Universal DNA methylation age across mammalian tissues

Aging, often considered a result of random cellular damage, can be accurately estimated using DNA methylation profiles, the foundation of pan-tissue epigenetic clocks. Here, we demonstrate the development of universal pan-mammalian clocks, using 11,754 methylation arrays from our Mammalian Methylation Consortium, which encompass 59 tissue types across 185 mammalian species. These predictive models estimate mammalian tissue age with high accuracy (r > 0.96). Age deviations correlate with human mortality risk, mouse somatotropic axis mutations and caloric restriction. We identified specific cytosines with methylation levels that change with age across numerous species. These sites, highly enriched in polycomb repressive complex 2-binding locations, are near genes implicated in mammalian development, cancer, obesity and longevity. Our findings offer new evidence suggesting that aging is evolutionarily conserved and intertwined with developmental processes across all mammals.

Identifying key gait features associated with the radiological grade of knee osteoarthritis

PURPOSE

Knee osteoarthritis (KOA) is characterized by pain and decreased gait function. This study assessed key features that can be used as mechanical biomarkers for KOA severity and progression. The identified features were validated statistically and were further examined by developing a classification model based on a machine-learning algorithm.

METHODS

The study included 227 volunteers with various grades of KOA. The severity of KOA was graded using the Kellgren-Lawrence (KL) system. A total of 165 features were extracted from the gait data. The key features were selected using neighborhood component analysis. The selected features were validated using the t-test. Then, the features were examined by building a classification model using a random forest algorithm.

RESULTS

Twenty features were identified that could discriminate the grade of KOA, including nine features extracted from the knee joint, seven from the hip, two from the ankle and two from the spatiotemporal gait parameters. The t-test showed that some features differed significantly between health and sever group, while some were significantly different among the severe group, and others were significantly different for all KL grades. The areas under the receiver operating characteristic curves for classification were 0.974, 0.992, 0.845, 0.894, and 0.905 for KL grades 0 through 4, respectively.

CONCLUSION

Key gait features reflecting the grade of KOA were identified. The results of the statistical analysis and machine-learning algorithm show that the features can discriminate the severity of disease according to the KL grade.

The cut-off analysis using visual analogue scale and cepstral assessments on severity of voice disorder

Purpose: The aims of this study were to: (1) determine the visual analogue scale (VAS) and cepstrum peak prominence (CPP) cut-off points on the ratings of numerical scale (NS) related to the severity of voice disorder ratings and (2) verify the discriminative power of these cut-off points for distinguishing between different severities of voice disorder. Methods: Auditory-perceptual severity assessments (VAS and four-point NS) of 214 voice samples were performed by three speech-language pathologists and CPP parameters were used for the acoustic analysis. Both VAS and CPP cut-off points were obtained using receiver operating characteristic (ROC) curve analyses, based on their correspondence with NS ratings. Results: A high level of inter- and intra-rater reliability was found for the auditory-perceptual assessments of both VAS and NS. The VAS cut-off points for overall severity (OS), between normal variation and mild/moderate severity, mild/moderate and moderate severity, and moderate and severe severity were 32.7, 51.7, and 71.7 points, respectively, and CPP cut-off points were 7.050, 4.651, and 2.989 points, respectively. Areas under the ROC curves demonstrated excellent specificity and sensitivity of all cut-off points. Conclusions: The VAS and CPP cut-off points of OS of voice disorder demonstrated a high power to discriminate between different severities of voice disorder. The results of this study suggested cut-off points for clinical use.

The role of the maxillary sinus on the voice

The objective of the study was to determine the effect of the maxillary sinus on the voice. The prospective study was conducted at an academic secondary referral center. A prospective chart review of 43 patients (17 males, 26 females) who conducted a voice recording and survey before and 3 months after middle meatal antrostomy whose lesion was confined to the maxillary sinus. Subjective voice changes were surveyed using a questionnaire. After phonation [∧m ma: the Korean pronunciation of 'mother'], [Nu Na: the Korean pronunciation of 'sister'], we analyzed the nasal consonant [m] of [∧m ma] and nasalized vowel [a] of [∧m ma] and [a] of [Nu Na]. In the poll conducted, the change rates for males and females were 41.1 % (7/17) and 15.4 % (4/26), respectively; of the male patients, 85.7 % (6/7) felt that the sound quality was better and 14.3 % (1/6) that it was worse. However, all the female patients felt it was better. Among of the patients with an improved voice, reduced nasal sound was the most frequent observation. In an objective analysis, a tendency to lowered frequencies was observed for nasalized vowels after surgery. Significant differences were observed at second formant frequencies of [a] of [∧m ma] and first formant frequencies of [a] of [Nu Na] in female subjects (P < 0.005). Our findings indicated that the maxillary sinus plays a role in the modification of voice quality. Preoperative counseling is important for patients concerning expected changes in the voice after maxillary sinus surgery.

Voice examination in patients with decreased high pitch after thyroidectomy

Decreased high pitch after thyroidectomy due to injury of the external branch of superior laryngeal nerve (EBSLN) may be a critical, especially to professional voice users. The author studied the usefulness of VRP (voice range profile) and MDVP (multi-dimensional voice program) to evaluate patients who have decreased high pitch after thyroidectomy. A study was performed with 58 females and 9 males who underwent voice assessment between January 2008 and June 2009. The patients were classified as the group of female with no decreased high pitch (group A, n = 52), decreased high pitch (group B, n = 6) and the group of male with no decreased high pitch (group C, n = 9). VRP and laryngeal electromyogram (EMG) was performed in group B.

RESULTS

The preoperative frequency range of group A and B were statistically not different. In Group B, the result of VRP showed that the frequency range was 443.11 ± 83.97, 246.67 ± 49.41, 181.37 ± 80.13 Hz showing significant decrease after the surgery compared to that of the preoperative result. (P < 0.05) In addition, the intensity range was 22.25 ± 2.87, 15.25 ± 2.22, 16.25 ± 2.63 dB respectively showing significant postoperative decrease. (P < 0.05) EMG of the cricothyroid muscle of group B showed decreased potential with 3 patients, normal potential in 2, and the other patient refused to take the examination. In group A and C, the result of VRP revealed no significant difference between the preoperative and postoperative result. VRP is a noninvasive, quick, and practical test to demonstrate decreased frequency range visually and helps to evaluate EBSLN injury in patient with thyroidectomy.

Examining the effect of length/width ratio on the hydro-dynamic behaviour in a DAF system using CFD and ADV techniques

Dissolved air flotation (DAF) is a solid-liquid separation system that uses fine bubbles rising from the bottom to remove particles in water. In this study, we investigated the effect of L/W(L; length, W; width) on the hydrodynamic behavior in a DAF system using CFD (computational fluid dynamics) and ADV (acoustic Doppler velocimetry) technique. The factual full-scale DAF system, L/W ratio of 1:1, was selected and various UW ratio conditions (2:1, 3:1,4:1 and 5:1) were simulated with CFD. For modelling, 2-phase (gas-liquid) flow equations for the conservation of mass, momentum and turbulence quantities were solved using a Eulerian-Eulerian approach based on the assumption that a very small particle is applied in the DAF system. Also, for verification of CFD simulation results, we measured the actual velocity at some points in the full-scale DAF system with the ADV technique. Both the simulation and the measurement results were in good accordance with each other. We concluded that the L/W ratio and outlet geometry play an important role for flow pattern and fine bubble distribution in the flotation zone. In the ratio of 1:1, the dead zone is less than those in other cases. On the other hand, in the ratio of 5:1, the fine bubbles were more evenly distributed.

Application of the flotation process to thicken the sludge from a DAF plant

Dissolved air flotation (DAF) was evaluated for thickening of the sludges from a water treatment plant which uses DAF. Solid flux theory for gravity thickening was applied to the solid flux of DAF sludge. The higher the polymer dosage, at fixed solid concentration, the greater the rising velocity becomes. When applied with solid flux equations, a similar relationship to that of gravity thickening has been found. However, the values were much higher than in gravity thickening, because both the inflow solid concentration and the floating velocity were higher than for settled sludge. With this result, the proper dosage of polymer could be derived from the relationship between total solid flux and withdrawal velocity of DAF sludge.

Dissemination of transferable CTX-M-type extended-spectrum beta-lactamase-producing Escherichia coli in Korea

AIMS

Among 365 Escherichia coli isolated in 2003, 31 cefotaxime-resistant isolates were obtained from clinical specimens taken from adults hospitalized in Busan, Korea. Six extended-spectrum beta-lactamase (ESBL)-producing isolates were investigated further to determine the mechanism of resistance.

METHODS AND RESULTS

These isolates were analysed by antibiotic susceptibility testing, pI determination, plasmid profiles, transconjugation test, PCR-restriction fragment length polymorphism (RFLP), enterobacterial repetitive consensus (ERIC)-PCR and DNA sequencing. All six of these isolates were found to contain the CTX-M-type ESBL genes. Five clinical isolates and their transconjugants produced CTX-M-3. One clinical isolate (K17391) and its transconjugant (trcK17391) produced CTX-M-15. Five clinical isolates also produced another TEM-1. One clinical isolate (K12776) also contained another TEM-52. CTX-M-3 ESBL gene was responsible for the resistance to piperacillin, cephalothin, cefotaxime, cefepime and aztreonam. CTX-M-15 or TEM-52 was especially responsible for the resistance to ceftazidime.

CONCLUSIONS

These results appear to represent the in vivo evolution of CTX-M-type beta-lactamase genes (bla(CTX-M-3) --> bla(CTX-M-15)) under the selective pressure of antimicrobial therapy (especially ceftazidime). PCR-RFLP is a reliable method to discriminate CTX-M-15 gene from CTX-M-3 gene. ERIC-PCR analysis revealed that dissemination of CTX-M-3 was not due to a clonal outbreak of a resistant strain but to the intra-species spread of resistance to piperacillin, cephalothin, cefotaxime, cefepime and aztreonam in Korea.

SIGNIFICANCE AND IMPACT OF THE STUDY

This is the first report of the occurrence of CTX-M-1 cluster ESBLs in Korea. A more comprehensive survey of these ESBL types from Korea is urgently needed because of the in vivo evolution of CTX-M-15 from CTX-M-3. The emergence of these CTX-M-type ESBLs suggests that diagnostic laboratories should screen for ESBLs with ceftazidime as well as cefotaxime; they should still perform clavulanate synergy tests on resistant isolates.

Regulation of osteoclast differentiation by the redox-dependent modulation of nuclear import of transcription factors

This study sought to characterize the reduced glutathione (GSH)/oxidized GSSG ratio during osteoclast differentiation and determine whether changes in the intracellular redox status regulate its differentiation through a RANKL-dependent signaling pathway. A progressive decrease of the GSH/GSSG ratio was observed during osteoclast differentiation, and the phenomenon was dependent on a decrease in total glutathione via downregulation of expression of the gamma-glutamylcysteinyl synthetase modifier gene. Glutathione depletion by L-buthionine-(S,R)-sulfoximine (BSO) was found to inhibit osteoclastogenesis by blocking nuclear import of NF-kappaB and AP-1 in RANKL-propagated signaling and bone pit formation by increasing BSO concentrations in mature osteoclasts. Furthermore, intraperitoneal injection of BSO in mice resulted in an increase in bone density and a decrease of the number of osteoclasts in bone. Conversely, glutathione repletion with either N-acetylcysteine or GSH enhanced osteoclastogenesis. These findings indicate that redox status decreases during osteoclast differentiation and that this modification directly regulates RANKL-induced osteoclastogenesis.

Investigation of a nosocomial outbreak of Acinetobacter baumannii producing PER-1 extended-spectrum beta-lactamase in an intensive care unit

We investigated an outbreak of Acinetobacter baumannii in an adult intensive care unit of Kosin University Gospel Hospital in Busan, Republic of Korea. The outbreak involved 10 cases of infection by A. baumannii producing PER-1 extended-spectrum beta-lactamase over a seven-month period, and was caused by a single pulsed-field gel electrophoresis clone. The epidemic isolates were characterized by slight synergy between clavulanic acid and cefepime. Isoelectric focusing of crude bacterial extracts detected two nitrocefin-positive bands with pI values of 8.0 and 5.3. Polymerase chain reaction amplification and characterization of the amplicons by restriction analysis and direct sequencing indicated that the epidemic isolates carried a bla(PER-1) determinant. The epidemic isolates were characterized by a multidrug-resistant phenotype that remained unchanged over the outbreak, including penicillins, beta-lactam/beta-lactamase inhibitor, extended-spectrum cephalosporins and monobactams. Isolation of infected patients and appropriate carbapenem therapy were successful in ending the outbreak. Our report indicates that the bla(PER-1) resistance determinant may become an emerging therapeutic problem.

Intracellular glutathione status regulates mouse bone marrow monocyte-derived macrophage differentiation and phagocytic activity

Although a redox shift can regulate the development of cells, including proliferation, differentiation, and survival, the role of the glutathione (GSH) redox status in macrophage differentiation remains unclear. In order to elucidate the role of a redox shift, macrophage-like cells were differentiated from the bone marrow-derived monocytes that were treated with a macrophage colony stimulating factor (M-CSF or CSF-1) for 3 days. The macrophagic cells were characterized by a time-dependent increase in three major symptoms: the number of phagocytic cells, the number of adherent cells, and the mRNA expression of c-fms, a M-CSF receptor that is one of the macrophage-specific markers and mediates development signals. Upon M-CSF-driven macrophage differentiation, the GSH/GSSG ratio was significantly lower on day 1 than that observed on day 0 but was constant on days 1-3. To assess the effect of the GSH-depleted and -repleted status on the differentiation and phagocytosis of the macrophages, GSH depletion by BSO, a specific inhibitor of the de novo GSH synthesis, inhibited the formation of the adherent macrophagic cells by the down-regulation of c-fms, but did not affect the phagocytic activity of the macrophages. To the contrary, GSH repletion by the addition of NAC, which is a GSH precursor, or reduced GSH in media had no effect on macrophage differentiation, and led to a decrease in the phagocytic activity. Furthermore, we observed that there is checkpoint that is capable of releasing from the inhibition of the formation of the adherent macrophagic cells according to GSH depletion by BSO. Summarizing, these results indicate that the intracellular GSH status plays an important role in the differentiation and phagocytosis of macrophages.

Investigation of extended-spectrum beta-lactamases produced by clinical isolates of Klebsiella pneumoniae and Escherichia coli in Korea

AIMS

Isolates obtained from various regions in Korea in 2002 were identified and their susceptibility to extended-spectrum cephalosporins, monobactams and/or cephamycins was studied along with any production of extended-spectrum beta-lactamases (ESBLs).

METHODS AND RESULTS

Bacteria identified by the conventional techniques and Vitek GNI card were Klebsiella pneumoniae and Escherichia coli. Using disk diffusion and double-disk synergy tests, we found that 39.2% of strains produced ESBLs. About 52% of isolates transferred resistance to ceftazidime by conjugation. Banding patterns of PCR amplification with the designed primers showed that 837- and 259-bp fragments specific to bla(TEM) genes were amplified in 63.3% of strains. 929- and 231-bp fragments (bla(SHV)), 847- and 520-bp fragments (bla(CMY)), 597- and 858-bp fragments (bla(CTX-M)) were amplified in 61.5, 17.3 and 7.7% of strains respectively. About 51.9% of strains contained more than two types of beta-lactamase genes. Especially, one strain contained bla(TEM), bla(CMY) and bla(CTX-M) genes.

SIGNIFICANCE

Resistance mechanisms to beta-lactams, comprising mostly ESBL production, lead to the resistance against even recently developed beta-lactams in enterobacteria, which is now a serious threat to antibiotic therapy. The high prevalence of bla(CMY) genes and multidrug-resistant genes may also make therapeutic failure and lack of eradiation of these strains by extended-spectrum cephalosporins or cephamycins.

Study on size distribution of total aerosol and water-soluble ions during an Asian dust storm event at Jeju Island, Korea

Soil dust particles transported from loess regions of the Asian continent, called Asian dust, highly influences the air quality of north-eastern Asia and the northern Pacific Ocean. In order to investigate the effects of these dust storms on the chemical composition of atmospheric aerosol particles with different size, measurements of size distributions of total aerosol and major ion species were carried out on Jeju Island, Korea during April 2001. Juju Island was chosen for the study because the levels of emissions of anthropogenic air pollutants are very low. A 5-stage cascade impactor was used to sample size-fractionated aerosol particles. Samples were analyzed for major water-soluble ions using Dionex DX-120 ion chromatograph. The average mass concentration of total aerosol was found to be 24.4 and 108.3 microg m(-3) for non-Asian dust and Asian dust periods, respectively. The total aerosol size distribution, measured during the non-Asian dust period, was bimodal, whereas the coarse particles dominated the size distribution of total aerosol during the Asian dust period. It was found that SO4(2-), NH4+ and K+ were mainly distributed in fine particles, while Cl-, NO3-, Na+, Mg2+ and Ca2+ were in coarse particles. Although SO4(2-) was mainly distributed in fine particles, during the Asian dust period, the concentrations in coarse particles were significantly increased. This indicates heterogeneous oxidation of SO2 on wet surfaces of basic soil dust particles. The NH4+ was found to exist as (NH4)2SO4 in fine particles, with a molar ratio of NH4+ to SO4(2-) of 2.37 and 1.52 for non-Asian dust and Asian dust periods, respectively. Taking into account the proximity of the sampling site to the sea, and the observed chloride depletion, coarse mode nitrate, during the non-Asian dust period, is assumed to originate from the reaction of nitric acid with sodium chloride on the surfaces of sea-salt particles although the chloride depletion was not shown to be large enough to prove this assumption. During the Asian dust period, however, chloride depletion was much smaller, indicating coarse nitrate particles were mainly produced by the reaction of nitric acid with surfaces of basic soil particles. Most chloride and sodium components were shown to originate from sea-salt particles. Asian dust aerosols, arriving at Jeju Island, contained considerable amounts of sea-salt particles as they passed over the Yellow Sea. Ca2+ was shown to be the most abundant species in Asian dust particles.

A case study of dissolved air flotation for seasonal high turbidity water in Korea

A DAF (Dissolved-Air-Flotation) process has been designed considering raw water quality characteristics in Korea. Although direct filtration is usually operated, DAF is operated when freshwater algae blooms occur or raw water turbidity becomes high. Pre-sedimentation is operated in case when the raw water turbidity is very high due to rainstorms. A main feature of this plant is that the operation mode can be changed (controlled) based on the characteristics of the raw water to optimize the effluent quality and the operation costs. Treatment capacity (surface loading rate) and efficiency of DAF was found to be better than the conventional sedimentation process. Moreover, low-density particles (algae and alum flocs) are easily separated while the removal of them by sedimentation is more difficult. One of the main concerns for DAF operation is a high raw water turbidity. DAF is not adequate for raw water, which is more turbid than 100 NTU. In order to avoid this problem, pre-sedimentation basins are installed in the DAF plant to decrease the turbidity of the DAF inflow. For simulation of the actual operation, bench and full-scale tests were performed for highly turbid water conditions. Consequently, it is suggested that pre-sedimentation with optimum coagulation prior to DAF is the appropriate treatment scheme.

Dietary supplementation of (+)-catechin protects against UVB-induced skin damage by modulating antioxidant enzyme activities

PURPOSE

The aim of this study was to investigate the effects of dietary supplementation with (+)-catechin on cutaneous antioxidant enzymes and the skin damage caused by UVB irradiation.

METHODS

BALB/c mice were divided into three groups. Each group was fed a regular diet (RD) or a 2% catechin-supplemented diet for either 2 weeks (2CSD) or 4 weeks (4CSD) ad libitum prior to UVB irradiation. Skin was removed for the antioxidant enzyme assay, hematoxylin and eosin staining, and the TEM analysis before and at various time points after UVB (200 mJ/cm2) irradiation.

RESULTS

Before UVB irradiation, the superoxide dismutase (SOD) and catalase (CAT) activities of the 2CSD and the 4CSD groups were found to be lower than those of the RD group, whereas the glutathione peroxidase (GPx) activity of the 4CSD group was higher than those of the RD and the 2CSD groups (P<0.05). The SOD and CAT activities of the RD group decreased after UVB irradiation, while those of the 2CSD and the 4CSD groups increased immediately after irradiation and then decreased (P<0.05). Immediately after UVB irradiation, the GPx activities of the 4CSD and the 2CSD groups increased, but that of the RD group decreased. The GPx activity of all three groups showed a tendency to return to pre-UVB irradiation levels with time. Light microscopic findings of the RD group showed epidermal thinning and apoptotic cells at 24 h after UVB irradiation and mostly necrotic cells at 48 h, whereas only moderate thickening of the epidermis was observed in the 2CSD group at 48 h after irradiation. An electron microscopic examination produced similar findings. At 48 h after irradiation, nearly all epidermal cells seemed to be damaged in the RD group as compared to the 2CSD group.

CONCLUSION

These results demonstrate that dietary supplementation with (+)-catechin could protect epidermal cells against UVB-induced damage by modulating antioxidant enzyme activities.

Zantedeschia mosaic virus causing leaf mosaic symptom in calla lily is a new potyvirus

Anovel virus, Zantedeschia mosaic virus (ZaMV-KR), causing mosaic and malformation symptoms was isolated from calla lily ( Zantedeschia spp.) in Korea and its biological and molecular properties were characterized. The virus was distinct from Dasheen mosaic virus, an Araceae-infecting potyvirus, by serological and sequence analyses. Multiple alignments of the CP amino acid sequence between the virus and other potyviruses showed 51.8 to 62.1% identity. Phylogenetic analyses of the CP revealed that the virus could be clustered with Plum pox virus and Turnip mosaic virus. Sequence comparison of the CP gene between the virus and three other ZaMV isolates from Taiwan showed over 93.9% identity, and most of amino acids changes occurred in the N-terminal region. Sequence comparison of 3' NTR revealed homology levels of 27.0 to 47.9% between the virus and other potyviruses. Our results support ZaMV as a distinct species of the genus Potyvirus.

Zucchini green mottle mosaic virus is a new tobamovirus; comparison of its coat protein gene with that of kyuri green mottle mosaic virus

A novel virus we call zucchini green mottle mosaic virus (ZGMMV) was isolated from zucchini squash and its properties were determined. The size and shape of its virions, and other properties suggest that the virus is a tobamovirus. The coat protein (CP) genes of ZGMMV and kyuri green mottle mosaic virus (KGMMV), which also infects zucchini squash plants, were cloned and their nucleotides sequences were determined. The CP genes of ZGMMV and KGMMV are composed of 161 amino acid residues, and they share 77.6% amino acid identity. Western blot analysis showed that the two viruses are serologically related but not identical. Comparison of the sequences with those of sixteen other tobamoviruses revealed that the two viruses had much higher identity to cucumber green mottle mosaic virus (CGMMV), another tobamovirus infectious to cucurbit plants, than other tobamoviruses. The nucleotide and amino acid sequences of ZGMMV were from 29.5 to 78.4% and from 29.3 to 77.6% identical, respectively, to those of other tobamoviruses. The predicted virion assembly origins of the two tobamoviruses were located in the CP region of the genomic RNAs, and the predicted secondary structures were more similar to that of CGMMV than those of other tobamoviruses. The seventeen tobamo-viruses could be classified into three main subgroups based on the phylogenetic tree analysis on the CP gene, and ZGMMV and KGMMV formed a third subgroup together with CGMMV and sunn-hemp mosaic virus (SHMV). These results show that ZGMMV is a previously unknown member of the Tobamovirus genus.

Outbreak of rat mite dermatitis in medical students

BACKGROUND

The tropical rat mite, Ornithonyssus bacoti (0. bacoti), is an ectoparasite on many rodents, but when the rodent is not available, humans may become the victim of the mite's bite. The bite induces a nonspecific dermatitis; therefore, it is not easy to diagnose rat mite dermatitis unless the parasites are found.

MATERIALS AND METHODS

Ten cases of rat mite dermatitis were found in medical students who had studied in the same room of the library. Their nonspecific dermatitis consisted of small papules, and parasites were found in the skin or in the environment. The mites were collected and identified as O. bacoti, female. Histopathologic studies showed moderate perivascular lymphohistiocytic infiltrations intermingled with some eosinophils. The presence of rodents in or around the room was confirmed by the students, but there had been no preceding rodent eradication. Although the rats were not captured in the library, insecticides were sprayed, and no further problem with either mites or dermatitis developed during the follow-up period.

CONCLUSIONS

Rat mite dermatitis can occur in clusters that involve a common source of exposure to the rat mite epidemiologically. Prompt identification of rat mites and the eradication of mites and rodents from the environment can prevent further spreading of the disease.