Phylogenetic characterization of novel transport protein families revealed by genome analyses

As a result of recent genome sequencing projects as well as detailed biochemical, molecular genetic and physiological experimentation on representative transport proteins, we have come to realize that all organisms possess an extensive but limited array of transport protein types that allow the uptake of nutrients and excretion of toxic substances. These proteins fall into phylogenetic families that presumably reflect their evolutionary histories. Some of these families are restricted to a single phylogenetic group of organisms and may have arisen recently in evolutionary time while others are found ubiquitously and may be ancient. In this study we conduct systematic phylogenetic analyses of 26 families of transport systems that either had not been characterized previously or were in need of updating. Among the families analyzed are some that are bacterial-specific, others that are eukaryotic-specific, and others that are ubiquitous. They can function by either a channel-type or a carrier-type mechanism, and in the latter case, they are frequently energized by coupling solute transport to the flux of an ion down its electrochemical gradient. We tabulate the currently sequenced members of the 26 families analyzed, describe the properties of these families, and present partial multiple alignments, signature sequences and phylogenetic trees for them all.

Ferroptosis-Related Gene Signature Predicts Glioma Cell Death and Glioma Patient Progression

Glioma is a fatal brain tumor characterized by rapid proliferation and treatment resistance. Ferroptosis is a newly discovered programmed cell death and plays a crucial role in the occurrence and progression of tumors. In this study, we identified ferroptosis specific markers to reveal the relationship between ferroptosis-related genes and glioma by analyzing whole transcriptome data from Chinese Glioma Genome Atlas, The Cancer Genome Atlas dataset, GSE16011 dataset, and the Repository of Molecular Brain Neoplasia Data dataset. Nineteen ferroptosis-related genes with clinical and pathological features of glioma were identified as highly correlated. Functional assays in glioma cell lines indicated the association of ferroptosis with temozolomide resistance, autophagy, and glioma cell migration. Therefore, the identified ferroptosis-related genes were significantly correlated with glioma progression.

Effects of ginsenoside Rb1 on central cholinergic metabolism

Ginsenosides, the saponins of ginseng, are bioactive ingredients which exert many beneficial effects. One ginsenoside, Rb1, extracted from North American ginseng (Panax quinquefolium L.), partially prevents the memory deficits induced by a cholinergic agent (scopolamine) in rats. In vitro studies show that Rb1 has no effect on quinuclidinyl benzylate binding or on acetylcholinesterase activity, but facilitates the release of acetylcholine (ACh) from hippocampal slices. The increase in ACh release is associated with an increased uptake of choline into nerve endings; however, calcium influx is unaltered. The ability of Rb1 to prevent memory deficits may be related to facilitation of ACh metabolism in the central nervous system.

Bacterial invasion into dentinal tubules of human vital and nonvital teeth

The difference in resistance to bacterial invasion into the dentinal tubules between vital and nonvital teeth has not been determined. This study was conducted to clarify the effect of vital pulp on bacterial invasion into the dentinal tubules. The specimens were 19 intact pairs of bilateral upper third molars of 19 healthy, young adult male volunteers. In each case, 30 or 150 days before extraction, pulpectomies and root canal fillings were carried out unilaterally and a class V cavity involving the dentin was made on the palatal surface of both the pulpectomized tooth and the nonpulpectomized opposite tooth. The cavities were left unprotected to expose them to oral flora until the extractions were done, and the extracted teeth were examined histologically. When extraction followed 150-day exposure to the oral flora, there was a statistically significant difference in the bacterial invasion rate between the vital and nonvital teeth. It was postulated that vital teeth were much more resistant to bacterial invasion into the dentinal tubules than were nonvital teeth, thereby suggesting that the vital pulp plays some important role in this process.

Vasopressin and PGE(2) regulate activity of apical 70 pS K(+) channel in thick ascending limb of rat kidney

Vasopressin and prostaglandin E(2) (PGE(2)) are involved in regulating NaCl reabsorption in the thick ascending limb (TAL) of the rat kidney. In the present study, we used the patch-clamp technique to study the effects of vasopressin and PGE(2) on the apical 70 pS K(+) channel in the rat TAL. Addition of vasopressin increased the channel activity, defined as NP(o), from 1.11 to 1.52 (200 pM) and 1.80 (500 pM), respectively. The effect of vasopressin can be mimicked by either forskolin (1-5 microM) or 8-bromo-cAMP/dibutyryl-cAMP (8-Br-cAMP/DBcAMP) (200-500 microM). Moreover, the effects of cAMP and vasopressin were not additive and application of 10 microM H-89 abolished the effect of vasopressin. This suggests that the effect of vasopressin is mediated by a cAMP-dependent pathway. Applying 10 nM PGE(2) alone had no significant effect on the channel activity. However, PGE(2) (10 nM) abolished the stimulatory effect of vasopressin. The PGE(2)-induced inhibition of the vasopressin effect was the result of decreasing cAMP production because addition of 200 microM 8-Br-cAMP/DBcAMP reversed the PGE(2)-induced inhibition. In addition to antagonizing the vasopressin effect, high concentrations of PGE(2) reduced channel activity in the absence of vasopressin by 33% (500 nM) and 51% (1 microM), respectively. The inhibitory effect of high concentrations of PGE(2) was not the result of decreasing cAMP production because adding the membrane-permeant cAMP analog failed to restore the channel activity. In contrast, inhibiting protein kinase C (PKC) with calphostin C (100 nM) abolished the effect of 1 microM PGE(2). We conclude that PGE(2) inhibits apical K(+) channels by two mechanisms: 1) low concentrations of PGE(2) attenuate the vasopressin-induced stimulation mainly by reducing cAMP generation, and 2) high concentrations of PGE(2) inhibit the channel activity by a PKC-dependent pathway.

Biosorption of uranium(VI) by a mangrove endophytic fungus Fusarium sp. #ZZF51 from the South China Sea

The uranium(VI) accumulation was studied in detail by using the biomass of mangrove endophytic fungus Fusarium sp.#ZZF51 from the South China Sea. The uranium(VI) biosorption process onto the tested fungus powders was optimized at pH 4.0, adsorption time 60 min, and uranium(VI) initial concentration 50 mg L⁻¹ with 61.89% of removal efficiency. According to Fourier transform infrared spectra for the tested fungus before and after loaded with uranium(VI), the results showed that both of hydroxyl and carboxyl groups acted as the important roles in the adsorption process. In addition, the experimental data were analyzed by using parameter and kinetic models, and it was obtained that the Langmuir isotherm model and the pseudo-second-order kinetic model provided better correlation with the experimental data for adsorption of uranium(VI).

The ZmCLA4 gene in the qLA4-1 QTL controls leaf angle in maize (Zea mays L.)

Maize architecture is a major contributing factor to their high level of productivity. Maize varieties with an erect-leaf-angle (LA) phenotype, which increases light harvesting for photosynthesis and grain-filling, have elevated grain yields. Although a large body of information is available on the map positions of quantitative trait loci (QTL) for LA, little is known about the molecular mechanism of these QTL. In this study, the ZmCLA4 gene, which is responsible for the qLA4-1 QTL associated with LA, was identified and isolated by fine mapping and positional cloning. The ZmCLA4 gene is an orthologue of LAZY1 in rice and Arabidopsis. Sequence analysis revealed two SNPs and two indel sites in ZmCLA4 between the D132 and D132-NIL inbred maize lines. Association analysis showed that C/T/mutation667 and CA/indel965 were strongly associated with LA. Subcellular localization verified the functions of a predicted transmembrane domain and a nuclear localization signal in ZmCLA4. Transgenic maize plants with a down-regulated ZmCLA4 RNAi construct and transgenic rice plants over-expressing ZmCLA4 confirmed that the ZmCLA4 gene located in the qLA4 QTL regulated LA. The allelic variants of ZmCLA4 in the D132 and D132-NIL lines exhibited significant differences in leaf angle. ZmCLA4 transcript accumulation was higher in D132-NIL than in D132 during all the developmental stages and was negatively correlated with LA. The gravitropic response was increased and cell shape and number at the leaf and stem junctions were altered in D132-NIL relative to D132. These findings suggest that ZmCLA4 plays a negative role in the control of maize LA through the alteration of mRNA accumulation, leading to altered shoot gravitropism and cell development. The cloning of the gene responsible for the qLA4-1 QTL provides information on the molecular mechanisms of LA in maize and an opportunity for the improvement of plant architecture with regard to LA through maize breeding.

Differential north to south gastric cancer-duodenal ulcer gradient in China. China Ulcer Study Group

There are suggestions that duodenal ulcer protects individuals from gastric cancer and that rice is ulcerogenic while wheat is gastro-protective. We aimed to examine the relationship of gastric cancer, duodenal and gastric ulcers in different geographical regions in China and identified dietary risk factors for duodenal ulcer and gastric cancer. The prevalence of peptic ulcer and gastric cancer among symptomatic patients in eight major cities, four each from the north and the south representing all the six defined regions of China were studied. Endoscopy and case records over a 10 year period were reviewed and cases of confirmed duodenal and gastric ulcer and gastric cancer, together with the total number of endoscopies performed per year, were recorded. Rates were expressed as cases/1000 endoscopies. Results were compared to another epidemiological study on diet and mortality in the same regions in China conducted at the same time. Duodenal ulcer rates were 2.4-fold higher in southern China than northern China, whereas gastric cancer rates were 1.6-fold higher in the north than in the south. Correlation studies showed for the first time an inverse linear relationship between the gastric cancer rates and the duodenal ulcer rates (r=-0.8076, P=0.015), as well as the duodenal ulcer: gastric ulcer ratios (r=-0.9133, P=0.002). Gastric ulcer rates were higher in southern China but did not correlate with the gastric cancer rates (r=0.1455, P=0.731). Duodenal ulcer rates were found to be related to daily rice intake (r=0.8554, P=0.029) and inversely related to daily wheat flour intake (r=-0.8472, P=0.033). Gastric cancer rates were not related to any dietary risk factors tested. We concluded there was an inverse relationship between gastric cancer rates and duodenal ulcer rates. Although duodenal ulceration and gastric cancer are both linked to Helicobacter pylori infection, the findings of this study indicate independent additional aetiological factors for the pathogenesis of these conditions. Dietary factors such as rice or wheat intake may play a role.

Polarized absorption spectra of single-walled 4 A carbon nanotubes aligned in channels of an AlPO(4)-5 single crystal

We report the polarized optical absorption spectra of single-walled 4 A carbon nanotubes arrayed in the channels of an AlPO (4)-5 single crystal. When the light electric field (E) is polarized parallel to the tube direction (c), the spectra display a sharp peak at 1.37 eV, with two broadbands at 2.1 and 3.1 eV. In the E perpendicular c configuration, the tube is nearly transparent in the measured energy region 0.5-4.1 eV. The optical dipole selection rules are discussed, and the absorption bands are assigned to the dipole transitions between the Van Hove singularities. The measured absorption spectra agreed well with the ab initio calculations of band structure based on the local density function approximation.

Molecular characterization of Newcastle disease viruses isolated from recent outbreaks in Taiwan

A reverse transcription-polymerase chain reaction (RT-PCR) was described which amplified a portion of the F and HN genes of Newcastle disease virus (NDV) isolated from recent outbreaks in Taiwan. The F protein plays an important role in determining the virulence of NDV strains. Sequencing of a region specifying the F protein cleavage site was therefore undertaken and this verified the correlation between deduced amino sequences and pathogenicity. Analysis of the deduced amino acid sequences of the F protein cleavage site showed that all recent Taiwanese isolates in 1999 were velogenic viruses. All the virulent viruses have the amino acid sequence 112RRQKR116 for the C-terminus of the F2 protein and phenylanine (F) at the N-terminus of the F1 protein, residue 117. A phylogenetic tree based on the nucleotide sequences of the F gene revealed that recent Taiwanese NDV isolates responsible for recent outbreaks were classified into two distant genotypes (VI and VII). Genotype VI virus is the first finding in Taiwan and has a highly genetic similarity to European isolates, suggesting that they might have originated from a common ancestor.

Identification of the sigma C-encoded gene of avian reovirus by nested PCR and restriction endonuclease analysis

A nested reverse transcription (RT)-polymerase chain reaction with subsequent restriction endonuclease analysis was developed for identification of the sigma C-encoded gene of avian reoviruses (ARV). PCR products derived from the sigma C-encoded gene of all tested ARVs resulted in a specific DNA band of 1023 bp, indicating that there were no apparent insertions or deletions in this region. Amplification with the nested primer pairs S1M-S1N and S1P-S1N generated 330 and 239 bp, respectively. PCR products amplified from the sigma C-encoded of all tested ARVs isolates were further confirmed by Southern blot hybridization and restriction endonuclease analysis. PCR amplified cDNA fragment (1023 bp) cleaved with Pst I generated two fragments of 565 and 458 bp. The amplified sigma C-encoded gene of ARV was subcloned into PQE 32 vector for further study of its antigenicity and immunogenicity. The sensitivity of RT-PCR was examined on nucleic acids from the ARV infected cell cultures. The detection limit was 10(0) to 10(-1) TCID50 of ARV in a ethidium bromide stained gel and could be increased further to 10(-1) to 10(-2) TCID50 of ARV by Southern blot hybridization using a digoxigenin-labeled cDNA probe. The sensitivity increased approximately 10(3) to 10(4) folds when the cDNA was reamplified with two sets of nested primers.

Induction of heat-shock response and alterations of protein phosphorylation by a novel topoisomerase II inhibitor, withangulatin A, in 9L rat brain tumor cells

Withangulatin A is a newly identified in vitro topoisomerase II inhibitor isolated from the Chinese antitumor herb Physalis angulata. In vivo, it was found to be cytotoxic, capable of suppressing general protein synthesis and of inducing the synthesis of a small set of proteins including those generated by heat-shock treatment. The 70 kDa protein generated by withangulatin A was unequivocally identified as the heat-shock protein 70 (HSP70) since both proteins migrated to the same position on two-dimensional polyacrylamide gels, could be recognized by a monoclonal antibody to human HSP70, and exhibited identical peptide maps. The induction of protein synthesis by withangulatin A was regulated at the transcriptional level since it was aborted in cells pre-treated with actinomycin D. However, the initiation of this process did not require de novo protein synthesis since it was not affected by cycloheximide. Other cellular effect of withangulatin A was alterations of protein phosphorylation including an enhancement of phosphorylation of a 65 kDa protein which was also detected in the heat-shocked cells. Moreover, this process was observed within 7.5 min after the initial heat treatment which is much faster than the onset of HSP synthesis. Therefore, increased phosphorylation of the 65 kDa protein may represent one of the earliest signals generated by both heat-shock and withangluatin A and may be involved in the upstream regulation of heat-shock response in cells.

Comparison of complications in cranioplasty with various materials: a systematic review and meta-analysis

Objective: Meta-analysis to evaluate complications in the use of autogenous bone and bone substitutes and to compare bone substitutes, specifically HA, polyetheretherketone (PEEK) and titanium materials.Methods: Search of PubMed, Cochrane, Embase and Google scholar to identify all citations from 2010 to 2019 reporting complications regarding materials used in cranioplasty.Results: 20 of 2266 articles met the inclusion criteria, including a total of 2913 patients. The odds of overall complication were significantly higher in the autogenous bone group (n = 214/644 procedures, 33.2%) than the bone substitute groups (n = 116/436 procedures, 26.7%, CI 1.29-2.35, p < 0.05). In bone substitutes groups, there was no significant difference in overall complication rate between HA and Ti (OR, 1.2; 95% CI, 0.47-3.14, p = 0.69). PEEK has lower overall complication rates (OR, 0.51; 95% CI, 0.30-0.87, p = 0.01) and lower implant exposure rates (OR, 0.17; 95% CI, 0.06-0.53, p = 0.002) than Ti, but there was no significant difference in infection rates and postoperative hematoma rates.Conclusions: Cranioplasty is associated with high overall complication rates with the use of autologous bone grafts compared with bone substitutes. PEEK has a relatively low overall complication rates in substitutes groups, but still high infection rates and postoperative hematoma rates. Thus, autologous bone grafts should only be used selectively, and prospective long-term studies are needed to further refine a better material in cranioplasty.

Structure and genomic organization of porcine RACK1 gene

The cDNA encoding porcine RACK1 protein was isolated from porcine spleen cDNA library. The deduced protein sequence of porcine RACK1 cDNA shows that it contains 317 amino acid residues, and shares nearly 100% identity with its vertebrate counterparts. Noticeably, the RACK1 protein was differentially expressed in various porcine tissues. High expression of RACK1 protein was observed in the tissues including thymus, pituitary, spleen and liver, whereas there was no detectable expression in muscle. The genomic DNA of porcine RACK1 with approximate 7.5 kb was constructed by both polymerase chain reaction amplification and genomic library screening. It consists of eight exons intervened by seven introns, and most of the intron/exon splice sites conform to the GT/AG rule. The promoter region contains functional serum response element, YY1-like binding site and AP1 site, which is supported by the finding that the expression of RACK1 gene in cultured porcine ST cells has a serum response as well as a TPA response.

Detection of hepatitis C virus RNA sequences in B-cell non-Hodgkin lymphoma

Serologic testing shows that hepatitis C virus (HCV) may have a role in the pathogenesis of B-cell non-Hodgkin lymphomas (B-cell NHLs). We tried to demonstrate HCV RNA sequences in paraffin-embedded tissue from B-cell NHLs by reverse-transcription double polymerase chain reaction (RT-PCR) and Southern blotting. We studied 31 consecutive cases of B-cell NHLs; lymph nodes from 32 patients with diseases other than B-cell NHL were negative controls. Positive-strand HCV RNA was tested with primers for the 5' untranslated region. Replicative negative strand HCV RNA was tested with strand-specific RT-PCR for the 5' untranslated region. Immunohistochemical staining for HCV was done using an antibody to HCV core protein. Positive-strand HCV RNA was detected in 8 patients with B-cell NHL; negative-strand HCV RNA was detected in 6 of these cases, indicating viral replication. All control cases were negative for HCV RNA. Immunohistochemistry showed no staining of lymphoma cells for HCV core proteins in any case. HCV and B-cell NHLs may be associated. RT-PCR on paraffin-embedded lymphoma tissue is an alternative method of testing for HCV. The value of immunohistochemistry could not be ascertained. The exact role of HCV in the pathogenesis of B-cell NHL needs to be studied further.

Detection of genetic variations in serotype I isolates of infectious bursal disease virus using polymerase chain reaction and restriction endonuclease analysis

Reverse transcription with polymerase chain reaction (PCR) followed by restriction endonuclease analysis detected genetic variations among serotype I isolates of infectious bursal disease virus (IBDV). Using a set of synthetic primers derived from the large genome segment of APHIS-IBDV, the hypervariable region (AccI-SpeI fragment) located in the VP2 gene was amplified. With all strains, a cDNA fragment of approximately 643 bp was amplified, indicating that there were no apparent deletions or insertions in this region among isolates. Fragments amplified from 9 isolates were digested with 14 restriction enzymes. Restriction fragment profiles generated by restriction enzymes NaeI, StuI, TaqI, and SacI, showed genetic variations among isolates. This study provided a simple and sensitive method for detection of genetic variations among isolates that are closely related serologically and could not be differentiated using current serologic methods.

Household gas cooking: a risk factor for respiratory illnesses in preschool children

AIMS

To explore the association of household gas cooking and respiratory illnesses in preschool children and their relation to outdoor air pollution.

METHODS

Cross-sectional study among households that used gas stoves for cooking in two housing estates with contrasting air qualities in Hong Kong. A structured questionnaire was administered to parents of 426 children aged 0-6 years on their exposure to gas cooking and passive smoking, and the prevalence of respiratory illnesses.

RESULTS

A total of 111 children (26.1%) were reported to have one or more respiratory illnesses (allergic rhinitis, asthma, bronchitis, sinusitis, and pneumonia). Of these, 21 (18.9%), 41 (36.9%), and 49 (44.1%) children were from households that cooked once, twice, and three times a day with gas. Hierarchical logistic regression models adjusting for socioeconomic, demographic, and indoor risk factors including passive smoking showed that household gas cooking was positively associated with respiratory illnesses. There was a dose-response relation between the frequency of gas cooking and the prevalence of respiratory illnesses in the estate with lower outdoor air pollution (OR = 6.1 and 3.2 respectively, for cooking three and two meals a day, compared to one meal a day). This relation was not observed in the more polluted estate. The association between the presence of a cigarette smoker in the household and the prevalence of respiratory illnesses was not significant.

CONCLUSIONS

As gas cooking is common in urban households, the findings could have important public health implications.

Expression and activation of caspase-3/CPP32 in CD34(+) cord blood cells is linked to apoptosis after growth factor withdrawal

Caspase-3/CPP32, a member of the interleukin-1 converting enzyme (ICE) family, is considered an executioner protease in mammalian cells during apoptosis. Although expression and activation of caspase-3/CPP32 protein have been studied in many tissues and leukemia cell lines, this has not been explored in primitive hematopoietic CD34(+) cells. In this study, we evaluated expression and activation of caspase-3/CPP32 protein in CD34(+) cells from cord blood (CB) during apoptosis induced by growth factor deprivation. Reverse transcriptase-polymerase chain reaction (RT-PCR), Western blot, and flow cytometry analysis were used in this study to determine the expression of caspase-3/CPP32 in CD34(+) CB cells during apoptosis. Our results demonstrated that caspase-3/CPP32 mRNA was constitutively expressed at a very low level in freshly isolated CD34(+) cells. Expression of caspase-3/CPP32 mRNA and protein was upregulated when these cells were first expanded in suspension culture with growth factors for 3 days. However, only the 32 kDa inactive caspase-3/CPP32 proenzyme was detected in the freshly isolated CD34(+) cells and after 3 days expansion with cytokines. Within 12 hours after growth factor withdrawal from expanded cells caspase-3/CPP32 was activated and a cleavage 20 kDa protein was detected; a poly(ADP-ribose) polymerase (PARP) was cleaved by activated caspase-3/CPP32. Activation of caspase-3/CPP32 and apoptosis upon growth factor withdrawal were inhibited/reduced by the caspase inhibitors, z-VAD-fmk and DEVD-CHO. These results demonstrate that caspase-3/CPP32 is involved in apoptosis of primitive CB CD34(+) cells but may not be the only mechanism involved.

Gall-bladder wall thickening in patients with liver cirrhosis

Gall-bladder wall thickening is commonly seen in patients with cirrhosis, but its exact causes have not been well established. We evaluated clinical, biochemical and haemodynamic data of patients with cirrhosis with respect to the presence of thickening of the gall-bladder wall. After excluding patients who presented with gallstones, acute or chronic cholecystitis, heart failure, a serum creatinine level greater than 2 mg/dL and/or a serum alanine aminotransferase level greater than 400 U/L, 77 patients with cirrhosis (75 male, two female; mean age 58 +/- 8 years) were enrolled in the study. Clinical, biochemical, ultrasound and haemodynamic data were obtained in every patient. Forty-one (53%) of 77 patients with cirrhosis had gall-bladder wall thickening (> 4 mm). Compared with patients with a normal gall-bladder wall, patients with gall-bladder wall thickening had significantly lower serum albumin levels (3.6 +/- 0.6 vs 2.9 +/- 0.7 gm/dL, respectively; P < 0.05), a longer prothrombin time (13 +/- 6 vs 16 +/- 6 s, respectively; P < 0.05), more patients with Child-Pugh class C (6 vs 37%, respectively; P < 0.05) and more patients with ascites (8 vs 50%, respectively; P < 0.05). In addition, compared with patients with a normal gall-bladder wall, those patients with gall-bladder wall thickening had a higher hepatic venous pressure gradient (13.9 +/- 4.5 vs 17.1 +/- 4.1 mmHg, respectively; P < 0.01) and a lower systemic vascular resistance (SVR; 1144 +/- 332 vs 1010 +/- 318 dyn.s/cm5, respectively; P < 0.05). Using a multivariate analysis, the presence of ascites and SVR lower than 900 dyn.s/cm5 were independently correlated with the presence of gall-bladder wall thickening, while a hepatic vein pressure gradient greater than 10 mmHg had only a marginally significant association. The presence of ascites, decreased SVR and portal hypertension are related to the occurrence of gall-bladder wall thickening in patients with cirrhosis, indicating that the development of gall-bladder wall thickening may be multifactorial.

Prognostic Correlation of Autophagy-Related Gene Expression-Based Risk Signature in Patients with Glioblastoma

Purpose

Autophagy plays a vital role in cancer initiation, malignant progression, and resistance to treatment; however, autophagy-related gene sets have rarely been analyzed in glioblastoma. The purpose of this study was to evaluate the prognostic significance of autophagy-related genes in patients with glioblastoma.

Patients and methods

Here, we collected whole transcriptome expression data from the Chinese Glioma Genome Atlas (CGGA) and The Cancer Genome Atlas (TCGA) datasets to explore the relationship between autophagy-related gene expression and glioblastoma prognosis. R language was the primary analysis and drawing tool.

Results

We screened 531 autophagy-related genes and identified 14 associated with overall survival in data from 986 patients with glioblastoma. Patients could be clustered into two groups (high and low risk) using expression data from the 14 associated genes, based on significant differences in clinicopathology and prognosis. Next, we constructed a signature based on the 14 genes and found that most patients designated high risk using our gene signature were IDH wild-type, MGMT promoter non-methylated, and likely to have more malignant tumor subtypes (including classical and mesenchymal subtypes). Survival analysis indicated that patients in the high-risk group had dramatically shorter overall survival compared with their low-risk counterparts. Cox regression analysis further confirmed the independent prognostic value of our 14 gene signature. Moreover, functional and ESTIMATE analyses revealed enrichment of immune and inflammatory responses in the high-risk group.

Conclusion

In this study, we identified a novel autophagy-related signature for the prediction of prognosis in patients with glioblastoma.

A new compound, withangulatin A, promotes type II DNA topoisomerase-mediated DNA damage

Withangulatin A, a new compound with a known chemical structure and from the antitumor Chinese herb Physalis angulata L, was found to act on topoisomerase II to induce topoisomerase II-mediated DNA damage in vitro. It has two effective dosage ranges of approximate 0.5 and 20 microM, with about one-third the activity of 20 microM VM-26.

PAHs contamination and bacterial communities in mangrove surface sediments of the Jiulong River Estuary, China

Sixteen sediment samples collected from eight transects in a mangrove swamp of the Jiulong River Estuary, Fujian, China were investigated for their content of polycyclic aromatic hydrocarbons (PAHs) and the biodegradation potential of the indigenous microorganisms. The bacterial community structures in the mangrove sediments and in enrichment cultures were also investigated. The results showed that the total PAHs concentration of mangrove sediments ranged from 280 to 1074 ng g(-1) dry weight, that the PAHs composition pattern in the mangrove sediments was dominated by high molecular weight PAH components (4-6 rings), and that Benzo[ghi]perylene and Indeno[1,2,3-cd]pyrene were the most dominant at different stations. Abundant PAH-degrading bacteria were found in all the stations, the values of phenanthrene-degrading bacteria ranged from 5.85 x 10(4) to 7.80 x 10(5) CFU g(-1) dry weight, fluoranthene-degrading bacteria ranged from 5.25 x 10(4) to 5.79 x 10(5) CFU g(-1) dry weight, pyrene-degrading bacteria ranged from 3.10 x 10(4) to 6.97 x 10(5) CFU g(-1) dry weight and the benzo(a)pyrene-degrading bacteria ranged from 5.25 x 10(4) to 7.26 x 10(5) CFU g(-1) dry weight. DGGE analysis of PCR-amplified 16S rDNA gene fragments confirmed that there was a remarkable shift in the composition of the bacterial community due to the addition of the different model PAH compound phenanthrene (three ring PAH), fluoranthene(four ring PAH), pyrene(four ring PAH) and benzo(a)pyrene(five ring PAH) during enrichment batch culture. Eleven strains were obtained with different morphology and different degradation ability. The presence of common bands for microbial species in the cultures and in the native mangrove sediment DNA indicated that these strains could be potential in situ PAH-degraders.

Enhancement of electrolarynx speech using adaptive noise cancelling based on independent component analysis

The electrolarynx provides a valuable means of verbal communication for people who cannot use their natural voice-production mechanism, but technology has changed very little since it was introduced in the 1950s. The presence of background noise degrades the resulting speech. In this study background noise was reduced by a new method, independent component analysis-based adaptive noise cancelling, which can remove noise components of the primary input signal based on statistical independence, by incorporating both second-order and higher-order statistics. The method shows better performance than the conventional least mean square algorithm. Acoustic analysis of the denoised electrolarynx speech revealed a significant reduction in the amount of background noise. Results from the perceptual evaluations indicated that the new filtering technique produced a noticeable improvement in the acceptability of the electrolarynx speech in a quiet environment (from 1.75 to 2.49, arbitrary units) or a noisy environment (from 0.59 to 1.82). In general, there was no significant improvement or degradation in intelligibility in the quiet environment (from 52.7 to 53.3). However, the processing did improve the intelligibility in a babble-noise environment (from 24.9 to 40.6). The improvement in acceptability and intelligibility may increase the communication ability of the user in daily situations.