a stress response strategy of repressing unhelpful biotic stress responses and focusing on the promotion of those responses important for salt tolerance. To identify histone marks altered by the priming salinity treatment, a genome-wide profiling of histone 3 lysine 4 dimethylation (H3K4me2), H3K4me3, and histone 3 lysine 9 acetylation (H3K9ac) was performed. Our integrative analyses revealed that priming induced drastic alterations in these histone marks, which coordinately modified the stress response, ion homeostasis, and cell wall modification. Furthermore, transcriptional network analyses unveiled epigenetically modified networks which mediate the strategic downregulation of defense responses. Altering the histone acetylation status using a chemical inhibitor could elicit the priming-like transcriptional responses in non-primed seedlings, confirming the importance of histone marks in forming the priming response.

Increased copy number of gibberellin 2-oxidase 8 genes reduced trailing growth and shoot length during soybean domestication

Copy number variations (CNVs) play important roles in crop domestication. However, there is only very limited information on the involvement of CNVs in soybean domestication. Trailing growth and long shoots are soybean adaptations for natural habitats but cause lodging that hampers yield in cultivation. Previous studies have focused on Dt1/2 affecting the indeterminate/determinate growth habit, whereas the possible role of the gibberellin pathway remained unclear. In the present study, quantitative trait locus (QTL) mapping of a recombinant inbred population of 460 lines revealed a trailing-growth-and-shoot-length QTL. A CNV region within this QTL was identified, featuring the apical bud-expressed gibberellin 2-oxidase 8A/B, the copy numbers of which were positively correlated with expression levels and negatively with trailing growth and shoot length, and their effects were demonstrated by transgenic soybean and Arabidopsis thaliana. Based on the fixation index, this CNV region underwent intense selection during the initial domestication process.

Drivers of carbon flux in drip irrigation maize fields in northwest China

BACKGROUND

Under the escalating threat to sustainable development from the global increase in carbon dioxide concentrations, the variations in carbon flux in the farmland ecosystem and their influencing factors have attracted global attention. Over the past few decades, with the development of eddy covariance technology, the carbon fluxes of farmlands have been determined in many countries. However, studies are very limited for drip irrigation maize the arid regions in northwestern China, which covers a large area where a mixed mode of agriculture and grazing is practiced.

RESULTS

To study the effects of drip irrigation on the net ecosystem productivity (NEE), ecosystem respiration (ER), gross primary production (GPP) and net biome productivity (NBP) in the arid regions of northwestern China, we measured the carbon flux annually from 2014 to 2018 using an eddy covariance system. Our results showed that the maize field carbon flux exhibited single-peak seasonal patterns during the growing seasons. During 2014-2018, the NEE, ER and GPP of the drip-irrigated maize field ranged between - 407 ~ - 729 g C m^-2, 485.46 ~ 975.46 g C m^-2, and 1068.23 ~ 1705.30 g C m^-2. In four of the 5 study years, the ER released back to the atmosphere was just over half of the carbon fixed by photosynthesis. The mean daily NEE, ER and GPP were significantly correlated with the net radiation (Rn), air temperature (Ta), leaf area index (LAI) and soil moisture (SWC). The results of path analysis showed that leaf area index is the main driving force of seasonal variation of carbon flux. When harvested removals were considered, the annual NBP was - 234 g C m^-2, and the drip-irrigated maize field was a carbon source.

CONCLUSIONS

This study shows the variation and influencing factors of NEE, ER and GPP in the growth period of spring maize under film drip irrigation in arid areas of northwest China. The ecosystem was a carbon sink before maize harvest, but it was converted into a carbon source considering the carbon emissions after harvest. The variation of carbon flux was influenced by both environmental and vegetation factors, and its leaf area index was the main driver that affects the seasonal variation of carbon flux.

The soybean plasma membrane-localized cation/H+ exchanger GmCHX20a plays a negative role under salt stress

Cation/H+ -exchanger (CHX) perform diverse functions in plants, including being a part of the protective mechanisms to cope with salt stress. GmCHX1 has been previously identified as the causal gene in a major salt-tolerance quantitative trait locus (QTL) in soybean, but little is known about another close paralog, GmCHX20a, found in the same QTL. In this study, GmCHX20a was characterized along with GmCHX1. The expression patterns of the two genes and the direction of Na+ flux directed by overexpression of these two transporters are different, suggesting that they are functionally distinct. The ectopic expression of GmCHX20a led to an increase in salt sensitivity and osmotic tolerance, which was consistent with its role in increasing Na+ uptake into the root. Although this seems counter-intuitive, it may in fact be part of the mechanism by which soybean could counter act the effects of osmotic stress, which is commonly manifested in the initial stage of salinity stress. On the other hand, GmCHX1 from salt-tolerant soybean was shown to protect plants via Na+ exclusion under salt stress. Taken together these results suggest that GmCHX20a and GmCHX1 might work complementally through a concerted effort to address both osmotic stress and ionic stress as a result of elevated salinity.

Photodynamic therapy on prostate cancer cells involve mitochondria membrane proteins

OBJECTIVE

Photodynamic therapy for prostate cancer has emerged, however the evaluation of its mechanism of action has not yet been clarified. This study aims to explore the mechanism and significance of photodynamic therapy on prostate cancer in vitro.

METHODS

Cultured prostate cancer cells were divided into two groups: untreated and photodynamic therapy treatment. The protein of each group was extracted and analyzed by MALDI-TOF/MSMS method. The significantly expressed proteins were identified in the NCBI human protein database. The change of mitochondrial membrane permeability after photodynamic treatment was examined by transmission electron microscopy.

RESULTS

The total protein content and band distribution of photodynamic treatment group were similar to the control group. Two mitochondrial membrane proteins were down-regulated significantly. They are mitochondrial heat shock protein (HSP60) (Entrez Gene ID: 31542947, PI 5.7, MW: 61016.4, Protein Score: 354, Protein Score C.I.%:100), and voltage-dependent anion channel (VDAC) (Entrez Gene ID: 340201, PI 7.49, MW: 31574.6, Protein Score: 178, Protein Score C.I.%:100). Transmission electron microscopy showed the loss of integrity of mitochondrial membranes.

CONCLUSIONS

Photodynamic therapy changes mitochondrial membrane permeability, leading to the eventual death of cancer cells. The regulation of proteins related to mitochondrial membrane permeability may become an indicator of the efficacy of photodynamic therapy.

Impacts of genomic research on soybean improvement in East Asia

It has been commonly accepted that soybean domestication originated in East Asia. Although East Asia has the historical merit in soybean production, the USA has become the top soybean producer in the world since 1950s. Following that, Brazil and Argentina have been the major soybean producers since 1970s and 1990s, respectively. China has once been the exporter of soybean to Japan before 1990s, yet she became a net soybean importer as Japan and the Republic of Korea do. Furthermore, the soybean yield per unit area in East Asia has stagnated during the past decade. To improve soybean production and enhance food security in these East Asian countries, much investment has been made, especially in the breeding of better performing soybean germplasms. As a result, China, Japan, and the Republic of Korea have become three important centers for soybean genomic research. With new technologies, the rate and precision of the identification of important genomic loci associated with desired traits from germplasm collections or mutants have increased significantly. Genome editing on soybean is also becoming more established. The year 2019 marked a new era for crop genome editing in the commercialization of the first genome-edited plant product, which is a high-oleic-acid soybean oil. In this review, we have summarized the latest developments in soybean breeding technologies and the remarkable progress in soybean breeding-related research in China, Japan, and the Republic of Korea.

Analysis of Soybean Long Non-Coding RNAs Reveals a Subset of Small Peptide-Coding Transcripts

Long non-coding RNAs (lncRNAs) are defined as non-protein-coding transcripts that are at least 200 nucleotides long. They are known to play pivotal roles in regulating gene expression, especially during stress responses in plants. We used a large collection of in-house transcriptome data from various soybean (Glycine max and Glycine soja) tissues treated under different conditions to perform a comprehensive identification of soybean lncRNAs. We also retrieved publicly available soybean transcriptome data that were of sufficient quality and sequencing depth to enrich our analysis. In total, RNA-sequencing data of 332 samples were used for this analysis. An integrated reference-based, de novo transcript assembly was developed that identified ∼69,000 lncRNA gene loci. We showed that lncRNAs are distinct from both protein-coding transcripts and genomic background noise in terms of length, number of exons, transposable element composition, and sequence conservation level across legume species. The tissue-specific and time-specific transcriptional responses of the lncRNA genes under some stress conditions may suggest their biological relevance. The transcription start sites of lncRNA gene loci tend to be close to their nearest protein-coding genes, and they may be transcriptionally related to the protein-coding genes, particularly for antisense and intronic lncRNAs. A previously unreported subset of small peptide-coding transcripts was identified from these lncRNA loci via tandem mass spectrometry, which paved the way for investigating their functional roles. Our results also highlight the present inadequacy of the bioinformatic definition of lncRNA, which excludes those lncRNA gene loci with small open reading frames from being regarded as protein-coding.

High-Throughput Mass Spectrometric Analysis of the Whole Proteome and Secretome From Sinorhizobium fredii Strains CCBAU25509 and CCBAU45436

Sinorhizobium fredii is a dominant rhizobium on alkaline-saline land that can induce nitrogen-fixing symbiotic root nodules in soybean. Two S. fredii strains, CCBAU25509 and CCBAU45436, were used in this study to facilitate in-depth analyses of this species and its interactions with soybean. We have previously completed the full assembly of the genomes and detailed transcriptomic analyses for these two S. fredii strains, CCBAU25509 and CCBAU45436, that exhibit differential compatibility toward some soybean hosts. In this work, we performed high-throughput Orbitrap analyses of the whole proteomes and secretomes of CCBAU25509 and CCBAU45436 at different growth stages. Our proteomic data cover coding sequences in the chromosome, chromid, symbiotic plasmid, and other accessory plasmids. In general, we found higher levels of protein expression by genes in the chromosomal genome, whereas proteins encoded by the symbiotic plasmid were differentially accumulated in bacteroids. We identified secreted proteins from the extracellular medium, including seven and eight Nodulation Outer Proteins (Nops) encoded by the symbiotic plasmid of CCBAU25509 and CCBAU45436, respectively. Differential host restriction of CCBAU25509 and CCBAU45436 is regulated by the allelic type of the soybean Rj2(Rfg1) protein. Using sequencing data from this work and available in public databases, our analysis confirmed that the soybean Rj2(Rfg1) protein has three major allelic types (Rj2/rfg1, rj2/Rfg1, rj2/rfg1) that determine the host restriction of some Bradyrhizobium diazoefficiens and S. fredii strains. A mutant defective in the type 3 protein secretion system (T3SS) in CCBAU25509 allowed this strain to nodulate otherwise-incompatible soybeans carrying the rj2/Rfg1 allelic type, probably by disrupting Nops secretion. The allelic forms of NopP and NopI in S. fredii might be associated with the restriction imposed by Rfg1. By swapping the NopP between CCBAU25509 and CCBAU45436, we found that only the strains carrying NopP from CCBAU45436 could nodulate soybeans carrying the rj2/Rfg1 allelic type. However, no direct interaction between either forms of NopP and Rfg1 could be observed.

A reference-grade wild soybean genome

Efficient crop improvement depends on the application of accurate genetic information contained in diverse germplasm resources. Here we report a reference-grade genome of wild soybean accession W05, with a final assembled genome size of 1013.2 Mb and a contig N50 of 3.3 Mb. The analytical power of the W05 genome is demonstrated by several examples. First, we identify an inversion at the locus determining seed coat color during domestication. Second, a translocation event between chromosomes 11 and 13 of some genotypes is shown to interfere with the assignment of QTLs. Third, we find a region containing copy number variations of the Kunitz trypsin inhibitor (KTI) genes. Such findings illustrate the power of this assembly in the analysis of large structural variations in soybean germplasm collections. The wild soybean genome assembly has wide applications in comparative genomic and evolutionary studies, as well as in crop breeding and improvement programs.

Transcriptomic reprogramming in soybean seedlings under salt stress

To obtain a comprehensive understanding of transcriptomic reprogramming under salt stress, we performed whole-transcriptome sequencing on the leaf and root of soybean seedlings subjected to salt treatment in a time-course experiment (0, 1, 2, 4, 24, and 48 hr). This time series dataset enabled us to identify important hubs and connections of gene expressions. We highlighted the analysis on phytohormone signaling pathways and their possible crosstalks. Differential expressions were also found among those genes involved in carbon and nitrogen metabolism. In general, the salt-treated seedlings slowed down their photosynthetic functions and ramped up sugar catabolism to provide extra energy for survival. Primary nitrogen assimilation was shut down whereas nitrogen resources were redistributed. Overall, the results from the transcriptomic analyses indicate that the plant uses a multipronged approach to overcome salt stress, with both fast-acting, immediate physiological responses, and longer term reactions that may involve metabolic adjustment.

Modelling predicts that soybean is poised to dominate crop production across Africa

The superior agronomic and human nutritional properties of grain legumes (pulses) make them an ideal foundation for future sustainable agriculture. Legume-based farming is particularly important in Africa, where small-scale agricultural systems dominate the food production landscape. Legumes provide an inexpensive source of protein and nutrients to African households as well as natural fertilization for the soil. Although the consumption of traditionally grown legumes has started to decline, the production of soybeans (Glycine max Merr.) is spreading fast, especially across southern Africa. Predictions of future land-use allocation and production show that the soybean is poised to dominate future production across Africa. Land use models project an expansion of harvest area, whereas crop models project possible yield increases. Moreover, a seed change in farming strategy is underway. This is being driven largely by the combined cash crop value of products such as oils and the high nutritional benefits of soybean as an animal feed. Intensification of soybean production has the potential to reduce the dependence of Africa on soybean imports. However, a successful "soybean bonanza" across Africa necessitates an intensive research, development, extension, and policy agenda to ensure that soybean genetic improvements and production technology meet future demands for sustainable production.

Proteomic analysis reveals that pheophorbide a-mediated photodynamic treatment inhibits prostate cancer growth by hampering GDP-GTP exchange of ras-family proteins

BACKGROUND

We previously reported that pheophorbide a (PhA), excited by 630 nm light, significantly inhibited the growth of prostate cancer cells. In this study, we employed whole-cell proteomics to investigate photodynamic treatment (PDT)-related proteins.

METHODS

Two-dimensional gel electrophoresis (2-DE) coupled with tandem mass spectrometry was employed to reveal the proteins involved in PhA-mediated PDT in LNCaP and PC-3 prostate cancer cells.

RESULTS

After PhA-PDT treatment, decreased expression of translationally-controlled tumor protein (TCTP) was found in both PC-3 and LNCaP whole-cell proteomes. In contrast, human rab GDP dissociation inhibitor (GDI) in LNCaP cells and ras-related homologs GDI in PC-3 cells were up-regulated.

CONCLUSIONS

GDP-GTP exchange is an underlying target of photodynamic treatment in prostate cancer cells.

Genome-Wide Analyses of the Soybean F-Box Gene Family in Response to Salt Stress

The F-box family is one of the largest gene families in plants that regulate diverse life processes, including salt responses. However, the knowledge of the soybean F-box genes and their roles in salt tolerance remains limited. Here, we conducted a genome-wide survey of the soybean F-box family, and their expression analysis in response to salinity via in silico analysis of online RNA-sequencing (RNA-seq) data and quantitative reverse-transcription polymerase chain reaction (qRT-PCR) to predict their potential functions. A total of 725 potential F-box proteins encoded by 509 genes were identified and classified into 9 subfamilies. The gene structures, conserved domains and chromosomal distributions were characterized. There are 76 pairs of duplicate genes identified, including genome-wide segmental and tandem duplication events, which lead to the expansion of the number of F-box genes. The in silico expression analysis showed that these genes would be involved in diverse developmental functions and play an important role in salt response. Our qRT-PCR analysis confirmed 12 salt-responding F-box genes. Overall, our results provide useful information on soybean F-box genes, especially their potential roles in salt tolerance.

Comparison of Small RNA Profiles of Glycine max and Glycine soja at Early Developmental Stages

Small RNAs, including microRNAs (miRNAs) and phased small interfering RNAs (phasiRNAs; from PHAS loci), play key roles in plant development. Cultivated soybean, Glycine max, contributes a great deal to food production, but, compared to its wild kin, Glycine soja, it may lose some genetic information during domestication. In this work, we analyzed the sRNA profiles of different tissues in both cultivated (C08) and wild soybeans (W05) at three stages of development. A total of 443 known miRNAs and 15 novel miRNAs showed varying abundances between different samples, but the miRNA profiles were generally similar in both accessions. Based on a sliding window analysis workflow that we developed, 50 PHAS loci generating 55 21-nucleotide phasiRNAs were identified in C08, and 46 phasiRNAs from 41 PHAS loci were identified in W05. In germinated seedlings, phasiRNAs were more abundant in C08 than in W05. Disease resistant TIR-NB-LRR genes constitute a very large family of PHAS loci. PhasiRNAs were also generated from several loci that encode for NAC transcription factors, Dicer-like 2 (DCL2), Pentatricopeptide Repeat (PPR), and Auxin Signaling F-box 3 (AFB3) proteins. To investigate the possible involvement of miRNAs in initiating the PHAS-phasiRNA pathway, miRNA target predictions were performed and 17 C08 miRNAs and 15 W05 miRNAs were predicted to trigger phasiRNAs biogenesis. In summary, we provide a comprehensive description of the sRNA profiles of wild versus cultivated soybeans, and discuss the possible roles of sRNAs during soybean germination.

Genomewide Approach Validates Thiopurine Methyltransferase Activity Is a Monogenic Pharmacogenomic Trait

We performed a genomewide association study (GWAS) of primary erythrocyte thiopurine S-methyltransferase (TPMT) activity in children with leukemia (n = 1,026). Adjusting for age and ancestry, TPMT was the only gene that reached genomewide significance (top hit rs1142345 or 719A>G; P = 8.6 × 10^-61 ). Additional genetic variants (in addition to the three single-nucleotide polymorphisms [SNPs], rs1800462, rs1800460, and rs1142345, defining TPMT clinical genotype) did not significantly improve classification accuracy for TPMT phenotype. Clinical mercaptopurine tolerability in 839 patients was related to TPMT clinical genotype (P = 2.4 × 10^-11 ). Using 177 lymphoblastoid cell lines (LCLs), there were 251 SNPs ranked higher than the top TPMT SNP (rs1142345; P = 6.8 × 10^-5 ), revealing a limitation of LCLs for pharmacogenomic discovery. In a GWAS, TPMT activity in patients behaves as a monogenic trait, further bolstering the utility of TPMT genetic testing in the clinic.

Neglecting legumes has compromised human health and sustainable food production

The United Nations declared 2016 as the International Year of Pulses (grain legumes) under the banner 'nutritious seeds for a sustainable future'. A second green revolution is required to ensure food and nutritional security in the face of global climate change. Grain legumes provide an unparalleled solution to this problem because of their inherent capacity for symbiotic atmospheric nitrogen fixation, which provides economically sustainable advantages for farming. In addition, a legume-rich diet has health benefits for humans and livestock alike. However, grain legumes form only a minor part of most current human diets, and legume crops are greatly under-used. Food security and soil fertility could be significantly improved by greater grain legume usage and increased improvement of a range of grain legumes. The current lack of coordinated focus on grain legumes has compromised human health, nutritional security and sustainable food production.

Neglecting legumes has compromised human health and sustainable food production

The United Nations declared 2016 as the International Year of Pulses (grain legumes) under the banner 'nutritious seeds for a sustainable future'. A second green revolution is required to ensure food and nutritional security in the face of global climate change. Grain legumes provide an unparalleled solution to this problem because of their inherent capacity for symbiotic atmospheric nitrogen fixation, which provides economically sustainable advantages for farming. In addition, a legume-rich diet has health benefits for humans and livestock alike. However, grain legumes form only a minor part of most current human diets, and legume crops are greatly under-used. Food security and soil fertility could be significantly improved by greater grain legume usage and increased improvement of a range of grain legumes. The current lack of coordinated focus on grain legumes has compromised human health, nutritional security and sustainable food production.

Molecular phylogeny and dynamic evolution of disease resistance genes in the legume family

Background

Legumes are the second-most important crop family in agriculture for its economic and nutritional values. Disease resistance (R-) genes play an important role in responding to pathogen infections in plants. To further increase the yield of legume crops, we need a comprehensive understanding of the evolution of R-genes in the legume family.

Results

In this study, we developed a robust pipeline and identified a total of 4,217 R-genes in the genomes of seven sequenced legume species. A dramatic diversity of R-genes with structural variances indicated a rapid birth-and-death rate during the R-gene evolution in legumes. The number of R-genes transiently expanded and then quickly contracted after whole-genome duplications, which meant that R-genes were sensitive to subsequent diploidization. R proteins with the Coiled-coil (CC) domain are more conserved than others in legumes. Meanwhile, other types of legume R proteins with only one or two typical domains were subjected to higher rates of loss during evolution. Although R-genes evolved quickly in legumes, they tended to undergo purifying selection instead of positive selection during evolution. In addition, domestication events in some legume species preferentially selected for the genes directly involved in the plant-pathogen interaction pathway while suppressing those R-genes with low occurrence rates.

Conclusions

Our results provide insights into the dynamic evolution of R-genes in the legume family, which will be valuable for facilitating genetic improvements in the disease resistance of legume cultivars.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-016-2736-9) contains supplementary material, which is available to authorized users.

QTLs Regulating the Contents of Antioxidants, Phenolics, and Flavonoids in Soybean Seeds Share a Common Genomic Region

Soybean seeds are a rich source of phenolic compounds, especially isoflavonoids, which are important nutraceuticals. Our study using 14 wild- and 16 cultivated-soybean accessions shows that seeds from cultivated soybeans generally contain lower total antioxidants compared to their wild counterparts, likely an unintended consequence of domestication or human selection. Using a recombinant inbred population resulting from a wild and a cultivated soybean parent and a bin map approach, we have identified an overlapping genomic region containing major quantitative trait loci (QTLs) that regulate the seed contents of total antioxidants, phenolics, and flavonoids. The QTL for seed antioxidant content contains 14 annotated genes based on the Williams 82 reference genome (Gmax1.01). None of these genes encodes functions that are related to the phenylpropanoid pathway of soybean. However, we found three putative Multidrug And Toxic Compound Extrusion (MATE) transporter genes within this QTL and one adjacent to it (GmMATE1-4). Moreover, we have identified non-synonymous changes between GmMATE1 and GmMATE2, and that GmMATE3 encodes an antisense transcript that expresses in pods. Whether the polymorphisms in GmMATE proteins are major determinants of the antioxidant contents, or whether the antisense transcripts of GmMATE3 play important regulatory roles, awaits further functional investigations.

Proteins interacting with mitochondrial ATP-dependent Lon protease (MAP1) in Magnaporthe oryzae are involved in rice blast disease

The ATP-dependent Lon protease is involved in many physiological processes. In bacteria, Lon regulates pathogenesis and, in yeast, Lon protects mitochondia from oxidative damage. However, little is known about Lon in fungal phytopathogens. MAP1, a homologue of Lon in Magnaporthe oryzae, was recently identified to be important for stress resistance and pathogenesis. Here, we focus on a novel pathogenic pathway mediated by MAP1. Based on an interaction system between rice and a tandem affinity purification (TAP)-tagged MAP1 complementation strain, we identified 23 novel fungal proteins from infected leaves using a TAP approach with mass spectrometry, and confirmed that 14 of these proteins physically interact with MAP1 in vivo. Among these 14 proteins, 11 candidates, presumably localized to the mitochondria, were biochemically determined to be substrates of MAP1 hydrolysis. Deletion mutants were created and functionally analysed to further confirm the involvement of these proteins in pathogenesis. The results indicated that all mutants showed reduced conidiation and sensitivity to hydrogen peroxide. Appressorial formations were not affected, although conidia from certain mutants were morphologically altered. In addition, virulence was reduced in four mutants, enhanced (with lesions forming earlier) in two mutants and remained unchanged in one mutant. Together with the known virulence-related proteins alternative oxidase and enoyl-CoA hydratase, we propose that most of the Lon-interacting proteins are involved in the pathogenic regulation pathway mediated by MAP1 in M. oryzae. Perturbation of this pathway may represent an effective approach for the inhibition of rice blast disease.

Identification of a novel salt tolerance gene in wild soybean by whole-genome sequencing

Using a whole-genome-sequencing approach to explore germplasm resources can serve as an important strategy for crop improvement, especially in investigating wild accessions that may contain useful genetic resources that have been lost during the domestication process. Here we sequence and assemble a draft genome of wild soybean and construct a recombinant inbred population for genotyping-by-sequencing and phenotypic analyses to identify multiple QTLs relevant to traits of interest in agriculture. We use a combination of de novo sequencing data from this work and our previous germplasm re-sequencing data to identify a novel ion transporter gene, GmCHX1, and relate its sequence alterations to salt tolerance. Rapid gain-of-function tests show the protective effects of GmCHX1 towards salt stress. This combination of whole-genome de novo sequencing, high-density-marker QTL mapping by re-sequencing and functional analyses can serve as an effective strategy to unveil novel genomic information in wild soybean to facilitate crop improvement.

Identification of a novel salt tolerance gene in wild soybean by whole-genome sequencing

Using a whole-genome-sequencing approach to explore germplasm resources can serve as an important strategy for crop improvement, especially in investigating wild accessions that may contain useful genetic resources that have been lost during the domestication process. Here we sequence and assemble a draft genome of wild soybean and construct a recombinant inbred population for genotyping-by-sequencing and phenotypic analyses to identify multiple QTLs relevant to traits of interest in agriculture. We use a combination of de novo sequencing data from this work and our previous germplasm re-sequencing data to identify a novel ion transporter gene, GmCHX1, and relate its sequence alterations to salt tolerance. Rapid gain-of-function tests show the protective effects of GmCHX1 towards salt stress. This combination of whole-genome de novo sequencing, high-density-marker QTL mapping by re-sequencing and functional analyses can serve as an effective strategy to unveil novel genomic information in wild soybean to facilitate crop improvement.

Expression of an apoplast-localized BURP-domain protein from soybean (GmRD22) enhances tolerance towards abiotic stress

The BURP-domain protein family comprises a diverse group of plant-specific proteins that share a conserved BURP domain at the C terminus. However, there have been only limited studies on the functions and subcellular localization of these proteins. Members of the RD22-like subfamily are postulated to associate with stress responses due to the stress-inducible nature of some RD22-like genes. In this report, we used different transgenic systems (cells and in planta) to show that the expression of a stress-inducible RD22-like protein from soybean (GmRD22) can alleviate salinity and osmotic stress. We also performed detailed microscopic studies using both fusion proteins and immuno-electron microscopic techniques to demonstrate the apoplast localization of GmRD22, for which the BURP domain is a critical determinant of the subcellular localization. The apoplastic GmRD22 interacts with a cell wall peroxidase and the ectopic expression of GmRD22 in both transgenic Arabidopsis thaliana and transgenic rice resulted in increased lignin production when subjected to salinity stress. It is possible that GmRD22 regulates cell wall peroxidases and hence strengthens cell wall integrity under such stress conditions.

Recent developments of genomic research in soybean

Soybean is an important cash crop with unique and important traits such as the high seed protein and oil contents, and the ability to perform symbiotic nitrogen fixation. A reference genome of cultivated soybeans was established in 2010, followed by whole-genome re-sequencing of wild and cultivated soybean accessions. These efforts revealed unique features of the soybean genome and helped to understand its evolution. Mapping of variations between wild and cultivated soybean genomes were performed. These genomic variations may be related to the process of domestication and human selection. Wild soybean germplasms exhibited high genomic diversity and hence may be an important source of novel genes/alleles. Accumulation of genomic data will help to refine genetic maps and expedite the identification of functional genes. In this review, we summarize the major findings from the whole-genome sequencing projects and discuss the possible impacts on soybean researches and breeding programs. Some emerging areas such as transcriptomic and epigenomic studies will be introduced. In addition, we also tabulated some useful bioinformatics tools that will help the mining of the soybean genomic data.

A study of JAK2 (V617F) gene mutation in patients with chronic myeloproliferative disorders

BACKGROUND AND AIMS

Chronic myeloproliferative diseases (MPDs) are heterogenous group of haematological malignant disorders. It is now a well recognized fact that the JAK2 (V617F) mutation occurs in majority of the patients with polycythaemia vera (PV) and half of those with myelofibrosis and essential thrombocythaemia. The presence of JAK2 (V617F) mutation is considered an important criterion for the exclusion of secondary-reactive from clonal disorders. In the present uni-institutional study, we analyzed the JAK2 (V617F) mutation status in the ethnic Malay and Chinese patients who were diagnosed as MPDs.

MATERIALS AND METHODS

The study was performed on known cases of chronic MPDs either at diagnosis or during the follow-up. A total of 45 cases were studied with informed consent. The allele specific PCR, ARMS-PCR and RQ-PCR methods were used.

RESULTS

The frequency of the JAK2 (V617F) mutation varied between the MPD subtypes, with the mutation being most frequent in PV (95.8%) and 39% showed homozygous mutant allele. The mutation was detected in 52.9% cases of ET, of which 36.4% were homozygous for the mutant allele and 1 case of MF was homozygous for the mutant allele.

CONCLUSION

Screening for the mutation in all cases suspected of chronic MPD could be beneficial in differentiating patients with reactive erthrocytosis or thrombocytosis from the true clonal MPDs especially polycythaemia vera.

Prevalence of uridine glucuronosyl transferase 1A1 (UGT1A1) mutations in Malay neonates with severe jaundice

A number of genetic risk factors have been implicated in the development of neonatal severe hyperbilirubinaemia. This includes mutations in the uridine glucoronosyl transferase 1A1 (UGT1A1) gene which is responsible for unconjugated hyperbilirubinemia in Gilbert's Syndrome. We studied the prevalence of UGT1A1 gene mutations in a group of Malay neonates to determine whether they are risk factors to severe neonatal jaundice. One hundred and twenty-five Malay neonates with severe hyperbilirubinemia were studied. Ninety-eight infants without severe hyperbilirubinaemia were randomly selected from healthy Malay term infants (controls). DNA from EDTA cord blood samples were examined for UGT1A1 mutations nt211G > A and nt247T > C using established Taqman SNP genotyping assays and the UGT1A1*28 variant was detected by the Agilent 2100 bioanalyzer. All samples were also screened for common Malay G6PD variants using established techniques. The frequency of UGT1A1 211G > A mutation is significantly higher in the severely hyperbilirubinemic group (13%) than the control group (4%; p = 0.015) and all the positive cases were heterozygous for the mutation. There was no significant difference in the frequency of UGT1A1*28 mutation between the severely hyperbilirubinemic (3.5%) and the control group (0.01%; p = 0.09). None of the neonates in both groups carried the nt247 T > C mutation. The prevalence of G6PD mutation was significantly higher in the severely jaundiced group than control (9% vs 4%; p = 0.04). In conclusion, nt 211 G > A alleles constitute at least 12% of UGT1A1 mutations underlying unconjugated hyperbilirubinemia and appears to be a significant independent risk factor associated with severe neonatal hyperbilirubinemia in the Malay newborns.

Real-time quantification for BCR-ABL transcripts in chronic myeloid leukaemia patients in UKMMC, Malaysia

Molecular pathogenesis of chronic myeloid leukemia (CML) is well established and molecular monitoring for patients with CML has become an important practice in the management of patients on imatinib therapy. In the present study, we report the use of RQ-PCR method for detection of BCR-ABL fusion gene for our CML cases. We performed a two-step RQ-PCR on bone marrow aspirates or peripheral blood of 37 CML patients. Quantitative expression of BCR-ABL fusion gene was carried out relative to the expression of a housekeeping gene as endogenous control to compensate for uneven cell numbers, RNA quality, or variations in reverse transcription efficiencies. Twenty-four of these patients were pre-treated with hydroxyurea or alpha interferon prior to the imatinib therapy. Their BCR-ABL fusion gene levels were monitored for 18 months. All samples processed were evaluable. The PCR amplification efficiency of the ABL gene is 90.5% (0.2158) and the BCR-ABL gene, 93.4% (0.1573).

Resequencing of 31 wild and cultivated soybean genomes identifies patterns of genetic diversity and selection

We report a large-scale analysis of the patterns of genome-wide genetic variation in soybeans. We re-sequenced a total of 17 wild and 14 cultivated soybean genomes to an average of approximately ×5 depth and >90% coverage using the Illumina Genome Analyzer II platform. We compared the patterns of genetic variation between wild and cultivated soybeans and identified higher allelic diversity in wild soybeans. We identified a high level of linkage disequilibrium in the soybean genome, suggesting that marker-assisted breeding of soybean will be less challenging than map-based cloning. We report linkage disequilibrium block location and distribution, and we identified a set of 205,614 tag SNPs that may be useful for QTL mapping and association studies. The data here provide a valuable resource for the analysis of wild soybeans and to facilitate future breeding and quantitative trait analysis.

Tonoplast-located GmCLC1 and GmNHX1 from soybean enhance NaCl tolerance in transgenic bright yellow (BY)-2 cells

Genes encoding ion transporters that regulate ion homeostasis in soybean have not been carefully investigated. Using degenerate primers, we cloned a putative chloride channel gene (GmCLC1) and a putative Na+/H+ antiporter gene (GmNHX1) from soybean. Confocal microscopic studies using yellow fluorescent fusion proteins revealed that GmCLC1 and GmNHX1 were both localized on tonoplast. The expressions of GmCLC1 and GmNHX1 were both induced by NaCl or dehydration stress imposed by polyethylene glycol (PEG). Using mitochondrial integrity and cell death as the damage indicators, a clear alleviation under NaCl stress (but not PEG stress) was observed in both GmCLC1 and GmNHX1 transgenic cells. Using fluorescent dye staining and quenching, respectively, a higher concentration of chloride ion (Cl-) or sodium ion (Na+) was observed in isolated vacuoles in the cells of GmCLC1 and of GmNHX1 transgenic lines. Our result suggested that these vacuolar-located ion transporters function to sequester ions from cytoplasm into vacuole to reduce its toxic effects.

An intelligent tutoring system for trauma management (Trauma-Teach): a preliminary report

Trauma-Teach is an interactive software for tutoring surgical trainees on medical trauma management procedures. Users of the system interact with a virtual patient suffering from trauma injuries. The task of the user is to stabilise the virtual patient, discover the underlying injuries and decide on an appropriate management plan. Artificial intelligence techniques are used to simulate the patient's pulmonary and cardiovascular systems in real time, determine the responses and results of treatments and diagnostics accordingly, model the patient deterioration if wrong actions are taken, and give a measure of reality to the system by selecting actual trauma cases from the hospital's database.

GmPAP3, a novel purple acid phosphatase-like gene in soybean induced by NaCl stress but not phosphorus deficiency

Purple acid phosphatases (PAPs) are commonly found in plants, but the physiological functions of different classes of PAPs are not thoroughly understood. In the present study, we identified a novel gene, GmPAP3, from salt-stressed soybean using suppression subtractive hybridization (SSH) techniques. Protein sequence alignment studies and phylogenetic analysis strongly suggested that GmPAP3 belongs to the group of plant PAPs and PAP-like proteins that are distinct from those of fungi and animals. In addition, the invariable consensus metal binding residues of PAPs were all conserved in GmPAP3. Surprisingly, analysis of protein sorting signals showed that a putative mitochondrion targeting transit peptide is present on GmPAP3. Northern blot analysis revealed that NaCl stress causes a general induction of GmPAP3 expression in both roots and leaves of various cultivated (Glycine max) and wild (Glycine soja) soybean varieties. Further test using two genetically unrelated cultivated soybean varieties showed that the expression pattern of GmPAP3 is distinct from other PAP genes in soybeans. NaCl stress and oxidative stress but not phosphorus (P) starvation induces the expression of GmPAP3. These results suggest that the physiological role of GmPAP3 might be related to the adaptation of soybean to NaCl stress, possibly through its involvement in reactive oxygen species (ROS) forming and/or scavenging or stress-responding signal transduction pathways.

A training workshop on late-stage dementia care for family caregivers

Training workshops have been considered a useful intervention in helping family caregivers of people with dementia to cope with the stress of caregiving. However, there are no reports in the literature with regard to training and support of families specifically looking after individuals who are in the late stage of dementia. This paper reports the experience and evaluation of a training workshop aimed at preparing family caregivers for late-stage dementia care. Eighty-eight percent of the participants completed the client satisfaction questionnaire. The results from the questionnaire gave a very positive response, showing 90.9 percent of respondents were satisfied with the workshop, and 77.3 percent of respondents indicated that their caregiving needs were met. Eleven participants who attended this workshop joined a focus group feedback session. The Kruskal-Wallis test found no significant differences between the overall profile of the participants and that of the focus group in terms of age, gender, educational background, whether they were primary caregivers, for whom they cared (e.g., parents or spouse), or whether the care recipient stayed at home or in a nursing home. Findings from the focus group session provide a somewhat different picture from that of the questionnaire. Three focus group participants provided more critical comments of the workshop. Although the majority of the focus group agreed that the workshop had been useful, they disagreed on whether it is necessary to discuss psychosocial issues in this workshop. Findings from the focus group have enabled the project team to reflect on their design and operation of the workshop and provided valuable insight for future development as well as for further study.

The importance of hemoglobin levels during radiotherapy for carcinoma of the cervix

BACKGROUND

It is unclear whether blood transfusion can overcome the negative impact of anemia before or during radiotherapy (RT) in patients with carcinoma of the cervix. The objective of this retrospective study was to examine the impact of anemia and blood transfusion on 605 patients with carcinoma of the cervix treated with radical RT at 7 centers across Canada in 1989, 1990, and 1992.

METHODS

The data collected included hemoglobin (Hgb) levels from the time of diagnosis to the end of therapy; blood transfusions administered; and identifiable patient-, tumor-, and treatment-related factors. Survival, disease free survival, and pelvic control analyses were evaluated by univariate and multivariate analysis.

RESULTS

The median follow-up was 41 months (range, 0-92 months). Presenting Hgb level, average weekly nadir Hgb (AWNH) during RT, and blood transfusion were correlated significantly with local control, disease free survival, and overall survival on univariate analysis. However, the AWNH remained significant on multivariate analysis, whereas Hgb at presentation and blood transfusion did not. The 5-year survival was 74% for patients with an AWNH >/= 120 g/L, 52% for patients with AWNH levels 110-119 g/L inclusive, and 45% for patients with AWNH levels < 110 g/L (P < 0.0001). At each Hgb level, patients who were transfused and maintained a specific Hgb level had a survival rate that was not significantly different from patients who were at that level spontaneously. There was a significant reduction in both pelvic and distant recurrence (P < 0.0001 and P < 0.0006, respectively) in patients whose AWNH level during RT was >/= 120 g/L compared with < 120 g/L. A reduction in the rate of distant recurrence was observed in patients with and without pelvic recurrence.

CONCLUSIONS

AWNH is highly predictive of outcome for patients treated with RT for carcinoma of the cervix. Blood transfusion appears to overcome the negative prognostic effects of low presenting Hgb levels and AWNH levels.

Effects of radiation on the longitudinal trends of total serum cholesterol levels in the atomic bomb survivors

The effects of radiation on the long-term trends of the total serum cholesterol levels of the Hiroshima and Nagasaki atomic bomb survivors were examined using data collected in the Adult Health Study over a 28-year period (1958-1986). The growth-curve method was used to model the longitudinal age-dependent changes in cholesterol levels. For each sex, temporal trends of cholesterol levels were characterized with respect to age, body mass index, city and birth year. We then examined whether the temporal trends differed by radiation dose. We showed that the mean growth curve of cholesterol levels for the irradiated subjects were significantly higher than that for the unirradiated subjects, and that the increase was greater for women than for men. No difference in dose response was detected between Hiroshima and Nagasaki. An increased mean level of cholesterol was evident for irradiated women in general, but a notable increase was apparent in males only for the youngest birth cohort of 1935-1945. The difference in the mean cholesterol levels between the irradiated and unirradiated subjects diminished past 70 years of age. It is not known whether this is due to natural progression or is an artifact of nonrandom variation in the rate of participation in the examinations. The maximum predicted increase at 1 Gy for women occurred at age 52 years for the 1930 cohort: 2.5 mg/dl (95% CI 1.6-3.3 mg/dl) for Hiroshima and 2.3 mg/dl (95% CI 1.5-3.1 mg/dl) for Nagasaki. The corresponding increase for men occurred at age 29 years for the 1940 cohort: 1.6 mg/dl (95% CI 0.4-2.8) for Hiroshima and 1.4 mg/dl (95% CI 0.3-2.6) for Nagasaki. Controlling for cigarette smoking did not alter the dose-response relationship. Although the difference in the mean growth curves of the irradiated and unirradiated groups was statistically significant, there was a considerable overlap in the individual growth curves of the two groups. The significant sex difference and the greater magnitude of radiation effects in women suggest that hormonal changes resulting from radiation exposure, such as accelerated menopause, is an area worth investigating to delineate the mechanisms underlying the increased cholesterol levels of the irradiated female subjects. This increase may also partially explain the increased rate of coronary heart disease seen in the atomic bomb survivors.

Cancer of the tonsil: the results of ipsilateral radiation treatment

BACKGROUND AND PURPOSE

The use of ipsilateral irradiation techniques to treat patients with carcinoma of the tonsil reduces the acute radiation reaction in the contralateral pharynx and late damage to the contralateral salivary tissue. However, this may also spare microscopic disease in apparently uninvolved contralateral lymph nodes. The purpose of this study was to analyse the survival and recurrence rates and sites of recurrance in a group of patients with carcinoma of the tonsil treated with ipsilateral techniques.

MATERIALS AND METHODS

Between 1975 and 1993, 271 patients with invasive squamous cell cancer of the tonsil were referred to the Vancouver Cancer Centre (VCC). One hundred and seventy-eight received ipsilateral radiation treatment. Three received surgery only, six post-operative radiation, 12 supportive treatment only and 72 bilateral radiation treatment. In the absence of bilateral neck nodes and extensive lymphodenopathy, field sizes were generally kept small to include the primary tumour and the first echelon of nodes. The most common dose was 60 Gy in 25 daily fractions in 5 weeks (2.4 Gy per day).

RESULTS AND DISCUSSION

The disease specific survival for all patients treated by radical radiation treatment was 61% at 5 years. For the 178 patients who received ipsilateral radiation treatment the overall primary tumour control rate by ipsilateral radiation treatment alone was 75% and for T1 and T2 tumours 84%. Eight (7.5%) of 101 of these patients with N0 nodes at presentation and without prior failure at the primary site, developed nodal recurrence (four within the initially radiated high dose volume). Two developed contralateral nodes, and two developed field edge nodal recurrence, one cured by surgery. In 54 patients with N1 disease, five developed nodal recurrence, two within field, two contralateral, one of whom was cured by surgery, and one at field edge. In 23 patients with N2a, N2b or N3 disease node control was achieved from radiation treatment in 11 and two more were cured by surgery. All nodal failures were within the radiated volume. Overall, 10 of the 25 patients with nodal failure were cured by subsequent surgery.

CONCLUSIONS

Ipsilateral treatment of patients with carcinoma of the tonsil gives survival results that are at least as good as those reported with bilateral treatment with fewer side effects and a very low risk of failure in the contralateral neck.

Dissemination of an evidence-based intervention manual to improve managed care mammography rates

After collaborating with the Centers for Disease Control and Prevention to develop an evidence-based mammography intervention manual, the dissemination of the manual in a managed care setting was assessed. Using qualitative methods (in-depth interviews), factors were examined that motivated use of the manual by the quality improvement units of eight Prudential HealthCare health plans. Seven of the plans implemented more intensive interventions after having received the manual than in the previous year. Factors that facilitated use of the manual and implementation of recommendations included: internal motivation, support of senior level management, adequate resources (time, personnel, and funds) to support interventions, and the organization and content of the manual itself.

Pretreatment assessment and dental management of patients with nasopharyngeal carcinoma

Patients who present with nasopharyngeal carcinoma (NPC) require through oral and dental assessment prior to treatment of the malignancy. We assessed the oral status of 57 consecutive patients with a diagnosis of NPC. In this study, identified risk factors for NPC were seen to be different in Asian versus non-Asian patients. Epstein-Barr virus seropositivity was seen in all Asian patients and in 69% of non-Asian patients (P = 0.00006), and reported alcohol use was greater in the non-Asian patients. In this study it was found that 68% of dentate patients required dental extractions primarily due to periodontal disease. Even in patients who reported receiving regular dental care (28%) extractions prior to radiation therapy were suggested. Oral complications of radiation therapy were reported by 84% of patients, with the most common being xerostomia. Clinical diagnosis of candidiasis (16%), rampant caries (10% of dentate patients) and difficulties with dentures (25% of denture wearers) were noted. In addition to pretreatment assessment, continuing oral and dental management is needed for patients with NPC.

Topical bleomycin for the treatment of dysplastic oral leukoplakia

BACKGROUND

Because malignant transformation of dysplastic oral leukoplakia has been reported in up to 43% of cases, these lesions must be managed.

METHODS

This study evaluated the use of topical 1% bleomycin in dimethylsulfoxide for the treatment of dysplastic oral lesions. Bleomycin was applied once daily for 14 consecutive days to lesions of the oral mucosa in 19 patients. Immediate posttreatment biopsies and the clinical response were evaluated and clinical follow-up was conducted for as long as possible.

RESULTS

The mean age of the patients at diagnosis was 59.4 years and 74% were tobacco users. Seventy-five percent of patients had resolution of dysplasia at follow-up biopsy, with a mean improvement of two histologic grades of dysplasia after topical chemotherapy. Ninety-four percent of the patients attained at least partial responses. After a mean follow-up period of 3.4 years, 31.6% of patients had no clinically visible lesions and 47.4% of patients had clinically benign lesions of homogeneous leukoplakia or minimal visible leukoplakia. In 2 patients (11%) malignant transformation occurred a mean of 1.75 years after bleomycin treatment.

CONCLUSIONS

Topical bleomycin may prevent the potential progression of leukoplakia through dysplasia to carcinoma. Close follow-up of all patients with dysplasia is required.

Cancer mortality following treatment for adult hyperthyroidism. Cooperative Thyrotoxicosis Therapy Follow-up Study Group

CONTEXT

High-dose iodine 131 is the treatment of choice in the United States for most adults with hyperthyroid disease. Although there is little evidence to link therapeutic (131)I to the development of cancer, its extensive medical use indicates the need for additional evaluation.

OBJECTIVE

To evaluate cancer mortality among hyperthyroid patients, particularly after (131)I treatment.

DESIGN

A retrospective cohort study.

SETTING

Twenty-five clinics in the United States and 1 clinic in England.

PATIENTS

A total of 35 593 hyperthyroid patients treated between 1946 and 1964 in the original Cooperative Thyrotoxicosis Therapy Follow-up Study; 91 % had Graves disease, 79% were female, and 65% were treated with (131)I.

MAIN OUTCOME MEASURE

Standardized cancer mortality ratios (SMRs) after 3 treatment modalities for hyperthyroidism.

RESULTS

Of the study cohort, 50.5% had died by the end of follow-up in December 1990. The total number of cancer deaths was close to that expected based on mortality rates in the general population (2950 vs 2857.6), but there was a small excess of mortality from cancers of the lung, breast, kidney, and thyroid, and a deficit of deaths from cancers of the uterus and the prostate gland. Patients with toxic nodular goiter had an SMR of 1.16 (95% confidence interval [CI], 1.03-1.30). More than 1 year after treatment, an increased risk of cancer mortality was seen among patients treated exclusively with antithyroid drugs (SMR, 1.31; 95% CI, 1.06-1.60). Radioactive iodine was not linked to total cancer deaths (SMR, 1.02; 95% CI, 0.98-1.07) or to any specific cancer with the exception of thyroid cancer (SMR, 3.94; 95% CI, 2.52-5.86).

CONCLUSIONS

Neither hyperthyroidism nor (131)I treatment resulted in a significantly increased risk of total cancer mortality. While there was an elevated risk of thyroid cancer mortality following (131)I treatment, in absolute terms the excess number of deaths was small, and the underlying thyroid disease appeared to play a role. Overall, (131)I appears to be a safe therapy for hyperthyroidism.

Cancer incidence after retinoblastoma. Radiation dose and sarcoma risk

CONTEXT

There is a substantial risk of a second cancer for persons with hereditary retinoblastoma, which is enhanced by radiotherapy.

OBJECTIVE

To examine long-term risk of new primary cancers in survivors of childhood retinoblastoma and quantify the role of radiotherapy in sarcoma development.

DESIGN

Cohort incidence study of patients with retinoblastoma followed for a median of 20 years, and nested case-control study of a radiation dose-response relationship for bone and soft tissue sarcomas.

SETTING/PARTICIPANTS

A total of 1604 patients with retinoblastoma who survived at least 1 year after diagnosis, identified from hospital records in Massachusetts and New York during 1914 to 1984.

RESULTS

Incidence of subsequent cancers was statistically significantly elevated only in the 961 patients with hereditary retinoblastoma, in whom 190 cancers were diagnosed, vs 6.3 expected in the general population (relative risk [RR], 30 [95% confidence interval, 26-47]). Cumulative incidence (+/-SE) of a second cancer at 50 years after diagnosis was 51.0% (+/-6.2%) for hereditary retinoblastoma, and 5.0% (+/-3.0%) for nonhereditary retinoblastoma. All 114 sarcomas of diverse histologic types occurred in patients with hereditary retinoblastoma. For soft tissue sarcomas, the RRs showed a stepwise increase at all dose categories, and were statistically significant at 10 to 29.9 Gy and 30 to 59.9 Gy. A radiation risk for all sarcomas combined was evident at doses above 5 Gy, rising to 10.7-fold at doses of 60 Gy or greater (P<.05).

CONCLUSIONS

Genetic predisposition has a substantial impact on risk of subsequent cancers in retinoblastoma patients, which is further increased by radiation treatment. A radiation dose-response relationship is demonstrated for all sarcomas and, for the first time in humans, for soft tissue sarcomas. Retinoblastoma patients should be examined for new cancers and followed into later life to determine whether their extraordinary cancer risk extends to common cancers of adulthood.

Longitudinal trends in total serum cholesterol levels in a Japanese cohort, 1958-1986

The 28-year follow-up of a Japanese cohort, having collected vast amounts of data collected on total serum cholesterol (TC), provided an exceptional opportunity to examine TC temporal trends. The longitudinal statistical method of growth-curve analysis was used to elucidate the age-related changes in TC levels and to characterize these trends in relation to sex, birth cohort, time period, place of residence, and body mass index (BMI). Japanese TC levels at initial examination were remarkably lower than those in western countries. During the study period from 1958 to 1986, TC levels increased dramatically with age in both sexes. The slope of the cholesterol growth curve was steeper for women than for men, with the difference growing larger after age 40 years. Drastic changes in Japanese behavior and lifestyle, especially westernization of the diet, are thought to have affected the TC values as time-period effects. As a result of this temporal change, which affected different cohorts at different ages, TC values were higher in members of the younger cohort. The increase of the TC values as time-period effects were larger in earlier period than in later period. These time-period effects appeared to be almost similar in men and women. The TC growth curves also varied by city of residence. Subjects in urban areas had higher TC values than subjects in rural areas. Changes associated with BMI from 1958 to 1986 were only partially responsible for the increased steepness of the TC growth curve.

Benign thyroid tumors: general risk factors and their effects on radiation risk estimation

The authors examined risk factors for benign thyroid nodules and their influence on radiation effects among 544 subjects who were exposed to childhood radiation treatment for benign head and neck conditions at a Chicago, Illinois hospital during 1939-1962. In follow-up through 1991, benign thyroid nodules were diagnosed in 131 patients. The risk of benign nodules was elevated in women (relative risk (RR) = 2.2, 95% confidence interval (CI) 1.6-3.2), Jews (RR = 1.7, 95% CI 1.2-2.5), college graduates (RR = 1.8, 95% CI 1.2-2.8), and subjects whose mother had cancer (RR = 1.7, 95% CI 1.2-2.5). There were increasing trends for risk with increasing body mass index in women and decreasing height in men. Risk was increased for women who never married (RR = 3.7, 95% CI 1.6-7.3) or who never had a full-term pregnancy (RR = 2.0, 95% CI 1.1-3.3). A significant radiation dose-response relationship was observed that was not modified by sex, education, Jewish religion, or reproductive factors. The data suggest that there are genetic, life-style (including ascertainment), and hormonal factors associated with the development of benign thyroid nodules.

Relationship between cataracts and epilation in atomic bomb survivors

Among 1713 atomic bomb survivors who underwent ophthalmological examinations from 1963-1964, the risk of cataract formation per unit dose of radiation was significantly greater for those who reported hair loss of 67% or more after exposure (the epilation group) than for those who reported less or no hair loss (the no-epilation group) (P < 0.01). Such an epilation effect has also been associated with leukemia mortality and the frequency of chromosome aberrations. Although this might be interpreted as indicating differential sensitivity to radiation between the epilation group and the no-epilation group, it could also be explained by imprecision in dose estimates. We have calculated that a 48% random error in DS86 dose estimates could be in accordance with the dose-response relationship for the prevalence of cataracts in the epilation group or the no-epilation group. Possible mechanisms for variation in radiosensitivity are discussed.

Incidence of benign gastrointestinal tumors among atomic bomb survivors

Using the Hiroshima and Nagasaki tumor and tissue registries, benign tumors of the stomach, colon, and rectum were identified among members of the Life Span Study cohort of atomic bomb survivors. During the period 1958-1989, a total of 470 cases with histologically confirmed benign gastrointestinal tumors (163 stomach, 215 colon, and 92 rectum) were identified among approximately 80,000 Life Span Study members with known radiation doses, who were alive in 1958. Restricting the analysis to adenomatous tumors not detected at autopsy, a dose-response relation was observed for stomach tumors (excess relative risk at 1 sievert (ERR1Sv) = 0.53; 95% confidence interval (CI) -0.01 to 1.43). However, there was little evidence of a dose response for colon tumors (ERR1Sv = 0.14; 95% CI -0.20 to 0.76), and no evidence was present for rectal tumors (ERR1Sv = -0.25; 95% CI undetermined to 0.80). The excess relative risk (ERR) for benign tumors of the stomach is consistent with the excess found for stomach cancer. For cancer of the rectum, the dose response was not significant, but the point estimate of the excess relative risk was positive. The excess relative risk for benign colon tumors is less than that reported for colon cancer (ERR1Sv = 0.72). The authors observed a dramatic increase in colon tumors detected after 1985, suggesting that the relatively recent introduction of colonoscopy may be influencing these results.