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

Biotechnol Bioeng. 2018 Apr 28;:

Authors: Rupp O, MacDonald ML, Li S, Dhiman H, Polson S, Griep S, Heffner K, Hernandez I, Brinkrolf K, Jadhav V, Samoudi M, Hao H, Kingham B, Goesmann A, Betenbaugh MJ, Lewis NE, Borth N, Lee KH

Abstract
Accurate and complete genome sequences are essential in biotechnology to facilitate genome-based cell engineering efforts. The current genome assemblies for Cricetulus griseus, the Chinese hamster, are fragmented and replete with gap sequences and misassemblies, consistent with most short-read based assemblies. Here, we completely resequenced C. griseus using Single Molecule Real Time (SMRT) sequencing and merged this with Illumina-based assemblies. This generated a more contiguous and complete genome assembly than either technology alone, reducing the number of scaffolds by >28-fold, with 90% of the sequence in the 122 longest scaffolds. Most genes are now found in single scaffolds, including up- and downstream regulatory elements, enabling improved study of noncoding regions. With >95% of the gap sequence filled, important CHO cell mutations have been detected in draft assembly gaps. This new assembly will be an invaluable resource for continued basic and pharmaceutical research.

PMID: 29704459 [PubMed - as supplied by publisher]

IL-31 is crucial for induction of pruritus, but not inflammation, in contact hypersensitivity.

Sci Rep. 2018 Apr 27;8(1):6639

Authors: Takamori A, Nambu A, Sato K, Yamaguchi S, Matsuda K, Numata T, Sugawara T, Yoshizaki T, Arae K, Morita H, Matsumoto K, Sudo K, Okumura K, Kitaura J, Matsuda H, Nakae S

Abstract
IL-31, which is a member of the IL-6 family of cytokines, is produced mainly by activated CD4+ T cells, in particular activated Th2 cells, suggesting a contribution to development of type-2 immune responses. IL-31 was reported to be increased in specimens from patients with atopic dermatitis, and IL-31-transgenic mice develop atopic dermatitis-like skin inflammation, which is involved in the pathogenesis of atopic dermatitis. However, the role of IL-31 in development of contact dermatitis/contact hypersensitivity (CHS), which is mediated by hapten-specific T cells, including Th2 cells, is not fully understood. Therefore, we investigated this using IL-31-deficient (Il31-/-) mice, which we newly generated. We demonstrated that the mice showed normal migration and maturation of skin dendritic cells and induction of hapten-specific T cells in the sensitization phase of FITC-induced CHS, and normal induction of local inflammation in the elicitation phase of FITC- and DNFB-induced CHS. On the other hand, those mice showed reduced scratching frequency and duration during FITC- and/or DNFB-induced CHS. Our findings suggest that IL-31 is responsible for pruritus, but not induction of local skin inflammation, during CHS induced by FITC and DNFB.

PMID: 29703903 [PubMed - in process]

Population size changes and selection drive patterns of parallel evolution in a host-virus system.

Nat Commun. 2018 Apr 27;9(1):1706

Authors: Frickel J, Feulner PGD, Karakoc E, Becks L

Abstract
Predicting the repeatability of evolution remains elusive. Theory and empirical studies suggest that strong selection and large population sizes increase the probability for parallel evolution at the phenotypic and genotypic levels. However, selection and population sizes are not constant, but rather change continuously and directly affect each other even on short time scales. Here, we examine the degree of parallel evolution shaped through eco-evolutionary dynamics in an algal host population coevolving with a virus. We find high degrees of parallelism at the level of population size changes (ecology) and at the phenotypic level between replicated populations. At the genomic level, we find evidence for parallelism, as the same large genomic region was duplicated in all replicated populations, but also substantial novel sequence divergence between replicates. These patterns of genome evolution can be explained by considering population size changes as an important driver of rapid evolution.

PMID: 29703896 [PubMed - in process]

Next generation microbiological risk assessment-Potential of omics data for hazard characterisation.

Int J Food Microbiol. 2018 Apr 12;:

Authors: Haddad N, Johnson N, Kathariou S, Métris A, Phister T, Pielaat A, Tassou C, Wells-Bennik MHJ, Zwietering MH

Abstract
According to the World Health Organization estimates in 2015, 600 million people fall ill every year from contaminated food and 420,000 die. Microbial risk assessment (MRA) was developed as a tool to reduce and prevent risks presented by pathogens and/or their toxins. MRA is organized in four steps to analyse information and assist in both designing appropriate control options and implementation of regulatory decisions and programs. Among the four steps, hazard characterisation is performed to establish the probability and severity of a disease outcome, which is determined as function of the dose of toxin and/or pathogen ingested. This dose-response relationship is subject to both variability and uncertainty. The purpose of this review/opinion article is to discuss how Next Generation Omics can impact hazard characterisation and, more precisely, how it can improve our understanding of variability and limit the uncertainty in the dose-response relation. The expansion of omics tools (e.g. genomics, transcriptomics, proteomics and metabolomics) allows for a better understanding of pathogenicity mechanisms and virulence levels of bacterial strains. Detection and identification of virulence genes, comparative genomics, analyses of mRNA and protein levels and the development of biomarkers can help in building a mechanistic dose-response model to predict disease severity. In this respect, systems biology can help to identify critical system characteristics that confer virulence and explain variability between strains. Despite challenges in the integration of omics into risk assessment, some omics methods have already been used by regulatory agencies for hazard identification. Standardized methods, reproducibility and datasets obtained from realistic conditions remain a challenge, and are needed to improve accuracy of hazard characterisation. When these improvements are realized, they will allow the health authorities and government policy makers to prioritize hazards more accurately and thus refine surveillance programs with the collaboration of all stakeholders of the food chain.

PMID: 29703417 [PubMed - as supplied by publisher]

Simple paired heavy- and light-chain antibody repertoire sequencing using endoplasmic reticulum microsomes.

Genome Med. 2018 Apr 27;10(1):34

Authors: Devulapally PR, Bürger J, Mielke T, Konthur Z, Lehrach H, Yaspo ML, Glökler J, Warnatz HJ

Abstract
Existing methods for paired antibody heavy- and light-chain repertoire sequencing rely on specialized equipment and are limited by their commercial availability and high costs. Here, we report a novel simple and cost-effective emulsion-based single-cell paired antibody repertoire sequencing method that employs only basic laboratory equipment. We performed a proof-of-concept using mixed mouse hybridoma cells and we also showed that our method can be used for discovery of novel antigen-specific monoclonal antibodies by sequencing human CD19+ B cell IgM and IgG repertoires isolated from peripheral whole blood before and seven days after Td (Tetanus toxoid/Diphtheria toxoid) booster immunization. We anticipate broad applicability of our method for providing insights into adaptive immune responses associated with various diseases, vaccinations, and cancer immunotherapies.

PMID: 29703216 [PubMed - in process]

Development of a computational promoter with highly efficient expression in tumors.

BMC Cancer. 2018 Apr 27;18(1):480

Authors: Ho SY, Chang BH, Chung CH, Lin YL, Chuang CH, Hsieh PJ, Huang WC, Tsai NM, Huang SC, Liu YK, Lo YC, Liao KW

Abstract
BACKGROUND: Gene therapy is a potent method to increase the therapeutic efficacy against cancer. However, a gene that is specifically expressed in the tumor area has not been identified. In addition, nonspecific expression of therapeutic genes in normal tissues may cause side effects that can harm the patients' health. Certain promoters have been reported to drive therapeutic gene expression specifically in cancer cells; however, low expression levels of the target gene are a problem for providing good therapeutic efficacy. Therefore, a specific and highly expressive promoter is needed for cancer gene therapy.
METHODS: Bioinformatics approaches were utilized to analyze transcription factors (TFs) from high-throughput data. Reverse transcription polymerase chain reaction, western blotting and cell transfection were applied for the measurement of mRNA, protein expression and activity. C57BL/6JNarl mice were injected with pD5-hrGFP to evaluate the expression of TFs.
RESULTS: We analyzed bioinformatics data and identified three TFs, nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB), cyclic AMP response element binding protein (CREB), and hypoxia-inducible factor-1α (HIF-1α), that are highly active in tumor cells. Here, we constructed a novel mini-promoter, D5, that is composed of the binding sites of the three TFs. The results show that the D5 promoter specifically drives therapeutic gene expression in tumor tissues and that the strength of the D5 promoter is directly proportional to tumor size.
CONCLUSIONS: Our results show that bioinformatics may be a good tool for the selection of appropriate TFs and for the design of specific mini-promoters to improve cancer gene therapy.

PMID: 29703163 [PubMed - in process]

Identification of a novel fused gene family implicates convergent evolution in eukaryotic calcium signaling.

BMC Genomics. 2018 Apr 27;19(1):306

Authors: Chen F, Zhang L, Lin Z, Cheng ZM

Abstract
BACKGROUND: Both calcium signals and protein phosphorylation responses are universal signals in eukaryotic cell signaling. Currently three pathways have been characterized in different eukaryotes converting the Ca2+ signals to the protein phosphorylation responses. All these pathways have based mostly on studies in plants and animals.
RESULTS: Based on the exploration of genomes and transcriptomes from all the six eukaryotic supergroups, we report here in Metakinetoplastina protists a novel gene family. This family, with a proposed name SCAMK, comprises SnRK3 fused calmodulin-like III kinase genes and was likely evolved through the insertion of a calmodulin-like3 gene into an SnRK3 gene by unequal crossover of homologous chromosomes in meiosis cell. Its origin dated back to the time intersection at least 450 million-year-ago when Excavata parasites, Vertebrata hosts, and Insecta vectors evolved. We also analyzed SCAMK's unique expression pattern and structure, and proposed it as one of the leading calcium signal conversion pathways in Excavata parasite. These characters made SCAMK gene as a potential drug target for treating human African trypanosomiasis.
CONCLUSIONS: This report identified a novel gene fusion and dated its precise fusion time in Metakinetoplastina protists. This potential fourth eukaryotic calcium signal conversion pathway complements our current knowledge that convergent evolution occurs in eukaryotic calcium signaling.

PMID: 29703146 [PubMed - in process]

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circRNA expression analysis in lung adenocarcinoma: Comparison of paired fresh frozen and formalin-fixed paraffin-embedded specimens.

Biochem Biophys Res Commun. 2018 Apr 18;:

Authors: Zhang F, Zhao X, Dong H, Xu J

Abstract
Circular RNA (circRNAs) is a novel class of endogenous non-coding RNAs which is widely involved in carcinogenesis. Archived formalin-fixed paraffin-embedded (FFPE) specimens represent valuable resources for cancer research. Currently there is a lack of systematic analysis on the feasibility of circRNAs expression analysis using FFPE samples. Here, we reported the first comparison study of circRNA expression from paired fresh frozen and FFPE specimens of lung adenocarcinoma. circRNAs expression of paired lung adenocarcinoma and adjacent normal samples, starting from either fresh frozen or FFPE materials, were analyzed via a high-throughput circRNA microarray. Hierarchical clustering was performed on samples. qRT-PCR was used to confirm the differentially expressed circRNAs. The circRNA regulation networks were built by bioinformatics tools for several candidate circRNAs. Our results demonstrated that there was a good correlation in circRNAs expression analysis utilizing fresh frozen or FFPE tissues. Tumors and adjacent normal tissues can be clustered correctly by the differentially expressed circRNAs in fresh frozen or FFPE groups. Furthermore, three differentially expressed circRNAs, hsa_circRNA_100421, hsa_circRNA_104329 and hsa_circRNA_101969 were verified by qRT-PCR assay. Bioinformatics analysis was also applied to predict the circRNA-miRNA-protein coding gene interaction network for each of above circRNAs. To the best of our knowledge, this is the first report demonstrating that the circRNAs microarray analysis, starting from FFPE specimens, is comparable with that based on fresh frozen samples. Therefore FFPE specimen represents a good substitute for fresh frozen tissue, especially when fresh frozen specimen is limited.

PMID: 29679573 [PubMed - as supplied by publisher]

Foxd1 is required for terminal differentiation of anterior hypothalamic neuronal subtypes.

Dev Biol. 2018 Apr 18;:

Authors: Newman EA, Kim DW, Wan J, Wang J, Qian J, Blackshaw S

Abstract
Although the hypothalamus functions as a master homeostat for many behaviors, little is known about the transcriptional networks that control its development. To investigate this question, we analyzed mice deficient for the Forkhead domain transcription factor Foxd1. Foxd1 is selectively expressed in neuroepithelial cells of the prethalamus and hypothalamus prior to the onset of neurogenesis, and is later restricted to neural progenitors of the prethalamus and anterior hypothalamus. During early stages of neurogenesis, we observed that Foxd1-deficient mice showed reduced expression of Six3 and Vax1 in anterior hypothalamus, but overall patterning of the prethalamus and hypothalamus is unaffected. After neurogenesis is complete, however, a progressive reduction and eventual loss of expression of molecular markers of the suprachiasmatic, paraventricular and periventricular hypothalamic is observed. These findings demonstrate that Foxd1 acts in hypothalamic progenitors to allow sustained expression of a subset of genes selectively expressed in mature neurons of the anterior hypothalamus.

PMID: 29679559 [PubMed - as supplied by publisher]

Comparative genomics provides insights into the lifestyle and reveals functional heterogeneity of dark septate endophytic fungi.

Sci Rep. 2018 Apr 20;8(1):6321

Authors: Knapp DG, Németh JB, Barry K, Hainaut M, Henrissat B, Johnson J, Kuo A, Lim JHP, Lipzen A, Nolan M, Ohm RA, Tamás L, Grigoriev IV, Spatafora JW, Nagy LG, Kovács GM

Abstract
Dark septate endophytes (DSE) are a form-group of root endophytic fungi with elusive functions. Here, the genomes of two common DSE of semiarid areas, Cadophora sp. and Periconia macrospinosa were sequenced and analyzed with another 32 ascomycetes of different lifestyles. Cadophora sp. (Helotiales) and P. macrospinosa (Pleosporales) have genomes of 70.46 Mb and 54.99 Mb with 22,766 and 18,750 gene models, respectively. The majority of DSE-specific protein clusters lack functional annotation with no similarity to characterized proteins, implying that they have evolved unique genetic innovations. Both DSE possess an expanded number of carbohydrate active enzymes (CAZymes), including plant cell wall degrading enzymes (PCWDEs). Those were similar in three other DSE, and contributed a signal for the separation of root endophytes in principal component analyses of CAZymes, indicating shared genomic traits of DSE fungi. Number of secreted proteases and lipases, aquaporins, and genes linked to melanin synthesis were also relatively high in our fungi. In spite of certain similarities between our two DSE, we observed low levels of convergence in their gene family evolution. This suggests that, despite originating from the same habitat, these two fungi evolved along different evolutionary trajectories and display considerable functional differences within the endophytic lifestyle.

PMID: 29679020 [PubMed - in process]

Feedback between tissue packing and neurogenesis in the zebrafish neural tube.

Development. 2018 Apr 20;:

Authors: Hiscock TW, Miesfeld JB, Mosaliganti KR, Link BA, Megason SG

Abstract
Balancing the rate of differentiation and proliferation in developing tissues is essential to produce organs of robust size and composition. Whilst many molecular regulators have been established, how these connect to physical and geometrical aspects of tissue architecture is poorly understood. Here, using high-resolution timelapse imaging, we find that changes to cell geometry associated with dense tissue packing play a significant role in regulating differentiation rate in the zebrafish neural tube. Specifically, progenitors that are displaced away from the apical surface due to crowding tend to differentiate, in a Notch-dependent manner. Using simulations we show that interplay between progenitor density, cell shape, and changes in differentiation rate could naturally result in negative feedback control on progenitor cell number. Given these results, we suggest a model whereby differentiation rate is regulated by density dependent effects on cell geometry to: 1) correct variability in cell number, and 2) balance the rates of proliferation and differentiation over development to "fill" the available space.

PMID: 29678815 [PubMed - as supplied by publisher]

Activation and Polarity Control of PIN-FORMED Auxin Transporters by Phosphorylation.

Trends Plant Sci. 2018 Apr 17;:

Authors: Barbosa ICR, Hammes UZ, Schwechheimer C

Abstract
Auxin controls almost every aspect of plant development. Auxin is distributed within the plant by passive diffusion and active cell-to-cell transport. PIN-FORMED (PIN) auxin efflux transporters are polarly distributed in the plasma membranes of many cells, and knowledge about their distribution can predict auxin transport and explain auxin distribution patterns, even in complex tissues. Recent studies have revealed that phosphorylation is essential for PIN activation, suggesting that PIN phosphorylation needs to be taken into account in understanding auxin transport. These findings also ask for a re-examination of previously proposed mechanisms for phosphorylation-dependent PIN polarity control. We provide a comprehensive summary of the current knowledge on PIN regulation by phosphorylation, and discuss possible mechanisms of PIN polarity control in the context of recent findings.

PMID: 29678589 [PubMed - as supplied by publisher]