Next-generation sequencing analysis of the Tineola bisselliella larval gut transcriptome reveals candidate enzymes for keratin digestion

The clothes moth Tineola bisselliella is one of a few insects that can digest keratin, leading to the destruction of clothing, textiles and artwork. The mechanism of keratin digestion is not yet fully understood, partly reflecting the lack of publicly available genomic and transcriptomic data. Here we present a high-quality gut transcriptome of T. bisselliella generated from larvae reared on keratin-rich and keratin-free diets. The overall transcriptome consists of 428,221 contigs that were functionally annotated and screened for candidate enzymes involved in keratin utilization. As a mechanism for keratin digestion, we identified cysteine synthases, cystathionine β-synthases and cystathionine γ-lyases. These enzymes release hydrogen sulfite, which may reduce the disulfide bonds in keratin. The dataset also included 27 differentially expressed contigs with trypsin domains, among which 20 were associated with keratin feeding. Finally, we identified seven collagenases that were upregulated on the keratin-rich diet. In addition to this enzymatic repertoire potentially involved in breaking down keratin, our analysis of poly(A)-enriched and poly(A)-depleted transcripts suggested that T. bisselliella larvae possess an unstable intestinal microbiome that may nevertheless contribute to keratin digestion

A reference genome for the Chinese hamster based on a hybrid assembly strategy

Accurate and complete genome sequences are essential in biotechnology, especially to facilitate genome-based cell engineering efforts for the main production host of biotherapeutic proteins, Chinese hamster ovary (CHO) cells. While genome-enabled CHO cell engineering efforts promise to enhance drug production, the current genome assemblies for Cricetulus griseus, the Chinese hamster, are highly fragmented and replete with gap sequences and misassemblies, consistent with most short-read based assemblies. Here we have completely re-sequenced the Chinese hamster, C. griseus, using Single Molecule Real Time (SMRT) long-read technology and merged this assembly with Illumina-based assemblies. Please download the file below for full content

Redirecting T Cells to Ewing's Sarcoma Family of Tumors by a Chimeric NKG2D Receptor Expressed by Lentiviral Transduction or mRNA Transfection

We explored the possibility to target Ewing's sarcoma family of tumors (ESFT) by redirecting T cells. To this aim, we considered NKG2D-ligands (NKG2D-Ls) as possible target antigens. Detailed analysis of the expression of MICA, MICB, ULBP-1, -2, and -3 in fourteen ESFT cell lines revealed consistent expression of at least one NKG2D-L. Thus, for redirecting T cells, we fused a CD3ζ/CD28-derived signaling domain to the ectodomain of NKG2D, however, opposite transmembrane orientation of this signaling domain and NKG2D required inverse orientation fusion of either of them. We hypothesized that the particularly located C-terminus of the NKG2D ectodomain should allow reengineering of the membrane anchoring from a native N-terminal to an artificial C-terminal linkage. Indeed, the resulting chimeric NKG2D receptor (chNKG2D) was functional and efficiently mediated ESFT cell death triggered by activated T cells. Notably, ESFT cells with even low NKG2D-L expression were killed by CD8pos and also CD4pos cells. Both, mRNA transfection and lentiviral transduction resulted in high level surface expression of chNKG2D. However, upon target-cell recognition receptor surface levels were maintained by tranfected RNA only during the first couple of hours after transfection. Later, target-cell contact resulted in strong and irreversible receptor down-modulation, whereas lentivirally mediated expression of chNKG2D remained constant under these conditions. Together, our study defines NKG2D-Ls as targets for a CAR-mediated T cell based immunotherapy of ESFT. A comparison of two different methods of gene transfer reveals strong differences in the susceptibility to ligand-induced receptor down-modulation with possible implications for the applicability of RNA transfection

The complete genome sequence of Corynebacterium pseudotuberculosis FRC41 isolated from a 12-year-old girl with necrotizing lymphadenitis reveals insights into gene-regulatory networks contributing to virulence

Trost E, Ott L, Schneider J, et al. The complete genome sequence of Corynebacterium pseudotuberculosis FRC41 isolated from a 12-year-old girl with necrotizing lymphadenitis reveals insights into gene-regulatory networks contributing to virulence. BMC Genomics. 2010;11(1): 728

Deinococcus geothermalis: The Pool of Extreme Radiation Resistance Genes Shrinks

Bacteria of the genus Deinococcus are extremely resistant to ionizing radiation (IR), ultraviolet light (UV) and desiccation. The mesophile Deinococcus radiodurans was the first member of this group whose genome was completely sequenced. Analysis of the genome sequence of D. radiodurans, however, failed to identify unique DNA repair systems. To further delineate the genes underlying the resistance phenotypes, we report the whole-genome sequence of a second Deinococcus species, the thermophile Deinococcus geothermalis, which at its optimal growth temperature is as resistant to IR, UV and desiccation as D. radiodurans, and a comparative analysis of the two Deinococcus genomes. Many D. radiodurans genes previously implicated in resistance, but for which no sensitive phenotype was observed upon disruption, are absent in D. geothermalis. In contrast, most D. radiodurans genes whose mutants displayed a radiation-sensitive phenotype in D. radiodurans are conserved in D. geothermalis. Supporting the existence of a Deinococcus radiation response regulon, a common palindromic DNA motif was identified in a conserved set of genes associated with resistance, and a dedicated transcriptional regulator was predicted. We present the case that these two species evolved essentially the same diverse set of gene families, and that the extreme stress-resistance phenotypes of the Deinococcus lineage emerged progressively by amassing cell-cleaning systems from different sources, but not by acquisition of novel DNA repair systems. Our reconstruction of the genomic evolution of the Deinococcus-Thermus phylum indicates that the corresponding set of enzymes proliferated mainly in the common ancestor of Deinococcus. Results of the comparative analysis weaken the arguments for a role of higher-order chromosome alignment structures in resistance; more clearly define and substantially revise downward the number of uncharacterized genes that might participate in DNA repair and contribute to resistance; and strengthen the case for a role in survival of systems involved in manganese and iron homeostasis

Virtual optimisation for improved production planning

Brinkrolf J, Mittag T, Joppen R, Dr\ A, Pietsch K-H, Hammer B. Virtual optimisation for improved production planning. In: New Challenges in Neural Computation. 2016

Risk of Transmission of MRSA on Contact Surfaces in Ambulance

The gram-positive bacterium methicillin-resistant Staphylococcus aureus (MRSA) is one of the most frequent causes of treatment-associated nosocomial infections. The incidence of MRSA among the population and in hospitalised patients is growing worldwide. Ambulance service is an interface between the enviroment, outpatient treatment and inpatient treatment of patients. What is the probability that MRSA is applied by the patient on contact surfaces in ambulance vehicles in compliance with an infection control concept and what are risk contact surfaces in the ambulance vehicle? We studied defined contact surfaces in 30 ambulances after transport of a MRSA positive patients. In the control group 15 ambulances were examined after transport with unknown MRSA status. The sampling was carried out before the final disinfection, genotyping of MRSA strains were carried out within the Euregio MRSA-net project. In three transports with known MRSA status of the patient we found on four contact surfaces in the vehicles a nosocomial MRSA strain with the same genotype of previously transported patient. In the control group, we detected an incidental finding of a nosocomial MRSA strain on the disinfectant dispenser. The risk areas identified were all close to the patient and all hand-related areas of the staff. All sampling was carried out before the final disinfection. In 10% MRSA is transmitted from patient to near patient and all hand contact surfaces in the ambulance vehicle. A targeted disinfection, as well as an infection control concept are sufficient to eliminate MRSA transmission on contact surfaces in the ambulance vehicle