A fuzzy-set-theory-based approach to analyse species membership in DNA barcoding

Reliable assignment of an unknown query sequence to its correct species remains a methodological problem for the growing field of DNA barcoding. While great advances have been achieved recently, species identification from barcodes can still be unreliable if the relevant biodiversity has been insufficiently sampled. We here propose a new notion of species membership for DNA barcoding-fuzzy membership, based on fuzzy set theory-and illustrate its successful application to four real data sets (bats, fishes, butterflies and flies) with more than 5000 random simulations. Two of the data sets comprise especially dense species/population-level samples. In comparison with current DNA barcoding methods, the newly proposed minimum distance (MD) plus fuzzy set approach, and another computationally simple method, 'best close match', outperform two computationally sophisticated Bayesian and BootstrapNJ methods. The new method proposed here has great power in reducing false-positive species identification compared with other methods when conspecifics of the query are absent from the reference database.

Be alert to tuberculosis-mediated glomerulonephritis: a retrospective study

Mycobacterium tuberculosis infection causing glomerulonephritis is a rare disorder. This retrospective study analyzed the clinical characteristics of patients diagnosed with tuberculosis-mediated glomerulonephritis (TB-GN) between 2002 and 2009, as well as the diagnostic tools used. These findings were then compared with those of patients with primary glomerulonephritis (P-GN). The records of all patients were reviewed. The diagnosis of TB-GN was based on renal hematuria and/or proteinuria and cure after antituberculosis therapy alone plus urine culture positive for M. tuberculosis, demonstration of typical tubercle granulomas on renal biopsy specimens, or the detection of M. tuberculosis DNA by polymerase chain reaction (PCR) on renal specimens. Forty-six patients with TB-GN and 49 patients with P-GN were included. Compared with patients in the P-GN group, most (76%) patients with TB-GN had a history of TB. Systemic symptoms were much more frequent in patients with TB-GN than local genitourinary symptoms. Serological testing showed a statistical difference between the two groups. Immunoglobulin A nephropathy was found in the majority (72%) of patients with TB-GN. M. tuberculosis DNA detection was positive in 39 (84.8%) patients, a much higher positive rate of diagnosis than that with urine culture for M. tuberculosis. The manifestation of TB-GN is atypical and nonspecific. It warrants a high index of suspicion when patients with renal hematuria and proteinuria fail to respond to standard treatments for P-GN. Clinicians should pay close attention to the medical history and results of special laboratory tests. M. tuberculosis DNA detection on renal biopsy specimens should be considered in order to confirm the diagnosis of TB-GN.

Bilateral Knee Lipoma Arborescens Combined with Osteoarthritis in Elderly Patients

Here, three cases of combined lipoma arborescens (LA) — a rare neoplastic lesion of the synovium — and osteoarthritis (OA) with bilateral knee involvement in elderly patients are reported. The clinical, magnetic resonance imaging and histological characteristics of this rare condition are described. Limited by the similarity of symptoms between LA and OA and the low sensitivity of X-ray for discerning LA, it was found that a diagnosis of LA could be easily missed. Follow-up data suggested that the treatment of LA was not jeopardized even if the diagnosis was not made preoperatively, since the lesion is easily discerned intraoperatively. The definitive treatment of synovectomy can then be performed without recurrence of the lesion. Based on the evidence of the sequence of symptoms and the progression of untreated LA with static OA at follow up, it is suggested that the aetiology of LA is secondary to OA in elderly patients.

Rheological and fractal characteristics of unconditioned and conditioned water treatment residuals

The rheological and fractal characteristics of raw (unconditioned) and conditioned water treatment residuals (WTRs) were investigated in this study. Variations in morphology, size, and image fractal dimensions of the flocs/aggregates in these WTR systems with increasing polymer doses were analyzed. The results showed that when the raw WTRs were conditioned with the polymer CZ8688, the optimum polymer dosage was observed at 24 kg/ton dry sludge. The average diameter of irregularly shaped flocs/aggregates in the WTR suspensions increased from 42.54 μm to several hundred micrometers with increasing polymer doses. Furthermore, the aggregates in the conditioned WTR system displayed boundary/surface and mass fractals. At the optimum polymer dosage, the aggregates formed had a volumetric average diameter of about 820.7 μm, with a one-dimensional fractal dimension of 1.01 and a mass fractal dimension of 2.74 on the basis of the image analysis. Rheological tests indicated that the conditioned WTRs at the optimum polymer dosage showed higher levels of shear-thinning behavior than the raw WTRs. Variations in the limiting viscosity (η(∞)) of conditioned WTRs with sludge content could be described by a linear equation, which were different from the often-observed empirical exponential relationship for most municipal sludge. With increasing temperature, the η(∞) of the raw WTRs decreased more rapidly than that of the raw WTRs. Good fitting results for the relationships between lgη(∞)∼T using the Arrhenius equation indicate that the WTRs had a much higher activation energy for viscosity of about 17.86-26.91 J/mol compared with that of anaerobic granular sludge (2.51 J/mol) (Mu and Yu, 2006). In addition, the Bingham plastic model adequately described the rheological behavior of the conditioned WTRs, whereas the rheology of the raw WTRs fit the Herschel-Bulkley model well at only certain sludge contents. Considering the good power-law relationships between the limiting viscosity and sludge content of the conditioned WTRs, their mass fractal dimensions were calculated through the models proposed by Shih et al. (1990), which were 2.48 for these conditioned WTR aggregates. The results demonstrate that conditioned WTRs behave like weak-link flocs/aggregates.

In vivo effect of 5-HT₇ receptor agonist on pyramidal neurons in medial frontal cortex of normal and 6-hydroxydopamine-lesioned rats: an electrophysiological study

The 5-hydroxytryptamine (5-HT)-7 receptor began to be cloned and pharmacologically characterized close to 20 years ago. It couples positively via G-proteins to adenylyl cyclase and activation of this receptor increases neuronal excitability, and several studies have shown that degeneration of the nigrostriatal pathway leads to an impairment of 5-HT system. Here we reported that systemic and local administration of 5-HT₇ receptor agonist AS 19 produced excitation, inhibition and no change in the firing rate of pyramidal neurons in medial prefrontal cortex (mPFC) of normal and 6-hydroxydopamine-lesioned rats. In normal rats, the mean response of the pyramidal neurons to AS 19 by systemic and local administration in mPFC was excitatory. The inhibitory effect by systemic administration of AS 19 was reversed by GABA(A) receptor antagonist picrotoxinin. Systemic administration of picrotoxinin excited all the neurons examined in normal rats, and after treatment with picrotoxinin, the local administration of AS 19 further increased the firing rate of the neurons. In the lesioned rats, systemic administration of AS 19, at the same doses, also increased the mean firing rate of the pyramidal neurons. However, cumulative dose producing excitation in the lesioned rats was higher than that of normal rats. Systemic administration of AS 19 produced inhibitory effect in the lesioned rats, which was partially reversed by picrotoxinin. The local administration of AS 19, at the same dose, did not change the firing rate of the neurons in the lesioned rats. Systemic administration of picrotoxinin and the local administration of AS 19 did not affect the firing rate of the neurons in the lesioned rats. These results indicate that activity of mPFC pyramidal neurons is regulated through activation of 5-HT₇ receptor by direct or indirect action, and degeneration of the nigrostriatal pathway leads to decreased response of these neurons to AS 19, suggesting dysfunction and/or down-regulation of 5-HT₇ receptor on the pyramidal neurons and GABA interneurons in the lesioned rats.

Cross talk between activation of microglia and astrocytes in pathological conditions in the central nervous system

Microglia and astrocytes in the central nervous system are now recognized as active participants in various pathological conditions such as trauma, stroke, or chronic neurodegenerative disorders. Their activation is closely related with the development and severity of diseases. Interestingly, activation of microglia and astrocytes occurs with a spatially and temporarily distinct pattern. The present review explores the cross talk in the process of their activation. Microglia, activated earlier than astrocytes, promote astrocytic activation. On the other hand, activated astrocytes not only facilitate activation of distant microglia, but also inhibit microglial activities. Molecules contributing to their intercommunication include interleukin-1 (IL-1), adenosine triphosphate (ATP), and transforming growth factor beta (TGF-β). A better understanding about the cross talk between activation of microglia and astrocytes would be helpful to elucidate the role of glial cells in pathological conditions, which could accelerate the development of treatment for various diseases.

First Report of Fusarium cerealis Causing Fusarium Head Blight on Barley in China

The fungus Fusarium cerealis (Cooke) Sacc. (1886) (synonym F. crookwellense L.W. Burgess, P.E. Nelson et Toussoun (1982)) is one of the causal agents of Fusarium head blight (FHB), a significant fungal disease of small grains and maize in many countries (3). Miller et al. identified trichothecene chemotypes from three F. cerealis (F. crookwellense) strains collected from Chinese wheat in 1991 (2). However, there have been no other reports of this Fusarium species in China since then. The disease has been an important threat to the production of wheat and barley in China, and has caused yield losses of approximately 212,000 t (data from China National Agro-Technical Extension and Service Center) in 2008, one of the most severe FHB epidemic years in Chinese wheat in the past 10 years. Scabby heads of barley and wheat were collected from Yuxi and Zhaotong in Yunnan Province, respectively, in 2008. Each of 15 strains was isolated from a different spike of barley and eight isolates were derived from different wheat spikes. All strains were single spored. On the basis of a multilocus genotyping assay (4), all 15 isolates from barley and six of the eight strains from wheat were identified as F. cerealis with the nivalenol (NIV) genotype. To validate this result, partial translation elongation factor (TEF-1α, ~700 bp) gene sequences of isolates were generated (GenBank Accession Nos. HQ824369 and HQ824370) and then compared with the FUSARIUM-ID database (1). The TEF-1α sequences of all 21 isolates were highly conserved and showed 100% identity with the sequences of F. cerealis in the database. A pathogenicity test was performed on a winter wheat cultivar, Yangmai158, using a three-replicate randomized complete block design in Langfang Experimental Farm. Langfang is not an FHB-endemic area and is very dry, with almost no infection source in normal years. At anthesis, the central floret of each of five spikes was injected with 20 μl of a conidial suspension (10⁶ macroconidia/ml) of each isolate in each block, such that 105 spikes were injected per block. An equal amount of water was injected into five heads in each block as a control. The inoculated spikes were enclosed in sandwich bags misted with water for 3 days to ensure infection by the inoculated pathogen and prevent infections from other sources. The plots were misted twice daily after inoculation. The average night and day temperatures were 19.0 and 25.2°C, respectively. Typical FHB symptoms (light tan or bleached spikelets, bases of infected spikelets, and portions of the rachis were dark brown), which were observed in the heads inoculated with F. cerealis 7 days after inoculation, were similar to the original symptoms in the sampling sites. The control plants remained asymptomatic. F. cerealis was reisolated from the infected heads, indicating it was the pathogen causing this disease. To our knowledge, this is the first report of F. cerealis causing FHB on barley in China, and also the first time that a high proportion of F. cerealis strains were isolated from one sampling site (15 of 15 in Yuxi and 6 of 8 in Zhaotong). More isolates must be collected in Yunnan Province and further studies conducted to gain a better understanding of the spatial and temporal dynamics of this pathogen. References: (1) D. M. Geiser et al. Eur. J. Plant Pathol. 110:473, 2010. (2) J. D. Miller et al. Mycologia 83:121, 1991. (3) D. W. Parry et al. Plant Pathol. 44:207, 1995. (4) T. J. Ward et al. Fungal Genet. Biol. 45:473, 2008.

Electronic structure of warm dense copper studied by ultrafast x-ray absorption spectroscopy

We use time-resolved x-ray absorption spectroscopy to investigate the unoccupied electronic density of states of warm dense copper that is produced isochorically through the absorption of an ultrafast optical pulse. The temperature of the superheated electron-hole plasma, which ranges from 4000 to 10 000 K, was determined by comparing the measured x-ray absorption spectrum with a simulation. The electronic structure of warm dense copper is adequately described with the high temperature electronic density of state calculated by the density functional theory. The dynamics of the electron temperature is consistent with a two-temperature model, while a temperature-dependent electron-phonon coupling parameter is necessary.

New Measurement of the π0 radiative decay width

High precision measurements of the differential cross sections for π0 photoproduction at forward angles for two nuclei, 12C and 208Pb, have been performed for incident photon energies of 4.9-5.5 GeV to extract the π0→γγ decay width. The experiment was done at Jefferson Lab using the Hall B photon tagger and a high-resolution multichannel calorimeter. The π0→γγ decay width was extracted by fitting the measured cross sections using recently updated theoretical models for the process. The resulting value for the decay width is Γ(π0→γγ)=7.82±0.14(stat)±0.17(syst)  eV. With the 2.8% total uncertainty, this result is a factor of 2.5 more precise than the current Particle Data Group average of this fundamental quantity, and it is consistent with current theoretical predictions.

O45-regulation of osteoblast differentiation and ECM remodeling by Bmp2/4 in vitro

Both of bone morphogenetic proteins 2 and 4 (Bmp2 and Bmp4) are two closely related members of the transforming growth factor beta superfamily and play diverse roles in normal and pathological processes. However, detail understandings of mechanisms through which Bmp2 and Bmp4 exert their effects remain elusive due to their functional compensations each other. To study roles of Bmp2/Bmp4 in osteoblast differentiation and extracellular matrix (ECM) remodeling, calvarial osteoblasts from Bmp2/4 conditional mice with Cre recombinase recognition site (loxP) were isolated and transfected with simian virus 40 large T antigen to generate immortalized BMP2C/C4C/C (iBMP2 C/C/4C/C) osteoblast lines. The BMP2/4 genes in the iBMP2 C/C/4C/C cells were double knocked out by Ad-Cre recombinase infection. Differentiation and mineralization of iBMP2C/C/4C/C knock-out (iBmp2C/C/4C/C KO) cells were detected by alkaline phosphatase (ALP) and alizarin (ALZ) red S staining analyses. ECM remodeling was also observed in fluorescent microscope. Cell differentiation was dramatically decreased in the iBMP2C/C/4C/C KO cells compared to that of the iBMP2C/C/4C/C osteoblasts. Mineralization was also reduced in these KO cells by ALZ staining. Furthermore, Bmp2/4 double knock-out cells have major defects in remodeling the ECM as reflected by changes in collagen type I processing. Here we for the first time demonstrate the establishment of iBmp2C/C/4C/C KO osteoblasts. Cell differentiation and mineralization in the iBmp2C/C/4C/C KO cells were decreased. Furthermore, ECM processing in these KO cells was impaired. This indicates that BMP2/4 play important roles in osteoblast differentiation and ECM remodeling.

Exercise impacts brain-derived neurotrophic factor plasticity by engaging mechanisms of epigenetic regulation

We have evaluated the possibility that the action of voluntary exercise on the regulation of brain-derived neurotrophic factor (BDNF), a molecule important for rat hippocampal learning, could involve mechanisms of epigenetic regulation. We focused the studies on the Bdnf promoter IV, as this region is highly responsive to neuronal activity. We have found that exercise stimulates DNA demethylation in Bdnf promoter IV, and elevates levels of activated methyl-CpG-binding protein 2, as well as BDNF mRNA and protein in the rat hippocampus. Chromatin immunoprecipitation assay showed that exercise increases acetylation of histone H3, and protein assessment showed that exercise elevates the ratio of acetylated :total for histone H3 but had no effects on histone H4 levels. Exercise also reduces levels of the histone deacetylase 5 mRNA and protein implicated in the regulation of the Bdnf gene [N.M. Tsankova et al. (2006)Nat. Neurosci., 9, 519-525], but did not affect histone deacetylase 9. Exercise elevated the phosphorylated forms of calcium/calmodulin-dependent protein kinase II and cAMP response element binding protein, implicated in the pathways by which neural activity influences the epigenetic regulation of gene transcription, i.e. Bdnf. These results showing the influence of exercise on the remodeling of chromatin containing the Bdnf gene emphasize the importance of exercise on the control of gene transcription in the context of brain function and plasticity. Reported information about the impact of a behavior, inherently involved in the daily human routine, on the epigenome opens exciting new directions and therapeutic opportunities in the war against neurological and psychiatric disorders.

Cadmium directly induced mitochondrial dysfunction of human embryonic kidney cells

Cadmium (Cd) is the major component of polluted environment, which has numerous undesirable effects on health. Cd could induce apoptosis of HEK293 cells, and the mitochondria may play a key role. However, the mode of action is unclear. In the present study, we aimed to evaluate the ability of the Cd to induce dysfunction of mitochondria. We examined the effect of cadmium chloride (1, 5 and 10 μM) on mitochondrial membrane permeability and potential as well as oxidative stress markers in mitochondria isolated from HEK293 cells. We found that Cd could directly increase in permeability and decrease in membrane potential of mitochondria, even resulted in mitochondrial swelling, and that Cd could inhibit the activities of ATPase, lactate dehydrogenase (LDH), superoxide dismutase (SOD) and glutathione peroxidase (GSH-Px), enhanced the levels of reactive oxygen species (ROS) and lipid peroxidation (LPO). On the whole, the results show that Cd can directly lead to mitochondrial dysfunction of HEK293 cells, including increased permeability, inhibiting respiration and evoking oxidative stress. Thus, for the first time, this paper makes an overall analysis of Cd-induced changes of structure and function of isolated mitochondria. Our findings may also have general implications in Cd-induced apoptosis by mitochondria pathway.

Evidence for significantly enhancing reduction of Azo dyes in Escherichia coli by expressed cytoplasmic Azoreductase (AzoA) of Enterococcus faecalis

Although cytoplasmic azoreductases have been purified and characterized from various bacteria, little evidence demonstrating that these azoreductases are directly involved in azo dye reduction in vivo is known. In order to evaluate the contribution of the enzyme to azo dye reduction in vivo, experiments were conducted to determine the effect of a recombinant cytoplasmic azoreductase (AzoA) from Enterococcus faecalis expressed in Escherichia coli on the rate of metabolism of Methyl Red, Ponceau BS and Orange II. The intact cells that contained IPTG induced AzoA had a higher rate of dye reduction with increases of 2 (Methyl Red), 4 (Ponceau BS) and 2.6 (Orange II)-fold compared to noninduced cells, respectively. Metabolites of Methyl Red isolated from induced cultures were identified as N,N-dimethyl-p-phenylenediamine and 2-aminobenzoic acid through liquid chromatography electrospray ionization tandem mass spectrometry (LC/ESI-MS/MS) analyses. In conclusion, our data demonstrate that AzoA from Ent. faecalis is capable of increasing the reduction of azo dyes in intact E. coli cells and that cytoplasmic azoreductase is involved in bacterial dye degradation in vivo.

Time-resolved demagnetization of Co2MnSi observed using x-ray magnetic circular dichroism and an ultrafast streak camera

The demagnetization dynamics of the Heusler alloy Co(2)MnSi was studied using picosecond time-resolved x-ray magnetic circular dichroism. The sample was excited using femtosecond laser pulses. In contrast to the sub-picosecond demagnetization of the metal ferromagnet Ni, substantially slower demagnetization with a time constant of 3.5 ± 0.5 ps was measured. This could be explained by a spin-dependent band gap inhibiting the spin-flip scattering of hot electrons in Co(2)MnSi, which is predicted to be half-metallic. A universal demagnetization time constant was measured across a range of pump power levels.

Glycosaminoglycan chain of dentin sialoprotein proteoglycan

Dentin sialophosphoprotein (DSPP) is processed into dentin sialoprotein (DSP) and dentin phosphoprotein. A molecular variant of rat DSP, referred to as "HMW-DSP", has been speculated to be a proteoglycan form of DSP. To determine if HMW-DSP is the proteoglycan form of DSP and to identify the glycosaminoglycan side-chain attachment site(s), we further characterized HMW-DSP. Chondroitinase ABC treatment reduced the migration rate for portions of rat HMW-DSP to the level of DSP. Disaccharide analysis showed that rat HMW-DSP contains glycosaminoglycan chains made of chondroitin-4-sulfate and has an average of 31-32 disaccharides/mol. These observations confirmed that HMW-DSP is the proteoglycan form of DSP (renamed "DSP-PG"). Edman degradation and mass spectrometric analyses of tryptic peptides from rat DSP-PG, along with substitution analyses of candidate Ser residues in mouse DSPP, confirmed that 2 glycosaminoglycan chains are attached to Ser(241) and Ser(253) in the rat, or Ser(242) and Ser(254) in the mouse DSPP sequence.

The novel estrogen-induced gene EIG121 regulates autophagy and promotes cell survival under stress

We previously identified a novel estrogen-induced gene, EIG121, as being differentially regulated in endometrioid and nonendometrioid endometrial carcinoma. The function of EIG121 was unknown. Using a tetracycline-inducible system, we found that overexpression of EIG121, but not of LacZ, caused a profound suppression of cell growth. Subcellular fractionation and immunofluroscent labeling indicated that EIG121 was a transmembrane protein localized in the plasma membrane-late endosome–lysosome compartments. Deletion of the putative transmembrane domain abolished the membrane association. In cells overexpressing EIG121, cytoplasmic vacuoles accumulated after EIG121 induction, and the autophagosome marker LC3 translocated into punctuate, dot-like structures. Electron microscopy revealed that in cells overexpressing EIG121, autophagosomes were markedly increased. Overexpression of EIG121 also increased the cells containing acidic vesicles and induced lysosomal degradation of long-lived proteins. In MCF-7 cells, both EIG121 and LC3 were rapidly degraded by a lysosomal mechanism after starvation. Knockdown of EIG121 blocked starvation-induced LC3 degradation. By itself, knockdown of EIG121 did not affect cell survival. When combined with starvation or cytotoxic agents, EIG121 knockdown greatly increased apoptosis. Our results suggest that EIG121 is associated with the endosome–lysosome compartments and may have an important role in autophagy. Under unfavorable conditions such as starvation and exposure to cytotoxic agents, EIG121 may protect cells from cell death by upregulating the autophagy pathway.