Transpiration of grapevines and co-habitating cover crop and weed species in a vineyard. A “snapshot” at diurnal trends

The objective of this study was to quantify transpiration rates of two cover crops, Festuca rubra subsp. rubra  (red fescue) and Medicago lupulina (black medick) and 4 weeds, Chenopodium album (fat hen), Cirsium arvense (creeping thistle), Malva neglecta (common mallow) and Taraxacum officinale (dandelion) occurring in a mixed stand in a commercial steep-slope, North-South oriented vineyard as compared to vines, cv. Riesling near Johannisberg (Rheingau), Germany. Leaf transpiration (E) was measured directly on the cover crop and weed species with a portable gas exchange measurement system. Grapevine transpiration was measured concomitantly using custommade Granier-type xylem sap flow gauges. Measurements were conducted on two days in August (15th and 22nd) in 2001 under hot and sunny conditions. All herbaceous species presented a similar diurnal pattern of E, with low values in the morning and afternoon and peak values between 12 and 15 h. In contrast E of grapevines peaked mid-morning (between 8 and 10 h) remained relatively stable until mid-afternoon (16 h) before decreasing continuously until darkness. Significant differences in E between the herbaceous species were observed throughout the day. In general transpiration rates were highest for M. neglecta and lowest for C. arvense, T. officinale and F. rubra subsp. rubra. We estimated the projected leaf area indices (leaf area per surface area covered) for each species and calculated possible transpiration rates for pure stands assuming that all leaves were well exposed. Potential transpiration rates ranged from about 1 mm d-1 (one l m-2 of soil surface) for F. rubra subsp. rubra to = 5 mm d-1 for M. neglecta as compared to only 0.9 mm d-1 for grapevine. These results underline the importance of appropriate cover crop species and the control of some weed species with respect to water use.

Complete Draft Genome Sequence of the Actinobacterium Nocardiopsis sinuspersici UTMC102 (DSM 45277T), Which Produces Serine Protease.

Tokovenko B, Rückert C, Kalinowski J, et al. Complete Draft Genome Sequence of the Actinobacterium Nocardiopsis sinuspersici UTMC102 (DSM 45277T), Which Produces Serine Protease. Genome Announc. 2017;5(20): e00362-17.The genome sequence of alkalohalophilic actinobacterium Nocardiopsis sinuspersici UTMC102 is provided. N. sinuspersici UTMC102 produces a highly active serine alkaline protease, and contains at least 11 gene clusters encoding the biosynthesis of secondary metabolites. The N. sinuspersici UTMC102 genome was assembled into a single chromosomal scaffold

Complete genome sequence of Paenibacillus riograndensis SBR5T, a Gram-positive diazotrophic rhizobacterium

AbstractPaenibacillus riograndensis is a Gram-positive rhizobacterium which exhibits plant growth promoting activities. It was isolated from the rhizosphere of wheat grown in the state of Rio Grande do Sul, Brazil. Here we announce the complete genome sequence of P. riograndensis strain SBR5T. The genome of P. riograndensis SBR5T consists of a circular chromosome of 7,893,056bps. The genome was finished and fully annotated, containing 6705 protein coding genes, 87 tRNAs and 27 rRNAs. The knowledge of the complete genome helped to explain why P. riograndensis SBR5T can grow with the carbon sources arabinose and mannitol, but not myo-inositol, and to explain physiological features such as biotin auxotrophy and antibiotic resistances. The genome sequence will be valuable for functional genomics and ecological studies as well as for application of P. riograndensis SBR5T as plant growth-promoting rhizobacterium

The complete genome sequence of the acarbose producer Actinoplanes sp. SE50/110

Schwientek P, Szczepanowski R, Rückert C, et al. The complete genome sequence of the acarbose producer Actinoplanes sp. SE50/110. BMC Genomics. 2012;13(1): 112.Background Actinoplanes sp. SE50/110 is known as the wild type producer of the alpha-glucosidase inhibitor acarbose, a potent drug used worldwide in the treatment of type-2 diabetes mellitus. As the incidence of diabetes is rapidly rising worldwide, an ever increasing demand for diabetes drugs, such as acarbose, needs to be anticipated. Consequently, derived Actinoplanes strains with increased acarbose yields are being used in large scale industrial batch fermentation since 1990 and were continuously optimized by conventional mutagenesis and screening experiments. This strategy reached its limits and is generally superseded by modern genetic engineering approaches. As a prerequisite for targeted genetic modifications, the complete genome sequence of the organism has to be known. Results Here, we present the complete genome sequence of Actinoplanes sp. SE50/110 [GenBank:CP003170], the first publicly available genome of the genus Actinoplanes, comprising various producers of pharmaceutically and economically important secondary metabolites. The genome features a high mean G + C content of 71.32% and consists of one circular chromosome with a size of 9,239,851 bp hosting 8,270 predicted protein coding sequences. Phylogenetic analysis of the core genome revealed a rather distant relation to other sequenced species of the family Micromonosporaceae whereas Actinoplanes utahensis was found to be the closest species based on 16S rRNA gene sequence comparison. Besides the already published acarbose biosynthetic gene cluster sequence, several new non-ribosomal peptide synthetase-, polyketide synthase- and hybrid-clusters were identified on the Actinoplanes genome. Another key feature of the genome represents the discovery of a functional actinomycete integrative and conjugative element. Conclusions The complete genome sequence of Actinoplanes sp. SE50/110 marks an important step towards the rational genetic optimization of the acarbose production. In this regard, the identified actinomycete integrative and conjugative element could play a central role by providing the basis for the development of a genetic transformation system for Actinoplanes sp. SE50/110 and other Actinoplanes spp. Furthermore, the identified non-ribosomal peptide synthetase- and polyketide synthase-clusters potentially encode new antibiotics and/or other bioactive compounds, which might be of pharmacologic interest

Chronic pancreatitis of the pancreatic remnant is an independent risk factor for pancreatic fistula after distal pancreatectomy

Background: There is an ongoing debate about the best closure technique after distal pancreatectomy (DP). The aim of the closure is to prevent the formation of a clinically relevant post-operative pancreatic fistula (POPF). Stapler technique seems to be equal compared with hand-sewn closure of the remnant. For both techniques, a fistula rate of approximately 30% has been reported. Methods: We retrospectively analyzed our DPs between 01/2000 and 12/2010. In all cases, the pancreatic duct was over sewn with a separately stitched ligation of the pancreatic duct (5*0 PDS) followed by a single-stitched hand-sewn closure of the residual pancreatic gland. The POPF was classified according to the criteria of the International Study Group for Pancreatic Fistula (ISGPF). Univariate and multivariate analyses of potential risk factors for the formation of POPF were performed. Indications for operations included cystic tumors (n = 53), neuroendocrine tumors (n = 27), adenocarcinoma (n = 22), chronic pancreatitis (n = 9), metastasis (n = 6), and others (n = 7). Results: During the period, we performed 124 DPs (♀ = 74, ♂ = 50). The mean age was 57.5 years (18–82). The POPF rates according to the ISGPF criteria were: no fistula, 54.8% (n = 68); grade A, 24.2% (n = 30); grade B, 19.3% (n = 24); and grade C, 1.7% (n = 2). Therefore, in 21.0% (n = 26) of the cases, a clinically relevant pancreatic fistula occurred. The mean postoperative stay was significantly higher after grade B/C fistula (26.3 days) compared with no fistula/grade A fistula (13.7 days) (p < 0.05). The uni- and multivariate analyses showed chronic pancreatitis of the pancreatic remnant to be an independent risk factor for the development of POPF (p = 0.004 OR 7.09). Conclusion: By using a standardized hand-sewn closure technique of the pancreatic remnant after DP with separately stitched ligation of the pancreatic duct, a comparably low fistula rate can be achieved. Signs of chronic pancreatitis of the pancreatic remnant may represent a risk factor for the development of a pancreatic fistula after DP and therefore an anastomosis of the remnant to the intestine should be considered

Transcriptome analysis of thermophilic methylotrophic Bacillus methanolicus MGA3 using RNA-sequencing provides detailed insights into its previously uncharted transcriptional landscape

Irla M, Neshat A, Brautaset T, Rückert C, Kalinowski J, Wendisch VF. Transcriptome analysis of thermophilic methylotrophic Bacillus methanolicus MGA3 using RNA-sequencing provides detailed insights into its previously uncharted transcriptional landscape. BMC Genomics. 2015;16(1): 73.Background Bacillus methanolicus MGA3 is a thermophilic, facultative ribulose monophosphate (RuMP) cycle methylotroph. Together with its ability to produce high yields of amino acids, the relevance of this microorganism as a promising candidate for biotechnological applications is evident. The B. methanolicus MGA3 genome consists of a 3,337,035 nucleotides (nt) circular chromosome, the 19,174 nt plasmid pBM19 and the 68,999 nt plasmid pBM69. 3,218 protein-coding regions were annotated on the chromosome, 22 on pBM19 and 82 on pBM69. In the present study, the RNA-seq approach was used to comprehensively investigate the transcriptome of B. methanolicus MGA3 in order to improve the genome annotation, identify novel transcripts, analyze conserved sequence motifs involved in gene expression and reveal operon structures. For this aim, two different cDNA library preparation methods were applied: one which allows characterization of the whole transcriptome and another which includes enrichment of primary transcript 5′-ends. Results Analysis of the primary transcriptome data enabled the detection of 2,167 putative transcription start sites (TSSs) which were categorized into 1,642 TSSs located in the upstream region (5′-UTR) of known protein-coding genes and 525 TSSs of novel antisense, intragenic, or intergenic transcripts. Firstly, 14 wrongly annotated translation start sites (TLSs) were corrected based on primary transcriptome data. Further investigation of the identified 5′-UTRs resulted in the detailed characterization of their length distribution and the detection of 75 hitherto unknown cis-regulatory RNA elements. Moreover, the exact TSSs positions were utilized to define conserved sequence motifs for translation start sites, ribosome binding sites and promoters in B. methanolicus MGA3. Based on the whole transcriptome data set, novel transcripts, operon structures and mRNA abundances were determined. The analysis of the operon structures revealed that almost half of the genes are transcribed monocistronically (940), whereas 1,164 genes are organized in 381 operons. Several of the genes related to methylotrophy had highly abundant transcripts. Conclusion The extensive insights into the transcriptional landscape of B. methanolicus MGA3, gained in this study, represent a valuable foundation for further comparative quantitative transcriptome analyses and possibly also for the development of molecular biology tools which at present are very limited for this organism

Open Field Exercise Testing in Pediatric Congenital Heart Disease Patients: A Subsumption of Cardiovascular Parameters

Heart failure is a common phenomenon in congenital heart disease patients. Cardiopulmonary exercise testing is used for a reliable assessment of heart failure but is still challenging, especially for young children. Implementing mobile cardiopulmonary exercise testing (CPET) can close that diagnostic gap. While average values for healthy children have already been published, this study aims to describe typical ranges of cardiovascular performance parameters of young children with congenital heart disease performing an 8-min running cardiopulmonary exercise test. Children aged 4–8 years with common congenital heart defects after corrective surgery (Tetralogy of Fallot; transposition of the great arteries and univentricular hearts after palliation) were included. The outdoor running protocol consisted of slow walking, slow jogging, fast jogging, and maximum speed running. Each exercise was performed for 2 min, except the last, in which children were instructed to keep up maximal speed as long as possible. A total of 78 children (45 male/33 female, mean age 6,24) with congenital heart disease participated in the study, of which 97% completed the CPET successfully. A detailed description of participating patients, including data on cardiac function and subjective fitness levels, is given to help physicians use this method to classify their patients. This study presents a typical range for cardiovascular performance parameters in a population of 4–8-year-old children with congenital heart disease tested in a newly developed outdoor running protocol for CPET.Open Access funding enabled and organized by Projekt DEAL.Universitätsklinikum Leipzig (8929

Chassis organism from Corynebacterium glutamicum – a top-down approach to identify and delete irrelevant gene clusters

Unthan S, Baumgart M, Radek A, et al. Chassis organism from Corynebacterium glutamicum – a top-down approach to identify and delete irrelevant gene clusters. Biotechnology Journal. 2015;10(2):290-301

Proposal of a Standardized Questionnaire to Structure Clinical Peer Reviews of Mortality and Failure of Rescue in Pancreatic Surgery

Background: Quality management tools such as clinical peer reviews facilitate root cause analysis and may, ultimately, help to reduce surgery-related morbidity and mortality. This study aimed to evaluate the reliability of a standardized questionnaire for clinical peer reviews in pancreatic surgery. Methods: All cases of in-hospital-mortality following pancreatic surgery at two high-volume centers (n = 86) were reviewed by two pancreatic surgeons. A standardized mortality review questionnaire was developed and applied to all cases. In a second step, 20 cases were randomly assigned to an online re-review that was completed by seven pancreatic surgeons. The overall consistency of the results between the peer review and online re-review was determined by Cohen’s kappa (κ). The inter-rater reliability of the online re-review was assessed by Fleiss’ kappa (κ). Results: The clinical peer review showed that 80% of the patient mortality was related to surgery. Post-operative pancreatic fistula (POPF) (36%) followed by post-pancreatectomy hemorrhage (PPH) (22%) were the most common surgical underlying (index) complications leading to in-hospital mortality. Most of the index complications yielded in abdominal sepsis (62%); 60% of the cases exhibited potential of improvement, especially through timely diagnosis and therapy (42%). There was a moderate to substantial strength of agreement between the peer review and the online re-review in regard to the category of death (surgical vs. non-surgical; κ = 0.886), type of surgical index complication (κ = 0.714) as well as surgical and non-surgical index complications (κ = 0.492 and κ = 0.793). Fleiss’ kappa showed a moderate to substantial inter-rater agreement of the online re-review in terms of category of death (κ = 0.724), category of common surgical index complications (κ = 0.455) and surgical index complication (κ = 0.424). Conclusion: The proposed questionnaire to structure clinical peer reviews is a reliable tool for root cause analyses of in-hospital mortality and may help to identify specific options to improve outcomes in pancreatic surgery. However, the reliability of the peer feedback decreases with an increasing specificity of the review questions