Compact SAW aerosol generator

In this work, we discuss and demonstrate the principle features of surface acoustic wave (SAW) aerosol generation, based on the properties of the fluid supply, the acoustic wave field and the acoustowetting phenomena. Furthermore, we demonstrate a compact SAW-based aerosol generator amenable to mass production fabricated using simple techniques including photolithography, computerized numerical control (CNC) milling and printed circuit board (PCB) manufacturing. Using this device, we present comprehensive experimental results exploring the complexity of the acoustic atomization process and the influence of fluid supply position and geometry, SAW power and fluid flow rate on the device functionality. These factors in turn influence the droplet size distribution, measured here, that is important for applications including liquid chromatography, pulmonary therapies, thin film deposition and olfactory displays.

[Impact of a Senso-Motoric Intervention in COPD-Patients Participating in an Outpatient Pulmonary Rehabilitation Program: A Randomized Controlled Trial]

Objective Exercise training provides a cornerstone of pulmonary rehabilitation (PR) in COPD-patients. However, the components of the training are not yet fully investigated. We conducted a randomized controlled trial to investigate the effectiveness of a sensory-motoric training (SMT) in comparison to a conventional strength training (KT) according to the physical performance. Patients and Methods: 43 COPD patients were randomized and participated either in the intervention group (SMT = 30 minutes SMT per day) or in the control group (KT = 30 minutes KT per day). The SMT was performed as circuit training with five stations. The primary endpoint was the difference between T1 (start of the PR) and T2 (end of the PR) in 5-Times Sit-to-stand test (5-STST) in the intergroup comparison. Secondary endpoints were the intra- and intergroup comparisons of T1 and T2 in the 6-Minute Walk Test (6-MWT), COPD Assessment Test (CAT), St. George Respiratory Questionnaire (SGRQ), Hospital Anxiety- and Depression Scale (HADS) and in lung function. Results No significant differences were seen in the results of the 5-STST between the groups. Likewise, in the 6-MWT, SGRQ, CAT, HADS and lung function. The intragroup comparison between T1 and T2 showed significant differences in 5-STST, 6-MWT, SGRQ, CAT and HADS in both groups. The differences in lung function were not significantly, neither in the inter- nor in the intragroup comparison. Conclusion Similarly to a conventional strength training improvements in exercise capacity could be achieved with a SMT during PR in COPD patients. Further studies are necessary to define the role of the SMT in regards to postural control.

Highly efficient methane generation from untreated microalgae biomass

BACKGROUND

The fact that microalgae perform very efficiently photosynthetic conversion of sunlight into chemical energy has moved them into the focus of regenerative fuel research. Especially, biogas generation via anaerobic digestion is economically attractive due to the comparably simple apparative process technology and the theoretical possibility of converting the entire algal biomass to biogas/methane. In the last 60 years, intensive research on biogas production from microalgae biomass has revealed the microalgae as a rather challenging substrate for anaerobic digestion due to its high cell wall recalcitrance and unfavorable protein content, which requires additional pretreatment and co-fermentation strategies for sufficient fermentation. However, sustainable fuel generation requires the avoidance of cost/energy intensive biomass pretreatments to achieve positive net-energy process balance.

RESULTS

Cultivation of microalgae in replete and limited nitrogen culture media conditions has led to the formation of protein-rich and low protein biomass, respectively, with the last being especially optimal for continuous fermentation. Anaerobic digestion of nitrogen limited biomass (low-N BM) was characterized by a stable process with low levels of inhibitory substances and resulted in extraordinary high biogas, and subsequently methane productivity [750 ± 15 and 462 ± 9 mL_N g^-1 volatile solids (VS) day^-1, respectively], thus corresponding to biomass-to-methane energy conversion efficiency of up to 84%. The microbial community structure within this highly efficient digester revealed a clear predominance of the phyla Bacteroidetes and the family Methanosaetaceae among the Bacteria and Archaea, respectively. The fermentation of replete nitrogen biomass (replete-N BM), on the contrary, was demonstrated to be less productive (131 ± 33 mL_N CH₄ g^-1VS day^-1) and failed completely due to acidosis, caused through high ammonia/ammonium concentrations. The organization of the microbial community of the failed (replete-N) digester differed greatly compared to the stable low-N digester, presenting a clear shift to the phyla Firmicutes and Thermotogae, and the archaeal population shifted from acetoclastic to hydrogenotrophic methanogenesis.

CONCLUSIONS

The present study underlines the importance of cultivation conditions and shows the practicability of microalgae biomass usage as mono-substrate for highly efficient continuous fermentation to methane without any pretreatment with almost maximum practically achievable energy conversion efficiency (biomass to methane).Graphical abstractGrowth condition dependence of anaerobic conversion efficiency of microalgae biomass to methane.

Complete genome sequence of the actinomycete Actinoalloteichus hymeniacidonis type strain HPA 177T isolated from a marine sponge

Actinoalloteichus hymeniacidonis HPA 177T is a Gram-positive, strictly aerobic, black pigment producing and spore-forming actinomycete, which forms branching vegetative hyphae and was isolated from the marine sponge Hymeniacidon perlevis. Actinomycete bacteria are prolific producers of secondary metabolites, some of which have been developed into anti-microbial, anti-tumor and immunosuppressive drugs currently used in human therapy. Considering this and the growing interest in natural products as sources of new drugs, actinomycete bacteria from the hitherto poorly explored marine environments may represent promising sources for drug discovery. As A. hymeniacidonis, isolated from the marine sponge, is a type strain of the recently described and rare genus Actinoalloteichus, knowledge of the complete genome sequence enables genome analyses to identify genetic loci for novel bioactive compounds. This project, describing the 6.31 Mbp long chromosome, with its 5346 protein-coding and 73 RNA genes, will aid the Genomic Encyclopedia of Bacteria and Archaea project.

Non-canonical integration events in Pichia pastoris encountered during standard transformation analysed with genome sequencing

The non-conventional yeast Pichia pastoris is a popular host for recombinant protein production in scientific research and industry. Typically, the expression cassette is integrated into the genome via homologous recombination. Due to unknown integration events, a large clonal variability is often encountered consisting of clones with different productivities as well as aberrant morphological or growth characteristics. In this study, we analysed several clones with abnormal colony morphology and discovered unpredicted integration events via whole genome sequencing. These include (i) the relocation of the locus targeted for replacement to another chromosome (ii) co-integration of DNA from the E. coli plasmid host and (iii) the disruption of untargeted genes affecting colony morphology. Most of these events have not been reported so far in literature and present challenges for genetic engineering approaches in this yeast. Especially, the presence and independent activity of E. coli DNA elements in P. pastoris is of concern. In our study, we provide a deeper insight into these events and their potential origins. Steps preventing or reducing the risk for these phenomena are proposed and will help scientists working on genetic engineering of P. pastoris or similar non-conventional yeast to better understand and control clonal variability.

Deciphering the Transcriptional Response Mediated by the Redox-Sensing System HbpS-SenS-SenR from Streptomycetes

The secreted protein HbpS, the membrane-embedded sensor kinase SenS and the cytoplasmic response regulator SenR from streptomycetes have been shown to form a novel type of signaling pathway. Based on structural biology as well as different biochemical and biophysical approaches, redox stress-based post-translational modifications in the three proteins were shown to modulate the activity of this signaling pathway. In this study, we show that the homologous system, named here HbpSc-SenSc-SenRc, from the model species Streptomyces coelicolor A3(2) provides this bacterium with an efficient defense mechanism under conditions of oxidative stress. Comparative analyses of the transcriptomes of the Streptomyces coelicolor A3(2) wild-type and the generated hbpSc-senSc-senRc mutant under native and oxidative-stressing conditions allowed to identify differentially expressed genes, whose products may enhance the anti-oxidative defense of the bacterium. Amongst others, the results show an up-regulated transcription of genes for biosynthesis of cysteine and vitamin B₁₂, transport of methionine and vitamin B₁₂, and DNA synthesis and repair. Simultaneously, transcription of genes for degradation of an anti-oxidant compound is down-regulated in a HbpSc-SenSc-SenRc-dependent manner. It appears that HbpSc-SenSc-SenRc controls the non-enzymatic response of Streptomyces coelicolor A3(2) to counteract the hazardous effects of oxidative stress. Binding of the response regulator SenRc to regulatory regions of some of the studied genes indicates that the regulation is direct. The results additionally suggest that HbpSc-SenSc-SenRc may act in concert with other regulatory modules such as a transcriptional regulator, a two-component system and the Streptomyces B₁₂ riboswitch. The transcriptomics data, together with our previous in vitro results, enable a profound characterization of the HbpS-SenS-SenR system from streptomycetes. Since homologues to HbpS-SenS-SenR are widespread in different actinobacteria with ecological and medical relevance, the data presented here will serve as a basis to elucidate the biological role of these homologues.

Temperature and layer thickness dependent in situ investigations on epindolidione organic thin-film transistors

We report on in situ performance evaluations as a function of layer thickness and substrate temperature for bottom-gate, bottom-gold contact epindolidione organic thin-film transistors on various gate dielectrics. Experiments were carried out under ultra-high vacuum conditions, enabling quasi-simultaneous electrical and surface analysis. Auger electron spectroscopy and thermal desorption spectroscopy (TDS) were applied to characterize the quality of the substrate surface and the thermal stability of the organic films. Ex situ atomic force microscopy (AFM) was used to gain additional information on the layer formation and surface morphology of the hydrogen-bonded organic pigment. The examined gate dielectrics included SiO2, in its untreated and sputtered forms, as well as the spin-coated organic capping layers poly(vinyl-cinnamate) (PVCi) and poly((±)endo,exo-bicyclo[2.2.1]hept-5-ene-2,3-dicarboxylic acid, diphenylester) (PNDPE, from the class of polynorbornenes). TDS and AFM revealed Volmer-Weber island growth dominated film formation with no evidence of a subjacent wetting layer. This growth mode is responsible for the comparably high coverage required for transistor behavior at 90-95% of a monolayer composed of standing molecules. Surface sputtering and an increased sample temperature during epindolidione deposition augmented the surface diffusion of adsorbing molecules and therefore led to a lower number of better-ordered islands. Consequently, while the onset of charge transport was delayed, higher saturation mobility was obtained. The highest, bottom-contact configuration, mobilities of approximately 2.5 × 10-3cm2/Vs were found for high coverages (50 nm) on sputtered samples. The coverage dependence of the mobility showed very different characteristics for the different gate dielectrics, while the change of the threshold voltage with coverage was approximately the same for all systems. An apparent decrease of the mobility with increasing coverage on the less polar PNDPE was attributed to a change in molecular orientation from upright standing in the thin-film phase to tilted in the bulk phase. From temperature-dependent mobility measurements we calculated activation barriers for the charge transport between 110 meV and 160 meV, depending on the dielectric configuration.

Comparative transcriptome analysis of the biocontrol strain Bacillus amyloliquefaciens FZB42 as response to biofilm formation analyzed by RNA sequencing

The strain Bacillus amyloliquefaciens FZB42 is a plant growth promoting rhizobacterium (PGPR) and biocontrol agent known to keep infections of lettuce (Lactuca sativa) by the phytopathogen Rhizoctonia solani down. Several mechanisms, including the production of secondary metabolites possessing antimicrobial properties and induction of the host plant's systemic resistance (ISR), were proposed to explain the biocontrol effect of the strain. B. amyloliquefaciens FZB42 is able to form plaques (biofilm-like structures) on plant roots and this feature was discussed to be associated with its biocontrol properties. For this reason, formation of B. amyloliquefaciens biofilms was studied at the transcriptional level using high-throughput sequencing of whole transcriptome cDNA libraries from cells grown under biofilm-forming conditions vs. planktonic growth. Comparison of the transcriptional profiles of B. amyloliquefaciens FZB42 under these growth conditions revealed a common set of highly transcribed genes mostly associated with basic cellular functions. The lci gene, encoding an antimicrobial peptide (AMP), was among the most highly transcribed genes of cells under both growth conditions suggesting that AMP production may contribute to biocontrol. In contrast, gene clusters coding for synthesis of secondary metabolites with antimicrobial properties were only moderately transcribed and not induced in biofilm-forming cells. Differential gene expression revealed that 331 genes were significantly up-regulated and 230 genes were down-regulated in the transcriptome of B. amyloliquefaciens FZB42 under biofilm-forming conditions in comparison to planktonic cells. Among the most highly up-regulated genes, the yvqHI operon, coding for products involved in nisin (class I bacteriocin) resistance, was identified. In addition, an operon whose products play a role in fructosamine metabolism was enhanced in its transcription. Moreover, genes involved in the production of the extracellular biofilm matrix including exopolysaccharide genes (eps) and the yqxM-tasA-sipW operon encoding amyloid fiber synthesis were up-regulated in the B. amyloliquefaciens FZB42 biofilm. On the other hand, highly down-regulated genes in biofilms are associated with synthesis, assembly and regulation of the flagellar apparatus, the degradation of aromatic compounds and the export of copper. The obtained transcriptional profile for B. amyloliquefaciens biofilm cells uncovered genes involved in its development and enabled the assessment that synthesis of secondary metabolites among other factors may contribute to the biocontrol properties of the strain.

Integration event induced changes in recombinant protein productivity in Pichia pastoris discovered by whole genome sequencing and derived vector optimization

Background

The classic AOX1 replacement approach is still one of the most often used techniques for expression of recombinant proteins in the methylotrophic yeast Pichia pastoris. Although this approach is largely successful, it frequently delivers clones with unpredicted production characteristics and a work-intense screening process is required to find the strain with desired productivity.

Results

In this project 845 P. pastoris clones, transformed with a GFP expression cassette, were analyzed for their methanol-utilization (Mut)-phenotypes, GFP gene expression levels and gene copy numbers. Several groups of strains with irregular features were identified. Such features include GFP expression that is markedly higher or lower than expected based on gene copy number as well as strains that grew under selective conditions but where the GFP gene cassette and its expression could not be detected. From these classes of strains 31 characteristic clones were selected and their genomes sequenced. By correlating the assembled genome data with the experimental phenotypes novel insights were obtained. These comprise a clear connection between productivity and cassette-to-cassette orientation in the genome, the occurrence of false-positive clones due to a secondary recombination event, and lower total productivity due to the presence of untransformed cells within the isolates were discovered. To cope with some of these problems, the original vector was optimized by replacing the AOX1 terminator, preventing the occurrence of false-positive clones due to the secondary recombination event.

Conclusions

Standard methods for transformation of P. pastoris led to a multitude of unintended and sometimes detrimental integration events, lowering total productivity. By documenting the connections between productivity and integration event we obtained a deeper understanding of the genetics of mutation in P. pastoris. These findings and the derived improved mutagenesis and transformation procedures and tools will help other scientists working on recombinant protein production in P. pastoris and similar non-conventional yeasts.

Electronic supplementary material

The online version of this article (doi:10.1186/s12934-016-0486-7) contains supplementary material, which is available to authorized users.

Complete mitochondrial genome of the scleractinian coral Porites rus

Scleractinian corals of the genus Porites are found across a wide geographical range along the tropical seas. Some species of the genus such as Porites rus are important reef builders in coral reef ecosystems and display a remarkable stress tolerance. Despite their physiological particularities and ecological importance, there is a scarcity of molecular data for members of this genus. Here, we report the first complete mitochondrial genome of Porites rus (Genbank accession number LN864762) which is 18 647 bp in size. It has the typical coral mitochondrial gene arrangement, consisting of 14 protein-coding genes, with a GC content of 36.2%, 12 tRNAs and two rRNAs. The P. rus mitochondrial genome displays two groups: 1 intron in cox1 and nad5 genes. Phylogenetic analyses support the monophyly of the genus Porites. The complete mitochondrial genome will be helpful for addressing questions regarding mitochondrial gene evolution.

Isolation and genome sequencing of four Arctic marine Psychrobacter strains exhibiting multicopper oxidase activity

Background

Marine cold-temperature environments are an invaluable source of psychrophilic microbial life for new biodiscoveries. An Arctic marine bacterial strain collection was established consisting of 1448 individual isolates originating from biota, water and sediment samples taken at a various depth in the Barents Sea, North of mainland Norway, with an all year round seawater temperature of 4 °C. The entire collection was subjected to high-throughput screening for detection of extracellular laccase activity with guaiacol as a substrate.

Results

In total, 13 laccase-positive isolates were identified, all belonging to the Psychrobacter genus. From the most diverse four strains, based on 16S rRNA gene sequence analysis, all originating from the same Botryllus sp. colonial ascidian tunicate sample, genomic DNA was isolated and genome sequenced using a combined approach of whole genome shotgun and 8 kb mate-pair library sequencing on an Illumina MiSeq platform. The genomes were assembled and revealed genome sizes between 3.29 and 3.52 Mbp with an average G + C content of around 42 %, with one to seven plasmids present in the four strains. Bioinformatics based genome mining was performed to describe the metabolic potential of these four strains and to identify gene candidates potentially responsible for the observed laccase-positive phenotype. Up to two different laccase-like multicopper oxidase (LMCO) encoding gene candidates were identified in each of the four strains. Heterologous expression of P11F6-LMCO and P11G5-LMCO2 in Escherichia coli BL21 (DE3) resulted in recombinant proteins exhibiting 2,2'-azino-bis-3-ethylbenzothiazoline-6-sulphonic acid (ABTS) and guaiacol oxidizing activity.

Conclusions

Thirteen Psychrobacter species with laccase-positive phenotype were isolated from a collection of Arctic marine bacteria. Four of the isolates were genome sequenced. The overall genome features were similar to other publicly available Psychrobacter genome sequences except for P11G5 harboring seven plasmids. However, there were differences at the pathway level as genes associated with degradation of phenolic compounds, nicotine, phenylalanine, styrene, ethylbenzene, and ethanolamine were detected only in the Psychrobacter strains reported in this study while they were absent among the other publicly available Psychrobacter genomes. In addition, six gene candidates were identified by genome mining and shown to possess T1, T2 and T3 copper binding sites as the main signature of the three-domain laccases. P11F6-LMCO and P11G5-LMCO2 were recombinantly expressed and shown to be active when ABTS and guaiacol were used as substrates.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-016-2445-4) contains supplementary material, which is available to authorized users.

Taxonomic analysis of the microbial community in stored sugar beets using high-throughput sequencing of different marker genes

Post-harvest colonization of sugar beets accompanied by rot development is a serious problem due to sugar losses and negative impact on processing quality. Studies on the microbial community associated with rot development and factors shaping their structure are missing. Therefore, high-throughput sequencing was applied to describe the influence of environment, plant genotype and storage temperature (8°C and 20°C) on three different communities in stored sugar beets, namely fungi (internal transcribed spacers 1 and 2), Fusarium spp. (elongation factor-1α gene fragment) and oomycetes (internal transcribed spacers 1). The composition of the fungal community changed during storage mostly influenced by the storage temperature followed by a weak environmental effect. Botrytis cinerea was the prevalent species at 8°C whereas members of the fungal genera Fusarium and Penicillium became dominant at 20°C. This shift was independent of the plant genotype. Species richness within the genus Fusarium also increased during storage at both temperatures whereas the oomycetes community did not change. Moreover, oomycetes species were absent after storage at 20°C. The results of the present study clearly show that rot development during sugar beet storage is associated with pathogens well known as causal agents of post-harvest diseases in many other crops.

Optimizing pentacene thin-film transistor performance: Temperature and surface condition induced layer growth modification

In this work we present in situ electrical and surface analytical, as well as ex situ atomic force microscopy (AFM) studies on temperature and surface condition induced pentacene layer growth modifications, leading to the selection of optimized deposition conditions and entailing performance improvements. We prepared p++-silicon/silicon dioxide bottom-gate, gold bottom-contact transistor samples and evaluated the pentacene layer growth for three different surface conditions (sputtered, sputtered + carbon and unsputtered + carbon) at sample temperatures during deposition of 200 K, 300 K and 350 K. The AFM investigations focused on the gold contacts, the silicon dioxide channel region and the highly critical transition area. Evaluations of coverage dependent saturation mobilities, threshold voltages and corresponding AFM analysis were able to confirm that the first 3-4 full monolayers contribute to the majority of charge transport within the channel region. At high temperatures and on sputtered surfaces uniform layer formation in the contact-channel transition area is limited by dewetting, leading to the formation of trenches and the partial development of double layer islands within the channel region instead of full wetting layers. By combining the advantages of an initial high temperature deposition (well-ordered islands in the channel) and a subsequent low temperature deposition (continuous film formation for low contact resistance) we were able to prepare very thin (8 ML) pentacene transistors of comparably high mobility.

[Preliminary Short-term Results of an All-day Outpatient Pulmonary Rehabilitation Program in an Acute Hospital on Patients with Mild to Very Severe COPD]

INTRODUCTION

Positive effects of pulmonary rehabilitation on chronic obstructive pulmonary disease (COPD) are well known, and inpatient rehabilitation programs are the preferred modality in Germany. In this paper, we report on the recent results of a daily outpatient rehabilitation program offered at an acute hospital, the first of this kind in Germany. It is not known whether this kind of rehabilitation is an effective approach.

METHODS

32 consecutive COPD patients GOLD-stage II-IV, phenotype B-D (mean 64.5±21.9 years; 18 male, 14 female) completed a rehabilitation program of 19 (15-21) days conducted according to the recommendations of the National Accociation for Rehabilitation. In this prospective observational study, data (walking distance in the 6-MWD, BODE-Index, HADS-, BDI/TDI-, CAT-questionnaire) were collected at the beginning (T1) and at the end (T2) of the program and the results are presented in a pre- vs. post-analysis.

RESULTS

We found significant positive effects for most of the measured parameters, except for body plethysmography, diffusion capacity and blood gas. Especially the increase in the 6 min walking distance (6-MWD) was remarkable (T1: 485.78±158.24, T2: 527.97±146.75 m, p=0.0212). There were no adverse events or complications. All participants were able to complete the program properly.

CONCLUSION

Most of the measured parameters in COPD patients with stage II or worse disease improved significantly during the comprehensive outpatient rehabilitation program. A limitation of this study is the small number of cases, and further conclusions can only be made after examining a larger sample. The setting of this rehabilitation program in an acute hospital seems to be meaningful in an organisational and structural sense.

The effect of grape seed and grape marc meal extract on milk performance and the expression of genes of endoplasmic reticulum stress and inflammation in the liver of dairy cows in early lactation

During the periparturient phase, cows are typically in an inflammation-like condition, and it has been suggested that inflammation associated with the development of stress of the endoplasmic reticulum (ER) in the liver contributes to the development of fatty liver syndrome and ketosis. In the present study, we investigated the hypothesis that feeding grape seed and grape marc meal extract (GSGME) as a plant extract rich in flavonoids attenuates inflammation and ER stress in the liver of dairy cows. Two groups of cows received either a total mixed ration as a control diet or the same total mixed ration supplemented with 1% of GSGME over the period from wk 3 prepartum to wk 9 postpartum. Dry matter intake during wk 3 to 9 postpartum was not different between the 2 groups. However, the cows fed the diet supplemented with GSGME had an increased milk yield and an increased daily milk protein yield. Cows supplemented with GSGME moreover had a significantly reduced mRNA abundancy of fibroblast growth factor (FGF) 21, a stress hormone induced by various stress conditions, in the liver in wk 1 and 3 postpartum. In contrast, mRNA abundances of a total of 3 genes involved in inflammation and 14 genes involved in ER stress response, as well as concentrations of triacylglycerols and cholesterol, in liver samples of wk 1 and 3 postpartum did not differ between the 2 groups. Overall, this study shows that supplementation of GSGME did not influence inflammation or ER stress in the liver but increased milk yield, an effect that could be due to effects on ruminal metabolism.

SAW-based fluid atomization using mass-producible chip devices

Surface acoustic wave (SAW)-based fluid atomizers are ideally suited to generate micrometer-sized droplets without any moving parts or nozzles. Versatile application fields can be found for instance in biomedical, aerosol or thin film technology, including medical inhalators or particle deposition for advanced surface treatment. Such atomizers also show great potential for on-chip integration and can lead to economic production of hand-held and even disposable devices, with either a single functionality or integrated in more complex superior systems. However, this potential was limited in the past by fluid supply mechanisms inadequate for mass production, accuracy and reliability. In this work, we briefly discuss existing fluid supply methods and demonstrate a straightforward new approach suited for reliable and cost-effective mass-scale manufacturing of SAW atomizer chips. Our approach is based on a fluid supply at the boundary of the acoustic beam via SU-8 microchannels produced by a novel one-layer/double-exposure photolithography method. Using this technique, we demonstrate precise and stable fluid atomization with almost ideal aerosol plume geometry from a dynamically stabilized thin fluid film. Additionally, we demonstrate the possibility of in situ altering the droplet size distribution by controlling the amount of fluid available in the active region of the chip.

Deeply sequenced metagenome and metatranscriptome of a biogas-producing microbial community from an agricultural production-scale biogas plant

BACKGROUND

The production of biogas takes place under anaerobic conditions and involves microbial decomposition of organic matter. Most of the participating microbes are still unknown and non-cultivable. Accordingly, shotgun metagenome sequencing currently is the method of choice to obtain insights into community composition and the genetic repertoire.

FINDINGS

Here, we report on the deeply sequenced metagenome and metatranscriptome of a complex biogas-producing microbial community from an agricultural production-scale biogas plant. We assembled the metagenome and, as an example application, show that we reconstructed most genes involved in the methane metabolism, a key pathway involving methanogenesis performed by methanogenic Archaea. This result indicates that there is sufficient sequencing coverage for most downstream analyses.

CONCLUSIONS

Sequenced at least one order of magnitude deeper than previous studies, our metagenome data will enable new insights into community composition and the genetic potential of important community members. Moreover, mapping of transcripts to reconstructed genome sequences will enable the identification of active metabolic pathways in target organisms.

Complete genome sequence of Rhodococcus erythropolis BG43 (DSM 46869), a degrader of Pseudomonas aeruginosa quorum sensing signal molecules

Rhodococcus erythropolis BG43 was isolated from soil and characterized as a degrader of the quorum sensing signal molecules 2-heptyl-3-hydroxy-4(1H)-quinolone (the Pseudomonas quinolone signal, PQS) and 2-heptyl-4(1H)-quinolone, produced by Pseudomonas aeruginosa. The complete genome of R. erythropolis BG43 consists of a circular chromosome and three plasmids, one of them circular and two linear ones. In total, 6158 protein-coding regions were identified. With this genome sequence, the genetic basis of its quorum-quenching ability and possible biotechnological applications can be explored further.

Draft genome sequence of Talaromyces islandicus ("Penicillium islandicum") WF-38-12, a neglected mold with significant biotechnological potential

Talaromyces (Penicillium) islandicus is a common mold found in stored rice or cereals. It has a highly versatile metabolism characterized by the secretion of numerous biopolymer degrading enzymes, mycotoxins, and anthraquinones that altogether offer a broad range of potential industrial applications. Here, we report the draft genome sequence of Talaromyces islandicus, which provides the basis of a biotechnological usage of this species.

Improved genome sequence of the phytopathogenic fungus Rhizoctonia solani AG1-IB 7/3/14 as established by deep mate-pair sequencing on the MiSeq (Illumina) system

The phytopathogenic fungus Rhizoctonia solani AG1-IB of the phylum Basidiomycota affects various economically important crops comprising bean, rice, soybean, figs, cabbage and lettuce. The R. solani isolate 7/3/14 of the anastomosis group AG1-IB was deeply resequenced on the Illumina MiSeq system applying the mate-pair mode to improve its genome sequence. Assembly of obtained sequence reads significantly reduced the amount of scaffolds and improved the genome sequence of the isolate compared to the previous sequencing approach. The genome sequence of the AG1-IB isolate 7/3/14 now provides an up-graded basis to analyze genome features predicted to play a role in pathogenesis and for the development of strategies to antagonize the pathogenic impact of this fungus.

Complete genome sequence of Streptomyces lividans TK24

Streptomyces lividans TK24 is the standard host for the heterologous expression of a number of different proteins and antibiotic-synthesizing enzymes. As such, it is often used as an experimental microbial cell factory for the production of secreted heterologous proteins including human cytokines and industrial enzymes, and of several antibiotics. It accepts methylated DNA and is an ideal Streptomyces cloning system. Here, we report the complete genome sequence of S. lividans TK24 that includes a plasmid-less genome of 8.345Mbp (72.24% G+C content).

Complete genome sequence of the methanogenic neotype strain Methanobacterium formicicum MF(T.)

The neotype strain Methanobacterium formicicum MF(T) (DSM1535), a hydrogenotrophic methanogenic Archaeon, was isolated from a domestic sewage sludge digestor in Urbana (IL, USA). Here, the complete genome sequence of the methanogen is reported. The genome is 2,478,074bp in size, featuring a GC content of 41.23%. M. formicicum MF(T) encodes several genes predicted to be involved in adaptation to abiotic stress such as high osmolarity. The strain MF(T) is of biotechnological importance since M. formicicum strains are often found in production-scale biogas plants and it is suggested as a starter culture for the anaerobic biomethanation process.

In situ preparation, electrical and surface analytical characterization of pentacene thin film transistors

The fabrication of organic thin film transistors with highly reproducible characteristics presents a very challenging task. We have prepared and analyzed model pentacene thin film transistors under ultra-high vacuum conditions, employing surface analytical tools and methods. Intentionally contaminating the gold contacts and SiO2 channel area with carbon through repeated adsorption, dissociation, and desorption of pentacene proved to be very advantageous in the creation of devices with stable and reproducible parameters. We mainly focused on the device properties, such as mobility and threshold voltage, as a function of film morphology and preparation temperature. At 300 K, pentacene displays Stranski-Krastanov growth, whereas at 200 K fine-grained, layer-like film growth takes place, which predominantly influences the threshold voltage. Temperature dependent mobility measurements demonstrate good agreement with the established multiple trapping and release model, which in turn indicates a predominant concentration of shallow traps in the crystal grains and at the oxide-semiconductor interface. Mobility and threshold voltage measurements as a function of coverage reveal that up to four full monolayers contribute to the overall charge transport. A significant influence on the effective mobility also stems from the access resistance at the gold contact-semiconductor interface, which is again strongly influenced by the temperature dependent, characteristic film growth mode.

Complete genome sequence of Bacillus methanolicus MGA3, a thermotolerant amino acid producing methylotroph

Bacillus methanolicus MGA3 was isolated from freshwater marsh soil and characterised as a thermotolerant and methylotrophic L-glutamate producer. The complete genome consists of a circular chromosome and the two plasmids pBM19 and pBM69. It includes genomic information about C1 metabolism and amino acid biosynthetic pathways.

Draft genome sequence of Sinorhizobium meliloti RU11/001, a model organism for flagellum structure, motility and chemotaxis

Sinorhizobium meliloti of the order Rhizobiales is a symbiotic nitrogen-fixing bacterium nodulating plants of the genera Medicago, Trigonella and Melilotus and hence is of great agricultural importance. In its free-living state it is motile and capable of modulating its movement patterns in response to chemical attractants. Here, the draft genome consisting of a circular chromosome, the megaplasmids pSymA and pSymB and three accessory plasmids of Sinorhizobium meliloti RU11/001, a model organism for flagellum structure, motility and chemotaxis, is reported.

Transcriptomics of cortical gray matter thickness decline during normal aging

INTRODUCTION

We performed a whole-transcriptome correlation analysis, followed by the pathway enrichment and testing of innate immune response pathway analyses to evaluate the hypothesis that transcriptional activity can predict cortical gray matter thickness (GMT) variability during normal cerebral aging.

METHODS

Transcriptome and GMT data were available for 379 individuals (age range=28-85) community-dwelling members of large extended Mexican American families. Collection of transcriptome data preceded that of neuroimaging data by 17 years. Genome-wide gene transcriptome data consisted of 20,413 heritable lymphocytes-based transcripts. GMT measurements were performed from high-resolution (isotropic 800 μm) T1-weighted MRI. Transcriptome-wide and pathway enrichment analysis was used to classify genes correlated with GMT. Transcripts for sixty genes from seven innate immune pathways were tested as specific predictors of GMT variability.

RESULTS

Transcripts for eight genes (IGFBP3, LRRN3, CRIP2, SCD, IDS, TCF4, GATA3, and HN1) passed the transcriptome-wide significance threshold. Four orthogonal factors extracted from this set predicted 31.9% of the variability in the whole-brain and between 23.4 and 35% of regional GMT measurements. Pathway enrichment analysis identified six functional categories including cellular proliferation, aggregation, differentiation, viral infection, and metabolism. The integrin signaling pathway was significantly (p<10(-6)) enriched with GMT. Finally, three innate immune pathways (complement signaling, toll-receptors and scavenger and immunoglobulins) were significantly associated with GMT.

CONCLUSION

Expression activity for the genes that regulate cellular proliferation, adhesion, differentiation and inflammation can explain a significant proportion of individual variability in cortical GMT. Our findings suggest that normal cerebral aging is the product of a progressive decline in regenerative capacity and increased neuroinflammation.

Controlling the wetting properties of the Asakura-Oosawa model and applications to spherical confinement

We demonstrate for the Asakura-Oosawa model and an extension of this model that uses continuous rather than hard potentials, how wetting properties at walls can be easily controlled. By increasing the interaction range of the repulsive wall potential acting on the colloids (while keeping the polymer-wall interactions constant) polymers begin to substitute colloids at walls and the system can be driven from complete wetting of colloids via partial wetting to complete wetting of polymers. As an application, we discuss the morphology and wetting behavior of colloid-polymer mixtures in spherical confinement. We apply the recently developed 'ensemble switch method' where the Hamiltonian is extended to a combination of a system with walls and of a system without walls to calculate the surface excess free energies of colloid-rich and polymer-rich phases. The contact angle then is inferred from Young's equation.

Non-compliant maxillary protraction by orthodontic micro-implants

AIM

Delaire-type facemask is still the appliance of choice for non surgical paediatric Class III treatment. However, it entails great aesthetical problems and is totally dependent on patient compliance. A new modified maxillary protractor was then designed: it is monomaxillary, fixed, implant-supported, aesthetically pleasing and it does not require patient compliance. The aims of this study were to evaluate the clinical use and analyse the effects of a new appliance called Fixed Maxillary Protractor. The device aims at obtaining a forward movement of the maxillary dento-alveolar component in non-compliant paediatric patients, when mandible retrusion cannot be pursued.

CASE REPORT

A non-compliant patient aged 4 years 11 months with mild skeletal and predominant dento-alveolar Class III malocclusion with maxillary deficiency, anterior crossbite and complete deciduous dentition was treated for 10 months. The appliance, anchored by 2 micro-implants in the posterior palatal region, consisted of an acrylic plate, a lingual splint, 2 TMA springs that delivered a posterior-anterior force, 2 anterior security devices and 2 occlusal bite raising splints on the deciduous molars. The treatment yielded a slightly overcorrected Class I incisal relationship. Increase in SNA angle (2°) and a decrease in SNB angle (1°) resulted in an increase in ANB angle (3°). Increases in Wits appraisal of 4 mm and in overjet of 7 mm were obtained. A correction of the anterior crossbite the a posterior sliding of the mandible due to the crossbite correction were observed. An anticlockwise rotation of the maxilla and a mild increase in the anterior facial height were achieved: the treatment effects are similar to those obtained with the Delaire-type facemask, but the amount of postero-anterior correction is lower.

DISCUSSION AND CONCLUSION

The Fixed Maxillary Protractor is effective for the treatment of mild-moderate Class III malocclusion with maxillary deficiency in non-compliant paediatric patients.

Attachment limited versus diffusion limited nucleation of organic molecules: Hexaphenyl on sputter-modified mica

The nucleation and growth of organic molecules is usually discussed in the framework of diffusion limited aggregation (DLA). In this letter we demonstrate for the rod-like organic molecules hexaphenyl (6P) on sputter-modified mica, that under specific experimental conditions the nucleation has to be described by attachment limited aggregation (ALA). The crucial parameter for the growth mode is the roughness of the substrate surface, as induced by ion sputtering. With decreasing surface roughness the diffusion probability of the molecules increases and the growth mode changes from DLA to ALA. This was derived from the deposition rate dependence of the island density. A critical size of i = 7 molecules was determined for the nucleation of 6P on a moderately sputtered mica surface.

[Indication for and verification of hearing aid benefit using modern methods of speech audiometry in German]

The current guidelines for hearing aid supply in Germany employ the often criticised Freiburg monosyllabic speech test (FBE) in quiet. This test can be replaced with the monosyllabic rhyme test by von Wallenberg and Kollmeier (WaKo) in quiet and by the measurement of a speech reception threshold in an interfering noise at a moderate level (45 dB SPL) using either the Göttingen or the Oldenburg sentence test (criterion: 2 dB improvement in SNR, "signal-to-noise ratio"). This procedure was investigated in a group of 38 participants with a sensorineural hearing impairment (mild, moderate or severe hearing loss) and 11 volunteers with normal hearing. On average, comparable indications were achieved. Participants with a mild hearing loss and a selective problem with listening in interfering noise were assessed more fairly.

Capillary condensation in cylindrical pores: Monte Carlo study of the interplay of surface and finite size effects

When a fluid that undergoes a vapor to liquid transition in the bulk is confined to a long cylindrical pore, the phase transition is shifted (mostly due to surface effects at the walls of the pore) and rounded (due to finite size effects). The nature of the phase coexistence at the transition depends on the length of the pore: for very long pores, the system is axially homogeneous at low temperatures. At the chemical potential where the transition takes place, fluctuations occur between vapor- and liquidlike states of the cylinder as a whole. At somewhat higher temperatures (but still far below bulk criticality), the system at phase coexistence is in an axially inhomogeneous multidomain state, where long cylindrical liquid- and vaporlike domains alternate. Using Monte Carlo simulations for the Ising/lattice gas model and the Asakura-Oosawa model of colloid-polymer mixtures, the transition between these two different scenarios is characterized. It is shown that the density distribution changes gradually from a double-peak structure to a triple-peak shape, and the correlation length in the axial direction (measuring the equilibrium domain length) becomes much smaller than the cylinder length. The (rounded) transition to the disordered phase of the fluid occurs when the axial correlation length has decreased to a value comparable to the cylinder diameter. It is also suggested that adsorption hysteresis vanishes when the transition from the simple domain state to the multidomain state of the cylindrical pore occurs. We predict that the difference between the pore critical temperature and the hysteresis critical temperature should increase logarithmically with the length of the pore.

Sorption Properties of Natural Sulfides with Respect to Technetium

Technetium sorption properties of Fe2+-bearing minerals and different metal sulfides were studied by batch and column experiments. Pure stibnite (SbS3), pyrrhotite (FeS), pyrite (FeS2), galena (PbS) and loell ingite (FeAs2) fix Tc to a great extent (> 95 % of TcO4- starting inventory). They appear to be favourable backfill materials for redox-sensitive radionucli-des. Physico-chemical processes of fixation and possible fixation modes are discussed.