Impact of unemployment on cardiovascular mortality in united states: a nationwide county-level analysis 2010–2019

Background

Unemployment has been linked with a myriad of adverse health outcomes; however, its population-level impact on cardiovascular mortality (CVM), particularly amongst various demographic subgroups, remains understudied.

Purpose

To determine the impact of county unemployment levels on CVM rates, in overall and between different demographic subgroups.

Methods

We utilized the CDC WONDER database tool to retrieve county-level CVM rates for U.S. counties between 2010 and 2019. The County Health Rankings project was used to retrieve data on unemployment levels in each county as well as other characteristics used in an adjusted multivariate model. Generalized linear mixed models using Poisson regression were used to estimate the impact of unemployment on county-level CVM using relative (incidence rate ratios; IRR) and absolute (additional yearly deaths; AYD) measures.

Results

From 2010 to 2019, a total of 2904 U.S. counties (64.2% white; 50.81% female) with data available on CVM and unemployment levels were analyzed. In a multivariate model adjusted for demographic composition, CV risk, socioeconomic, environmental, and healthcare-access factors, unemployment was significantly associated with higher levels of CVM (IRR: 1.026; 95% CI: 1.018 to 1.033; 6.00 AYD). The relative impact of unemployment was strongest in elderly Blacks (IRR: 1.051; 95% CI: 1.029 to 1.074), middle-aged whites (IRR: 1.050; 95% CI: 1.032 to 1.067), and middle-aged females (IRR: 1.046; 95% CI: 1.018 to 1.075). The absolute impact of unemployment was highest in elderly Blacks (AYD: 94.70), elderly Whites (AYD: 35.30), and elderly females (AYD: 32.70). On a relative basis, the impact was more pronounced in the middle-aged (IRR: 1.030; 95% CI: 1.015 to 1.044) compared to the elderly (IRR: 1.022; 95% CI: 1.014 to 1.030), females (IRR: 1.026; 95% CI: 1.017 to 1.036) compared to males (IRR: 1.022; 95% CI: 1.014 to 1.031), and Blacks (IRR: 1.036; 95% CI: 1.016 to 1.057) compared to Whites (IRR: 1.030; 95% CI: 1.022 to 1.038).

Conclusion(s)

Unemployment is significantly associated with county-level CVM, and this impact is most pronounced in vulnerable demographic subgroups, namely females and Blacks. Efforts to reduce unemployment levels may significantly lower the burden of cardiovascular disease, particularly in groups most strongly affected by health disparities.

Funding Acknowledgement

Type of funding sources: None.

Impact of sexually transmitted infections on cardiovascular mortality in united states: a nationwide county-level analysis 2011–2019

Background

Sexually Transmitted Infections (STIs) are associated with a significantly increased risk of morbidity and mortality; however, its population-level effect on cardiovascular mortality (CVM), particularly amongst various demographic subgroups, remains unknown.

Purpose

To assess the impact of county STIs levels on CVM rates, in overall and between different patient groups stratified by age, sex and race.

Methods

The CDC WONDER database tool was utilized to retrieve age adjusted county-level CVM rates (ACVM) for U.S. counties between 2011 and 2019. Data on STIs were provided by the County Health Rankings project database. STIs is the number of newly diagnosed chlamydia (the most common STI in north America) cases per 100,000 population in a county. Rates measure the number of events in a given time period (generally one year) divided by the average number of people at risk during that period. The Behavioral risk Factors Surveillance System and County Health Rankings project were used to retrieve county data on demographics, CV risk, socioeconomic, environmental, and health care access factors. Generalized linear mixed models using Poisson regression were used to estimate the impact of unemployment on county-level CVM using relative (incidence rate ratios; IRR) and absolute (additional yearly deaths; AYD) measures.

Results

Of 3143 U.S. counties, a total of 2890 counties (62.09% white; 50.76% female; 14.12% aged ≥65) with data available on ACVM and STIs levels were analyzed. In a multivariate model adjusted for demographic composition, CV risk, socioeconomic, environmental, and healthcare-access factors, STIs were significantly associated with higher levels of ACVM (IRR: 1.015; 95% CI: 1.007 to 1.022; 3.40 AYD). Additionally, this association was relatively higher in the middle-aged [45–64] (IRR: 1.016; 95% CI: 1.002 to 1.030) compared to the elderly [≥65] (IRR: 1.010; 95% CI: 1.002 to 1.018), males (IRR: 1.013; 95% CI: 1.004 to 1.021) compared to females (IRR: 1.011; 95% CI: 1.002 to 1.020), and non-Hispanic Blacks (IRR: 1.026; 95% CI: 1.011 to 1.040) compared to non-Hispanic Whites (IRR: 1.010; 95% CI: 1.002 to 1.018). Notably, the relative impact of STIs was highest in middle-aged non-Hispanic Blacks (IRR: 1.038; 95% CI: 1.013 to 1.063; AYD: 10.50), and middle-aged males (IRR: 1.021; 95% CI: 1.006 to 1.037; AYD: 4.30), (Figure).

Conclusions

STIs is robustly associated with county-level ACVM, independent from several important confounders. This impact is most prominent in vulnerable demographic subgroups, namely middle-aged, males, and Blacks. Efforts to reduce STIs levels may significantly lower the burden of cardiovascular mortality attributable to STIs, particularly in groups most frequently affected by health disparities.

Funding Acknowledgement

Type of funding sources: None.

Genome Assembly and Analysis of the Flavonoid and Phenylpropanoid Biosynthetic Pathways in Fingerroot Ginger (Boesenbergia rotunda)

Boesenbergia rotunda (Zingiberaceae), is a high-value culinary and ethno-medicinal plant of Southeast Asia. The rhizomes of this herb have a high flavanone and chalcone content. Here we report the genome analysis of B. rotunda together with a complete genome sequence as a hybrid assembly. B. rotunda has an estimated genome size of 2.4 Gb which is assembled as 27,491 contigs with an N50 size of 12.386 Mb. The highly heterozygous genome encodes 71,072 protein-coding genes and has a 72% repeat content, with class I TEs occupying ~67% of the assembled genome. Fluorescence in situ hybridization of the 18 chromosome pairs at the metaphase showed six sites of 45S rDNA and two sites of 5S rDNA. An SSR analysis identified 238,441 gSSRs and 4604 EST-SSRs with 49 SSR markers common among related species. Genome-wide methylation percentages ranged from 73% CpG, 36% CHG and 34% CHH in the leaf to 53% CpG, 18% CHG and 25% CHH in the embryogenic callus. Panduratin A biosynthetic unigenes were most highly expressed in the watery callus. B rotunda has a relatively large genome with a high heterozygosity and TE content. This assembly and data (PRJNA71294) comprise a source for further research on the functional genomics of B. rotunda, the evolution of the ginger plant family and the potential genetic selection or improvement of gingers.

Prognosticating outcome using magnetic resonance imaging in patients with moderate to severe traumatic brain injury: a machine learning approach

INTRODUCTION

Over the last decade advancements in computer processing have enabled the application of machine learning (ML) to complex medical problems. Convolutional neural networks (CNN), a type of ML, have been used to interrogate medical images for variety of purposes. In this study, we aimed to investigate the potential application of CNN in prognosticating patients with traumatic brain injury (TBI).

METHODS

Patients with moderate to severe TBI and evidence of diffuse axonal injury (DAI) were selected retrospectively. A CNN model was developed using a training subgroup and a holdout subgroup was used as a testing dataset. We reported the model characteristics including area under the receiver operating characteristic curve (AUC).

RESULTS

We included a total of 38 patient, of which we generated 725 MRI sections. We developed a CNN model based on a modified AlexNet architecture that interpreted the brain stem injury to generate outcome predictions. The model was able to predict GOS outcomes with a specificity of 0.43 and a sensitivity of 0.997. It showed an AUC of 0.917.

CONCLUSION

The utilization of machine learning MRI analysis for prognosticating patients with TBI is a valued method that require further investigation. This will require multicentre collaboration to generate large datasets.

Isolation and characterization of bacteria residing in the oral, gut, and fecal samples of different pheasant species

There is a paucity of research conducted on microbial prevalence in pheasants. The microbiota of captive birds has zoonotic significance and must be characterize. Present study is therefore planned to assess the microbiota from oral, fecal and gut content of captive avian species. It will be helpful in characterization of harmful microbes. Different samples taken from oral, gut and feces of ring-necked pheasants (Phasianus colchicus), green pheasants (Phasianus versicolor), golden pheasant (Chrysolophus pictus) and silver pheasant (Lophura nycthemera). Samples were collected, diluted, and inoculated onto different agar plates (MacConkey, SS agar, MSA and nutrient agar) for cultivation of bacterial species. Colonies of E.coli, Staphylococcus spp. Brachyspira spp. and Campylobacter spp were observed based on colony morphology. Colony forming unit showed E. coli as frequently found bacteria in fecal, oral and gut contents of all the above pheasants. The overall significance difference was found among bacterial species of golden pheasants, green pheasant, ring-necked pheasant, and silver pheasants. It was concluded that E.coli is predominant isolated from heathy pheasants followed by Campylobacter, Staphylococcus and Brachyspira.

COVID-19 Pandemic and Food Safety Issues in Pakistan

The article's abstract is not available.  

Cross-genera amplification and identification of Colpodella sp. with Cryptosporidium primers in fecal samples of zoo felids from northeast China

The protozoans include many intracellular human pathogens. Accurate detection of these pathogens is necessary to treat the diseases. In clinical epidemiology, molecular identification of protozoan is considered a more reliable and rapid method for identification than microscopy. Among these protozoans, Cryptosporidium considered being one of the important water-borne zoonotic pathogens and a major cause of a diarrheal disease named cryptosporidiosis in humans, domestic animals, and wild animals. This study was aimed to identify Cryptosporidium in zoo felids (N= 56) belonging to different zoo of China, but accidentlly Colpodella was encountered in the zoo felids sample and phylogenetic data confirmed this unexpected amplification from fecal samples using two-step nested-PCR. Phylogenetic analysis revealed the fact about the specific primers used previously by many researchers and cross-genera amplification. We came to know that genetically sequenced amplicon gives more accurate identification of species. This study suggests more investigation on Colpodella which has been neglected previously but gains the attention of researchers after identified from humans and animals and has been known to correlate with neurological symptoms in patients.

468 IMPROVING ADVANCE CARE PLANNING SKILLS IN JUNIOR DOCTORS

Introduction

Junior doctors are increasingly encountering Advance Care Planning (ACP) when they look after frail, older or multi-morbid patients during their hospital rotations. However, there remains a lack of formal training and resources, particularly with DNACPR discussions and when engaging patients and their loved ones with Emergency Health Care Planning (EHCP). We aimed to assess the need for ACP, improve the infrastructure by which ACP is delivered, and better support junior doctors to have these difficult conversations.

Method

Discharges from the Geriatrics Department at Kettering General Hospital were reviewed initially in May 2019 and again in January 2020 following intervention. We introduced a focused communication skills training session delivered at departmental teaching, which included a combination of simulation training and lectures. We additionally designed and implemented an EHCP template to aid junior doctors’ discussions. This could also be copied to the discharge letter, to facilitate safe transfer of care to primary care.

Results

In May 2019 of 32 patients, 100% met at least one SPICTTM criterion, with median of 4 criteria, thus indicating a high need for ACP in this cohort. Despite this, only one discharge letter included an EHCP and two had a request for GP colleagues to complete one. Evaluation of discharges again in January of 2020 reconfirmed a similar need for ACP, but following our interventions, the number of EHCP’s performed had increased. Of 22 identified patients 4 had a completed EHCP and 3 were requested for completion by their GP. Qualitative questionnaires demonstrated an improvement in both knowledge and confidence amongst junior doctors following the training session.

Conclusion

We have shown that there is a necessity for ACP to be considered for Geriatrics inpatients, and that providing structure and training in this challenging area offers benefit to both patients and junior doctors.

Optimization of culture conditions for in vitro adventitious roots and selected flavonoids production in Boesenbergia rotunda liquid suspension culture

Boesenbergia rotunda (L.) Mansf. is one of the unique monocotyledonous perennial plant species belonging to the ginger (Zingiberaceae) family. Locally known as ‘Temu Kunci’ in Malaysia and Indonesia, this medicinal plant has been widely used in Asian dishes, particularly as a condiment or as traditional natural medicines. The important medicinal properties of B. rotunda majorly derived from flavonoids which are highly sought as pharmaceuticals. In this study, culture conditions for the growth of adventitious roots in liquid suspension cultures were optimized. The highest adventitious root production was achieved when cultured with initial inoculum density of 1.5 g and pH value at 5.8 after five weeks of culture. HPLC analysis discovered that production of valuable flavonoid compounds (pinostrobin, cardamonin and panduratin A) was significantly higher when the adventitious roots were cultured with initial inoculum density of 1.5 g whereas the initial pH medium did not significantly affect flavonoid production.

A New Plant Expression System for Producing Pharmaceutical Proteins

In the past decade, interest in the production of recombinant pharmaceutical proteins in plants has tremendously progressed because plants do not harbor mammalian viruses, are economically competitive, easily scalable, and capable of carrying out complex post-translational modifications required for recombinant pharmaceutical proteins. Mucuna bracteata is an essential perennial cover crop species widely planted as an underground cover in oil palm and rubber plantations. As a legume, they have high biomass, thrive in its habitat, and can fix nitrogen. Thus, M. bracteata is a cost-efficient crop that shows ideal characteristics as a platform for mass production of recombinant protein. In this study, we established a new platform for the transient production of a recombinant protein in M. bracteata via vacuum-assisted agro-infiltration. Five-week-old M. bracteata plants were vacuum infiltrated with Agrobacterium tumefaciens harboring a plasmid that encodes for an anti-toxoplasma immunoglobulin (IgG) under different parameters, including trifoliate leaf positional effects, days to harvest post-infiltration, and the Agrobacterium strain used. Our results showed that vacuum infiltration of M. bracteata plant with A. tumefaciens strain GV3101 produced the highest concentration of heterologous protein in its bottom trifoliate leaf at 2 days post-infiltration. The purified anti-toxoplasma IgG was then analyzed using Western blot and ELISA. It was demonstrated that, while structural heterogeneity existed in the purified anti-toxoplasma IgG from M. bracteata, its transient expression level was two-fold higher than the model platform, Nicotiana benthamiana. This study has laid the foundation towards establishing M. bracteata as a potential platform for the production of recombinant pharmaceutical protein.

Enhancing flavonoid production by promiscuous activity of prenyltransferase, BrPT2 from Boesenbergia rotunda

Flavonoids and prenylated flavonoids are active components in medicinal plant extracts which exhibit beneficial effects on human health. Prenylated flavonoids consist of a flavonoid core with a prenyl group attached to it. This prenylation process is catalyzed by prenyltranferases (PTs). At present, only a few flavonoid-related PT genes have been identified. In this study, we aimed to investigate the roles of PT in flavonoid production. We isolated a putative PT gene (designated as BrPT2) from a medicinal ginger, Boesenbergia rotunda. The deduced protein sequence shared highest gene sequence homology (81%) with the predicted homogentisate phytyltransferase 2 chloroplastic isoform X1 from Musa acuminata subsp. Malaccensis. We then cloned the BrPT2 into pRI vector and expressed in B. rotunda cell suspension cultures via Agrobacterium-mediated transformation. The BrPT2-expressing cells were fed with substrate, pinostrobin chalcone, and their products were analyzed by liquid chromatography mass spectrometry. We found that the amount of flavonoids, namely alpinetin, pinostrobin, naringenin and pinocembrin, in BrPT2-expressing cells was higher than those obtained from the wild type cells. However, we were unable to detect any targeted prenylated flavonoids. Further in-vitro assay revealed that the reaction containing the BrPT2 protein produced the highest accumulation of pinostrobin from the substrate pinostrobin chalcone compared to the reaction without BrPT2 protein, suggesting that BrPT2 was able to accelerate the enzymatic reaction. The finding of this study implied that the isolated BrPT2 may not be involved in the prenylation of pinostrobin chalcone but resulted in high yield and production of other flavonoids, which is likely related to enzyme promiscuous activities.

Group B streptococcus infection in a sudden unexpected death of infancy - the importance of microbiological investigation at post-mortem

Group B streptococcus (GBS) is a common cause of infection in newborns and in early infants. However, GBS infection in an infant older than three months is infrequently reported in the literature. We reported a case of an apparently well six-month-old infant who died of sudden death due to GBS pneumonia, diagnosed at autopsy. The six-month-old, apparently well male infant was brought in dead to the Emergency Department. He underwent medicolegal autopsy four hours after death, as part of an overall sudden unexpected death in infancy investigation (SUDI). Apart from whitish froth oozing out of both nostrils, he appeared to be well-nourished infant without any deformity, syndromic features or obvious suspicious marks of injury externally. Internal examination showed generalized hyperinflated with patchy consolidation of upper and middle lobes of bilateral lung. Multiple matted mesenteric lymphadenopathy were also detected. Blood and lung tissue specimens collected under aseptic technique yielded growth of GBS. Post-mortem histology from consolidated lungs confirmed pneumonic features while mesenteric lymph nodes showed reactive changes inkeeping with underlying infective process. Death was attributed to GBS pneumonia. This case highlights the importance of a detailed autopsy in sudden unexpected death in infancy (SUDI) and the crucial role of post-mortem microbiological study in such cases. Relevant autopsy protocols that need to be employed during microbiological sampling are briefly discussed.

Expression and DNA methylation of SERK, BBM, LEC2 and WUS genes in in vitro cultures of Boesenbergia rotunda (L.) Mansf

The process of somatic embryogenesis and plant regeneration involve changes in gene expression and have been associated with changes in DNA methylation. Here, we report the expression and DNA methylation patterns of SOMATIC EMBRYOGENESIS RECEPTOR-LIKE KINASE (SERK), BABY BOOM (BBM), LEAFY COTYLEDON 2 (LEC2) and WUSCHEL (WUS) in meristematic block of newly emerged shoots from rhizome, embryogenic and non-embryogenic calli, prolonged cell suspension culture, ex vitro leaf, and in vitro leaf of regenerated plants of Boesenbergia rotunda. Among all seven samples, based on qRT-PCR, the highest level of expression of SERK, BBM and LEC2 was in embryogenic callus, while WUS was most highly expressed in meristematic block tissue followed by embryogenic callus. Relatively lower expression was observed in cell suspension culture and watery callus for SERK, LEC2 and WUS and in in vitro leaf for BBM. For gene specific methylation determined by bisulfite sequencing data, embryogenic callus samples had the lowest levels of DNA methylation at CG, CHG and CHH contexts of SERK, LEC2 and WUS. We observed negative correlation between DNA methylation at the CG and CHG contexts and the expression levels of SERK, BBM, LEC2 and WUS. Based on our results, we suggest that relatively higher expression and lower level of DNA methylation of SERK, BBM, LEC2 and WUS are associated with somatic embryogenesis and plant regeneration in B. rotunda.

In vitro shoot regeneration and analysis of biochemical, antioxidant and anticancer properties of Ananas comosus var. MD2

Pineapple (Ananas comosus (L.) Merr.) is one of the most important crops in the world. Although the phytochemical compounds of pineapple fruits have been extensively studied, little attention was paid on other parts of the plant. In this study, we developed an efficient in vitro regeneration procedures for A. comosus var. MD2 as well as analyzed the phytochemical composition, antioxidant and anticancer activities in field-grown and in vitro leaf samples. Leaf base explants cultured on Murashige and Skoog medium containing 1.0 mg/L IBA and 2.0 mg/L BAP produced the highest percentage of shoot response (100%) with a mean number of 6 microshoots per explant. Biochemical analysis showed that in vitro leaf samples contained higher amount of carotenoids and anthocyanins but lower total phenolic content and DPPH radical scavenging activity than field-grown leaves. Flavonoids, tannins, sterols and alkaloids were detected in both field-grown and in vitro leaf samples. The methanolic extracts from both samples exhibited low cytotoxic activity against human ovarian SKOV-3 and human breast MCF-7 cancer cells. These results suggested that pineapple leaves might not be suitable to serve as chemotherapeutic agent and further exploitation on other secondary metabolites is required.

Hypothyroidism during second-line treatment of multidrug-resistant tuberculosis: a prospective study

SETTING

Hypothyroidism is an adverse effect of certain anti-tuberculosis drugs.

DESIGN

This is a prospective study of the frequency and possible pathomechanisms associated with hypothyroidism due to second-line treatment of multidrug-resistant tuberculosis. Fifty human immunodeficiency virus negative patients and 20 controls were included. All participants underwent ultrasonography of the thyroid and measurement of thyroid stimulating hormone (TSH). TSH levels were checked every 3 months. If hypothyroidism was present, T3, T4 and thyroid peroxidase autoantibodies were measured, and imaging extended to scintigraphy and repeated ultrasonography.

RESULTS

Before treatment, 7 patients (14%) and 1 control (5%) were hypothyreotic. During the first 6 months of treatment, TSH levels increased in 41 patients (82%), 39 (78%) had values above the normal range and 19 (38%) had overt hypothyroidism. As none of the patients had signs of autoimmune thyroiditis, interaction with anti-tuberculosis drugs was assumed to be the cause of hypothyroidism. Nine patients died during treatment, all of whom had developed hypothyroidism. In seven, the metabolic situation at their death was known, and they had become euthyreotic following levothyroxine substitution.

CONCLUSION

TSH levels should be checked before initiating anti-tuberculosis treatment and after 3 and 6 months to start timely replacement of levothyroxine. Further studies are needed to elucidate the exact pathomechanism involved in hypothyroidism and whether hypothyroidism can be used as predictor of treatment failure.

Complete Chloroplast Genome Sequence of Corroborates Structural Heterogeneity of Inverted Repeats in Wild Progenitors of Cultivated Bananas and Plantains

Complete genome sequencing of cytoplasmically inherited chloroplast DNA provides novel insights into the origins of clonally propagated crops such as banana and plantain ( spp.). This study describes the structural organization of the chloroplast genome of Colla and its phylogenetic relationship with other wild progenitors of the domesticated banana cultivars. The chloroplast genome was sequenced using Illumina HiSeq 2000 platform, followed by a combination of de novo short-read assembly and reference-guided mapping of contigs to generate complete plastome sequence. The chloroplast genome is 169,503 bp in length, exhibits a typical quadripartite structural organization with a large single-copy (LSC; 87,828 bp) region and a small single-copy (SSC; 11,547 bp) region interspersed between inverted repeat (IRa/b; 35,064 bp) regions. Overall, its gene content, size, and gene order were identical to that of Colla with extensive expansion of the inverted repeat-small single-copy (IR-SSC) junctions. Comparative analyses revealed the conserved IRa-SSC expansion in three wild species and members of the order Zingiberales. In contrast, IRb-SSC expansion was conspicuously absent in the sister taxon Nee and related species of Zingiberales. Interestingly, phylogenomic assessment based on whole-plastome and protein-coding gene sets have provided robust support for the association of and as a sister group, despite the variation in IRb-SSC expansion. Although the current study substantiates the infrageneric IRb-SSC fluctuations in Musaceae, extensive taxon sampling is necessary to confirm whether the accessions of section have undergone independent IRb-SSC expansion relative to section .

Amino Acid and Secondary Metabolite Production in Embryogenic and Non-Embryogenic Callus of Fingerroot Ginger (Boesenbergia rotunda)

Interest in the medicinal properties of secondary metabolites of Boesenbergia rotunda (fingerroot ginger) has led to investigations into tissue culture of this plant. In this study, we profiled its primary and secondary metabolites, as well as hormones of embryogenic and non-embryogenic (dry and watery) callus and shoot base, Ultra Performance Liquid Chromatography-Mass Spectrometry together with histological characterization. Metabolite profiling showed relatively higher levels of glutamine, arginine and lysine in embryogenic callus than in dry and watery calli, while shoot base tissue showed an intermediate level of primary metabolites. For the five secondary metabolites analyzed (ie. panduratin, pinocembrin, pinostrobin, cardamonin and alpinetin), shoot base had the highest concentrations, followed by watery, dry and embryogenic calli. Furthermore, intracellular auxin levels were found to decrease from dry to watery calli, followed by shoot base and finally embryogenic calli. Our morphological observations showed the presence of fibrils on the cell surface of embryogenic callus while diphenylboric acid 2-aminoethylester staining indicated the presence of flavonoids in both dry and embryogenic calli. Periodic acid-Schiff staining showed that shoot base and dry and embryogenic calli contained starch reserves while none were found in watery callus. This study identified several primary metabolites that could be used as markers of embryogenic cells in B. rotunda, while secondary metabolite analysis indicated that biosynthesis pathways of these important metabolites may not be active in callus and embryogenic tissue.

Transcripts and MicroRNAs Responding to Salt Stress in Musa acuminata Colla (AAA Group) cv. Berangan Roots

Physiological responses to stress are controlled by expression of a large number of genes, many of which are regulated by microRNAs. Since most banana cultivars are salt-sensitive, improved understanding of genetic regulation of salt induced stress responses in banana can support future crop management and improvement in the face of increasing soil salinity related to irrigation and climate change. In this study we focused on determining miRNA and their targets that respond to NaCl exposure and used transcriptome sequencing of RNA and small RNA from control and NaCl-treated banana roots to assemble a cultivar-specific reference transcriptome and identify orthologous and Musa-specific miRNA responding to salinity. We observed that, banana roots responded to salinity stress with changes in expression for a large number of genes (9.5% of 31,390 expressed unigenes) and reduction in levels of many miRNA, including several novel miRNA and banana-specific miRNA-target pairs. Banana roots expressed a unique set of orthologous and Musa-specific miRNAs of which 59 respond to salt stress in a dose-dependent manner. Gene expression patterns of miRNA compared with those of their predicted mRNA targets indicated that a majority of the differentially expressed miRNAs were down-regulated in response to increased salinity, allowing increased expression of targets involved in diverse biological processes including stress signaling, stress defence, transport, cellular homeostasis, metabolism and other stress-related functions. This study may contribute to the understanding of gene regulation and abiotic stress response of roots and the high-throughput sequencing data sets generated may serve as important resources related to salt tolerance traits for functional genomic studies and genetic improvement in banana.

Transcriptome profiling shows gene regulation patterns in a flavonoid pathway in response to exogenous phenylalanine in Boesenbergia rotunda cell culture

Background

Panduratin A extracted from Boesenbergia rotunda is a flavonoid reported to possess a range of medicinal indications which include anti-dengue, anti-HIV, anti-cancer, antioxidant and anti-inflammatory properties. Boesenbergia rotunda is a plant from the Zingiberaceae family commonly used as a food ingredient and traditional medicine in Southeast Asia and China. Reports on the health benefits of secondary metabolites extracted from Boesenbergia rotunda over the last few years has resulted in rising demands for panduratin A. However large scale extraction has been hindered by the naturally low abundance of the compound and limited knowledge of its biosynthetic pathway.

Results

Transcriptome sequencing and digital gene expression (DGE) analysis of native and phenylalanine treated Boesenbergia rotunda cell suspension cultures were carried out to elucidate the key genes differentially expressed in the panduratin A biosynthetic pathway. Based on experiments that show increase in panduratin A production after 14 days post treatment with exogenous phenylalanine, an aromatic amino acid derived from the shikimic acid pathway, total RNA of untreated and 14 days post-phenylalanine treated cell suspension cultures were extracted and sequenced using next generation sequencing technology employing an Illumina-Solexa platform. The transcriptome data generated 101, 043 unigenes with 50, 932 (50.41%) successfully annotated in the public protein databases; including 49.93% (50, 447) in the non-redundant (NR) database, 34.63% (34, 989) in Swiss-Prot, 24,07% (24, 316) in Kyoto Encyclopedia of Genes and Genomes (KEGG) and 16.26% (16, 426) in Clusters of Orthologous Groups (COG). Through DGE analysis, we found that 14, 644 unigenes were up-regulated and 14, 379 unigenes down-regulated in response to exogenous phenylalanine treatment. In the phenylpropanoid pathway leading to the proposed panduratin A production, 2 up-regulated phenylalanine ammonia-lyase (PAL), 3 up-regulated 4-coumaroyl:coenzyme A ligase (4CL) and 1 up-regulated chalcone synthase (CHS) were found.

Conclusions

This is the first report of Boesenbergia rotunda de novo transcriptome data that could serve as a reference for gene or enzyme functional studies in the Zingiberaceae family. Although enzymes that are directly involved in the panduratin A biosynthetic pathway were not completely elucidated, the data provides an overall picture of gene regulation patterns leading to panduratin A production.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-984) contains supplementary material, which is available to authorized users.

Assessing frailty in the acute medical admission of elderly patients

BACKGROUND

Managing acute admission of frail older patients is a challenge in hospitals. Length of inpatient stay, inpatient mortality and the 90-day readmission rate are significant in this group of patients. The Comprehensive Geriatric Assessment (CGA), a multidisciplinary diagnostic and treatment process, is the best approach for identifying medical conditions, mental health, functional capacity and social circumstances in acute geriatric care.

METHODS

A review of the records of older patients aged 75 and over, acutely admitted to a district general hospital in England from 15 March 2012 to 16 April 2012 was conducted. We developed a frailty assessment tool and applied it to these patients, in order to determine who would be classified as frail. We then established if the patients meeting this criteria were then correctly assessed using the CGA. All patient data were processed and analysed using a statistical package for data analysis.

RESULTS

A total of 232 patients with a mean age of 84.25 ± 5.8 years were included. Out of these, 129 patients (55.6%) fulfilled the frailty criteria as determined with our frailty-assessment tool; 80.6% presented with lack of mobility over 24 hours, 69.8% were admitted with falls, 47.3% had known dementia or delirium and 45% were admitted from care homes. Patients aged over 85 years were more likely to have frailty compared with patients aged 75-85 years old (odds ratio [OR]: 4.78, 95% confidence interval [CI]: 2.6-8.6, p value >0.001). Patients assessed by a front door geriatric team were more likely to be reviewed with the CGA than those not seen by this team (adjusted OR 2.8, 95% CI: 1-7.6, p value=0.04).

CONCLUSION

The prevalence of frailty is high in acute admissions of older patients and it is important that they are properly identified and assessed with a CGA in order to ensure effective multidisciplinary care.

"A draft Musa balbisiana genome sequence for molecular genetics in polyploid, inter- and intra-specific Musa hybrids"

BACKGROUND

Modern banana cultivars are primarily interspecific triploid hybrids of two species, Musa acuminata and Musa balbisiana, which respectively contribute the A- and B-genomes. The M. balbisiana genome has been associated with improved vigour and tolerance to biotic and abiotic stresses and is thus a target for Musa breeding programs. However, while a reference M. acuminata genome has recently been released (Nature 488:213-217, 2012), little sequence data is available for the corresponding B-genome.To address these problems we carried out Next Generation gDNA sequencing of the wild diploid M. balbisiana variety 'Pisang Klutuk Wulung' (PKW). Our strategy was to align PKW gDNA reads against the published A-genome and to extract the mapped consensus sequences for subsequent rounds of evaluation and gene annotation.

RESULTS

The resulting B-genome is 79% the size of the A-genome, and contains 36,638 predicted functional gene sequences which is nearly identical to the 36,542 of the A-genome. There is substantial sequence divergence from the A-genome at a frequency of 1 homozygous SNP per 23.1 bp, and a high degree of heterozygosity corresponding to one heterozygous SNP per 55.9 bp. Using expressed small RNA data, a similar number of microRNA sequences were predicted in both A- and B-genomes, but additional novel miRNAs were detected, including some that are unique to each genome. The usefulness of this B-genome sequence was evaluated by mapping RNA-seq data from a set of triploid AAA and AAB hybrids simultaneously to both genomes. Results for the plantains demonstrated the expected 2:1 distribution of reads across the A- and B-genomes, but for the AAA genomes, results show they contain regions of significant homology to the B-genome supporting proposals that there has been a history of interspecific recombination between homeologous A and B chromosomes in Musa hybrids.

CONCLUSIONS

We have generated and annotated a draft reference Musa B-genome and demonstrate that this can be used for molecular genetic mapping of gene transcripts and small RNA expression data from several allopolyploid banana cultivars. This draft therefore represents a valuable resource to support the study of metabolism in inter- and intraspecific triploid Musa hybrids and to help direct breeding programs.

Construction of phosphomannose isomerase (PMI) transformation vectors and evaluation of the effectiveness of vectors in tobacco (Nicotiana tabacum L)

Phosphomannose isomerase (pmi) gene isolated from Escherichia coli allows transgenic plants carrying it to convert mannose-6- phosphate (from mannose), a carbon source that could not be naturally utilized by plants into fructose-6-phosphate which can be utilized by plants as a carbon source. This conversion ability provides energy source to allow the transformed cells to survive on the medium containing mannose. In this study, four transformation vectors carrying the pmi gene alone or in combination with the β-glucuronidase (gusA) gene were constructed and driven by either the maize ubiquitin (Ubi1) or the cauliflower mosaic virus (CaMV35S) promoter. Restriction digestion, PCR amplification and sequencing were carried out to ensure sequence integrity and orientation. Tobacco was used as a model system to study the effectiveness of the constructs and selection system. PMI11G and pMI3G, which carry gusA gene, were used to study the gene transient expression in tobacco. PMI3 construct, which only carries the pmi gene driven by CaMV35S promoter, was stably transformed into tobacco using biolistics after selection on 30 g 1(-1) mannose without sucrose. Transgenic plants were verified using PCR analysis.

ABBREVIATIONS

PMI/pmi - Phosphomannose isomerase, Ubi1 - Maize ubiquitin promoter, CaMV35S - Cauliflower mosaic virus 35S promoter, gusA - β-glucuronidase GUS reporter gene.

Patterns of radiotherapy practice in the management of gastric cancer: Preliminary findings from the Quality Research in Radiation Oncology (QRRO) GI Committee process surveys

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Background: The specific aim of the ACR QRRO survey was to determine the national patterns of radiotherapy (RT) practice in patients (pts) treated for stage IB–IV (non-metastatic) gastric cancer (GC).

Methods: A National Process Survey was conducted from randomly selected U.S. RT facilities to assess demographics, staging, geographic region, practice setting, and treatment through retrospective on-site record review of eligible GC cases treated from 2005-2007. Three clinical performance measures (CPMs): 1) use of CT-based treatment planning; 2) use of dose volume histograms (DVHs) to evaluate RT dose to the kidneys and liver; 3) completion of RT within the prescribed time frame were assessed. Three emerging quality indicators: 1) use of intensity modulated RT (IMRT); 2) use of image-guided tools (IGRT), other than CT, for RT target delineation; 3) use of preop RT were also assessed.

Results: CPMs were computed on data collected through Aug, 2010 for 250 eligible pts at 45 institutions. Median age was 62 years; 66% male; 60% Caucasian. 13% were AJCC 2002 stage I, 29% II, 32% IIIA, 10% IIIB and 12% IV. Most pts (43%) were treated at academic centers with 32% at large non-academic centers and 25% medium-small facilities. Almost all (99.5%) pts underwent CT-based planning and 75% had DVHs to evaluate normal tissue doses to the kidneys and liver. 70% completed RT within the prescribed time frame. IMRT and IGRT were used in 22% and 17% of pts, respectively. IGRT techniques included: PET (n = 20), MRI (n = 1), respiratory gating and/or 4D-CT (n = 22) and on-board imaging (n = 10). 19% of pts received preop RT.

Conclusions: Preliminary findings from QRRO's analysis of radiation practice patterns for non-metastatic gastric cancer indicate widespread adoption of CT-based planning with the use of DVHs to evaluate normal tissue doses. Moreover, most pts completed adjuvant RT in the prescribed time frame. Emerging RT techniques such as IMRT and IGRT were not routinely incorporated into clinical practice during the evaluated time period. These data will serve as a benchmark for future QRRO gastric cancer surveys.

No significant financial relationships to disclose.

Morphometric and molecular differentiation of Phlebotomus (Phlebotomus) sandflies

The closely related sandfly species of the subgenus Phlebotomus namely, Phlebotomus papatasi (Scopoli, 1786), Phlebotomus duboscqi Neveu-Lemair, 1906 and Phlebotomus bergeroti Parrot, 1934 (Diptera: Psychodidae), are major vectors of Leishmania major (Kinetoplastida: Trypanosomatidae), the causative agent of cutaneous leishmaniasis in the Old World. Although allopatric in most of their distribution, the three species exist sympatrically in many places in central and eastern Sudan. Males of the three species can be distinguished using morphological characters; however, females are much harder to identify, thus complicating epidemiological studies. We carried out a morphometric and a molecular study to determine reliable morphological features and develop a polymerase chain reaction (PCR) assay for distinguishing females of these species. Males and females from each species were collected from sites in Sudan, East Africa and from one site in Mali, West Africa. Males were analysed morphologically and 20 characters and 10 character ratios were used in a stepwise discriminant analysis. This led to the identification of four characters with high discriminant loading scores sufficient for accurate male species identification. Male DNA was then used for the development of a PCR-based species diagnostic based on the second internal transcribed spacer (ITS2) of the ribosomal DNA. A set of four primers was developed to generate fragment sizes that are specific to each species and can reliably identify females as well as hybrid DNA. Both the morphometric and the molecular findings of this study have important applications for studies of the epidemiology of cutaneous leishmaniasis.

Assessment of air quality of two metropolitan cities in Pakistan: Elemental analysis using INAA and AAS

For the assessment of air quality of two cities in Pakistan, Instrumental Neutron Activation Analysis (INAA) and Atomic Absorption Spectrometry (AAS) have been used. In all 26 elements were determined in suspended particulate matter (SPM) and soil samples. The SPM levels from different locations of Rawalpindi and Lahore indicate unhealthy to hazardous air quality much above the World Health Organization (WHO) guidelines. Metrological conditions and nature of soil that contains clay components mainly contribute to the inventory of the SPM elements of these cities. The calculated enrichment factors (EF) also indicate the dominance of the soil components. Contributions of inorganic elements due to heavy traffic with automotive exhaust and other commercial activities in this area have been identified. Areas of Qurtaba Chowk and Bank Square in Lahore in particular showed high EF for lead depicting burning of the automotive fuel and road dust. The accuracy and precision of the work has been maintained through the concurrent use of IAEA Reference Materials.