Vacuolar Degradation of Plant Organelles.

Plants continuously remodel and degrade their organelles due to damage from their metabolic activities and environmental stressors, as well as an integral part of their cell differentiation programs. Whereas certain organelles use local hydrolytic enzymes for limited remodeling, most of pathways that control the partial or complete dismantling of organelles rely on vacuolar degradation. Specifically, selective autophagic pathways play a crucial role in recognizing and sorting plant organelle cargo for vacuolar clearance, especially under cellular stress conditions induced by factors like heat, drought, and damaging light. In these short reviews, we discuss the mechanisms that control the vacuolar degradation of chloroplasts, mitochondria, endoplasmic reticulum, Golgi, and peroxisomes, with an emphasis on autophagy, recently discovered selective autophagy receptors for plant organelles, and crosstalk with other catabolic pathways.

VarEPS-Influ:an risk evaluation system of occurred and virtual variations of influenza virus genomes.

Influenza viruses undergo frequent genomic mutations, leading to potential cross-species transmission, phenotypic changes, and challenges in diagnostic reagents and vaccines. Accurately evaluating and predicting the risk of such variations remain significant challenges. To address this, we developed the VarEPS-Influ database, an influenza virus variations risk evaluation system (VarEPS-Influ). This database employs a 'multi-dimensional evaluation of mutations' strategy, utilizing various tools to assess the physical and chemical properties, primary, secondary, and tertiary structures, receptor affinity, antibody binding capacity, antigen epitopes, and other aspects of the variation's impact. Additionally, we consider space-time distribution, host species distribution, pedigree analysis, and frequency of mutations to provide a comprehensive risk evaluation of mutations and viruses. The VarEPS-Influ database evaluates both observed variations and virtual variations (variations that have not yet occurred), thereby addressing the time-lag issue in risk predictions. Our current one-stop evaluation system for influenza virus genomic variation integrates 1065290 sequences from 224 927 Influenza A, B and C isolates retrieved from public resources. Researchers can freely access the data at https://nmdc.cn/influvar/.

gcPathogen: a comprehensive genomic resource of human pathogens for public health.

Here, we present the manually curated Global Catalogue of Pathogens (gcPathogen), an extensive genomic resource designed to facilitate rapid and accurate pathogen analysis, epidemiological exploration and monitoring of antibiotic resistance features and virulence factors. The catalogue seamlessly integrates and analyzes genomic data and associated metadata for human pathogens isolated from infected patients, animal hosts, food and the environment. The pathogen list is supported by evidence from medical or government pathogenic lists and publications. The current version of gcPathogen boasts an impressive collection of 1 164 974 assemblies comprising 986 044 strains from 497 bacterial taxa, 4794 assemblies encompassing 4319 strains from 265 fungal taxa, 89 965 assemblies featuring 13 687 strains from 222 viral taxa, and 646 assemblies including 387 strains from 159 parasitic taxa. Through this database, researchers gain access to a comprehensive 'one-stop shop' that facilitates global, long-term public health surveillance while enabling in-depth analysis of genomes, sequence types, antibiotic resistance genes, virulence factors and mobile genetic elements across different countries, diseases and hosts. To access and explore the data and statistics, an interactive web interface has been developed, which can be accessed at https://nmdc.cn/gcpathogen/. This user-friendly platform allows seamless querying and exploration of the extensive information housed within the gcPathogen database.

Electron tomography of prolamellar bodies and their transformation into grana thylakoids in cryofixed Arabidopsis cotyledons.

The para-crystalline structures of prolamellar bodies (PLBs) and light-induced etioplast-to-chloroplast transformation have been investigated via electron microscopy. However, such studies suffer from chemical fixation artifacts and limited volumes of 3D reconstruction. Here, we examined Arabidopsis thaliana cotyledon cells by electron tomography (ET) to visualize etioplasts and their conversion into chloroplasts. We employed scanning transmission ET to image large volumes and high-pressure freezing to improve sample preservation. PLB tubules were arranged in a zinc blende-type lattice-like carbon atoms in diamonds. Within 2 h after illumination, the lattice collapsed from the PLB exterior and the disorganized tubules merged to form thylakoid sheets (pre-granal thylakoids), which folded and overlapped with each other to create grana stacks. Since the nascent pre-granal thylakoids contained curved membranes in their tips, we examined the expression and localization of CURT1 (CURVATURE THYLAKOID1) proteins. CURT1A transcripts were most abundant in de-etiolating cotyledon samples, and CURT1A was concentrated at the PLB periphery. In curt1a etioplasts, PLB-associated thylakoids were swollen and failed to form grana stacks. In contrast, PLBs had cracks in their lattices in curt1c etioplasts. Our data provide evidence that CURT1A is required for pre-granal thylakoid assembly from PLB tubules during de-etiolation, while CURT1C contributes to cubic crystal growth in the dark.

Fungal names: a comprehensive nomenclatural repository and knowledge base for fungal taxonomy.

Fungal taxonomy is a complex and rapidly changing subject, which makes proper naming of fungi challenging for taxonomists. A registration platform with a standardized and information-integrated database is a powerful tool for efficient research on fungal taxonomy. Fungal Names (FN, https://nmdc.cn/fungalnames/; launched in 2011) is one of the three official fungal nomenclatural repositories authorized by the International Nomenclature Committee for Fungi (NCF). Currently, FN includes >567 000 taxon names from >10 000 related journals and books published since 1596 and covers >147 000 collection records of type specimens/illustrations from >5000 preserving agencies. FN is also a knowledge base that integrates nomenclature information with specimens, culture collections and herbaria/fungaria, publications and taxonomists, and represents a summary of the history and recent advances in fungal taxonomy. Published fungal names are categorized based on well-accepted nomenclature rules and can be readily searched with different keywords and strategies. In combination with a standardized name checking tool and a sequence alignment-based identification package, FN makes the registration and typification of nomenclatural novelties of fungi convenient and accurate.

Dynamic Metabolons Using Stimuli-Responsive Protein Cages.

Naturally evolved metabolons have the ability to assemble and disassemble in response to environmental stimuli, allowing for the rapid reorganization of chemical reactions in living cells to meet changing cellular needs. However, replicating such capability in synthetic metabolons remains a challenge due to our limited understanding of the mechanisms by which the assembly and disassembly of such naturally occurring multienzyme complexes are controlled. Here, we report the synthesis of chemical- and light-responsive protein cages for assembling synthetic metabolons, enabling the dynamic regulation of enzymatic reactions in living cells. Particularly, a chemically responsive domain was fused to a self-assembled protein cage subunit, generating engineered protein cages capable of displaying proteins containing cognate interaction domains on their surfaces in response to small molecular cues. Chemical-induced colocalization of sequential enzymes on protein cages enhances the specificity of the branched deoxyviolacein biosynthetic reactions by 2.6-fold. Further, by replacing the chemical-inducible domain with a light-inducible dimerization domain, we created an optogenetic protein cage capable of reversibly recruiting and releasing targeted proteins onto and from the exterior of the protein cages in tens of seconds by on-off of blue light. Tethering the optogenetic protein cages to membranes enables the formation of light-switchable, membrane-bound metabolons, which can repeatably recruit-release enzymes, leading to the manipulation of substrate utilization across membranes on demand. Our work demonstrates a powerful and versatile strategy for constructing dynamic metabolons in engineered living cells for efficient and controllable biocatalysis.

VarEPS: an evaluation and prewarning system of known and virtual variations of SARS-CoV-2 genomes.

The genomic variations of SARS-CoV-2 continue to emerge and spread worldwide. Some mutant strains show increased transmissibility and virulence, which may cause reduced protection provided by vaccines. Thus, it is necessary to continuously monitor and analyze the genomic variations of SARS-COV-2 genomes. We established an evaluation and prewarning system, SARS-CoV-2 variations evaluation and prewarning system (VarEPS), including known and virtual mutations of SARS-CoV-2 genomes to achieve rapid evaluation of the risks posed by mutant strains. From the perspective of genomics and structural biology, the database comprehensively analyzes the effects of known variations and virtual variations on physicochemical properties, translation efficiency, secondary structure, and binding capacity of ACE2 and neutralizing antibodies. An AI-based algorithm was used to verify the effectiveness of these genomics and structural biology characteristic quantities for risk prediction. This classifier could be further used to group viral strains by their transmissibility and affinity to neutralizing antibodies. This unique resource makes it possible to quickly evaluate the variation risks of key sites, and guide the research and development of vaccines and drugs. The database is freely accessible at www.nmdc.cn/ncovn.

Sphingobium agri sp. nov., isolated from rhizospheric soil of eggplant.

A Gram-stain-negative, aerobic, short rod-shaped and motile bacterial strain, designated MAH-33T, was isolated from rhizospheric soil of eggplant. The colonies were observed to be yellow-coloured, smooth, spherical and 0.1-0.3 mm in diameter when grown on TSA agar medium for 2 days. Strain MAH-33T was found to be able to grow at 10-40 °C, at pH 5.0-10.0 and at 0-3.0 % NaCl (w/v). The strain was found to be positive for both oxidase and catalase tests. The strain was positive for hydrolysis of tyrosine and aesculin. According to the 16S rRNA gene sequence comparisons, the isolate was identified as a member of the genus Sphingobium and to be closely related to Sphingobium quisquiliarum P25T (98.4 % similarity), Sphingobium mellinum WI4T (97.8 %), Sphingobium fuliginis TKPT (97.3 %) and Sphingobium herbicidovorans NBRC 16415T (96.9 %). The novel strain MAH-33T has a draft genome size of 3 908 768 bp (28 contigs), annotated with 3689 protein-coding genes, 45 tRNA and three rRNA genes. The average nucleotide identity and digital DNA-DNA hybridization values between strain MAH-33T and closely related type strains were in the range of 79.8-81.6 % and 23.2-24.5 %, respectively. The genomic DNA G+C content was determined to be 62.2 %. The predominant isoprenoid quinone was ubiquinone 10. The major fatty acids were identified as C16 : 0 and summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c). The polar lipids identified in strain MAH-33T were phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol, sphingoglycolipid, phosphatidylcholine; one unknown phospholipid and one unknown lipid. On the basis of digital DNA-DNA hybridization, ANI value, genotypic analysis, chemotaxonomic and physiological data, strain MAH-33T represents a novel species within the genus Sphingobium, for which the name Sphingobium agri sp. nov. is proposed, with MAH-33T (=KACC 19973T = CGMCC 1.16609T) as the type strain.

Massilia agrisoli sp. nov., isolated from rhizospheric soil of banana.

A Gram-stain-negative, aerobic, short rod-shaped and motile novel bacterial strain, designated MAHUQ-52T, was isolated from the rhizospheric soil of a banana plant. Colonies grew at 10-35 °C (optimum, 28 °C), pH 6.0-9.5 (optimum, pH 7.0-7.5), and in the presence of 0-1.0 % NaCl (optimum 0 %). The strain was positive for catalase and oxidase tests, as well as hydrolysis of gelatin, casein, starch and Tween 20. Based on the results of phylogenetic analysis using 16S rRNA gene and genome sequences, strain MAHUQ-52T clustered together within the genus Massilia. Strain MAHUQ-52T was closely related to Massilia soli R798T (98.6 %) and Massilia polaris RP-1-19T (98.3 %). The novel strain MAHUQ-52T has a draft genome size of 4 677 454 bp (25 contigs), annotated with 4193 protein-coding genes, 64 tRNA and 19 rRNA genes. The genomic DNA G+C content was 63.0 %. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between strain MAHUQ-52T and closely related type strains were ≤88.4 and 35.8 %, respectively. The only respiratory quinone was ubiquinone-8. The major fatty acids were identified as C16 : 0 and summed feature 3 (C15 : 0 iso 2-OH and/or C16 : 1 ω7c). Strain MAHUQ-52T contained phosphatidylethanolamine, diphosphatidylglycerol and phosphatidylglycerol as the major polar lipids. On the basis of dDDH and ANI values, as well as genotypic, chemotaxonomic and physiological data, strain MAHUQ-52T represents a novel species within the genus Massilia, for which the name Massilia agrisoli sp. nov. is proposed, with MAHUQ-52T (=KACC 21999T=CGMCC 1.18577T) as the type strain.

gcType: a high-quality type strain genome database for microbial phylogenetic and functional research.

Taxonomic and functional research of microorganisms has increasingly relied upon genome-based data and methods. As the depository of the Global Catalogue of Microorganisms (GCM) 10K prokaryotic type strain sequencing project, Global Catalogue of Type Strain (gcType) has published 1049 type strain genomes sequenced by the GCM 10K project which are preserved in global culture collections with a valid published status. Additionally, the information provided through gcType includes >12 000 publicly available type strain genome sequences from GenBank incorporated using quality control criteria and standard data annotation pipelines to form a high-quality reference database. This database integrates type strain sequences with their phenotypic information to facilitate phenotypic and genotypic analyses. Multiple formats of cross-genome searches and interactive interfaces have allowed extensive exploration of the database's resources. In this study, we describe web-based data analysis pipelines for genomic analyses and genome-based taxonomy, which could serve as a one-stop platform for the identification of prokaryotic species. The number of type strain genomes that are published will continue to increase as the GCM 10K project increases its collaboration with culture collections worldwide. Data of this project is shared with the International Nucleotide Sequence Database Collaboration. Access to gcType is free at http://gctype.wdcm.org/.

Pseudomonas oryzagri sp. nov., isolated from a rice field soil.

A Gram-stain-negative, aerobic, rod-shaped and non-motile novel bacterial strain, designated MAHUQ-58T, was isolated from soil sample of a rice field. The colonies were observed to be light pink-coloured, smooth, spherical and 0.6-1.0 mm in diameter when grown on nutrient agar (NA) medium for 2 days. Strain MAHUQ-58T was found to be able to grow at 15-40 °C, at pH 5.5-10.0 and with 0-1.0 % NaCl (w/v). Cell growth occurred on tryptone soya agar, Luria-Bertani agar, NA, MacConkey agar and Reasoner's 2A agar. The strain was found to be positive for both oxidase and catalase tests. The strain was positive for hydrolysis of Tween 20 and l-tyrosine. According to the 16S rRNA gene sequence comparisons, the isolate was identified as a member of the genus Pseudomonas and to be closely related to Pseudomonas oryzae WM-3T (98.9 % similarity), Pseudomonas linyingensis LYBRD3-7T (97.7 %), Pseudomonas sagittaria JCM 18195 T (97.6 %) and Pseudomonas guangdongensis SgZ-6T (97.2 %). The novel strain MAHUQ-58T has a draft genome size of 4 536 129 bp (46 contigs), annotated with 4064 protein-coding genes, 60 tRNA genes and four rRNA genes. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between strain MAHUQ-58T and four closely related type strains were in the range of 85.5-89.5 % and 29.5-38.0 %, respectively. The genomic DNA G+C content was determined to be 67.0 mol%. The predominant isoprenoid quinone was ubiquinone 9. The major fatty acids were identified as C16:0, summed feature 3 (C16 : 1 ω6c and/or C16 : 1 ω7c) and summed feature 8 (C18 : 1 ω6c and/or C18 : 1 ω7c). On the basis of dDDH and ANI values, genotypic results, and chemotaxonomic and physiological data, strain MAHUQ-58T represents a novel species within the genus Pseudomonas, for which the name Pseudomonas oryzagri sp. nov. is proposed, with MAHUQ-58T (=KACC 22005T=CGMCC 1.18518T) as the type strain.

Allobacillus salarius sp. nov., and Allobacillus saliphilus sp. nov., isolated from shrimp paste (ka-pi) in Thailand.

Two strains of moderately halophilic, Gram-stain-positive and spore-forming rods, designated as SKP4-8T and SKP8-2T isolated from shrimp paste (Ka-pi), were taxonomic studied based on polyphasic approach. Strain SKP4-8T grew at pH 6.0-9.0 (optimum 7.0), at 25-45 °C (optimum 37 °C) and in 1-16% (w/v) NaCl (optimum 5-10%). Strain SKP8-2T grew at pH 6.0-9.0 (optimum 8.0), at 25-45 °C (optimum 37 °C) and in 0-20% (w/v) NaCl (optimum 3-10%). The strains contained meso-diaminopimelic acid in cell-wall peptidoglycan and the major menaquinone was MK-7. Strain SKP4-8T contained iso-C15:0, anteiso-C15:0 and iso-C17:0; and strain SKP8-2T contained anteiso-C15:0, iso-C15:0, iso-C16:0 and antesio-C17:0 as major cellular fatty acids. Phosphatidylglycerol, diphosphatidylglycerol, unknown phospholipids and an unknown glycolipid were detected as major polar lipids. On the basis of 16S rRNA gene sequence analysis, strains SKP4-8T and SKP8-2T belonged to the genus Allobacillus and were closely related to Allobacillus halotolerans LMG 24826T with 98.8% and 99.3% similarity, respectively. The comparative genome analysis based on average nucleotide identity (ANI) and digital DNA-DNA hybridization revealed that both strains showed the values below 95 and 70%, from each other and from Allobacillus halotolerans LMG 24826T, respectively. Based on the data from this polyphasic study, strains SKP4-8T and SKP8-2T represent novel species of the genus Allobacillus and the name Allobacillus salarius sp. nov. was proposed for SKP4-8T (= KCTC 33905T = LMG 30016T = TISTR 2499T); and Allobacillus saliphilus sp. nov. for SKP8-2T (= KCTC 33906T = LMG 29682T = TISTR 2558T).

gcMeta: a Global Catalogue of Metagenomics platform to support the archiving, standardization and analysis of microbiome data.

Meta-omics approaches have been increasingly used to study the structure and function of the microbial communities. A variety of large-scale collaborative projects are being conducted to encompass samples from diverse environments and habitats. This change has resulted in enormous demands for long-term data maintenance and capacity for data analysis. The Global Catalogue of Metagenomics (gcMeta) is a part of the 'Chinese Academy of Sciences Initiative of Microbiome (CAS-CMI)', which focuses on studying the human and environmental microbiome, establishing depositories of samples, strains and data, as well as promoting international collaboration. To accommodate and rationally organize massive datasets derived from several thousands of human and environmental microbiome samples, gcMeta features a database management system for archiving and publishing data in a standardized way. Another main feature is the integration of more than ninety web-based data analysis tools and workflows through a Docker platform which enables data analysis by using various operating systems. This platform has been rapidly expanding, and now hosts data from the CAS-CMI and a number of other ongoing research projects. In conclusion, this platform presents a powerful and user-friendly service to support worldwide collaborative efforts in the field of meta-omics research. This platform is freely accessible at https://gcmeta.wdcm.org/.

Three-dimensional reconstruction and comparison of vacuolar membranes in response to viral infection.

The vacuole is a unique plant organelle that plays an important role in maintaining cellular homeostasis under various environmental stress conditions. However, the effects of biotic stress on vacuole structure has not been examined using three-dimensional (3D) visualization. Here, we performed 3D electron tomography to compare the ultrastructural changes in the vacuole during infection with different viruses. The 3D models revealed that vacuoles are remodeled in cells infected with cucumber mosaic virus (CMV) or tobacco necrosis virus A Chinese isolate (TNV-AC ), resulting in the formation of spherules at the periphery of the vacuole. These spherules contain neck-like channels that connect their interior with the cytosol. Confocal microscopy of CMV replication proteins 1a and 2a and TNV-AC auxiliary replication protein p23 showed that all of these proteins localize to the tonoplast. Electron microscopy revealed that the expression of these replication proteins alone is sufficient to induce spherule formation on the tonoplast, suggesting that these proteins play prominent roles in inducing vacuolar membrane remodeling. This is the first report of the 3D structures of viral replication factories built on the tonoplasts. These findings contribute to our understanding of vacuole biogenesis under normal conditions and during assembly of plant (+) RNA virus replication complexes.

The Global Catalogue of Microorganisms (GCM) 10K type strain sequencing project: providing services to taxonomists for standard genome sequencing and annotation.

The World Federation of Culture Collections and the World Data Center for Microorganisms (wdcm) initiated an international community-led project to sequence and annotate newly described prokaryotic taxa. This sequencing project aims to cooperate with international culture collections and the International Journal of Systematic and Evolutionary Microbiology and contribute to the expansion of whole genome sequencing databases for type strains. It will provide global microbial taxonomists with free standard genome sequencing and annotation services. Taxonomists are encouraged to contact the wdcm and participant culture collections to submit a type strain sequencing proposal.

World data centre for microorganisms: an information infrastructure to explore and utilize preserved microbial strains worldwide.

The World Data Centre for Microorganisms (WDCM) was established 50 years ago as the data center of the World Federation for Culture Collections (WFCC)-Microbial Resource Center (MIRCEN). WDCM aims to provide integrated information services using big data technology for microbial resource centers and microbiologists all over the world. Here, we provide an overview of WDCM including all of its integrated services. Culture Collections Information Worldwide (CCINFO) provides metadata information on 708 culture collections from 72 countries and regions. Global Catalogue of Microorganism (GCM) gathers strain catalogue information and provides a data retrieval, analysis, and visualization system of microbial resources. Currently, GCM includes >368 000 strains from 103 culture collections in 43 countries and regions. Analyzer of Bioresource Citation (ABC) is a data mining tool extracting strain related publications, patents, nucleotide sequences and genome information from public data sources to form a knowledge base. Reference Strain Catalogue (RSC) maintains a database of strains listed in International Standards Organization (ISO) and other international or regional standards. RSC allocates a unique identifier to strains recommended for use in diagnosis and quality control, and hence serves as a valuable cross-platform reference. WDCM provides free access to all these services at www.wdcm.org.

aKMT Catalyzes Extensive Protein Lysine Methylation in the Hyperthermophilic Archaeon Sulfolobus islandicus but is Dispensable for the Growth of the Organism.

Protein methylation is believed to occur extensively in creanarchaea. Recently, aKMT, a highly conserved crenarchaeal protein lysine methyltransferase, was identified and shown to exhibit broad substrate specificity in vitro Here, we have constructed an aKMT deletion mutant of the hyperthermophilic crenarchaeon Sulfolobus islandicus The mutant was viable but showed a moderately slower growth rate than the parental strain under non-optimal growth conditions. Consistent with the moderate effect of the lack of aKMT on the growth of the cell, expression of a small number of genes, which encode putative functions in substrate transportation, energy metabolism, transcriptional regulation, stress response proteins, etc, was differentially regulated by more than twofold in the mutant strain, as compared with that in the parental strain. Analysis of the methylation of total cellular protein by mass spectrometry revealed that methylated proteins accounted for ∼2/3 (1,158/1,751) and ∼1/3 (591/1,757) of the identified proteins in the parental and the mutant strains, respectively, indicating that there is extensive protein methylation in S. islandicus and that aKMT is a major protein methyltransferase in this organism. No significant sequence preference was detected at the sites of methylation by aKMT. Methylated lysine residues, when visible in the structure, are all located on the surface of the proteins. The crystal structure of aKMT in complex with S-adenosyl-l-methionine (SAM) or S-adenosyl homocysteine (SAH) reveals that the protein consists of four α helices and seven ß sheets, lacking a substrate recognition domain found in PrmA, a bacterial homolog of aKMT, in agreement with the broad substrate specificity of aKMT. Our results suggest that aKMT may serve a role in maintaining the methylation status of cellular proteins required for the efficient growth of the organism under certain non-optimal conditions.

Genomic encyclopedia of bacteria and archaea: sequencing a myriad of type strains.

Microbes hold the key to life. They hold the secrets to our past (as the descendants of the earliest forms of life) and the prospects for our future (as we mine their genes for solutions to some of the planet's most pressing problems, from global warming to antibiotic resistance). However, the piecemeal approach that has defined efforts to study microbial genetic diversity for over 20 years and in over 30,000 genome projects risks squandering that promise. These efforts have covered less than 20% of the diversity of the cultured archaeal and bacterial species, which represent just 15% of the overall known prokaryotic diversity. Here we call for the funding of a systematic effort to produce a comprehensive genomic catalog of all cultured Bacteria and Archaea by sequencing, where available, the type strain of each species with a validly published name (currently∼11,000). This effort will provide an unprecedented level of coverage of our planet's genetic diversity, allow for the large-scale discovery of novel genes and functions, and lead to an improved understanding of microbial evolution and function in the environment.

TCRklass: a new K-string-based algorithm for human and mouse TCR repertoire characterization.

The next-generation sequencing technology has promoted the study on human TCR repertoire, which is essential for the adaptive immunity. To decipher the complexity of TCR repertoire, we developed an integrated pipeline, TCRklass, using K-string-based algorithm that has significantly improved the accuracy and performance over existing tools. We tested TCRklass using manually curated short read datasets in comparison with in silico datasets; it showed higher precision and recall rates on CDR3 identification. We applied TCRklass on large datasets of two human and three mouse TCR repertoires; it demonstrated higher reliability on CDR3 identification and much less biased V/J profiling, which are the two components contributing the diversity of the repertoire. Because of the sequencing cost, short paired-end reads generated by next-generation sequencing technology are and will remain the main source of data, and we believe that the TCRklass is a useful and reliable toolkit for TCR repertoire analysis.

Distribution of sialic acid receptors and experimental infections with different subtypes of influenza A viruses in Qinghai-Tibet plateau wild pika.

BACKGROUND: The plateau pika (Ochotona curzoniae) is a small rabbit-like mammal that lives at high altitudes in the Qinghai-Tibet plateau and is in close contact with birds. Following the outbreak of highly pathogenic avian influenza (HPAI) H5N1 during 2005 in the migratory birds of Qinghai Lake, two clades of H5N1 have been found in pikas. However, the influenza virus receptor distribution in different tissues of this animal and its susceptibility to influenza A viruses have remained unclear. METHODS: The sialic acid receptor distribution tropism in pika was investigated using fluorescent Sambucus nigra and biotinylated Maackia amurensis I and II. Furthermore, the replication of three influenza A viruses H1N1, H3N2, and H5N1 in this animal was examined by immunohistochemistry and RT-PCR. Morphological and histopathological changes caused by infection were also analyzed with hematoxylin and eosin (H & E) staining. RESULTS: Human influenza virus-recognizing SAα2,6Gal receptors are widely expressed in the lung, kidney, liver, spleen, duodenum, ileum, rectum, and heart, whereas avian influenza virus-recognizing SAα2,3Gal receptors are strongly expressed in the trachea and lung of pika. M1 could be detected in the lungs of pikas infected with H1N1, H3N2, and H5N1 by either immunostaining or RT-PCR, and in the brain of H5N1-infected pikas. Additionally, three subtypes of influenza A viruses were able to infect pika and caused varying degrees of pneumonia with epithelial desquamation and alveolar inflammatory cell infiltration. Slight pathological changes were observed in H1N1-infected lungs. A few small bronchi and terminal bronchioles were infiltrated by lymphocytic cells in H3N2-infected lungs. In contrast, serious lung damage, such as alveolar capillary hyperemia, edema, alveolar collapse, and lymphocytic infiltrations was observed in H5N1-infected group. Furthermore, neural system changes were present in the brains of H5N1-infected pikas. CONCLUSIONS: SAα2,6Gal receptors are extensively present in many of the tissues and organs in wild plateau pika, whereas SA2,3Gal-linked receptors are dominant on the tracheal epithelial cells. H1N1, H3N2, and H5N1 were able to infect pika and caused different degrees of pathogenic changes in the lungs. Altogether, these results suggest that wild pika has the potential to be a host for different subtypes of influenza A viruses.