Antibiotic-dependent instability of homeostatic plasticity for growth and environmental load

Reducing antibiotic usage in livestock animals has become an urgent issue worldwide to prevent antimicrobial resistance. Here, abuse of chlortetracycline (CTC), a versatile antibacterial agent, on the performance, blood components, fecal microbiota, and organic acid concentration in calves was investigated. Japanese Black calves were fed milk replacer containing CTC at 10 g/kg (CON) or 0 g/kg (EXP). Growth performance was not affected by CTC administration. However, CTC administration altered the correlation between fecal organic acids and bacterial genera. Machine learning methods such as association analysis, linear discriminant analysis, and energy landscape analysis revealed that CTC administration affected according to certain rules the population of various types of fecal bacteria. It is particularly interesting that the population of several methane-producing bacteria was high in the CON, and that of Lachnospiraceae, a butyrate-producing bacteria, was high in the EXP at 60 d of age. Furthermore, statistical causal inference based on machine learning data estimated that CTC treatment affects the entire intestinal environment, inhibiting butyrate production for growth and biological defense, which may be attributed to methanogens in feces. Thus, these observations highlight the multiple harmful impacts of antibiotics on intestinal health and the potential production of greenhouse gas in the calves

RiceFOX: A Database of Arabidopsis Mutant Lines Overexpressing Rice Full-Length cDNA that Contains a Wide Range of Trait Information to Facilitate Analysis of Gene Function

Identification of gene function is important not only for basic research but also for applied science, especially with regard to improvements in crop production. For rapid and efficient elucidation of useful traits, we developed a system named FOX hunting (Full-length cDNA Over-eXpressor gene hunting) using full-length cDNAs (fl-cDNAs). A heterologous expression approach provides a solution for the high-throughput characterization of gene functions in agricultural plant species. Since fl-cDNAs contain all the information of functional mRNAs and proteins, we introduced rice fl-cDNAs into Arabidopsis plants for systematic gain-of-function mutation. We generated >30,000 independent Arabidopsis transgenic lines expressing rice fl-cDNAs (rice FOX Arabidopsis mutant lines). These rice FOX Arabidopsis lines were screened systematically for various criteria such as morphology, photosynthesis, UV resistance, element composition, plant hormone profile, metabolite profile/fingerprinting, bacterial resistance, and heat and salt tolerance. The information obtained from these screenings was compiled into a database named ‘RiceFOX’. This database contains around 18,000 records of rice FOX Arabidopsis lines and allows users to search against all the observed results, ranging from morphological to invisible traits. The number of searchable items is approximately 100; moreover, the rice FOX Arabidopsis lines can be searched by rice and Arabidopsis gene/protein identifiers, sequence similarity to the introduced rice fl-cDNA and traits. The RiceFOX database is available at http://ricefox.psc.riken.jp/

In Silico Analysis of Correlations between Protein Disorder and Post-Translational Modifications in Algae

Recent proteome analyses have reported that intrinsically disordered regions (IDRs) of proteins play important roles in biological processes. In higher plants whose genomes have been sequenced, the correlation between IDRs and post-translational modifications (PTMs) has been reported. The genomes of various eukaryotic algae as common ancestors of plants have also been sequenced. However, no analysis of the relationship to protein properties such as structure and PTMs in algae has been reported. Here, we describe correlations between IDR content and the number of PTM sites for phosphorylation, glycosylation, and ubiquitination, and between IDR content and regions rich in proline, glutamic acid, serine, and threonine (PEST) and transmembrane helices in the sequences of 20 algae proteomes. Phosphorylation, O-glycosylation, ubiquitination, and PEST preferentially occurred in disordered regions. In contrast, transmembrane helices were favored in ordered regions. N-glycosylation tended to occur in ordered regions in most of the studied algae; however, it correlated positively with disordered protein content in diatoms. Additionally, we observed that disordered protein content and the number of PTM sites were significantly increased in the species-specific protein clusters compared to common protein clusters among the algae. Moreover, there were specific relationships between IDRs and PTMs among the algae from different groups

MINORITY REPORT: FUNCTIONAL CHARACTERIZATION OF A SUBSET OF EXTREMELY ALKALINE PROTEINS IN THE HUMAN PROTEOME

[Abstract] Whole-proteome distributions of the protein isoelectric point (pI) are not Gaussian but rather multimodal. In the present study, we performed functional characterization of an extremely alkaline protein modality (pI>11.5, n=503) in the human proteome. Here, we report that the majority of the extremely alkaline proteins (69%), which have predominantly nuclear or mitochondrial localization (80%), are involved in information storage and processing. These proteins were further classified in the functional groups of “Translation, ribosomal structure and biogenesis”, “RNA processing and modification”, and “Chromatin structure and dynamic”, according to the classification of Eukaryotic Orthologous Groups, KOGs. In addition, a lot of nuclear proteins in the analyzed subset (63%) bear the nucleolar localization signal. These data indicate that many of the extremely alkaline proteins localize to the nucleolus and are involved in ribosome biogenesis and RNA processing.Original Pape

Signal Deconvolution and Noise Factor Analysis Based on a Combination of Time–Frequency Analysis and Probabilistic Sparse Matrix Factorization

Nuclear magnetic resonance (NMR) spectroscopy is commonly used to characterize molecular complexity because it produces informative atomic-resolution data on the chemical structure and molecular mobility of samples non-invasively by means of various acquisition parameters and pulse programs. However, analyzing the accumulated NMR data of mixtures is challenging due to noise and signal overlap. Therefore, data-cleansing steps, such as quality checking, noise reduction, and signal deconvolution, are important processes before spectrum analysis. Here, we have developed an NMR measurement informatics tool for data cleansing that combines short-time Fourier transform (STFT; a time–frequency analytical method) and probabilistic sparse matrix factorization (PSMF) for signal deconvolution and noise factor analysis. Our tool can be applied to the original free induction decay (FID) signals of a one-dimensional NMR spectrum. We show that the signal deconvolution method reduces the noise of FID signals, increasing the signal-to-noise ratio (SNR) about tenfold, and its application to diffusion-edited spectra allows signals of macromolecules and unsuppressed small molecules to be separated by the length of the T2* relaxation time. Noise factor analysis of NMR datasets identified correlations between SNR and acquisition parameters, identifying major experimental factors that can lower SNR

Knockout of the Sendai virus C gene eliminates the viral ability to prevent the interferon-α/β-mediated responses

AbstractSendai virus (SeV) renders cells unresponsive to interferon (IFN)-α. To identify viral factors involved in this process, we examined whether recombinant SeVs, which could not express V protein, subsets of C proteins (C, C′, Y1 and Y2) or any of four C proteins, retained the capability of impeding IFN-α-mediated responses. Among these viruses, only the 4C knockout virus completely lost the ability to suppress the induction of IFN-α-stimulated gene products and the subsequent establishment of an anti-viral state. These findings reveal crucial roles of the SeV C proteins in blocking IFN-α-mediated responses

Large-scale collection and annotation of full-length enriched cDNAs from a model halophyte, <it>Thellungiella halophila</it>

<p>Abstract</p> <p>Background</p> <p><it>Thellungiella halophila </it>(also known as <it>Thellungiella salsuginea</it>) is a model halophyte with a small plant size, short life cycle, and small genome. It easily undergoes genetic transformation by the floral dipping method used with its close relative, <it>Arabidopsis thaliana</it>. <it>Thellungiella </it>genes exhibit high sequence identity (approximately 90% at the cDNA level) with Arabidopsis genes. Furthermore, <it>Thellungiella </it>not only shows tolerance to extreme salinity stress, but also to chilling, freezing, and ozone stress, supporting the use of <it>Thellungiella </it>as a good genomic resource in studies of abiotic stress tolerance.</p> <p>Results</p> <p>We constructed a full-length enriched <it>Thellungiella </it>(Shan Dong ecotype) cDNA library from various tissues and whole plants subjected to environmental stresses, including high salinity, chilling, freezing, and abscisic acid treatment. We randomly selected about 20 000 clones and sequenced them from both ends to obtain a total of 35 171 sequences. CAP3 software was used to assemble the sequences and cluster them into 9569 nonredundant cDNA groups. We named these cDNAs "RTFL" (RIKEN <it>Thellungiella </it>Full-Length) cDNAs. Information on functional domains and Gene Ontology (GO) terms for the RTFL cDNAs were obtained using InterPro. The 8289 genes assigned to InterPro IDs were classified according to the GO terms using Plant GO Slim. Categorical comparison between the whole Arabidopsis genome and <it>Thellungiella </it>genes showing low identity to Arabidopsis genes revealed that the population of <it>Thellungiella </it>transport genes is approximately 1.5 times the size of the corresponding Arabidopsis genes. This suggests that these genes regulate a unique ion transportation system in <it>Thellungiella</it>.</p> <p>Conclusion</p> <p>As the number of <it>Thellungiella halophila </it>(<it>Thellungiella salsuginea</it>) expressed sequence tags (ESTs) was 9388 in July 2008, the number of ESTs has increased to approximately four times the original value as a result of this effort. Our sequences will thus contribute to correct future annotation of the <it>Thellungiella </it>genome sequence. The full-length enriched cDNA clones will enable the construction of overexpressing mutant plants by introduction of the cDNAs driven by a constitutive promoter, the complementation of <it>Thellungiella </it>mutants, and the determination of promoter regions in the <it>Thellungiella </it>genome.</p