Amino Acid Sequence Of Region Research Articles

Engineering New Protease Inhibitors Using α2-Macroglobulin.

Protease inhibitors of the alpha-macroglobulin family (αM) have a unique mechanism that allows them to trap proteases that is dependent not on the protease's class, but rather on its cleavage specificity. Proteases trigger a conformational change in the αM protein by cleaving within a "bait region," resulting in the sequestering of the protease inside the αM molecule. This nonspecific inhibitory mechanism appears to have arisen early in the αM family, and the broad protease-trapping capacity that it allows may play a role in pathogen defense.Human α2-macroglobulin (A2M) is a tetrameric αM whose bait region is permissive to cleavage by most proteases, making it a broad-spectrum protease inhibitor. Recent work has demonstrated that the inhibitory capacity of A2M derives directly from its bait region sequence: modifying the bait region sequence to introduce or remove protease cleavage sites will modify A2M's inhibition of the relevant proteases accordingly. Thus, changing the amino acid sequence of the bait region presents an effective avenue for protein engineering of new protease inhibitors if the substrate specificity of the target protease is known. The design of new A2M-based protease inhibitors with tailored inhibitory capacities has potential applications in basic research and the clinic. In this chapter, we describe the general approach and considerations for the bait region engineering of A2M.

Whole-genome sequencing and phylogenetic analysis of coxsackievirus-A16 strains causing hand, foot and mouth disease (HFMD) in India.

Hand, foot and mouth disease (HFMD) is a common childhood infectious disease, caused by enteroviruses (EVs), which can present with typical or atypical lesions. The illness is self-limiting, but it can also have serious complications. Since 1997, HFMD infections have become endemic and have increased to epidemic proportions across the Asia Pacific region, including India. Coxsackievirus-A16 (CV-A16) outbreaks occurred in India from 2005 onwards, although the clinical symptoms were noticeably different during this period. Understanding the population dynamics of enteroviruses that cause HFMD is crucial in the post-polio era because one of the circulating strain may replace another as the dominant strain. The aim of this study is to describe the genetic features of the CV-A16 strains isolated from hand, foot and mouth disease (HFMD) patients in India. Reverse transcription PCR (RT-PCR) and cell-culture-based isolation of CV-A16 was done from the 55 clinical samples. The entire genome of the CV-A16 isolate was performed from the seven isolates. After the sequences were analysed, a phylogenetic tree was created using bioinformatics tools. The total genomic length obtained was 7411 base pairs (bp). Nucleotide similarity across various regions, including 5'UTR, P1, P2 and 3'UTR, ranged from 87.0-97.9 %, 77.0-95.4 %, 80.3-96.9 %, and 77.9-96.2 %, respectively. Correspondingly, similarities in the VP1 region's nucleotide and amino acid sequences were 91.4-96.4 % and 99.3-99.7 %, respectively. Phylogenetic analysis highlighted that CV-A16 strains identified in Pune, Maharashtra, were grouped within the same cluster. The analysed CV-A16 isolates in this study aligned with subgenotype B1c. These findings have far-reaching implications for the surveillance, prevention and management of HFMD and CV-A16. Monitoring the dynamics of CV-A16 strains, informed by the genetic characteristics identified here, will significantly impact strategies aimed at tackling HFMD and its associated public health challenges.

Porcine Astrovirus Detection and Characterization in Healthy and Diarrheic Pigs from Haryana, India

Background: Porcine astrovirus (PAstV) is an emerging pathogen detected from the feces of both healthy and diarrheic pigs with limited studies comparing the presence of PAstV and diarrhea in pigs. PAstV has been reported worldwide with a few reports from India. In addition, there are limited reports on variation in the amino acid sequence of the ORF2 region, which codes for viral capsid protein. The present study was aimed to study the presence of PAstV, association with diarrhea in pigs of various age groups and its molecular characterization from Haryana, a northern Indian state. Methods: A total of 176 rectal swabs of pigs were collected from different parts of Haryana. The samples were screened for PAstV by RT-PCR of the partial ORF1b/ORF2 genomic region. The positive samples were characterized by molecular typing and phylogenetic analysis. Result: In the present study, PAstV was detected in pigs in 16.47% of fecal samples, including 21/127 (16.53%) diarrheic and 8/49 (16.32%) non-diarrheic. The results indicated that weaning piglets were more susceptible to PAstV infection followed by suckling piglets. The phylogenetic analysis revealed the circulation of PAstV4 and PAstV2 lineages in Haryana. The study revealed endemic presence of virus in the region with high genetic diversity among the PAstV strains, suggesting a wide range of heterogeneity.

An amino acid substitution in HCV core antigen limits its use as a reliable measure of HCV infection compared with HCV RNA.

Hepatitis C virus (HCV) is a viral pathogen that causes chronic hepatitis, which can lead to cirrhosis and hepatocellular carcinoma. Detection of HCV RNA is the standard method used to diagnose the disease and monitor antiviral treatment. A quantification assay for the HCV core antigen (HCVcAg) has been proposed as a simplified alternative to the HCV RNA test for predicting active HCV infection, with the aim of achieving the global goal of eliminating hepatitis. The objective of this study was to determine the correlation between HCV RNA and HCVcAg, as well as the impact of amino acid sequence heterogeneity on HCVcAg quantification. Our findings demonstrated a strong positive correlation between HCV RNA and HCVcAg across all HCV genotypes (1a, 1b, 3a, and 6), with correlation coefficients ranging from 0.88 to 0.96 (p < 0.001). However, in some cases, samples with genotypes 3a and 6 exhibited lower HCVcAg levels than expected based on the corresponding HCV RNA values. Upon the core amino acid sequence alignment, it was observed that samples exhibiting low core antigen levels had an amino acid substitution at position 49, where threonine was replaced by either alanine or valine. Core mutation at this position may correlate with one of the epitope regions recognized by anti-HCV monoclonal antibodies. The present findings suggest that the utilization of HCVcAg as a standalone marker for HCV RNA might not provide adequate sensitivity for the detection of HCV infection, especially in cases where there are variations in the amino acid sequence of the core region and a low viral load of HCV RNA.

Gene expression and TCR amino acid sequences selected by HLA-A02:01-restricted CTLs specific to HTLV-1 in ATL patients.

Adult T-cell leukaemia/lymphoma (ATL) is an aggressive malignancy of peripheral T cells caused by human T-cell lymphotropic virus type-1 (HTLV-1). Tax is the most important regulatory protein for HTLV-1. We aimed to reveal a unique amino acid sequence (AA) of complementarity-determining region 3 (CDR3) of the T-cell receptor (TCR)β and TCRα chains of HLA-A*02:01-restricted Tax11-19 -specific cytotoxic T cells (Tax-CTLs). The gene expression profiles (GEP) of Tax-CTLs were assessed by the next-generation sequence (NGS) method with SMARTer technology. Tax-CTLs seemed to be oligoclonal, and their gene compositions were skewed. The unique motifs of 'DSWGK' in TCRα and 'LAG' in TCRβ at CDR3 were observed in almost all patients. Tax-CTL clones harbouring the 'LAG' motif with BV28 had a higher binding score than those without either of them, besides a higher binding score associated with longer survival. Tax-CTLs established from a single cell showed killing activities against Tax-peptide-pulsed HLA-A2+ T2 cell lines. GEP of Tax-CTLs revealed that genes associated with immune response activity were well preserved in long-term survivors with stable status. These methods and results can help us better understand immunity against ATL, and should contribute to future studies on the clinical application of adoptive T-cell therapies.

Preparation of IgE Antibody and Distribution of IgE+ Secretory Cells in the Palatine Tonsil of Bactrian Camel.

Allergic diseases induced by dust have seriously threatened human health, while Bactrian camels can live in a sandy environment for a long time. To prepare rabbit anti-Bactrian camel IgE antibody and explore the distribution characteristics of IgE+ secretory cells in the palatine tonsils, which lays a theoretical foundation for the distribution of local antibodies in the palatal tonsils of Bactrian camel and the study of immune function. In this study, the amino acid sequences of Bactrian camel IgE, IgA, IgM and IgG heavy chain constant regions were compared, and a specific IgE gene fragment were selected (447 bp). The recombinant plasmid pET-28a-IgE was induced in Escherichia coli BL21(DE3) by IPTG and its expression conditions were optimized. The antibody was prepared by immunizing rabbits with purified IgE recombinant protein, its titer and specificity were detected by indirect ELISA and Western blotting. Immunohistochemical and statistical methods investigated the distribution of IgE+ secretory cells in the palatine tonsils. The IgE recombinant protein was expressed in the form of inclusion bodies with a size of 16 kDa. The optimal IPTG induction concentration was 0.7 mmol/L and the induction time was 8 h. The titer of the antibody was 1:16000 by ELISA, and the antibody could specifically bind to the recombinant protein by Western blotting. IgE+ secretory cells were mainly distributed in the subepithelial compartments of reticulated crypt epithelium of the palatine tonsil of the Bactrian camel, followed by the subepithelial compartments of stratified squamous epithelium and occasionally in the extrafollicular region. The rabbit anti-Bactrian camel IgE polyclonal antibody was successfully prepared. It is confirmed that IgE exists in the palatine tonsils of Bactrian camels under normal living conditions. In addition, IgE+ secretory cells are mainly distributed in the subepithelial compartments of reticulated crypt epithelium of the palatine tonsil, which is consistent with the distribution characteristics of IgG+ and sIgA+ secretory cells in the palatal tonsils of the Bactrian camel.

Antibody proteomics

Antibodies represent an essential component of humoral immunity; therefore their study is important for molecular biology and medicine. The unique property of antibodies to specifically recognize and bind a certain molecular target (an antigen) determines their widespread application in treatment and diagnostics of diseases, as well as in laboratory and biotechnological practices. High specificity and affinity of antibodies is determined by the presence of primary structure variable regions, which are not encoded in the human genome and are unique for each antibody-producing B cell clone. Hence, there is little or no information about amino acid sequences of the variable regions in the databases. This differs identification of antibody primary structure from most of the proteomic studies because it requires either B cell genome sequencing or de novo amino acid sequencing of the antibody. The present review demonstrates some examples of proteomic and proteogenomic approaches and the methodological arsenal that proteomics can offer for studying antibodies, in particular, for identification of primary structure, evaluation of posttranslational modifications and application of bioinformatics tools for their decoding.

Tumor suppressor effect of an antibody on xenotransplanted sarcomatoid mesothelioma cells.

BackgroundAs mesothelioma generally has an unfavorable prognosis, further advances are needed to improve the outcomes in patients with mesothelioma. In the present study, we generated and characterized a monoclonal antibody that could inhibit mesothelioma cell proliferation in a xenotransplantation mouse model.MethodsWe generated monoclonal antibodies by immunizing mice with cultured mesothelioma cells. These antibodies were then characterized by immunofluorescence staining, immunohistochemical staining, secondary antibody‐drug conjugate assay, antibody inoculation in a xenotransplantation mesothelioma mouse model, and mass spectrometry followed by small interfering RNA (siRNA) analysis. 5' rapid amplification of complementary DNA ends followed by sequencing was performed to deduce the amino acid sequences of the variable regions of the light and heavy chains of AX10.ResultsAn IgG2b κ‐type AX10 antibody against the cell surface membrane of sarcomatoid mesothelioma cells was generated. AX10 immunoreactivity was detected in 12 out of 22 different mesothelioma tissue specimens, but there was little AX10 immunoreactivity in a normal human tissue array. AX10 decreased Matrigel invasion by MPM‐1 cells but did not affect cell proliferation. Notably, AX10 significantly inhibited the proliferation of MPM‐1 cells xenotransplanted into Severe combined immunodeficiency‐Nonobese diabetic mice. Matrix‐assisted laser desorption ionization time‐of‐flight mass spectrometry followed by siRNA silencing indicated that AX10 reacted to a unique alternatively spliced isoform of sarcolemma‐associated protein. AX10 is composed of as yet unregistered amino acid sequences in its variable region.ConclusionsAX10 could have therapeutic potential for patients with sarcomatoid mesothelioma.

Prediction of HIV sensitivity to monoclonal antibodies using aminoacid sequences and deep learning.

MotivationKnowing the sensitivity of a viral strain versus a monoclonal antibody is of interest for HIV vaccine development and therapy. The HIV strains vary in their resistance to antibodies, and the accurate prediction of virus-antibody sensitivity can be used to find potent antibody combinations that broadly neutralize multiple and diverse HIV strains. Sensitivity prediction can be combined with other methods such as generative algorithms to design novel antibodies in silico or with feature selection to uncover the sites of interest in the sequence. However, these tools are limited in the absence of in silico accurate prediction methods.ResultsOur method leverages the CATNAP dataset, probably the most comprehensive collection of HIV-antibodies assays, and predicts the antibody-virus sensitivity in the form of binary classification. The methods proposed by others focus primarily on analyzing the virus sequences. However, our article demonstrates the advantages gained by modeling the antibody-virus sensitivity as a function of both virus and antibody sequences. The input is formed by the virus envelope and the antibody variable region aminoacid sequences. No structural features are required, which makes our system very practical, given that sequence data is more common than structures. We compare with two other state-of-the-art methods that leverage the same dataset and use sequence data only. Our approach, based on neuronal networks and transfer learning, measures increased predictive performance as measured on a set of 31 specific broadly neutralizing antibodies.Availability and implementation https://github.com/vlad-danaila/deep_hiv_ab_pred/tree/fc-att-fix

Research advances in the plant TCP transcription factors

<p indent="0mm">Transcription factors (TFs) are a group of protein molecules that can bind to a specific gene with a specific sequence specificity, thus ensuring that the target gene is expressed at a specific time and in space at a specific intensity. The plant-specific TFs of the TCP family (for Teosinte branched 1 in corn, CYCLOIDEA (CYC) in snapdragon (<italic>Antirrhinum majus</italic>) and PROLIFERATING CELL FACTOR 1/2 in rice) are characterized by an N-terminal non-canonical beta helix-loop-helix (bHLH) domain known as the TCP domain, and regulate the spatiotemporal expression of genes by binding to specific promoter sequences. TCP TFs play important roles in regulating the development of roots, stems, leaves, flowers, fruits, and vascular tissues, and participate in physiological processes such as plant secondary metabolism, plant immunity, and the responses to biotic and abiotic stress. The TCP TF family is conserved and widespread in plants. Based on the TCP domain sequence, TCP TFs are categorized into Class I and Class II; based on the amino acid sequence of the basic region and bHLH domain, the Class II TCP TFs can be further divided into CINCINNATA (CIN)-like TCPs (CIN) and CYC-like TCPs (CYC-C). In recent years, increasing numbers of studies have shed light on how TCP TFs regulate plant growth and development, especially on the functions of upstream regulators and downstream target genes. Plants have evolved multiple ways to accurately regulate their downstream related factors, and their own gene expression is also strictly regulated. TCP genes have also been analyzed in various plants and found to take part in the regulation of circadian rhythms and the biosynthesis and signaling pathways of plant hormones, among other functions. Other studies have investigated the regulatory relationships between TCP TFs and microRNAs. Additionally, members of the TCP family are often functionally redundant, making it difficult to study their functions; therefore, gene-editing technology and high-throughput sequencing have opened up new avenues to study this TF family. Here, we summarize recent advances in our understanding of how TCP activity is translated to the dynamic spatiotemporal control of cell-fate determination, life-cycle transitions, dormancy release, seed germination, leaf development, outgrowth of shoot branches, growth-repressing microRNAs, and interactions with the chromatin remodeling machinery to modulate phytohormone responses. Furthermore, we discuss existing problems and future directions in TCP research, in particular the role of TCP-related protein modification in plant growth and development and stress responses. Finally, we provide perspectives on the future research that is needed to gain a deep understanding of the diverse regulatory networks of TCP TFs in plant growth and development.

Establishment of Membrane-Bound IgA1-Specific Antibody Possessing Antibody-Dependent Cellular Cytotoxicity Activity.

Therapeutic agents targeting B cells, such as rituximab, have been proven to be effective in several diseases. However, since this therapy targets the whole B cell population, there are still concerns about critical adverse events. Therefore, a new type of antibody that can specifically deplete a particular type of B cell may have the potential to become an efficient and safer therapy. Membrane-bound IgA1 (mIgA1) is expressed on soluble IgA1 (sIgA1) producing B cells and/or their precursor, B cells. Although most of the amino acid sequence in the N-terminal regions of the extracellular domains of mIgA1 and sIgA1 is shared, there is a membrane type-specific region, named the membrane-bound immunoglobulin isotype-specific (migis-α) region, at the membrane-proximal region of mIgA1. We hypothesized that the migis-α region would be a suitable antigen for therapeutic antibodies to target mIgA1-expressing B cells without binding to sIgA1, which may cause undesired adverse effects and poor pharmacokinetics (PK). We established two anti-migis-α monoclonal antibodies (mAbs), KM4641 and KM4644, by immunization of the synthetic peptide corresponding to an migis-α region. These mAbs both showed robust binding to mIgA1-expressing transfectant cells. As we expected, neither mAbs bound to sIgA1 and we found that the mAbs recognized different seven to eight amino acid sequences within the migis-α region. Furthermore, the rat-human chimeric type of both mAbs showed antibody-dependent cellular cytotoxicity against mIgA1-expressing transfectant cells. Taken together, this study showed that established mAbs have therapeutic potential in IgA-related diseases, such as IgA nephropathy.

Introduction of a PEGylated EPO conjugate as internal standard for EPO analysis in doping controls.

Immunopurification of doping control samples is a mandatory necessity in erythropoietin (EPO) analysis during a confirmation procedure; moreover, it has become common practice to also immunopurify samples for the initial testing procedure. Typically used materials (e.g., Stemcell purification plate and MAIIA purification kit) rely on anti-EPO antibodies for purification. Also, the detection of EPO after electrophoretic separation and western blotting is based on a monoclonal anti-EPO antibody, clone AE7A5, directed against a 26 amino acid sequence of the N-terminal region of human EPO. While the electrophoretic separation and blot transfer efficiency can be monitored with reference standards and quality control samples, it is presently not possible to monitor the functionality of the entire sample preparation procedure. The reliance on antibodies for both purification and detection has complicated the implementation of an internal standard (ISTD). In this study, customized EPO-polyethylene glycol (PEG) conjugates were synthesized as potential ISTDs and assessed as to their compatibility with existing sample preparation procedures for urine and blood sample analysis using the most common immunopurification techniques. Moreover, probing for the impact of the ISTD on sodium N-lauroylsarcosinate ("sarcosyl") polyacrylamide gel electrophoresis (SAR-PAGE)-based EPO analysis concerning potential interference with target analytes was conducted. The presented data demonstrate that a 12-kDa PEG residue attached to human EPO represents a particularly useful construct to serve as ISTD for erythropoietin-receptor agonist (ERA) analysis. The conjugate is applicable to both urine and blood testing using the commonly employed purification techniques, supporting and improving result interpretations especially concerning specimens where the natural abundance of human EPO is low.

Expression and diversity of the sialic acid-binding adhesin and its homologs associated with oral streptococcal infection.

Streptococcus gordonii, one of the early colonizers of oral biofilms, is involved in the development of dental caries, periodontal disease, and infective endocarditis. The Hsa adhesin of S. gordonii DL1 has the ability to bind strongly to the terminal sialic acid groups of host glycoproteins via the binding region, nonrepetitive region 2 (NR2), which is important for the pathogenicity of S. gordonii DL1. Low similarity with the NR2 of Hsa homologs among other streptococcal species has been reported. However, the reports have been limited to certain strains. This study attempted to assess frequency of the expression on the bacterial cell surface and to analyze the diversity of Hsa homologs among different wild strains of oral streptococci. We isolated 186 wild-type strains of oral streptococci from healthy volunteers and analyzed their hemagglutinating (HA) activity on human erythrocytes and their Hsa homologs and NR2 homologous regions by dot immunoblotting using anti-Hsa and anti-NR2 antisera, respectively. We found 30 strains reacted with anti-NR2 antiserum (NR2 positive) and determined the sequence of the NR2 regions. Many strains with high HA activity were also NR2 positive, suggesting that the NR2 region may be associated with HA activity. Among the NR2-positive strains, four different amino acid sequence patterns were observed, demonstrating diversity in the NR2 region. Notably, S. gordonii strains frequently possessed Hsa homologs and NR2-like antigens compared with other streptococci. It is speculated that the possessing frequency of Hsa homologs and the amino acid sequence of NR2 region may vary among streptococcal species.

Effects of cryptochrome-modulating compounds on circadian behavioural rhythms in zebrafish.

The circadian clock controls daily rhythms of various physiological processes, and impairment of its function causes many diseases including sleep disorders. Chemical compounds that regulate clock function are expected to be applied for treatment of circadian clock-related diseases. We previously identified small-molecule compounds KL001, KL101 and TH301 that lengthen the period of cellular circadian clock by directly targeting clock proteins cryptochromes (CRYs) in mammals. KL001 targets both CRY1 and CRY2 isoforms, while KL101 and TH301 are isoform-selective compounds and require CRY C-terminal region for their effects. For further application of these compounds, the effects on locomotor activity rhythms at the organismal level need to be investigated. Here we used zebrafish larvae as an in vivo model system and found that KL001 lengthened the period of locomotor activity rhythms in a dose-dependent manner. In contrast, KL101 and TH301 showed no effect on the period. The amino acid sequences of CRY C-terminal regions are diverged in zebrafish and mammals, supporting the importance of this region for the effects of KL101 and TH301. This study demonstrated efficacy of CRY modulation for controlling circadian behavioural rhythms in organisms and suggested species-dependent differences in the effects of isoform-selective CRY-modulating compounds.

The B-type natriuretic peptide of the Congo and Timneh grey parrot

In captivity, cardiovascular diseases are common in grey parrots. The diagnosis of these diseases in living birds is difficult, and new diagnostic possibilities would be desirable. The heart is an important endocrine organ in which cardiomyocytes synthetise B-type natriuretic peptide (BNP) and release it into the bloodstream. This hormone has a significant role in cardiovascular and body fluid regulation. The blood concentration of BNP is used in human medicine and small animal medicine as a diagnostic tool in the identification of heart diseases and as a prognostic marker for the risk of mortality. The nucleotide and amino acid sequence of BNP was described in Congo (n = 4) and Timneh (n = 3) grey parrots by PCR after RNA isolation from the atria and ventricles. The results showed a high similarity between the nucleotide sequences of the grey parrots’ BNP and the already known sequence of this hormone in chickens. The amino acid sequence of the mature peptide region is consistent in these three species. BNP plasma concentration could be a possible blood parameter for identifying clinically manifest cardiovascular diseases in grey parrots as it is in other species.

Identification of genes for variable regions of immunoglobulins that recognize sialylated glycans

We previously reported an antibody (clone ID: FR9, IgM-κ) that recognizes the sialyl oligosaccharide Neu5Acα2,6Galβ1,4GlcNAc as an epitope on glycoproteins and glycolipids. In the present study, we developed an antibody (clone ID: AFR45, IgM-κ) that recognizes Neu5Acα2,3Galβ1,4GlcNAc/Glc as an epitope on glycoproteins and glycolipids and compared the nucleotide and amino acid sequences of the immunoglobulin gene variable regions with those of FR9. The heavy chain variable (VH) regions of FR9 and AFR45 were encoded by different VH gene segments, each of which was composed of a characteristic D gene segment. The major differences between VH genes encoding various antibodies deposited in public databases and FR9 and AFR45 were identified in the D gene segment, indicating that D genes play a critical role in determining the epitope specificity of these antibodies. Surprisingly, although FR9 and AFR45 were obtained independently from different mice immunized with different immunogens, the light chain variable (VL) region nucleotide sequences were identical. The VL gene consisted of Igkv4-57 and Igkj4 gene segments (Igkv4-57j4), the sequences of which were identical to VL genes for a number of antibodies against meningococcal group C capsular polysaccharide deposited in public databases. As this polysaccharide is a sialic acid homopolymer, these results indicate that Igkv4-57j4 encodes a VL common to immunoglobulins that recognize sialylated glycans.

An unusual case of haemorrhagic bursa in a pullet flock associated with a genogroup 2 infectious bursal disease virus

ABSTRACT An unusual case of infectious bursal disease (IBD) was observed in eight-week-old commercial caged pullets. This flock (House 1) exhibited a one-day spike in mortality. On gross necropsy examination, enlarged, diffusely haemorrhagic bursas were observed. This lesion has been frequently described in cases of very virulent infectious bursal disease virus (vvIBDV). A five-week-old caged pullet flock (House 2) in an adjacent building did not display haemorrhagic bursa lesions. Microscopic examination of bursas from the eight-week-old pullets in House 1 showed marked diffuse haemorrhages and extensive lymphoid necrosis. Histopathology of bursas from the five-week-old pullets in House 2 showed severe, diffuse lymphoid depletion without haemorrhages. IBD ELISA results from birds in House 1 at 9 weeks had a GMT of 6395 and birds in House 2 had a GMT of 82 in the same timeframe. Diagnostic testing for avian influenza virus, Mycoplasma gallisepticum, Mycoplasma synoviae, virulent Newcastle disease virus, infectious bronchitis virus, infectious laryngotracheitis virus, chicken anaemia virus and fowl pox virus were negative. The predicted amino acid sequence of the hypervariable region of VP2 indicated the IBDV observed in both flocks (1/chicken/USA/1300OH/19 from House 1 and 1/chicken/USA/1301OH/19 from House 2) was identical and was not a vvIBDV. Their sequences were similar to a genogroup 2 IBDV from Ontario, Canada (EF138967). No mortality was observed when the 1/chicken/USA/1300OH/19 virus was inoculated into specific-pathogen-free (SPF), four-week-old pullets. Gross and microscopic lesions were observed in bursa tissue, but the bursal haemorrhages observed in the original field case were not reproduced in challenged SPF pullets.

Screening of Fv Antibodies with Specific Binding Activities to Monosodium Urate and Calcium Pyrophosphate Dihydrate Crystals for the Diagnosis of Gout and Pseudogout.

To date, medical diagnosis of gout and pseudogout has been performed by observing the crystals in the joint fluid of patients under a polarized microscope. Conventional diagnostic methods using a polarized microscope have disadvantages, such as time-consuming analysis, a high false negative rate, and difficulty in distinguishing gout with monosodium urate (MSU) crystals and pseudogout with calcium pyrophosphate dihydrate (CPPD) crystals in synovial fluids. In this study, a chromogenic assay for the diagnosis of gout and pseudogout, without the requirement of a polarized microscope and trained experts, was proposed using Fv antibodies with specific binding activities to MSU and CPPD crystals. The IgG VH chain Fv library with randomized complementarity-determining region 3 (CDR3) region was expressed on the outer membrane of Escherichia coli using autodisplay technology. The target Fv antibodies with binding activity to MSU and CPPD crystals were screened from the autodisplayed Fv library on the E. coli outer membrane, and five clones were selected. On the basis of the binding properties of the screened Fv antibodies, peptides with the selected clone of amino acid sequences of the CDR3 region (15 residues) were chemically synthesized. The binding properties of the synthetic peptides with amino acid sequences of CDR3 regions from the selected clones were analyzed using fluorescence imaging and flow cytometry, and the affinity constants (Kd) of each peptide for binding to MSU and CPPD crystals were calculated by fitting based on the isotherm model. A chromogenic assay configuration for gout and pseudogout was developed using synthetic peptides. In this chromogenic assay, synthetic peptides labeled with biotin and streptavidin-horseradish peroxidase (HRP) complex were used, and crystal detection was possible using a chromogenic reaction between HRP and a chromogenic substrate (TMB). Finally, gout and pseudogout were diagnosed by detecting MSU and CPPD crystals in the synovial fluid in the concentration range of 0-300 μg/mL.

Molecular Characterization of Small Ruminant Lentiviruses of Subtype A5 Detected in Naturally Infected but Clinically Healthy Goats of Carpathian Breed.

Small ruminant lentiviruses (SRLVs) are widespread in sheep and goats in Poland, and several subtypes were identified and molecularly characterized up to date. This is the first study that characterizes the molecular properties of A5 strains of SRLV detected in naturally infected, but clinically healthy, Carpathian goats. Segments from three genomic regions (gag, env, and LTR) were analyzed. Genetic distance, pairwise comparison, and phylogenetic analysis revealed that Polish SRLV A5 sequences are closely related to the Swiss and German A5 sequences suggesting a common origin. The epidemiological linkage was identified particularly between the small ruminants of Germany and Poland. Amino acid sequences of immunodominant regions in CA protein were well-conserved within analyzed strains; however, they showed some remarkable changes like substitution (D) to (E), at position 90 in Major Homology Region (MHR) and (T) to (S), at position 141 in epitope 3. In contrast, aa sequences of surface glycoprotein exhibited the highest variability confirming type-specific variation in SU5 epitope. Two deletions in the U3 region of A5 strains were noted: One (8 nt) located near the 5′ end of the U3 region and the other (29 nt) located in the central region of U3. Additionally, all A5 strains had specific deletion (10 nt) in the R region. Furthermore, we did not find a correlation between copies of the CAAAT motif and clinical manifestation in infected animals. These data showed some remarkable features in the viral genome of A5 strains, which may be related to the attenuated phenotype in vivo, characterized by the lack of any clinical signs in infected goats. Certainly, more studies are required to support the hypothesis that these A5 viruses are of low pathogenicity for goats. We want to focus our future studies on the analysis of the whole genomes of these isolates and their biological properties, as well as on clinicopathological studies of goats infected by A5 SRLV, aiming to clarify the pathogenic potential of these viruses.

Progress on genotyping of norovirus

Norovirus are now recognized as one of the main pathogens causing acute gastroenteritis in both developed and developing countries. However, norovirus are easily mutated and recombined, and have many genotypes. In early studies, norovirus were amplified and identified by amino acid sequence of VP1 region. It was found that norovirus were easily mutated and recombined in or near the overlapping regions of polymerase and capsid. A two regions genotyping method was positively proposed internationally. Depending on the 2 times standard deviation standard method for two regions identification, norovirus polymerase regions can be divided into 10 gene groups and 76 genotypes including 2 tentative gene groups and 16 tentative genotypes. The VP1 region can be divided into 12 gene groups and 53 genotypes including 2 tentative gene groups and 5 tentative genotypes. However, the tentative gene groups and genotypes need to be further identified and reclassified. In this article, characteristics of norovirus sequences, principles of different genotyping methods, methods of sequence amplification, on-line genotyping tools and the latest studies in norovirus genotypes are reviewed and introduced.