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Acinetobacter baumannii is an important bacterium that emerged as a significant nosocomial pathogen worldwide. The rise of A. baumannii was due to its multi-drug resistance (MDR), while it was difficult to treat multi-drug resistant A. baumannii with antibiotics, especially in pediatric patients for the therapeutic options with antibiotics were quite limited in pediatric patients. A. baumannii ST208 was identified as predominant sequence type of carbapenem resistant A. baumannii in the United States and China. As we knew, there was no complete genome sequence reproted for A. baumannii ST208, although several whole genome shotgun sequences had been reported. Here, we sequenced the 4087-kilobase (kb) chromosome and 112-kb plasmid of A. baumannii XH386 (ST208), which was isolated from a pediatric hospital in China. The genome of A. baumannii XH386 contained 3968 protein-coding genes and 94 RNA-only encoding genes. Genomic analysis and Minimum inhibitory concentration assay showed that A. baumannii XH386 was multi-drug resistant strain, which showed resistance to most of antibiotics, except for tigecycline. The data may be accessed via the GenBank accession number CP010779 and CP010780.
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Aquaporins (AQPs) are proteins that facilitate the transport of water, small neutral solutes and gases across membranes and have an important role in plant physiology and drought stress responses. The sugarcane (Saccharum spp.) transcriptome was searched for AQPs, also known as major intrinsic proteins. Phylogenetic analysis based on nucleotide sequences identified 33 isoforms that fit into four AQP subfamilies previously described for monocotyledonous: 13 plasma membrane intrinsic protein (PIPs), 11 tonoplast intrinsic proteins (TIPs), six nodulin 26-like intrinsic proteins (NIPs) and three small basic intrinsic proteins (SIPs). Among the PIPs, five proteins were classified as PIP1 type and eight were classified as PIP2 type. The expression profiles of three PIP2 isoforms (ShPIP2;1, ShPIP2;5 and ShPIP2;6), which are counterparts of previously described isoforms involved in drought stress in leaves of higher plants, were aligned with monocots and dicot PIP2 protein sequence showing high identity with maize proteins. Furthermore, the transcript abundance of these three genes was evaluated through quantitative PCR (qPCR) in two sugarcane genotypes (‘IACSP94-2094’ and ‘IACSP97-7065’) subjected to water deficit under field and greenhouse conditions. ShPIP2;1, ShPIP2;5 and ShPIP2;6 isoforms were responsive to water deficit and their expression patterns were dependent on genotype, experimental condition and duration of drought stress. Taken together, our results show that the three APQs have their expression in leaves changed under drought, suggesting that these proteins constitute an important target for functional characterization in sugarcane, particularly focusing the performance of plants under varying water availability.
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Combining whole genome data with previously obtained amplicon sequences has the potential to increase the resolution of phylogenetic analyses, particularly at low taxonomic levels or where recent divergence, rapid speciation or slow genome evolution has resulted in limited sequence variation. However, the integration of these types of data for large scale phylogenetic studies has rarely been investigated. Here we conduct a phylogenetic analysis of the whole chloroplast genome and two nuclear ribosomal loci for 65 Acacia species from across the most recent Acacia phylogeny. We then combine this data with previously generated amplicon sequences (four chloroplast loci and two nuclear ribosomal loci) for 508 Acacia species. We use several phylogenetic methods, including maximum likelihood bootstrapping (with and without constraint) and ExaBayes, in order to determine the success of combining a dataset of 4000bp with one of 189,000bp. The results of our study indicate that the inclusion of whole genome data gave a far better resolved and well supported representation of the phylogenetic relationships within Acacia than using only amplicon sequences, with the greatest support observed when using a whole genome phylogeny as a constraint on the amplicon sequences. Our study therefore provides methods for optimal integration of genomic and amplicon sequences.
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Recent work has demonstrated that subject motion produces systematic biases in the metrics computed by widely used morphometry software packages, even when the motion is too small to produce noticeable image artifacts. In the common situation where the control population exhibits different behaviors in the scanner when compared to the experimental population, these systematic measurement biases may produce significant confounds for between-group analyses, leading to erroneous conclusions about group differences. While previous work has shown that prospective motion correction can improve perceived image quality, here we demonstrate that, in healthy subjects performing a variety of directed motions, the use of the volumetric navigator (vNav) prospective motion correction system significantly reduces the motion-induced bias and variance in morphometry.
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Context-independent anti-hypusine antibodies that bind to the post-translational modification (PTM), hypusine, with minimal dependence on flanking amino acid sequences, were identified. The antibodies bind to both hypusine and deoxyhypusine or selectively to hypusine but not to deoxyhypusine. Phage display was used to further enhance the affinity of the antibodies. Affinity maturation of these anti-hypusine antibodies improved their performance in affinity capture of the only currently known hypusinated protein, eukaryotic translation initiation factor 5A. These anti-hypusine antibodies may have utility in the identification of novel hypusinated proteins. Crystal structures of the corresponding Fab fragments were determined in complex with hypusine- or deoxyhypusine-containing peptides. The hypusine or deoxyhypusine moiety was found to reside in a deep pocket formed between VH and VL domains of the Fab fragments. Interaction between the antibodies and hypusine includes an extensive hydrogen bond network. These are, to our knowledge, the first reported structures of context-independent anti-PTM antibodies in complex with the corresponding PTM.
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This study aims at investigating the potential use of comparative proteomics as a multi-marker approach of metal contamination, taking into account the potential confounding effect of water temperature. The major objective was to identify combinations of proteins specifically responding to a given metal, even if included in a metal mixture. The diagnostic approach was performed via the comparative analysis of protein expression on spot mapping provided by adult males of Gammarus pulex (Amphipoda, Crustacea) respectively exposed to arsenate (As), cadmium (Cd) or a binary mixture of these metals (AsCd) at three realistic temperatures (5, 10 and 15°C). Proteomic expression analysis was performed by Differential in-Gel Electrophoresis (2D-DiGE), and completed by an adapted inferential statistical approach. Combinations of under/over-expressed protein spots discriminated the metal identity. However, none of these spots discriminated both the individual metal effect (As or Cd) and its effect in metal mixture (AsCd) whatever the tested temperature. Some limits of the two-dimensional analysis of protein spot maps in G. pulex have been highlighted: (i) the presence of contaminating peptides and/or abundant “déja-vu” proteins which can mask the responses of other proteins of interest or (ii) the presence of post-translational modifications. An optimization of the experimental design (especially during the sample preparation) has been described for future investigations.
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Environmental DNA sampling (eDNA) has emerged as a powerful tool for detecting aquatic animals. Previous research suggests that eDNA methods are substantially more sensitive than traditional sampling. However, the factors influencing eDNA detection and the resulting sampling costs are still not well understood. Here we use multiple experiments to derive independent estimates of eDNA production rates and downstream persistence from brook trout (Salvelinus fontinalis) in streams. We use these estimates to parameterize models comparing the false negative detection rates of eDNA sampling and traditional backpack electrofishing. We find that using the protocols in this study eDNA had reasonable detection probabilities at extremely low animal densities (e.g., probability of detection 0.18 at densities of one fish per stream kilometer) and very high detection probabilities at population-level densities (e.g., probability of detection >0.99 at densities of ≥3 fish per 100m). This is substantially more sensitive than traditional electrofishing for determining the presence of brook trout and may translate into important cost savings when animals are rare. Our findings are consistent with a growing body of literature showing that eDNA sampling is a powerful tool for the detection of aquatic species, particularly those that are rare and difficult to sample using traditional methods.
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The trypanosomatid Phytomonas nordicus parasitizing the predatory bug Troilus luridus was described at the twilight of the morphotype-based systematics. Despite its monoxenous life cycle, this species was attributed to the dixenous genus Phytomonas due to the presence of long twisted promastigotes and development of flagellates in salivary glands. However, these characteristics were considered insufficient for proving the phytomonad nature of the species and therefore its description remained virtually unnoticed. Here, we performed molecular phylogenetic analyses using 18S ribosomal RNA (rRNA) gene and region containing internal trascribed spacers (ITS) 1 and 2 and convincingly demonstrated the affinity of P. nordicus to the genus Phytomonas. In addition, we investigated its development in the salivary glands. We argue that in many aspects the life cycle of monoxenous P. nordicus resembles that of its dixenous relatives represented by tomato-parasitizing Phytomonas serpens.
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The paper presents the algorithm for calculating the fatigue life taking into account the variability of coefficients occurring in the multiaxial fatigue criterion depending on the number of cycles to failure. The algorithm has been analysed under uniaxial cyclic loads and a combination of bending and torsion for four structural materials. Significant increase of convergence of calculated and experimental fatigue life using the new algorithm as compared to the classical approach for five selected multiaxial fatigue criteria based on a critical plane has been demonstrated.
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In recent years, the removal of electrocardiogram (ECG) interferences from electromyogram (EMG) signals has been given large consideration. Where the quality of EMG signal is of interest, it is important to remove ECG interferences from EMG signals. In this paper, an efficient method based on a combination of adaptive neuro-fuzzy inference system (ANFIS) and wavelet transform is proposed to effectively eliminate ECG interferences from surface EMG signals. The proposed approach is compared with other common methods such as high-pass filter, artificial neural network, adaptive noise canceller, wavelet transform, subtraction method and ANFIS. It is found that the performance of the proposed ANFIS–wavelet method is superior to the other methods with the signal to noise ratio and relative error of 14.97dB and 0.02 respectively and a significantly higher correlation coefficient (p<0.05).
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