Accelerated construction of stress relief music datasets using CNN and the Mel-scaled spectrogram

Listening to music is a crucial tool for relieving stress and promoting relaxation. However, the limited options available for stress-relief music do not cater to individual preferences, compromising its effectiveness. Traditional methods of curating stress-relief music rely heavily on measuring biological responses, which is time-consuming, expensive, and requires specialized measurement devices. In this paper, a deep learning approach to solve this problem is introduced that explicitly uses convolutional neural networks and provides a more efficient and economical method for generating large datasets of stress-relief music. These datasets are composed of Mel-scaled spectrograms that include essential sound elements (such as frequency, amplitude, and waveform) that can be directly extracted from the music. The trained model demonstrated a test accuracy of 98.7%, and a clinical study indicated that the model-selected music was as effective as researcher-verified music in terms of stress-relieving capacity. This paper underlines the transformative potential of deep learning in addressing the challenge of limited music options for stress relief. More importantly, the proposed method has profound implications for music therapy because it enables a more personalized approach to stress-relief music selection, offering the potential for enhanced emotional well-being.

Host Subcellular Organelles: Targets of Viral Manipulation

Viruses have evolved sophisticated mechanisms to manipulate host cell processes and utilize intracellular organelles to facilitate their replication. These complex interactions between viruses and cellular organelles allow them to hijack the cellular machinery and impair homeostasis. Moreover, viral infection alters the cell membrane's structure and composition and induces vesicle formation to facilitate intracellular trafficking of viral components. However, the research focus has predominantly been on the immune response elicited by viruses, often overlooking the significant alterations that viruses induce in cellular organelles. Gaining a deeper understanding of these virus-induced cellular changes is crucial for elucidating the full life cycle of viruses and developing potent antiviral therapies. Exploring virus-induced cellular changes could substantially improve our understanding of viral infection mechanisms.

Effect of internet-based vs. in-person multimodal interventions on patients with mild to moderate Alzheimer's disease: a randomized, cross-over, open-label trial

Objective

We aimed to investigate the effect of internet-based and in-person cognitive interventions on cognition, mood, and activities of daily living (ADL) on patients with mild to moderate Alzheimer's disease (AD) and examine whether internet-based intervention is as effective as the in-person intervention.

Methods

We recruited 52 patients with probable mild AD, of whom 42 completed the trial. We randomly divided participants into intervention and control groups at a 1:1 ratio and statistically compared the neuropsychological test results of the two groups. In addition, patients in the intervention group were randomly assigned to a 4 weeks internet-based or in-person intervention, with subsequent crossover to the other group for 4 weeks. We statistically analyzed and compared the neuropsychological test scores between internet-based and in-person interventions.

Results

Compared with the control group, the intervention group (internet-based and in-person) showed significantly improved profile in cognition (p < 0.001), depression (p < 0.001), anxiety (p < 0.001) and ADL (p < 0.001). In addition, the effect of the internet-based intervention on cognition (p = 0.918) and depression (p = 0.282) was not significantly different from that of the in-person intervention. However, in the Beck anxiety inventory (p = 0.009) and Seoul instrumental activity of daily living (p = 0.023), in-person intervention was more effective than internet-based intervention.

Conclusion

This study suggests that both types of cognitive intervention (in-person and internet-based) may be viable supplementary treatments along with approved pharmacological therapy. In terms of anxiety and ADL, the effect of the in-person interventions may be more effective than the-internet based interventions.

Somatic Variants in SVIL in Cerebral Aneurysms

Background and Objectives

While somatic mutations have been well-studied in cancer, their roles in other complex traits are much less understood. Our goal is to identify somatic variants that may contribute to the formation of saccular cerebral aneurysms.

Methods

We performed whole-exome sequencing on aneurysm tissues and paired peripheral blood. RNA sequencing and the CRISPR/Cas9 system were then used to perform functional validation of our results.

Results

Somatic variants involved in supervillin (SVIL) or its regulation were found in 17% of aneurysm tissues. In the presence of a mutation in theSVILgene, the expression level of SVIL was downregulated in the aneurysm tissue compared with normal control vessels. Downstream signaling pathways that were induced by knockdown ofSVILvia the CRISPR/Cas9 system in vascular smooth muscle cells (vSMCs) were determined by evaluating changes in gene expression and protein kinase phosphorylation. We found thatSVILregulated the phenotypic modulation of vSMCs to the synthetic phenotype via Krüppel-like factor 4 and platelet-derived growth factor and affected cell migration of vSMCs via the RhoA/ROCK pathway.

Discussion

We propose that somatic variants form a novel mechanism for the development of cerebral aneurysms. Specifically, somatic variants inSVILresult in the phenotypic modulation of vSMCs, which increases the susceptibility to aneurysm formation. This finding suggests a new avenue for the therapeutic intervention and prevention of cerebral aneurysms.

Predicting allergic diseases in children using genome-wide association study (GWAS) data and family history

The recent rise in the prevalence of chronic allergic diseases among children has increased disease burden and reduced quality of life, especially for children with comorbid allergic diseases. Predicting the occurrence of allergic diseases can help prevent its onset for those in high risk groups. Herein, we aimed to construct prediction models for asthma, atopic dermatitis (AD), and asthma-AD comorbidity (also known as atopic march) using a genome-wide association study (GWAS) and family history data from patients of Korean heritage. Among 973 patients and 481 healthy controls, we evaluated single nucleotide polymorphism (SNP) heritability for each disease using genome-based restricted maximum likelihood (GREML) analysis. We then compared the performance of prediction models constructed using Least Absolute Shrinkage and Selection Operator (LASSO) and penalized ridge regression methods. Our results indicate that the addition of family history risk scores to the prediction model greatly increase the predictability of asthma and asthma-AD comorbidity. However, prediction of AD was mostly attributable to GWAS SNPs.

Integrated genetic and epigenetic analyses uncover MSI2 association with allergic inflammation

BACKGROUND

The relationship between allergic and eosinophilic inflammation, either systemic or local, in allergic diseases remains unclear.

OBJECTIVE

We performed combined genome-wide association study (GWAS) and epigenome-wide (EWAS) for atopy and tissue eosinophilia to identify both genetic and epigenetic signatures between systemic and local allergic inflammation, and to capture global patterns of gene regulation.

METHODS

We included 126 subjects for atopy analysis and 147 for tissue eosinophilia analysis, as well as 18 normal nasal tissue samples. We identified differentially methylated positions (DMPs) and genes associated with atopy and tissue eosinophilia. Furthermore, we performed mendelian randomization analysis and penalized regression along with replication in an independent cohort.

RESULTS

EWAS identified genes, including Musashi RNA binding protein 2 (MSI2), associated with atopy, which contained enriched DMPs that genetically affect atopy. A direct association was observed between MSI2 single-nucleotide polymorphisms and atopy, as was a causal effect of changes in MSI2 expression and methylation on atopy, which was replicated in a Costa Rican population. Regarding tissue eosinophilia, EWAS identified genes with enriched DMPs directly contributing to tissue eosinophilia at the gene level, including CAMK1D. The gene ontology terms of the identified genes for both phenotypes encompassed immune-related terms.

CONCLUSION

EWAS combined with GWAS identified novel candidate genes, especially the methylation of MSI2, contributing to systemic allergic inflammation. Certain genes displayed a greater association with either systemic or local allergic inflammation; however, it is expected that a harmonized effect of these genes influences immune responses.

Long-term mortality of patients with tuberculosis in Korea

BACKGROUND: Long-term mortality following tuberculosis (TB) diagnosis in Korea remains unclear.METHODS: The present study used data from the National Health Insurance Service database, an extensive health-related database including most Korean residents. TB patients were identified using International Classification of Diseases, Tenth Revision coding (A15-19, U88.0-88.1) and the type of anti-TB drug(s) between 2003 and 2016. Long-term mortality and causes of death in TB patients were analysed.RESULTS: A total of 357 211 individuals had TB over the period from 2003 to 2016 and 103 682 died. The mean age of the cohort was 54.7 ± 20.7 years, and 59.8% were male. The survival probability of TB patients at 1, 5, and 10 years after diagnosis was 87.8%, 75.3%, and 63.3%, respectively. High mortality and TB-related death rates were especially prominent in the early stages after TB diagnosis. The overall standardized mortality ratio of TB patients to the general Korean population was 3.23 (95% confidence interval 3.21-3.25).CONCLUSION: Mortality in TB patients was especially high in the early stages of disease after TB diagnosis, and mostly due to TB. This figure was approximately three-times higher than the mortality rate in the general population.

Effects of Material Properties on Angular Distortion in Wire Arc Additive Manufacturing: Experimental and Computational Analyses

In wire arc additive manufacturing (AM), as in arc welding, arc heat thermally deforms substrates and articles. For industrial applications, deformation characteristics of various materials must be understood and appropriate materials and methods of reducing deformation must be devised. Therefore, angular distortions of different materials were investigated through bead-on-plate welding and finite element analysis. A model that simplifies temperature-dependent properties was developed to establish relationships between thermomechanical properties and angular distortion. A simplified model of temperature-dependent properties was used, and angular distortion characteristics were extensively investigated for different material properties and heat inputs. Coefficient of thermal expansion, density, and specific heat all notably affected angular distortion depending on heat input conditions. Results showed that during wire arc AM, flatness of both substrates and articles could vary depending on material properties, heat input, substrate thickness, and bead accumulation. Study findings can provide insight into deformation characteristics of new materials and how to mitigate thermal distortions.

Type-2 Diabetics Reduces Spatial Variation of Microbiome Based on Extracellur Vesicles from Gut Microbes across Human Body

As a result of advances in sequencing technology, the role of gut microbiota in the mechanism of type-2 diabetes mellitus (T2DM) has been revealed. Studies showing wide distribution of microbiome throughout the human body, even in the blood, have motivated the investigation of the dynamics in gut microbiota across the humans. Particularly, extracellular vesicles (EVs), lipid bilayer structures secreted from the gut microbiota, have recently come into the spotlight because gut microbe-derived EVs affect glucose metabolism by inducing insulin resistance. Recently, intestine hyper-permeability linked to T2DM has also been associated with the interaction between gut microbes and leaky gut epithelium, which increases the uptake of macromolecules like lipopolysaccharide from the membranes of microbes leading to chronic inflammation. In this article, we firstly investigate the co-occurrence of stool microbes and microbe-derived EVs across serum and urine in human subjects (N = 284), showing the dynamics and stability of gut derived EVs. Stool EVs are intermediate, while the bacterial composition in both urine and serum EVs is distinct from the stool microbiome. The co-occurrence of microbes was compared between patients with T2DM (N = 29) and matched in healthy subjects (N = 145). Our results showed significantly higher correlations in patients with T2DM compared to healthy subjects across stool, serum, and urine, which could be interpreted as the dysfunction of intestinal permeability in T2DM. Therefore, the significant correlation of EVs might give insight into the pathophysiological mechanisms of T2DM, as well as the role of EVs as a biomarker in the intestinal permeability of T2DM.

Large-Scale Genomics Reveals the Genetic Characteristics of Seven Species and Importance of Phylogenetic Distance for Estimating Pan-Genome Size

For more than a decade, pan-genome analysis has been applied as an effective method for explaining the genetic contents variation of prokaryotic species. However, genomic characteristics and detailed structures of gene pools have not been fully clarified, because most studies have used a small number of genomes. Here, we constructed pan-genomes of seven species in order to elucidate variations in the genetic contents of >27,000 genomes belonging to Streptococcus pneumoniae, Staphylococcus aureus subsp. aureus, Salmonella enterica subsp. enterica, Escherichia coli and Shigella spp., Mycobacterium tuberculosis complex, Pseudomonas aeruginosa, and Acinetobacter baumannii. This work showed the pan-genomes of all seven species has open property. Additionally, systematic evaluation of the characteristics of their pan-genome revealed that phylogenetic distance provided valuable information for estimating the parameters for pan-genome size among several models including Heaps' law. Our results provide a better understanding of the species and a solution to minimize sampling biases associated with genome-sequencing preferences for pathogenic strains.

Antioxidant, antibacterial, and anti-adhesive activities of biosurfactants isolated from Bacillus strains

Biosurfactants are surface-active compounds that display a range of physiological functions. The present study investigated the antioxidant, antimicrobial, and anti-adhesive or anti-biofilm potential of biosurfactants isolated from Bacillus subtilis VSG4 and Bacillus licheniformis VS16. The antioxidant activity of the biosurfactants was studied in vitro using 2,2-diphenyl-1-picrylhydrazyl (DPPH) and hydroxyl radicals. At 5 mg/mL of the biosurfactant concentration, the scavenging of DPPH and hydroxyl radicals was found to be between 69.1-73.5% and 63.3-69.8%, respectively. The biosurfactants also displayed significant antibacterial activities against both Gram-positive and Gram-negative bacteria. The anti-adhesive activities of the biosurfactants were evaluated against Staphylococcus aureus ATCC 29523, Salmonella typhimurium ATCC 19430, and Bacillus cereus ATCC 11778. The biosurfactants exhibited anti-adhesive activity, even at concentrations of 3-5 mg/mL. Moreover, both biosurfactants displayed notable anti-biofilm activities with a biofilm eradication percentage ranging from 63.9 to 80.03% for VSG4 biosurfactant, and from 61.1-68.4% for VS16 biosurfactant. Furthermore, VSG4 biosurfactant exhibited emulsification and surface tension stability over a wide range of pH (4-10) and temperature up to 100 °C. These results show that VSG4 and VS16 biosurfactants can be potentially used as natural antioxidants, antimicrobials, and/or anti-adhesive agents for food and biomedical applications.

Evaluation of 16S rRNA Databases for Taxonomic Assignments Using Mock Community

Taxonomic identification is fundamental to all microbiology studies. Particularly in metagenomics, which identifies the composition of microorganisms using thousands of sequences, its importance is even greater. Identification is inevitably affected by the choice of database. This study was conducted to evaluate the accuracy of three widely used 16S databases—Greengenes, Silva, and EzBioCloud—and to suggest basic guidelines for selecting reference databases. Using public mock community data, each database was used to assign taxonomy and to test its accuracy. We show that EzBioCloud performs well compared with other existing databases.

Analysis of Pre-transplant Resuscitation Factors Influencing Immediate Graft Function After Deceased Donor Kidney Transplantation

BACKGROUND

The management of a deceased donor in the intensive care unit before organ transplantation is important for the outcome of the recipient. Herein, we analyze the pre-transplant resuscitation factors managed before procurement that could influence graft function immediately after deceased-donor kidney transplantation (DDKT).

METHODS

A total of 271 DDKTs performed at Seoul St. Mary's Hospital, Korea, from January 2009 to March 2016 were reviewed. We divided the patients into a delayed graft function (DGF) group and a non-DGF group, and compared postoperative outcomes between the 2 groups. We also analyzed the predisposing factors of DGF using multivariate analysis.

RESULTS

A total of 36 cases developed DGF while 235 patients did not, and the demographic characteristics of the recipients in the two groups had no significant difference. Of the pre-transplant resuscitation factors, preoperative polyuria, the maximal levels of serum sodium and BUN, and transfer times were significantly higher in the DGF group (P < .001). In a multivariable analysis, preoperative polyuria (odds ratio 4.835, P = .036), elevated preoperative level of sodium (odds ratio 1.227, P = .001), and extended transfer times (odds ratio 1.001, P < .001) were the independent risk factors of the donor in pre-transplant resuscitation management associated with DGF.

CONCLUSIONS

Polyuria, high levels of sodium before procurement, and prolonged transfer times are independent risk factors for DGF after a DDKT. Active intervention and early implementation of the intensivist can help in managing these factors effectively and thus ultimately improve graft function.

Kidney Transplantation Using Expanded-Criteria Deceased Donors: A Comparison With Ideal Deceased Donors and Non-Expanded-Criteria Deceased Donors

PURPOSE

The use of expanded-criteria deceased-donor (ECD) kidneys must be evaluated within the objective perspective of critical organ shortage and graft function and survival. In this study, we aimed to compare the clinical outcomes of ECD reliance with concurrent use of ideal-criteria deceased donors (IDDs) and non-ECDs in adult renal transplantation.

METHODS

Between February 2000 and December 2015, we analyzed 405 deceased-donor renal transplants, specifically 129 grafts (31.9%) from ECDs, 233 grafts (57.5%) from non-ECDs, and 43 grafts (10.6%) from IDDs. ECDs were classified according to the United Network for Organ Sharing guidelines, while an IDD was defined as a younger person (10-39 years of age) with no medical risk factors who died from a traumatic head injury. Donor and recipient risk factors were separately analyzed and correlated with recipient graft function, and survival was evaluated.

RESULTS

ECDs were older (56.8 ± 6.3 years); showed increased incidence of hypertension, diabetes, and cerebrovascular brain death; and had a higher pre-retrieval serum creatinine level than the other groups. ECD kidney recipients were also older (50.6 ± 9.8 years), had a shorter waiting time (P = .031), and demonstrated a low frequency of re-transplantation (P = .028). Long-term renal function followed longitudinally was lower in ECD kidney recipients until five years after transplantation, while the glomerular filtration rate (GFR) level at 7 and 10 years did not differ significantly among the groups (P = .074 and .262, respectively). There were no significant differences in terms of graft survival (P = .394) or patient survival (P = .737) among the groups.

CONCLUSIONS

Although the long-term renal function followed longitudinally was lower in ECD kidney recipients, the use of renal grafts from ECDs is an acceptable method to resolve the disparity of critical organ shortage. However, the classification of the high-risk group should be updated with consideration given to differences in regional characteristics.

First report of carp oedema virus infection of koi (Cyprinus carpio haematopterus) in the Republic of Korea

Twenty-five koi (Cyprinus carpio haematopterus) bought from a wholesale fish market in Korea, showed lethargic behaviour and 100% mortality within 20 days. Carp oedema virus (CEV) was detected by PCR in all 25 koi. Results of detailed histopathological and clinical examinations of 17 koi indicated loss of body balance, severe infiltration of inflammatory cells into the inter-lamellar spaces of the gills and vacuolization and inclusion bodies in gill epithelial cells. Sequence analysis of PCR products of these koi showed up to 99% identity to the previously reported sequences, suggesting that the observed mass mortality resulted from koi sleepy disease (KSD) due to CEV infection. To the best of our knowledge, this study is the first report of KSD in the Republic of Korea. Partial sequences of 4a protein from the virus indicated that the present CEV detected in koi from Korea is more closely related to that from the UK and Poland than from Japan. The present findings indicate that the prevalence and spread of KSD must be closely monitored in both European and Asian countries to avoid potential economic losses to the global koi industry.

The association between season of birth, age at onset, and clozapine use in schizophrenia

OBJECTIVE

This study aimed to determine whether the rate of clozapine use, an indicator of refractoriness in schizophrenia, is associated with the season of birth and age at onset in patients with schizophrenia based on nationwide data.

METHODS

Patients with schizophrenia (n = 114 749) who received prescriptions for antipsychotic medication between 2008 and 2014 were retrospectively identified from the Korean National Health Insurance Service database. The study population was divided into three groups based on their age at the onset of schizophrenia (early, middle, and late onset). We assessed differences in the month of birth between patients and the general population. In addition, the cumulative clozapine use was calculated.

RESULTS

Compared to the late-onset schizophrenia group, the early- and middle-onset groups showed a higher probability of birth during the winter season. In addition, the early-onset group showed the highest cumulative clozapine use rate. In the middle-onset group, the initiation of clozapine use was significantly earlier for patients born in winter compared to those born in summer.

CONCLUSION

Our results indicate that the age at onset is an important factor in predicting the prognosis of schizophrenia patients. The season of birth also affects the prognosis, but with less robustness. Specifically, it appears that early disease onset and winter birth might be associated with poor outcomes in Korean patients with schizophrenia.

Triazolium cyclodextrin click cluster-resin conjugate: an enrichment material for phosphatidylinositol (3,4,5)-triphosphate

UltraLink was functionalized with a triazolium cyclodextrin click cluster (CCC) which provides a well-oriented, multivalent, positively charged binding site for PtdIns(3,4,5)P₃. MALDI TOF MS and LC ESI MS/MS MRM analysis of spiked PtdIns(3,4,5)P₃ in lipid extract suggest that triazolium CCC-UltraLink conjugate can be used as an enrichment material for PtdIns(3,4,5)P₃.

4-n-butylresorcinol enhances proteolytic degradation of tyrosinase in B16F10 melanoma cells

OBJECTIVE

4-n-butylresorcinol is a competitive inhibitor of tyrosinase and has been used as an antimelanogenic agent. However, its inhibition mechanism in intact cells is not fully understood. To elucidate the cellular mechanism, we compared in vitro and in vivo inhibitory effects of 4-n-butylresorcinol on tyrosinase activity.

METHODS

B16F10 melanoma cells were cultured in media containing α-MSH in the presence or absence of 4-n-butylresorcinol. Tyrosinase mRNA levels, protein levels and activity in B16F10 cells were compared by real-time PCR, immunostaining combined with western blot and colorimetric analysis, respectively. Melanin concentration was measured by colorimetry both in the cells and in the media. Tyrosinase glycosylation and proteolytic degradation were analysed by immunoblotting after cells were treated with Endo H/PNGase F and E64/proteasome inhibitors, respectively.

RESULTS

4-n-butylresorcinol inhibited tyrosinase activity and melanin synthesis more effectively in intact cells than in cell lysates. Western blotting and real-time RT-PCR showed that 4-n-butylresorcinol reduced protein levels, but not mRNA levels, of tyrosinase in B16F10 cells. 4-n-butylresorcinol showed no effect on the processing of tyrosinase glycosylation or on trafficking to melanosomes. However, treatment of B16F10 cells with E64 or proteasome inhibitor abrogated the 4-n-butylresorcinol-induced decrease of tyrosinase. Moreover, 4-n-butylresorcinol activated p38 MAPK, resulting in increased ubiquitination of tyrosinase.

CONCLUSION

4-n-butylresorcinol inhibits melanogenesis by enhancing proteolytic degradation of tyrosinase as well as competitive binding to tyrosinase. These findings will help to develop new, effective and safe chemicals for the treatment of hyperpigmentation disorders.

Long-term outcomes of locally or radically resected T1 colorectal cancer

AIM

Little is known about the long-term outcome of T1 colorectal cancer (CRC) following curative resection. The present study addressed the long-term outcome of locally or radically resected T1 CRCs.

METHOD

A total of 430 patients with T1 CRC who underwent local or radical resection were considered. Unfavourable histological factors were defined as positive resection margin, deep submucosal invasion, vascular invasion, Grade 3 and budding. The patients were classified as low-risk (unfavourable histological factor negative, n = 65) or high-risk (unfavourable histological factor positive, n = 365).

RESULTS

Over a median follow-up of 78.4 months, disease recurred in 16 (3.7%) patients in the high-risk group, and no recurrence in the low-risk group. Resection type and vascular invasion were significantly associated with recurrence. In the vascular invasion (+) high-risk group, both 5-year disease-free survival rate and 5-year overall survival rate were significantly associated with resection type (radical 94.6%, local 43.8%, P < 0.001, and radical 99.1%, local 66.7%, P < 0.001). In the vascular invasion (-) high-risk group, 5-year disease-free survival rate was also significantly associated with resection type (radical 98.9%, local 84.7%, P = 0.001). However, 5-year overall survival rate was not associated with resection type (radical 98.9%, local 95.2%, P = 0.816).

CONCLUSION

Local resection may be effective and oncologically safe in low-risk T1 CRC. Although additional surgery should be recommended for the locally resected high-risk T1 CRC cases, intensive surveillance without additional surgery and timely salvage operation may offer another treatment option, if vascular invasion is negative.

The prevalence of causative organisms of community-acquired urethritis in an age group at high risk for sexually transmitted infections in Korean Soldiers

OBJECTIVES

This study was designed to evaluate the causative organisms in young male soldiers with clinical signs and symptoms after sexual contact that suggests a diagnosis of urethritis.

METHODS

Between June 2012 and January 2015, male patients with urethritis symptoms that had resulted from sexual contact within 3 months participated in this study. All patients were evaluated using urinalysis and were screened for Neisseria gonorrhoeae (NG), Chlamydia trachomatis (CT), Ureaplasma urealyticum (UU), Mycoplasma genitalium (MG), Mycoplasma hominis (MH), herpes simplex virus (HSV) type II and Trichomonas vaginalis (TV) using multiplex PCR (mPCR) assay in order to detect sexually transmitted infections (STI) or pathogens.

RESULTS

A total of 436 male patients aged 18-28 years were included in the study. The median age was 22.0 years. The prevalence of STI pathogens were as follows: NG in 19.0%, CT in 36.6%, UU in 24.0%, MG in 21.5%, MH in 6.1%, HSV type II in 1.6%, TV in 0.2% and indeterminate STI pathogens in 9.4%. Coinfection of NG with non-NG was detected in 5.7% of the participants, while the coinfection rates for STI pathogens were: with CT in 3.4%, with UU in 2.7%, with MG in 0.2% and with MH in 0.2%.

CONCLUSIONS

CT was the most prevalent STI pathogen and coinfections of NG with non-NG appeared less frequently. The young male soldiers with urethritis should be administered suitable antibiotics for STI pathogens that were found by mPCR results, rather than an experimental combination of antibiotics for coinfections.

OrthoANI: An improved algorithm and software for calculating average nucleotide identity

Species demarcation in Bacteria and Archaea is mainly based on overall genome relatedness, which serves a framework for modern microbiology. Current practice for obtaining these measures between two strains is shifting from experimentally determined similarity obtained by DNA-DNA hybridization (DDH) to genome-sequence-based similarity. Average nucleotide identity (ANI) is a simple algorithm that mimics DDH. Like DDH, ANI values between two genome sequences may be different from each other when reciprocal calculations are compared. We compared 63 690 pairs of genome sequences and found that the differences in reciprocal ANI values are significantly high, exceeding 1 % in some cases. To resolve this problem of not being symmetrical, a new algorithm, named OrthoANI, was developed to accommodate the concept of orthology for which both genome sequences were fragmented and only orthologous fragment pairs taken into consideration for calculating nucleotide identities. OrthoANI is highly correlated with ANI (using BLASTn) and the former showed approximately 0.1 % higher values than the latter. In conclusion, OrthoANI provides a more robust and faster means of calculating average nucleotide identity for taxonomic purposes. The standalone software tools are freely available at http://www.ezbiocloud.net/sw/oat.

Burkholderia megalochromosomata sp. nov., isolated from grassland soil

A Gram-stain negative, rod-shaped, non-spore-forming, obligate aerobic bacterial strain, JC2949T, was isolated from grassland soil in Gwanak Mountain, Seoul, Republic of Korea. Phylogenetic analysis, based on 16S rRNA sequences, indicated that strain JC2949T belongs to the genus Burkholderia , showing highest sequence similarities with Burkholderia grimmiae R27T (98.8 %), Burkholderia cordobensis LMG 27620T (98.6 %), Burkholderia jiangsuensis MP-1TT (98.6 %), Burkholderia zhejiangensis OP-1T (98.5 %), Burkholderia humi LMG 22934T (97.5 %), Burkholderia terrestris LMG 22937T (97.3 %), Burkholderia telluris LMG 22936T (97.2 %) and Burkholderia glathei ATCC 29195T (97.0 %). The major fatty acids of strain JC2949T were C18 : 1ω7c, summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) and C16 : 0. Its predominant polar lipids were phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol and an unknown amino phospholipid. The dominant isoprenoid quinone was ubiquinone Q-8. The pairwise average nucleotide identity values between strain JC2949T and the genomes of 30 other species of the genus Burkholderia ranged from 73.4–90.4 %, indicating that the isolate is a novel genomic species within this genus. Based on phenotypic and chemotaxonomic comparisons, it is clear that strain JC2949T represents a novel species of the genus Burkholderia . We propose the name for this novel species to be Burkholderia megalochromosomata sp. nov. The type strain is JC2949T ( = KACC 17925T = JCM 19905T).

Improved pipeline for reducing erroneous identification by 16S rRNA sequences using the Illumina MiSeq platform

The cost of DNA sequencing has decreased due to advancements in Next Generation Sequencing. The number of sequences obtained from the Illumina platform is large, use of this platform can reduce costs more than the 454 pyrosequencer. However, the Illumina platform has other challenges, including bioinformatics analysis of large numbers of sequences and the need to reduce erroneous nucleotides generated at the 3'-ends of the sequences. These erroneous sequences can lead to errors in analysis of microbial communities. Therefore, correction of these erroneous sequences is necessary for accurate taxonomic identification. Several studies that have used the Illumina platform to perform metagenomic analyses proposed curating pipelines to increase accuracy. In this study, we evaluated the likelihood of obtaining an erroneous microbial composition using the MiSeq 250 bp paired sequence platform and improved the pipeline to reduce erroneous identifications. We compared different sequencing conditions by varying the percentage of control phiX added, the concentration of the sequencing library, and the 16S rRNA gene target region using a mock community sample composed of known sequences. Our recommended method corrected erroneous nucleotides and improved identification accuracy. Overall, 99.5% of the total reads shared 95% similarity with the corresponding template sequences and 93.6% of the total reads shared over 97% similarity. This indicated that the MiSeq platform can be used to analyze microbial communities at the genus level with high accuracy. The improved analysis method recommended in this study can be applied to amplicon studies in various environments using high-throughput reads generated on the MiSeq platform.

Large-scale evaluation of experimentally determined DNA G+C contents with whole genome sequences of prokaryotes

Historically, DNA G+C content has played a critical role in the description of bacterial and archaeal species. Despite its importance in prokaryote taxonomy, its accuracy has been questioned due to methodological heterogeneity and measurement errors of conventional methods. Here we investigated the extent of accuracy of experimentally determined DNA G+C contents by comparing the reference values calculated from whole genome sequences. The large-scale comparison revealed that G+C contents determined by high-performance liquid chromatography and buoyant density centrifugation methods were more similar to the genome-derived reference values than those generated by thermal denaturation method. However, there was a substantial degree of discrepancy in DNA G+C contents between values obtained by conventional methods and genome-derived reference values. The majority of the differences between them fell out of the acceptable range (i.e. 1 mol% G+C content difference) for species delimitation of prokaryotes. In contrast, when average nucleotide identity (ANI) was correlated to G+C difference among genomes, most G+C difference was confined to less than 1% within species. Therefore, erroneous conventional methods are not meaningful in the description of bacterial and archaeal species. For taxonomic purposes, DNA G+C content should be determined by calculating directly from high-quality genome sequences with at least 16× or higher sequencing depth of coverage.

The early protective effect of glutamine pretreatment and ischemia preconditioning in renal ischemia-reperfusion injury of rat

BACKGROUND

Heat shock proteins (HSP) play an important role in protecting cells against stress.

METHODS

Using a rat model, we tested the hypothesis that pretreatment with glutamine (Gln) and ischemia preconditioning (IPC) increase the expression of HSP resulting in attenuation of renal ischemia/reperfusion (I/R) injury. Sprague-Dawley rats were randomized into 4 groups [group I, Gln injection (+), IPC (+); group II, Gln injection (+), IPC (-); group III, saline injection (+), IPC (+); group IV, saline injection (+), IPC (-)]. Renal HSP70 expression was determined by Western blotting and kidney function was assessed by blood urea nitrogen and serum creatinine. Renal cross-sections were microscopically examined for tubular necrosis, exfoliation of tubular epithelial cells, cast formation, and monocyte infiltration.

RESULTS

Gln pretreatment increased intrarenal HSP expression (P = .031). In group I, tubulointerstitial abnormalities were clearly slighter compared with the other groups (P < .001).

CONCLUSION

Our experiments suggest that (1) a single dose of Gln could induce HSP expression and (2) IPC could relieve renal I/R injury. In addition, IPC combined with Gln pretreatment had a synergic protective effect against renal I/R injury.

Contrast-enhanced magnetic resonance angiography in the early period after kidney transplantation

Our objective was to evaluate the usefulness of three-dimensional (3-D) contrast-enhanced (CE) magnetic resonance angiography (MRA) to assess renal parenchyma, arterial inflow stenosis, and peritransplant fluid collections in the early period after kidney transplantation (KT). Between January 2010 and April 2011, we examined a consecutive series of 144 renal transplants using 3-D CE MRA at 14 days after KT. MRA showed parenchyma infarctions (n = 17, 11.8%), arterial inflow stenoses (n = 23, 16%), lymphoceles (n = 14, 9.7%), and hematomas (n = 6, 4.2%). The degree of renal transplant artery inflow stenosis was graded qualitatively based on diameter criterion; <50% = mild, 50% to 70% = moderate, and >70% = severe in 10 (6.9%), 5 (3.5%), and 8 (5.6%) subjects, respectively. The study recipients were divided into 3 groups according to the degree of renal artery inflow stenosis (group I: normal; group II: mild and moderate, <70%; group III: severe, >70%). Among group III patients who underwent digital subtraction angiography, 5 had percutaneous transluminal angioplasty or stenting performed after 1 month. Their mean resume creatinine levels at 1, 6, and 12 months after transplantation were not significantly different from those in the other groups (P = .391, .447, .110). The prevalence of graft loss (n = 2) was high in group III (P = .012), although the frequency of acute rejection episodes was not different among the groups (P = .890). The incidences of renal parenchyma infarction, peritransplant fluid collection and arterial inflow stenosis were unexpectedly high in the early period after KT. Thus, 3-D CE MRA provided a rapid global assessment of the renal parenchyma, transplant arterial system, and peritransplant fluid collection that can be helpful to detect or exclude many causes of renal transplant dysfunction.

Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes

Among available genome relatedness indices, average nucleotide identity (ANI) is one of the most robust measurements of genomic relatedness between strains, and has great potential in the taxonomy of bacteria and archaea as a substitute for the labour-intensive DNA-DNA hybridization (DDH) technique. An ANI threshold range (95-96%) for species demarcation had previously been suggested based on comparative investigation between DDH and ANI values, albeit with rather limited datasets. Furthermore, its generality was not tested on all lineages of prokaryotes. Here, we investigated the overall distribution of ANI values generated by pairwise comparison of 6787 genomes of prokaryotes belonging to 22 phyla to see whether the suggested range can be applied to all species. There was an apparent distinction in the overall ANI distribution between intra- and interspecies relationships at around 95-96% ANI. We went on to determine which level of 16S rRNA gene sequence similarity corresponds to the currently accepted ANI threshold for species demarcation using over one million comparisons. A twofold cross-validation statistical test revealed that 98.65% 16S rRNA gene sequence similarity can be used as the threshold for differentiating two species, which is consistent with previous suggestions (98.2-99.0%) derived from comparative studies between DDH and 16S rRNA gene sequence similarity. Our findings should be useful in accelerating the use of genomic sequence data in the taxonomy of bacteria and archaea.

The natural history of arteriovenous access and risk factors associated with access thrombosis after successful kidney transplantation

INTRODUCTION

The purpose of this study was to determine the natural history of arteriovenous (AV) access after successful kidney transplantation (KT) and to identify the risk factors of spontaneous access closure in kidney transplant recipients.

METHODS

We performed a retrospective review of 115 patients who underwent KT with functioning access from June 2010 to July 2012. AV access patency was checked and recorded daily during the hospital stay and at every visit to the outpatient clinic. Patients were divided into 2 groups according to the patency of access, and risk factors of access thrombosis were assessed. Access patency was followed up until patency was lost or the study was closed.

RESULTS

At the end of follow-up, 18 (15.7%) AV accesses had spontaneously closed. Mean time to closure was 119 ± 163 days, and 12 of 18 were closed within 90 days after KT. AV access spontaneously closed in 8.5% of male patients, compared with 27.3% of female patients (P = .007), 12.2% of cases with native access compared with 35.3% of cases with artificial access (P = .016), and 11.3% of cases with wrist access compared with 25.7% of cases with elbow access (P = .049). Spontaneously closed AV accesses tended to have a lower mean access flow compared with functioning accesses (P = .019). On multivariate analysis, female sex and AV access flow volume affected spontaneous AV access closure (odds ratio 4.749, 95% confidence interval 1.919-35.383, P = .008; odds ratio 0.998, 95% confidence interval 0.996-0.999, P = .010, respectively).

CONCLUSIONS

Our results suggest that AV access thrombosis occurs more frequently during the early postoperative period, particularly in female patients or patients with low flow access, whereas it is a rare event in male patients or patients with high access flow, especially in the late postoperative period.

EzEditor: a versatile sequence alignment editor for both rRNA- and protein-coding genes

EzEditor is a Java-based molecular sequence editor allowing manipulation of both DNA and protein sequence alignments for phylogenetic analysis. It has multiple features optimized to connect initial computer-generated multiple alignment and subsequent phylogenetic analysis by providing manual editing with reference to biological information specific to the genes under consideration. It provides various functionalities for editing rRNA alignments using secondary structure information. In addition, it supports simultaneous editing of both DNA sequences and their translated protein sequences for protein-coding genes. EzEditor is, to our knowledge, the first sequence editing software designed for both rRNA- and protein-coding genes with the visualization of biologically relevant information and should be useful in molecular phylogenetic studies. EzEditor is based on Java, can be run on all major computer operating systems and is freely available from http://sw.ezbiocloud.net/ezeditor/.

Validation of a scoring tool to predict drug-resistant pathogens in hospitalised pneumonia patients

BACKGROUND

Health care-associated pneumonia (HCAP) affects a heterogeneous group of patients in frequent contact with health care systems. However, HCAP criteria poorly predict infection with drug-resistant (DR) pathogens.

OBJECTIVE

To validate our previously reported risk-scoring model (predictive of DR pathogen infection) in patients admitted to hospital with pneumonia.

DESIGN

We evaluated 580 patients admitted with culture-positive bacterial pneumonia. We identified risk factors, evaluated the risk-scoring model's capacity to predict infection by DR pathogens and compared the model's diagnostic accuracy with that of current HCAP criteria.

RESULTS

DR pathogens were observed in 227/580 patients (39.1%). Of 269 HCAP patients, 153 (56.9%) were infected with DR pathogens. Overtreatment was more common in HCAP than in community-acquired pneumonia (58.7% vs. 41.2%, P < 0.001). Recent hospitalisation, admission from a long-term care facility, recent antibiotic treatment and tube feeding were independently associated with DR pathogens. For pathogen prediction, the risk-scoring model showed better diagnostic accuracy than HCAP criteria (area under receiver operating-characteristic curve = 0.723 vs. 0.673, P < 0.001).

CONCLUSION

According to current HCAP criteria, half of the HCAP patients were treated unnecessarily with broad-spectrum antibiotics. Risk scoring by stratifying risk factors could improve the identification of patients likely to be infected with DR pathogens.

Isolation and characterization of a lytic Myoviridae bacteriophage PAS-1 with broad infectivity in Aeromonas salmonicida

To search for candidate control agents against Aeromonas salmonicida subsp. salmonicida infections in aquaculture, one bacteriophage (phage), designated as PAS-1, was isolated from the sediment samples of the rainbow trout (Oncorhynchus mykiss) culture farm in Korea. The PAS-1 was morphologically classified as Myoviridae and possessed approximately 48 kb of double-strand genomic DNA. The phage showed broad host ranges to other subspecies of A. salmonicida as well as A. salmonicida subsp. salmonicida including antibiotic-resistant strains. Its latent period and burst size were estimated to be approximately 40 min and 116.7 PFU/cell, respectively. Furthermore, genomic and structural proteomic analysis of PAS-1 revealed that the phage was closely related to other Myoviridae phages infecting enterobacteria or Aeromonas species. The bacteriolytic activity of phage PAS-1 was evaluated using three subspecies of A. salmonicida strain at different doses of multiplicity of infection, and the results proved to be efficient for the reduction of bacterial growth. Based on these results, PAS-1 could be considered as a novel Aeromonas phage and might have potentiality to reduce the impacts of A. salmonicida infections in aquaculture.

Predictors for lymph node metastasis in T1 colorectal cancer

BACKGROUND AND STUDY AIMS

It is critical that the risk of lymph node metastasis (LNM) is evaluated for determining the suitability of endoscopic resection for T1 colorectal cancer (CRC). Reported risk factors for LNM in completely resected T1 CRC are deep submucosal invasion, grade 3, angiolymphatic invasion, and budding. The aim of the present study was to identify the histopathologic factors associated with LNM in T1 CRC.

PATIENTS AND METHODS

The study involved 435 patients with T1 CRC treated by endoscopic or surgical resection between January 2001 and April 2010 at the National Cancer Center, Korea. The 435 patients were classified into two groups - those undergoing surgical resection (n = 324) and those undergoing endoscopic resection (n = 111). In the surgically resected group, details regarding depth of submucosal invasion, angiolymphatic invasion, tumor grade, budding, and background adenoma (BGA) were evaluated with respect to presence or absence of LNM. In the endoscopically resected group, the results of follow-ups and additional salvage surgeries were studied.

RESULTS

In the surgically resected group, LNM was detected in 42 patients (13.0 %). Grade 3, angiolymphatic invasion, budding, and the absence of BGA were identified as factors associated with LNM in univariate and multivariate analyses (P < 0.05). Among the 50 patients in the endoscopically resected group with high risk, three were diagnosed as being LNM-positive during the follow-up period. There was no LNM in the endoscopically resected group with low risk.

CONCLUSIONS

Grade 3, angiolymphatic invasion, budding, and the absence of BGA are the risk factors that predict LNM in patients with T1 CRC. In cases where endoscopically resected T1 CRC has no risk factor, cautious follow-up could be recommended. However, if the tumor has any risk factor, additional surgical resection should be considered.

Does donor kidney to recipient body weight ratio influence long-term outcomes of living-donor kidney transplantation?

This study evaluated the effect of the donor kidney to recipient body weight (Kw/Rw) ratio on long-term graft function and survival. We investigated retrospectively whether there was any association between Kw/Rw ratio and long-term graft survival and function after a follow-up of >10 years. We studied a consecutive series of 123 adult-to-adult living kidney transplants. According to the Kw/Rw ratio, patients were divided into 3 groups: "low" (Kw/Rw <2.85; n = 29), "medium" (2.85 ≤ Kw/Rw < 4.04; n = 63), and "high" (≥4.04; n = 31). Among the 3 groups, the mean serum creatinine levels at 1 and 6 months as well as 1 year after transplantation were significantly lower among patients with a high Kw/Rw ratio than in those with a medium or low ratio, but serum creatinine levels at 3 and 5 years did not differ significantly (P = .394 and 0.620, respectively). Graft survival rates at 5 and 10 years after transplantation were significantly lower in the "low" group. We observed a significant association between Kw/Rw ratio and graft survival (P = .018). The Kw/Rw ratio is an important factor for long-term graft survival and early graft function. However, it did not significantly affect subsequent renal function.

Lymph node ratio is an independent prognostic factor in patients with rectal cancer treated with preoperative chemoradiotherapy and curative resection

PURPOSE

To evaluate the prognostic effect of lymph node ratio (LNR) in patients with locally advanced rectal cancer who were treated with curative resection after preoperative chemoradiotherapy (CRT).

METHODS

Between October 2001 and December 2007, 519 patients who had undergone curative resection of primary rectal cancer after preoperative CRT were enrolled. Of these, 154 patients were positive for lymph node (LN) metastasis and were divided into three groups according to the LNR (≤ 0.15 [n=80], 0.16-0.3 [n=44], >0.3 [n=30]) to evaluate the prognostic effect on overall survival (OS) and disease-free survival (DFS).

RESULTS

LNR (≤ 0.15, 0.16-0.3, and >0.3) was significantly associated with 5-year OS (90.3%, 75.1%, and 45.1%; p<0.001) and DFS (66.7%, 55.8%, and 21.9%; p<0.001) rates. In a multivariate analysis, LNR (≤ 0.15, 0.16-0.3, and >0.3) was a significant independent prognostic factor for OS (hazard ratios [HRs], 1, 3.609, and 8.197; p<0.001) and DFS (HRs, 1, 1.699, and 3.960; p<0.001). LNR had a prognostic impact on OS and DFS in patients with <12 harvested LNs, as well as in those with ≥ 12 harvested LNs (p<0.05).

CONCLUSION

LNR was a significant independent prognostic predictor for OS and DFS in patients with locally advanced rectal cancer who were treated with curative resection after preoperative CRT.

Comparative genomics of Neisseria weaveri clarifies the taxonomy of this species and identifies genetic determinants that may be associated with virulence

A group of bacterial strains formerly known as CDC group M-5 are opportunistic pathogens to humans. In 1993, a name, Neisseria weaveri, was proposed by two independent studies to harbor CDC group M-5 strains, namely N. weaveri Holmes et al. 1993 and N. weaveri Andersen et al. 1993, with two different 'type' strains. However, no study has been conducted on to the relatedness of the two 'type' strains, although the close relationship of the two taxa has long been accepted unofficially. Formally, the status of the name N. weaveri Andersen et al. 1993 is illegitimate because it is a later homonym of N. weaveri Holmes et al., 1993; but the name of the strain is still validly published. In this study, we attempt to resolve the confusion caused by the apparent duplication of the species N. weaveri (with different type strains) using whole genome shotgun sequencing. We also sought to gain insight into the genetic characteristics of N. weaveri by conducting comparative genomics. On the basis of genomic similarities revealed through a comparative genomic study, we propose that N. weaveri Andersen et al. 1993 should be re-classified as a later heterotypic synonym of N. weaveri Holmes et al., 1993.

Gene expression profiling of a cold-shocked earthworm Eisenia andrei

To identify genes that are modulated under cold-stress conditions in the earthworm Eisenia andrei, we performed a genome-wide analysis of gene expression in cold-shocked earthworms by using Serial Analysis of Gene Expression (SAGE). We identified 5,977 and 5,407 unique SAGE tags under normal and cold-stressed conditions, respectively. The majority of the SAGE tags did not match to any known expressed sequences, due to a paucity of expression data in earthworms. We converted the statistically significant SAGE tags for the cold-stressed condition into expressed sequence tags (ESTs), and the results showed that particular genes associated with energy homeostasis, cellular defense mechanisms, and ion balance were up-regulated or down-regulated. We constructed a regulatory network of some of these genes and identified rps-6 as a core gene in the cold-response regulatory-gene network. Our data provide a baseline for gene expression studies of cold shock in the Lumbricidae.

Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species

Despite recent advances in commercially optimized identification systems, bacterial identification remains a challenging task in many routine microbiological laboratories, especially in situations where taxonomically novel isolates are involved. The 16S rRNA gene has been used extensively for this task when coupled with a well-curated database, such as EzTaxon, containing sequences of type strains of prokaryotic species with validly published names. Although the EzTaxon database has been widely used for routine identification of prokaryotic isolates, sequences from uncultured prokaryotes have not been considered. Here, the next generation database, named EzTaxon-e, is formally introduced. This new database covers not only species within the formal nomenclatural system but also phylotypes that may represent species in nature. In addition to an identification function based on Basic Local Alignment Search Tool (blast) searches and pairwise global sequence alignments, a new objective method of assessing the degree of completeness in sequencing is proposed. All sequences that are held in the EzTaxon-e database have been subjected to phylogenetic analysis and this has resulted in a complete hierarchical classification system. It is concluded that the EzTaxon-e database provides a useful taxonomic backbone for the identification of cultured and uncultured prokaryotes and offers a valuable means of communication among microbiologists who routinely encounter taxonomically novel isolates. The database and its analytical functions can be found at http://eztaxon-e.ezbiocloud.net/.

Genomic sequence of infectious hypodermal and hematopoietic necrosis virus (IHHNV) KLV-2010-01 originating from the first Korean outbreak in cultured Litopenaeus vannamei

Due to the need to track and monitor genetic diversity, the genome of the infectious hypodermal and hematopoietic necrosis virus (IHHNV) strain KLV-2010-01 in cultured Litopenaeus vannamei shrimp that originated from the first Korean outbreak in 2010 was sequenced and analyzed. The genome, with a length of 3914 nucleotides, was sequenced from the Korean IHHNV. The genome encoded three large and overlapping open reading frames: ORF1 (NS-1) of 2001 bp, ORF2 (NS-2) of 1092 bp and ORF3 (capsid protein) of 990 bp. The overall organization, size and predicted amino acid sequence of the three ORFs in Korean IHHNV were highly similar to those of members of the infectious IHHNV group, and the most closely related strains were IHHNVs described from Ecuador and Hawaii. Additionally, phylogenetic analysis showed that the Korean IHHNV was clustered with lineage III in the infectious IHHNV group and was most similar to IHHNV isolates from Ecuador, China and Taiwan.

Prevalence and different characteristics of two serotypes of Streptococcus parauberis isolated from the farmed olive flounder, Paralichthys olivaceus (Temminck and Schlegel), in Korea

The prevalence of two serotypes of Streptococcus parauberis isolated from the olive flounder, Paralichthys olivaceus, was evaluated in a total of 29 isolates between 2003 and 2010 in Korea. Streptococcus parauberis isolates were divided into two serologically distinct types (serotype 1 and serotype 2), except for one strain (S1091), using an agglutination assay with rabbit antiserum, and serotype 1 was identified as the dominant type (24 of 29 isolates) in this study. To identify the characteristics of the two serotypes of S. parauberis, we conducted a biochemical test using the API 20 Strep kit, a transmission electron microscopy (TEM) assay, sequence analysis of 16S-23S rRNA intergenic spacer region (ISR) and a pathogenicity test. In TEM, both serotypes possessed polysaccharide capsule layers around the cell surface when bacterial cells were treated with a homologous serotype of rabbit antiserum. However, we were unable to discriminate serotype-specific biochemical characteristics and genetic characteristics of 16S-23S rRNA ISR between the two serotypes. In the pathogenicity test, the serotype 1 strains induced significantly higher mortality than the serotype 2 strains in olive flounder when experimentally inoculated via the intraperitoneal route.

Effect of dimethyl sulfoxide on cell cycle synchronization of goldfish caudal fin derived fibroblasts cells

Several studies have previously been conducted regarding cell cycle synchronization in mammalian somatic cells. However, limited work has been performed on the control of cell cycle stages in the somatic cells of fish. The aim of this study was to determine the cell cycle arresting effects of several dimethyl sulfoxide (DMSO) concentrations for different times on different cell cycle stages of goldfish caudal fin-derived fibroblasts. Results demonstrated that the cycling cells or control group (68.29%) yields significantly higher (p < 0.05) arrest in G0/G1 phase compared with the group treated for 24 h with different concentrations (0.5%, 1.0% or 1.5%) of DMSO (64.88%, 65.70%, 64.22% respectively). The cell cycle synchronization in the treatment of cells with 1.0% DMSO at 48 h (81.14%) was significantly higher than that in the groups treated for 24 h (76.82%) and the control group (77.90%). Observations showed that treatment of DMSO resulted in an increase in the proportion of cells at G0/G1 phase for 48 h of culture. However, high levels of apoptotic cells can be detected after 48 h of culture treated with 1% concentration of DMSO.

Antimicrobial activity of the constituents of Smallanthus sonchifolius leaves against methicillin-resistant Staphylococcus aureus

BACKGROUND AND OBJECTIVES

Methicillin-resistant Staphylococcus aureus (MRSA) has been a serious problem as its infection is associated with higher mortality and increase cost worldwide. In the present study, the antibacterial activity of enhydrin, polymatin B, allo-schkuhriolide from the leaves of Smallanthus sonchifolius was investigated.

MATERIAL AND METHODS

Enhydrin, polymatin B, allo-schkuhriolide from the leaves of Smallanthus sonchifolius were tested for antimicrobial activity using micro dilution broth method against 2 strains of ATCC 33591, ATCC 25923 and 15 strains of clinical isolates MRSA.

RESULTS

The antibacterial activity of Smallanthus sonchifolius can safely be attributed to enhydrin as polymatin B, and allo-schkuhriolide are not showing any activity against Staphylococcus aureus strains. The enhydrin showed good antibacterial activity against all tested strains (MIC = 125-500 microg/ml).

DISCUSSION

These results suggest that only enhydrin can be considered as an antibacterial drug against MRSA.

Effect of probiotic-, bacteriophage-, or organic acid-supplemented feeds or fermented soybean meal on the growth performance, acute-phase response, and bacterial shedding of grower pigs challenged with Salmonella enterica serotype Typhimurium

A 28-d experiment evaluated the growth performance, acute-phase response, and bacterial shedding patterns in pigs (n = 108; initially, 38.7 ± 6.7 kg) fed 6 treatment diets, including a control diet with no antimicrobial agents (CON), a positive control diet containing chlortetracycline, 100 mg/kg (CT), a diet containing anti-Salmonella Typhimurium bacteriophage, 3 × 10(9) plaque-forming units/kg of feed (ASB), Lactobacillus plantarum CJLP56, 6.5 × 10(8) cfu/kg of feed (LP), 0.2% microencapsulated organic acids (MOA), or 5% fermented soybean meal (FSM). Pigs were fed the diets for 2 wk before and 2 wk after challenging orally with Salmonella enterica serotype Typhimurium (SalT). Before bacterial challenge, ADFI was similar in all groups. After SalT challenge, ADFI of CON pigs was less (P < 0.05) than all other groups. Before challenge, pigs on MOA, FSM, and CT diets had greater (P < 0.05) ADG and G:F than CON pigs. After challenge (wk 3 to 4) and during the overall experimental period (wk 1 to 4), ADG of all treatment groups and G:F of all treatment groups except the LP group were greater (P < 0.05) than those of CON pigs. Relative to all other treatments, CON and LP pigs had greater (P < 0.05) bacterial shedding scores on d 7 after SalT challenge. At d 14 postchallenge, shedding scores declined (P < 0.05) in all treatment groups compared with CON pigs. Serum haptoglobin for all treatment groups increased from d 0 concentrations on d 6 postchallenge and declined to prechallenge concentrations on d 13 (P < 0.05). Circulating IGF-I concentrations declined from 2 to 6 d postchallenge and increased again by d 13 in ASB and LP groups, did not decline in FSM and CT groups, and continuously declined through d 13 in CON and LP groups (P < 0.05). However, in MOA group, IGF-I concentrations declined from preinfection concentrations on d 2, increased on d 4, and declined again until d 13 (P < 0.05). The serum concentrations of the cytokines IL-6 and IL-1β were not generally affected by SalT challenge. In conclusion, acute infection of growing pigs with SalT was associated with short-term febrile responses in most pigs and reductions in ADFI and ADG of CON pigs. Compared with the CON diet, ASB, FSM, and MOA diets had a similar benefit to the antibiotic-supplemented diet in improving the performance of growing pigs, especially after bacterial challenge. However, further work needs to be done to better understand their mode of action in this class of pigs.