Efficient Identification of Tembusu Virus CTL Epitopes in Inbred HBW/B4 Ducks Using a Novel MHC Class I-Restricted Epitope Screening Scheme.

The identification of MHC class I-restricted CTL epitopes in certain species, particularly nonmammals, remains a challenge. In this study, we developed a four-step identification scheme and confirmed its efficiency by identifying the Anpl-UAA*76-restricted CTL epitopes of Tembusu virus (TMUV) in inbred haplotype ducks HBW/B4. First, the peptide binding motif of Anpl-UAA*76 was determined by random peptide library in de novo liquid chromatography-tandem mass spectrometry, a novel nonbiased, data-independent acquisition method that we previously established. Second, a total of 38 TMUV peptides matching the motif were screened from the viral proteome, among which 11 peptides were conserved across the different TMUV strains. Third, the conserved TMUV peptides were refolded in vitro with Anpl-UAA*76 and Anpl-ß2-microglobulin to verify the results from the previous two steps. To clarify the structural basis of the obtained motif, we resolved the crystal structure of Anpl-UAA*76 with the TMUV NS3 peptide LRKRQLTVL and found that Asp34 is critical for the preferential binding of the B pocket to bind the second residue to arginine as an anchor residue. Fourth, the immunogenicity of the conserved TMUV peptides was tested in vivo using specific pathogen-free HBW/B4 ducks immunized with the attenuated TMUV vaccine. All 11 conserved TMUV epitopes could bind stably to Anpl-UAA*76 in vitro and stimulate the secretion of IFN-γ and lymphocyte proliferation, and three conserved and one nonconserved peptides were selected to evaluate the CTL responses in vivo by flow cytometry and their tetramers. We believe that this new scheme could improve the identification of MHC class I-restricted CTL epitopes, and our data provide a foundation for further study on duck anti-TMUV CTL immunity.

Selection, periodicity and potential function for Highly Iterative Palindrome-1 (HIP1) in cyanobacterial genomes.

Highly Iterated Palindrome 1 (HIP1, GCGATCGC) is hyper-abundant in most cyanobacterial genomes. In some cyanobacteria, average HIP1 abundance exceeds one motif per gene. Such high abundance suggests a significant role in cyanobacterial biology. However, 20 years of study have not revealed whether HIP1 has a function, much less what that function might be. We show that HIP1 is 15- to 300-fold over-represented in genomes analyzed. More importantly, HIP1 sites are conserved both within and between open reading frames, suggesting that their overabundance is maintained by selection rather than by continual replenishment by neutral processes, such as biased DNA repair. This evidence for selection suggests a functional role for HIP1. No evidence was found to support a functional role as a peptide or RNA motif or a role in the regulation of gene expression. Rather, we demonstrate that the distribution of HIP1 along cyanobacterial chromosomes is significantly periodic, with periods ranging from 10 to 90 kb, consistent in scale with periodicities reported for co-regulated, co-expressed and evolutionarily correlated genes. The periodicity we observe is also comparable in scale to chromosomal interaction domains previously described in other bacteria. In this context, our findings imply HIP1 functions associated with chromosome and nucleoid structure.

Event inference in multidomain families with phylogenetic reconciliation.

BACKGROUND: Reconstructing evolution provides valuable insights into the processes of gene evolution and function. However, while there have been great advances in algorithms and software to reconstruct the history of gene families, these tools do not model the domain shuffling events (domain duplication, insertion, transfer, and deletion) that drive the evolution of multidomain protein families. Protein evolution through domain shuffling events allows for rapid exploration of functions by introducing new combinations of existing folds. This powerful mechanism was key to some significant evolutionary innovations, such as multicellularity and the vertebrate immune system. A method for reconstructing this important evolutionary process is urgently needed. RESULTS: Here, we introduce a novel, event-based framework for studying multidomain evolution by reconciling a domain tree with a gene tree, with additional information provided by the species tree. In the context of this framework, we present the first reconciliation algorithms to infer domain shuffling events, while addressing the challenges inherent in the inference of evolution across three levels of organization. CONCLUSIONS: We apply these methods to the evolution of domains in the Membrane associated Guanylate Kinase family. These case studies reveal a more vivid and detailed evolutionary history than previously provided. Our algorithms have been implemented in software, freely available at http://www.cs.cmu.edu/˜durand/Notung.

Inferring duplications, losses, transfers and incomplete lineage sorting with nonbinary species trees.

MOTIVATION: Gene duplication (D), transfer (T), loss (L) and incomplete lineage sorting (I) are crucial to the evolution of gene families and the emergence of novel functions. The history of these events can be inferred via comparison of gene and species trees, a process called reconciliation, yet current reconciliation algorithms model only a subset of these evolutionary processes. RESULTS: We present an algorithm to reconcile a binary gene tree with a nonbinary species tree under a DTLI parsimony criterion. This is the first reconciliation algorithm to capture all four evolutionary processes driving tree incongruence and the first to reconcile non-binary species trees with a transfer model. Our algorithm infers all optimal solutions and reports complete, temporally feasible event histories, giving the gene and species lineages in which each event occurred. It is fixed-parameter tractable, with polytime complexity when the maximum species outdegree is fixed. Application of our algorithms to prokaryotic and eukaryotic data show that use of an incomplete event model has substantial impact on the events inferred and resulting biological conclusions. AVAILABILITY: Our algorithms have been implemented in Notung, a freely available phylogenetic reconciliation software package, available at http://www.cs.cmu.edu/~durand/Notung. CONTACT: mstolzer@andrew.cmu.edu.

Polydopamine-based molecular imprinting on silica-modified magnetic nanoparticles for recognition and separation of bovine hemoglobin.

Surface molecular imprinting, especially on the surface of silica-modified magnetic nanoparticles, has been proposed as a promising strategy for protein recognition and separation. Inspired by the self-polymerization of dopamine, we synthesized a polydopamine-based molecular imprinted film coating on silica-Fe(3)O(4) nanoparticles for recognition and separation of bovine hemoglobin (BHb). Magnetic molecularly imprinted nanoparticles (about 860 nm) possess a core-shell structure. Magnetic molecularly imprinted nanoparticles (MMIP) show a relatively high adsorption capacity (4.65 ± 0.38 mg g(-1)) and excellent selectivity towards BHb with a separation factor of 2.19. MMIP with high saturation magnetization (10.33 emu g(-1)) makes it easy to separate the target protein from solution by an external magnetic field. After three continuous adsorption and elution processes, the adsorption capacity of MMIP remained at 4.30 mg g(-1). Our results suggest that MMIPs are suitable for the removal of high abundance of protein and the enrichment of low abundance of protein in proteomics.

A new c.1845A→T of oncostatin M receptor-ß mutation and slightly enhanced oncostatin M receptor-ß expression in a Chinese family with primary localized cutaneous amyloidosis.

Primary localized cutaneous amyloidosis (PLCA) is a chronic itching skin disease with amyloid material deposited in the upper dermis. PLCA is more common in Southeast Asia and South America, where up to 10% of cases may be familial. Mutations of OSMR or IL31RA have been identified in PLCA. Here we detected a new OSMR mutation in a lichenoid PLCA family from north China. This is the first report of PLCA with gene mutation on the Chinese mainland. A heterozygous 1845A→T was found in exon 13 of the proband, causing p.Lys615Asn substitution, which was not found in screening 100 ethnically matched healthy controls. The particular mutated amino acid is well conserved throughout various evolutionary lineages, located within the second fibronectin III-like domain of oncostatin M receptor ß subunit (OSMRß), and in close vicinity to a previously reported mutation, p.Gly618Ala. Immunohistochemistry showed slightly enhanced OSMRß expression in the lesion of the proband. This study extends the knowledge of PLCA gene mutation and further supports the pathogenic role of OSMRß in PLCA.

Genetic diversity and evolution of goose astrovirus in the east of China.

Goose astrovirus (GAstV), an agent of fatal visceral gout in goslings, has been widely circulating in eastern China since 2017, but little is known about its genetic diversity and systematic evolution. In this study, we isolated and sequenced nine nearly full-length GAstV genomes and conducted comprehensive genetic diversity and evolutionary analysis and compared them with other reported GAstV sequences. Our results indicated that two genotypic species of GAstV were circulating in China, and GAstV-2 subgenotype II-c had arisen as the dominant genotype in Shandong province and across the whole country. Multiple alignments of GAstV amino acid sequences revealed several characteristic mutations in GAstV-2 II-c strains, as well as additional residues in the nine new isolates which varied over time. Phylogenetic analysis of three open reading frames demonstrated different evolutionary histories. Evidence of natural recombination was also detected in GAstV, with most of the recombination occurring in the GAstV-2 II-c subgenotype. Molecular adaptation analyses revealed that the evolution of GAstV was shaped by strong negative selection, although a number of amino acids, which potentially affect host infection and cell entry, were subjected to positive pressure. Overall, these findings improve our understanding of the epidemiology and evolution of GAstV and may help in the development of vaccines and diagnostics.

Genome-wide de novo prediction of cis-regulatory binding sites in prokaryotes.

Although cis-regulatory binding sites (CRBSs) are at least as important as the coding sequences in a genome, our general understanding of them in most sequenced genomes is very limited due to the lack of efficient and accurate experimental and computational methods for their characterization, which has largely hindered our understanding of many important biological processes. In this article, we describe a novel algorithm for genome-wide de novo prediction of CRBSs with high accuracy. We designed our algorithm to circumvent three identified difficulties for CRBS prediction using comparative genomics principles based on a new method for the selection of reference genomes, a new metric for measuring the similarity of CRBSs, and a new graph clustering procedure. When operon structures are correctly predicted, our algorithm can predict 81% of known individual binding sites belonging to 94% of known cis-regulatory motifs in the Escherichia coli K12 genome, while achieving high prediction specificity. Our algorithm has also achieved similar prediction accuracy in the Bacillus subtilis genome, suggesting that it is very robust, and thus can be applied to any other sequenced prokaryotic genome. When compared with the prior state-of-the-art algorithms, our algorithm outperforms them in both prediction sensitivity and specificity.

Computational analysis of LexA regulons in Cyanobacteria.

BACKGROUND: The transcription factor LexA plays an important role in the SOS response in Escherichia coli and many other bacterial species studied. Although the lexA gene is encoded in almost every bacterial group with a wide range of evolutionary distances, its precise functions in each group/species are largely unknown. More recently, it has been shown that lexA genes in two cyanobacterial genomes Nostoc sp. PCC 7120 and Synechocystis sp. PCC 6803 might have distinct functions other than the regulation of the SOS response. To gain a general understanding of the functions of LexA and its evolution in cyanobacteria, we conducted the current study. RESULTS: Our analysis indicates that six of 33 sequenced cyanobacterial genomes do not harbor a lexA gene although they all encode the key SOS response genes, suggesting that LexA is not an indispensable transcription factor in these cyanobacteria, and that their SOS responses might be regulated by different mechanisms. Our phylogenetic analysis suggests that lexA was lost during the course of evolution in these six cyanobacterial genomes. For the 26 cyanobacterial genomes that encode a lexA gene, we have predicted their LexA-binding sites and regulons using an efficient binding site/regulon prediction algorithm that we developed previously. Our results show that LexA in most of these 26 genomes might still function as the transcriptional regulator of the SOS response genes as seen in E. coli and other organisms. Interestingly, putative LexA-binding sites were also found in some genomes for some key genes involved in a variety of other biological processes including photosynthesis, drug resistance, etc., suggesting that there is crosstalk between the SOS response and these biological processes. In particular, LexA in both Synechocystis sp. PCC6803 and Gloeobacter violaceus PCC7421 has largely diverged from those in other cyanobacteria in the sequence level. It is likely that LexA is no longer a regulator of the SOS response in Synechocystis sp. PCC6803. CONCLUSIONS: In most cyanobacterial genomes that we analyzed, LexA appears to function as the transcriptional regulator of the key SOS response genes. There are possible couplings between the SOS response and other biological processes. In some cyanobacteria, LexA has adapted distinct functions, and might no longer be a regulator of the SOS response system. In some other cyanobacteria, lexA appears to have been lost during the course of evolution. The loss of lexA in these genomes might lead to the degradation of its binding sites.

Rapid DNA barcoding analysis of large datasets using the composition vector method.

BACKGROUND: Sequence alignment is the rate-limiting step in constructing profile trees for DNA barcoding purposes. We recently demonstrated the feasibility of using unaligned rRNA sequences as barcodes based on a composition vector (CV) approach without sequence alignment (Bioinformatics 22:1690). Here, we further explored the grouping effectiveness of the CV method in large DNA barcode datasets (COI, 18S and 16S rRNA) from a variety of organisms, including birds, fishes, nematodes and crustaceans. RESULTS: Our results indicate that the grouping of taxa at the genus/species levels based on the CV/NJ approach is invariably consistent with the trees generated by traditional approaches, although in some cases the clustering among higher groups might differ. Furthermore, the CV method is always much faster than the K2P method routinely used in constructing profile trees for DNA barcoding. For instance, the alignment of 754 COI sequences (average length 649 bp) from fishes took more than ten hours to complete, while the whole tree construction process using the CV/NJ method required no more than five minutes on the same computer. CONCLUSION: The CV method performs well in grouping effectiveness of DNA barcode sequences, as compared to K2P analysis of aligned sequences. It was also able to reduce the time required for analysis by over 15-fold, making it a far superior method for analyzing large datasets. We conclude that the CV method is a fast and reliable method for analyzing large datasets for DNA barcoding purposes.

Unifying mechanical and thermodynamic descriptions across the thioredoxin protein family.

We compare various predicted mechanical and thermodynamic properties of nine oxidized thioredoxins (TRX) using a Distance Constraint Model (DCM). The DCM is based on a nonadditive free energy decomposition scheme, where entropic contributions are determined from rigidity and flexibility of structure based on distance constraints. We perform averages over an ensemble of constraint topologies to calculate several thermodynamic and mechanical response functions that together yield quantitative stability/flexibility relationships (QSFR). Applied to the TRX protein family, QSFR metrics display a rich variety of similarities and differences. In particular, backbone flexibility is well conserved across the family, whereas cooperativity correlation describing mechanical and thermodynamic couplings between the residue pairs exhibit distinctive features that readily standout. The diversity in predicted QSFR metrics that describe cooperativity correlation between pairs of residues is largely explained by a global flexibility order parameter describing the amount of intrinsic flexibility within the protein. A free energy landscape is calculated as a function of the flexibility order parameter, and key values are determined where the native-state, transition-state, and unfolded-state are located. Another key value identifies a mechanical transition where the global nature of the protein changes from flexible to rigid. The key values of the flexibility order parameter help characterize how mechanical and thermodynamic response is linked. Variation in QSFR metrics and key characteristics of global flexibility are related to the native state X-ray crystal structure primarily through the hydrogen bond network. Furthermore, comparison of three TRX redox pairs reveals differences in thermodynamic response (i.e., relative melting point) and mechanical properties (i.e., backbone flexibility and cooperativity correlation) that are consistent with experimental data on thermal stabilities and NMR dynamical profiles. The results taken together demonstrate that small-scale structural variations are amplified into discernible global differences by propagating mechanical couplings through the H-bond network.

Computational prediction of cAMP receptor protein (CRP) binding sites in cyanobacterial genomes.

BACKGROUND: Cyclic AMP receptor protein (CRP), also known as catabolite gene activator protein (CAP), is an important transcriptional regulator widely distributed in many bacteria. The biological processes under the regulation of CRP are highly diverse among different groups of bacterial species. Elucidation of CRP regulons in cyanobacteria will further our understanding of the physiology and ecology of this important group of microorganisms. Previously, CRP has been experimentally studied in only two cyanobacterial strains: Synechocystis sp. PCC 6803 and Anabaena sp. PCC 7120; therefore, a systematic genome-scale study of the potential CRP target genes and binding sites in cyanobacterial genomes is urgently needed. RESULTS: We have predicted and analyzed the CRP binding sites and regulons in 12 sequenced cyanobacterial genomes using a highly effective cis-regulatory binding site scanning algorithm. Our results show that cyanobacterial CRP binding sites are very similar to those in E. coli; however, the regulons are very different from that of E. coli. Furthermore, CRP regulons in different cyanobacterial species/ecotypes are also highly diversified, ranging from photosynthesis, carbon fixation and nitrogen assimilation, to chemotaxis and signal transduction. In addition, our prediction indicates that crp genes in modern cyanobacteria are likely inherited from a common ancestral gene in their last common ancestor, and have adapted various cellular functions in different environments, while some cyanobacteria lost their crp genes as well as CRP binding sites during the course of evolution. CONCLUSION: The CRP regulons in cyanobacteria are highly diversified, probably as a result of divergent evolution to adapt to various ecological niches. Cyanobacterial CRPs may function as lineage-specific regulators participating in various cellular processes, and are important in some lineages. However, they are dispensable in some other lineages. The loss of CRPs in these species leads to the rapid loss of their binding sites in the genomes.

[Antipruritic mechanisms of pimecrolimus cream for facial dermatitis in adult women patients].

OBJECTIVE: To investigate the antipruritic mechanisms of pimecrolimus cream for women facial dermatitis. METHODS: Topical pimecrolimus cream 1% was applied in 52 women patients with facial dermatitis. The Investigators Global Assessment (IGA) score, severity of pruritus (SP) scores, and a basic syntax and molecular substrate (molecular psychophysics) of nociception and pruriception established by temperature-sensitive transient receptor potential (TRP) channels were used to evaluate the clinical signs, severity of pruritus, and skin sensory phenomenon. RESULTS: The IGA scores at day 1 and 4 of treatment and the SP score at day 1, 4, and 11 of treatment were significantly lower than the baseline scores before treatment (P < 0.05). Among these 52 patients, 28 (53.8%) showed positive capsaicin-like response (i.e., burning with consequent rapid amelioration of pruritus) at the application sites, 12 (23.1%) showed camphor-like response (i.e., warming with consequent rapid amelioration of pruritus), and 12 (23.1%) showed negative capsaicin-like response or negative camphor-like response. CONCLUSIONS: Treatment with pimecrolimus cream 1% can rapidly and effectively improve the signs and symptoms of facial dermatitis in adult women patients. Pimecrolimus cream 1% may act on the transient potential vanilloid 1 (TRPV1) receptor in the skin sensory afferents to induce capsaicin-like response or camphor-like response and then desensitizes TRPV1 and rapidly inhibits or alleviate itching.

Simultaneously quantifying intracellular FAD and FMN using a novel strategy of intrinsic fluorescence four-way calibration.

The simultaneous quantitative analysis of intracellular metabolic coenzymes flavin adenine dinucleotide (FAD) and flavin mononucleotide (FMN) is of interest because they participate in many electron-transfer reactions of metabolism. But, the simultaneous quantitative analysis of FAD and FMN is hard to be achieved by traditional analytical methods. This paper proposes a novel strategy of intrinsic fluorescence coupled with four-way calibration method for simultaneous quantitative analysis of intracellular metabolic coenzymes FAD and FMN. Through mathematical separation, this proposed analytical method efficiently achieved the simultaneous quantitative analysis of metabolic coenzymes FAD and FMN in the cell, despite the fact that uncalibrated spectral interferents coexist in the system. The predicted concentrations of FAD and FMN in the cell are 217.0 ±â€¯6.9 and 155.0 ±â€¯1.7 pmol/106 cells respectively, which were validated by the approved liquid chromatography-tandem mass spectrometry (LC-MS/MS) method. This analytical method with second-order advantage simply requires the cell solution to be diluted by a buffer, it could introduce an interesting analytical strategy for multianalyte direct quantitative analysis in complex biological systems. In addition, we explore the third-order advantage of four-way calibration by a comparative study based on this real fluorescence data. The comparisons indicate that a four-way calibration method can provide higher sensitivity and more resolving power than a three-way calibration method.

Characterization of duck (Anas platyrhynchos) MHC class I gene in two duck lines.

To enrich gene polymorphism ofDuMHCI and provide data for further studies on disease resistance, 14DuMHCI genes from Weishan Ma duck and Cherry Valley duck were cloned, and their characterization were investigated. The overall conservation of the 14 alleles could be observed within the sequences, and relative conservation were also displayed in the peptide-binding domain and CD8 interaction sites. Based on full-length amino acid homology, MHC class I from different duck lines could be divided into 13 gene groups and three novel gene groups existed.Moreover, 14 key variable residues corresponding to gene groups division were exhibited on the homology modelling constructed based on the resolved protein structure of DuMHC I. This study explicit the characteristics of DuMHC I in the two duck lines and could contribute to design effective diagnostics and vaccines for the species against various infections.

Photosynthesis performance, antioxidant enzymes, and ultrastructural analyses of rice seedlings under chromium stress.

The present study was conducted to examine the effects of increasing concentrations of chromium (Cr(6+)) (0, 25, 50, 100, and 200 µmol) on rice (Oryza sativa L.) morphological traits, photosynthesis performance, and the activities of antioxidative enzymes. In addition, the ultrastructure of chloroplasts in the leaves of hydroponically cultivated rice (O. sativa L.) seedlings was analyzed. Plant fresh and dry weights, height, root length, and photosynthetic pigments were decreased by Cr-induced toxicity (200 µM), and the growth of rice seedlings was starkly inhibited compared with that of the control. In addition, the decreased maximum quantum yield of primary photochemistry (Fv/Fm) might be ascribed to the decreased the number of active photosystem II reaction centers. These results were confirmed by inhibited photophosphorylation, reduced ATP content and its coupling factor Ca(2+)-ATPase, and decreased Mg(2+)-ATPase activities. Furthermore, overtly increased activities of antioxidative enzymes were observed under Cr(6+) toxicity. Malondialdehyde and the generation rates of superoxide (O2̄) also increased with Cr(6+) concentration, while hydrogen peroxide content first increased at a low Cr(6+) concentration of 25 µM and then decreased. Moreover, transmission electron microscopy showed that Cr(6+) exposure resulted in significant chloroplast damage. Taken together, these findings indicate that high Cr(6+)concentrations stimulate the production of toxic reactive oxygen species and promote lipid peroxidation in plants, causing severe damage to cell membranes, degradation of photosynthetic pigments, and inhibition of photosynthesis.

The preparation of magnetic molecularly imprinted nanoparticles for the recognition of bovine hemoglobin.

The protein imprinted technique combining surface imprinting and nano-sized supports materials is an attractive strategy for protein recognition and rapid separation. In this work, we imprinted bovine hemoglobin (BHb) on magnetic nanoparticles. With itaconic acid (IA) and acrylamide (AAm) as the monomers, the experiment was carried out in aqueous media via surface-imprinting technique. The effects of initial concentration and adsorption time over the adsorption capacity of both imprinted and non-imprinted nanoparticles were analyzed. The maximum adsorption capability of imprinted nanoparticles was found to be 77.6 mg g(-1), which was 3.1-4.3 times higher than that of the non-imprinted nanoparticles prepared at the same conditions. This resulted in the successful formation of imprinting cavities. Moreover, in selective adsorption experiment and competitive batch rebinding test, imprinted nanoparticles exhibited a high specific recognition of the template protein over the non-imprinted protein.

A novel alignment-free method for comparing transcription factor binding site motifs.

BACKGROUND: Transcription factor binding site (TFBS) motifs can be accurately represented by position frequency matrices (PFM) or other equivalent forms. We often need to compare TFBS motifs using their PFMs in order to search for similar motifs in a motif database, or cluster motifs according to their binding preference. The majority of current methods for motif comparison involve a similarity metric for column-to-column comparison and a method to find the optimal position alignment between the two compared motifs. In some applications, alignment-free methods might be preferred; however, few such methods with high accuracy have been described. METHODOLOGY/PRINCIPAL FINDINGS: Here we describe a novel alignment-free method for quantifying the similarity of motifs using their PFMs by converting PFMs into k-mer vectors. The motifs could then be compared by measuring the similarity among their corresponding k-mer vectors. CONCLUSIONS/SIGNIFICANCE: We demonstrate that our method in general achieves similar performance or outperforms the existing methods for clustering motifs according to their binding preference and identifying similar motifs of transcription factors of the same family.