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Abscisic acid (ABA) is an important phytohormone involved in plant growth, plant development, and the protection of plants against abiotic stresses. PYL/RCAR (pyrabactin resistance/pyr1-like/regulatory components of ABA receptor) is the receptor protein of ABA and the core component of the ABA signal transduction network. The PYL gene family has been identified and analyzed in many species, however, there is no report about the research on the whole genome-wide identification of the alfalfa (Medicago sativa L.) PYL gene family. Therefore, to explore the function of alfalfa PYL genes, 39 MsPYL genes were identified by analyzing the recently published genome of alfalfa. Using bioinformatics methods, we systematically analyzed the chromosome location, protein physicochemical properties, evolutionary relationship, conserved motifs, and response to low-temperature stress of the MsPYL family of alfalfa. The results showed that 39 alfalfa MsPYL genes were distributed on 24 chromosomes, and the analysis of gene duplication events showed that fragment duplication was predominant duplication in alfalfa MsPYL family gene expansion. The phylogenetic tree of MsPYL protein of alfalfa and the phylogenetic tree of PYL genes of 3 species show that the MsPYL gene family can be divided into 3 subfamilies, and the structures of the same subfamilies are relatively similar. The 39 MsPYL gene family members of alfalfa contain 10 Motifs. Motif1, Motif2, Motif3, and Motif5 are the conserved motifs shared by these genes; cis-regulatory elements in promoter regions indicate that regulatory elements related to transcription, cell cycle, development, hormone, and stress response are abundantly present in the MsPYL promoter sequences; Real-time fluorescence quantitative PCR analysis showed that the expression of MsPYL genes can be induced by low-temperature treatment. This study provides a reference for further exploring the structural and functional characterization of the alfalfa PYL gene family.

Clinical applications of precision oncology require accurate tests that can distinguish true cancer-specific mutations from errors introduced at each step of next-generation sequencing (NGS). To date, no bulk sequencing study has addressed the effects of cross-site reproducibility, nor the biological, technical and computational factors that influence variant identification. Here we report a systematic interrogation of somatic mutations in paired tumor–normal cell lines to identify factors affecting detection reproducibility and accuracy at six different centers. Using whole-genome sequencing (WGS) and whole-exome sequencing (WES), we evaluated the reproducibility of different sample types with varying input amount and tumor purity, and multiple library construction protocols, followed by processing with nine bioinformatics pipelines. We found that read coverage and callers affected both WGS and WES reproducibility, but WES performance was influenced by insert fragment size, genomic copy content and the global imbalance score (GIV; G > T/C > A). Finally, taking into account library preparation protocol, tumor content, read coverage and bioinformatics processes concomitantly, we recommend actionable practices to improve the reproducibility and accuracy of NGS experiments for cancer mutation detection.

With the development of urbanization,the intensity of human use of land is increasing,which in turn has an impact on habitat quality. Therefore, the study of synergistic changes in land use and habitat quality plays an important role in watershed ecological protection and high-quality development.Based on the data of remote sensing in the five phases of 1980,1990,2000,2010 and 2020,the paper studies land use changes, habitat quality changes and synergistic changes in the Zuli River Basin.(1)The land use type of Zuli River basin is dominated by grassland and arable land, which account for more than 90% of the total area of the basin;(2)The rate of change in watershed land use from 1980 to 2020 is Water > Construction Land > Woodland > Grassland > Arable Land, The rate of increase of water, construction land and forest land was 20.38%,6.97% and 5.23%, respectively.The reduction rates of cultivated land and grassland were 0.27% and 0.2% respectively;(3)land use transfer in the Zuli River Basin was divided into two phases. From 1980 to 2000, with the transfer of arable land and grassland, and the transfer of woodland and construction land, cultivated land and grassland diversions were 12.90km2 and 38.19km2.The transfer volume of woodland and construction land is 16.62 km2 and 24 km2 2000 to 2020 respectively. Grassland, woodland, construction land and water diversion, 96.78 km2;(4)the overall habitat quality of the Zuli River basin increased in 1980–2020.Average habitat quality scores were 0.502, 0.5, 0.49, 0.504 and 0.52 respectively,but from the point of view of the development process were reduced and then increased;(5)There is a synergistic relationship between land use and habitat quality, and the change of grassland area in the basin influences the change of habitat quality,which is expected to provide a basis for ecological protection, land use planning and ecological protection and high-quality development of the Yellow River basin. This study aims to provide a basis for ecological protection, land use planning and ecological protection and quality development of the Yellow River basin.

B-box (BBX) proteins are one of the zinc-finger transcription factor that plays a critical role in plant development, growth, and multiple stress responses. Although

PURPOSE: Several professional societies have published guidelines for the clinical interpretation of somatic variants, which specifically address diagnostic, prognostic, and therapeutic implications. While these guidelines for the clinical interpretation of variants include data types that may be used to determine the oncogenicity of a variant (e.g., population frequency, functional and in silico data or somatic frequency), they do not provide a direct, systematic, and comprehensive set of standards and rules to classify the oncogenicity of a somatic variant. This insufficient guidance leads to inconsistent classification of rare somatic variants in cancer, generates variability in their clinical interpretation and importantly impacts patient care. Therefore, it’s essential to address this unmet need. METHODS: Clinical Genome Resource (ClinGen) Somatic Cancer Clinical Domain Working Group and ClinGen Germline/Somatic Variant Subcommittee, the Cancer Genomics Consortium (CGC), and the Variant Interpretation for Cancer Consortium (VICC) used a consensus approach to develop a Standard Operating Procedure (SOP) for the classification of oncogenicity of somatic variants. RESULTS: This comprehensive SOP has been developed to improve consistency in somatic variant classification, and has been validated on 94 somatic variants in ten common cancer-related genes. CONCLUSION: The comprehensive SOP is now available for classification of oncogenicity of a somatic variant.

Materials with a quasi-one-dimensional stripy magnetic order often exhibit low crystal and magnetic symmetries, thus allowing the presence of various energy coupling terms and giving rise to macroscopic interplay between spin, charge, and phonon. In this work, we performed optical, electrical and magnetic characterizations combined with first-principles calculations on a van der Waals antiferromagnetic insulator chromium oxychloride (CrOCl). We detected the subtle phase transition behaviors of exfoliated CrOCl under varying temperature and magnetic field and clarified its controversial spin structures. We found that the antiferromagnetism and its air stability persist down to few-layer samples, making it a promising candidate for future 2D spintronic devices. Additionally, we verified the magnetoelastic coupling effect in CrOCl, allowing for the potential manipulation of the magnetic states via electric field or strain. These virtues of CrOCl provide us with an ideal platform for fundamental research on spin-charge, spin-phonon coupling, and spin-interactions.

In recent years, ecological concerns such as vegetation destruction, permafrost deterioration, and river drying have been paid much more attention to on the Yellow River Basin in China. Soil pH is regarded to be the fundamental variable among soil properties for vegetation growth, while net primary productivity (NPP) is also an essential indicator to reflect the healthy growth of vegetation. Due to the limitation of on-site samples, the spatial–temporal variations in soil pH and NPP, as well as their intrinsic mechanisms, remain unknown, especially in the Yellow River source area, China. Therefore, it is imperative to investigate the coupling relationship between soil pH and NPP of the area. The study coupled MODIS reflectance data (MOD09A1) with on-site soil pH to estimate spatial–temporal variations in soil pH, explore the response of NPP to soil pH, and assess the extent to which they contribute to grassland ecosystems, thus helping to fill knowledge gaps. Results indicated that the surface spectral reflectance for seven bands could express the geographic pattern of soil pH by applying a multiple linear regression equation; NPP exhibited an increasing trend while soil pH was the contrary in summer from 2000 to 2021. In summer, NPP was negatively correlated with soil pH and there was a lag effect in the response of NPP to soil pH, revealing a correlation between temperate steppes > montane meadows > alpine meadows > swamps in different grassland ecosystems. In addition, contribution indices for temperate steppes and montane meadows were positive whereas they were negative for swamps and alpine meadows, which are apparent findings. The contribution index of montane and alpine meadows was greater than that of temperate steppes and swamps. The approach of the study can enable managers to easily identify and rehabilitate alkaline soil and provides an important reference and practical value for ecological restoration and sustainable development of grassland ecosystems in alpine regions.

Precision oncology is the practice of interpreting the clinical significance of observed molecular changes in patient neoplasms, potentially impacting medical decision making and care. This process is labor-intensive and (among other challenges) involves accurately translating between variation representation conventions from one resource to the next. For example, differences in representations of Copy Number Variation (CNV) from genomic regions, cytogenomic bands, or gene features create challenges in knowledge matching due to lack of standards covering all of these modalities of observed variation.The Global Alliance for Genomics and Health (GA4GH; ga4gh.org) is an international collaborative of genomic data sharing initiatives (Driver Projects) developing genomic data sharing standards within a human rights framework. GA4GH recently published the Variation Representation Specification (VRS; pronounced “verse”), a standard for the computational representation of biomolecular variation. VRS is a terminology, schema, and associated conventions for creating uniquely identifiable and federatable representations of molecular variation. VRS has formal data classes well-suited to differentiating between variation on a single molecule (e.g. tandem duplications) from variation measured at a systemic level (e.g. genome-wide copy number variation). In addition to molecular sequence variation, VRS also supports variation on cytogenetic coordinate systems and genes, making it well-suited to representing variation associated with cancer biomarkers.We demonstrate the use of VRS to model reported gene-associated CNVs from the AACR Project GENIE cohort, to aid in the computational discovery of evidence from clinico-genomic knowledgebases with genomic or cytogenomic CNV representations. We highlight the use case of knowledge matching to the Atlas of Genetics and Cytogenetics in Oncology and Haematology (“the Atlas”; atlasgeneticsoncology.org), a cytogenetics resource historically driven by user website navigation. Using VRS search tools we developed for the Variant Interpretation for Cancer Consortium (VICC; cancervariants.org) GA4GH Driver Project, we found that 64% of GENIE samples with reported CNVs matched clinically relevant knowledge in the Atlas. This work was enabled by programmatic search tools leveraging standard VRS object structures, demonstrating how VRS enables collection of real-world evidence across more resources without manual interpretation or custom normalization methods. We conclude with a survey of open-source tools supporting this analysis as well as search of other clinico-genomic knowledgebases with VRS, including CIViC (civicdb.org), BRCA Exchange (brcaexchange.org), and the Molecular Oncology Almanac (moalmanac.org). Citation Format: Matthew Cannon, Kori Kuzma, James Stevenson, Jiachen Liu, Colin O'Sullivan, Bimal P. Chaudhari, Matthew Brush, Robert R. Freimuth, Tristan Nelson, Michael Baudis, Obi L. Griffith, Malachi Griffith, Lawrence Babb, Melissa S. Cline, Xuelu Liu, Brian Walsh, Alex H. Wagner. Introduction of the GA4GH Variation Representation Specification (VRS) and supporting tools for discovery and exchange of clinical genomic and cytogenomic knowledge in cancers [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1177.

Reproduction is an energetically costly phenomenon. Therefore, to optimize reproductive success, male birds invest enough energetic resources for maintaining well-developed testes. The hypothalamic-pituitary-thyroid (HPT) axis in birds can crosstalk with the hypothalamic-pituitary-gonadal (HPG) axis, thus orchestrating both the reproduction and metabolism. However, until now, how the free-living birds timely optimize both the energy metabolism and reproduction via HPT-axis is not understood. To uncover this physiological mechanism, we investigated the relationships among body mass, testis size, plasma hormones including thyroid-stimulating hormone (TSH), thyroxine (T4), triiodothyronine (T3), metabolites including glucose (Glu), triglyceride (TG), total cholesterol (TC), uric acid (UA), diencephalon mRNA expressions of type 2 (Dio2) and 3 (Dio3) iodothyronine deiodinase enzymes, thyrotropin-releasing hormone (TRH), thyroid-stimulating hormone (TSH), gonadotropin-releasing hormone I (GnRH-I), and gonadotropin-inhibitory hormone (GnIH) in a male Eurasian tree sparrow (ETS, Passer montanus). We found significantly larger testis size; elevated diencephalon Dio2 and TRH mRNA expressions, plasma T3, and UA levels; and significantly lowered Glu, TG, and TC levels during mating relative to the non-mating stages in male ETSs. However, Dio3, TSH, GnRH-I, and GnIH mRNA expression did not vary with the stage. Furthermore, life-history stage dependent variation in plasma T3 had both direct effects on the available energy substrates and indirect effects on body mass and testis size, indicating a complex regulation of metabolic pathways through the HPT- and HPG-axes. The identified differences and relationships in mRNA expression, plasma T3 and metabolites, and testis size in male ETSs contribute to our understanding how free-living birds adjust their molecular, endocrinal, and biochemical features to orchestrate their reproductive physiology and metabolism for the maintenance of well-developed testes.

China is undergoing rapid urbanization, which has caused undesirable urban sprawl and ecological deterioration. Urban growth boundaries (UGBs) are an effective measure to restrict the irrational urban sprawl and protect the green space. However, the delimiting method and control measures of the UGBs is at the exploratory stage in China. In this paper, a cellular automata model based on multi-criteria evaluation (MCE-CA) was proposed to delimit the UGBs. The MCE-CA model considers influencing factors related to urban growth and generates UGBs based on spatiotemporally dynamic simulations. The MCE-CA model was applied to generate the UGBs of Jiayuguan City in 2020 and 2030, the results show that the simulation accuracy is higher than 0.8 and the compactness increases to 0.23, which demonstrates that the MCE-CA model is an effective model for delimiting UGBs. Moreover, the MCE-CA model can corporate the contradiction between environmental protection and urban development, promoting urban smart growth and sustainable development. UGBs is an effective tool for China to realize ecological civilization construction and improve the spatial governance ability, and the MCE-CA model can be used to assist planners in delimiting future UGBs, this study provides a methodological reference for future research of UGBs in Chinese cities.

Citrus Huanglongbing (HLB, yellow shoot disease) is one of the most serious citrus diseases worldwide. To better improve the detection sensitivity, a droplet digital PCR (ddPCR) assay was developed for the rapid detection of ‘Candidatus Liberibacter asiaticus’ (Las), the putative causal agent of HLB. The detection of sensitivity comparison using positive plasmid indicated that ddPCR was superior to quantitative PCR (qPCR) for detecting and quantifying Las at low concentrations. The Las detection of 40 field samples also showed that six of 13 asymptomatic samples (46.15%) with high Ct value (>35) were positive by ddPCR. This methodology showed great potential for early HLB infection diagnosis.

Despite the well-established role of recurrent gene fusions as oncogenic drivers, current practices for characterizing and interpreting gene fusion events in clinical testing and in biomedical literature are inconsistent. From the conceptual definition of gene fusions to the salient elements that characterize these alterations, a lack of community-driven standards for the curation of gene fusions has resulted in a disparate landscape of fusion representations and supporting tools. Consequently, the evidence-based clinical evaluation of gene fusions requires extensive expert review for accurate interpretation of observed gene fusions with respect to putative evidence from biomedical literature. Furthermore, the lack of these standards inhibits the interoperability of tools, resources, and pipelines - impeding data sharing and downstream utility.To address these challenges, a cross-consortia initiative between the Variant Interpretation for Cancer Consortium and ClinGen was formed to develop a standard operating procedure (SOP) for the curation of gene fusions. The SOP is under development by an international and diverse set of experts in the representation, detection, and clinical interpretation of gene fusions. Participating stakeholders across academic, government, and industry sectors showcased challenges and solutions, and participated in community surveys and discussions to define and develop the SOP for this diverse class of alterations.An initial result of this effort was the precise molecular definition of genomic events and features constituting gene fusions. We distinguish these from similar but distinct classes of structural alterations through clinically-relevant examples. Next, we discuss our findings on community practices around the description and evaluation of gene fusions. We provide our recommendations for characterization and representation of gene fusions from these practices, and compare these recommendations to existing variant representation standards and formats (e.g. HGVS variant nomenclature). We also discuss the concurrent application of formats for standardized human- and machine-readable representations of gene fusion events.We conclude with discussion of the salient elements to enable rapid, scalable, and consistent evaluation of fusions curated from the biomedical literature. Recommendations are provided for the standardized capture of these elements to enable both intuitive and precise characterization of this diverse class of alterations in clinical reporting and literature. In summary, we provide a clinical-practice driven framework and nomenclature for gene fusions, including recommendations for human readability, computational precision, and data integrity within the SOP. This work is a substantial advancement towards standardized communication, investigation, and sharing of gene fusion data across clinical and research domains and specialties. Citation Format: Alex H. Wagner, Ioannis S. Vlachos, Dmitriy Sonkin, Panieh Terraf, Chimene Kesserwan, Andrea Sboner, Thomas Coard, Christian Reich, Deborah I. Ritter, Peter Horak, Ying S. Zou, Anna Tanska, Aaron M. Berlin, Anna Lu, Daniel Cameron, Heather E. Williams, Wan-Hsin Lin, Gokce Toruner, Arpad Danos, Jason Saliba, Huiling Xu, Xinjie Xu, Georgina Ryland, Michele Ceccarelli, Liying Zhang, Sarah Rapisardo, Catherine Rehder, Xuelu Liu, Aparna Pallavajjala, Nicole Park, Laveniya Satgunaseelan, Kristy Lee, Jie Liu, Obi Griffith, Robert R. Freimuth, Albrecht Stenzinger, Linda B. Baughn, Michael Baudis, Jennifer Lee, Marilyn Li, Angshumoy Roy, Gordana Raca. A standard operating procedure for the curation of gene fusions [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 449.

To investigate the impact of neuropsychiatric disorders on the effect of metoprolol on cardiac and motor function in chronic heart failure (CHF) patients.From February 2013 to April 2016, CHF patients with clinical mental disorders received metoprolol (23.75 or 47.5 mg, once daily, orally) at the Second Affiliated Hospital of Kunming Medical University. Mental status was confirmed by means of the Hospital Anxiety and Depression Scale (HADS) and the Copenhagen Burnout Inventory (CBI) scale. Cardiac function parameters such as systolic blood pressure (SBP), ejection fraction (EF) and cardiac index (CI) as well as motor function including the 6 meter walk test (6MWT) and the Veteran's Specific Activity Questionnaire (VSAQ) were assessed as primary outcomes of the study.A total of 154 patients (median age, 66.39 years; men, n = 101) were allocated into eight groups based on their mental status. There were no significant differences in heart rate (HR) or SBP control achieved by metoprolol in any groups compared with the control (patients with normal mental status). Furthermore, biphasic ejection fraction (EF) changes were observed in all the groups with a decrease in the first month and increase from the sixth month. However, this increase was significantly lower (p .001) than the EF achieved with metoprolol treatment in the control group except for the anxiety group. A similar pattern was seen for CI, 6MWT and VSAQ changes in all the groups. Patients in the anxiety group responded similarly to the patients with normal mental status.Depressive and high burnout symptoms, but not anxiety, lower the improvement of cardiac and motor function by metoprolol treatment in CHF.

Xuelu Liu,1 Xueming Lou,1 Xianliang Cheng,2 Yong Meng1 1Department of Cardiology, 2Department of Endocrinology, The Second Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, People’s Republic of China Background: Metoprolol treatment is well established for chronic heart failure (CHF) patients, but the central nervous system side effects are often a potential drawback.Objective: To investigate the impact of metoprolol treatment on change in mental status of CHF patients with clinical psychological disorders (such as depression, anxiety, and burnout syndrome).Methods: From February 2013 to April 2016, CHF patients with clinical mental disorders received metoprolol (23.75 or 47.5 mg, qd PO, dose escalated with 23.75 mg each time until target heart rate [HR]

To prospectively evaluate the impact of metoprolol achieved heart rate (HR) on cardiac-motor function and quality of life (QoL) in chronic heart failure (CHF) patients.Between February 2013 to April 2016, association of HR reduction with haemodynamic indices, motor function and QoL in CHF patients with HR80bpm receiving metoprolol 23.75mg or 47.5mgq.d was studied. Overall, 154 patients (median age, 66.39years; males, n=101; females, n=53) were enrolled, whose average resting HR decreased significantly from baseline value of 82.72±6.73 to 69.38±3.57, 67.72±2.61, 66.50±3.14 and 64.86±3.21bpm in the 1st, 3rd, 6th and 12th months post metoprolol intervention, respectively (P0.0001). Similarly, the ejection fraction (r=-0.6461, P0.0001), cardiac output (r=-0.5238, P0.0001), cardiac index (r=-0.5378, P0.0001) and veterans specific activity questionnaire scores (r=-0.4088, P0.0001) were significantly associated with the reduction in HR after 12months. The improvement in 6-min walk test was independent of HR reduction (P=0.005). Similarly, QoL as measured by short form-8 questionnaire (SF-8) but not Minnesota Living with Heart Failure was significantly improved at the 12th-month. However, this was not associated with the reductions in HR.Metoprolol achieved HR control was associated with improvement in cardiac performance and motor function but not QoL in patients with CHF.

&lsquo, Candidatus Liberibacter asiaticus&rsquo, (CLas) is one of the causal agents of citrus Huanglongbing (HLB), a bacterial disease of citrus trees that greatly reduces fruit yield and quality. CLas strains produce an array of currently uncharacterized Sec-dependent secretory proteins. In this study, the conserved chromosomally encoded protein CLIBASIA_03875 was identified as a novel Sec-dependent secreted protein. We show that CLIBASIA_03875 contains a putative Sec- secretion signal peptide (SP), a 29 amino acid residue located at the N-terminus, with a mature protein (m3875) of 22 amino acids found to localize in multiple subcellular components of the leaf epidermal cells of Nicotiana benthamiana. When overexpressed via a Potato virus X (PVX)-based expression vector in N. benthamiana, m3875 suppressed programmed cell death (PCD) and the H2O2 accumulation triggered by the pro-apoptotic mouse protein BAX and the Phytophthora infestans elicitin INF1. Overexpression also resulted in a phenotype of dwarfing, leaf deformation and mosaics, suggesting that m3875 has roles in plant immune response, growth, and development. Substitution mutagenesis of the charged amino acid (D7, R9, R11, and K22) with alanine within m3875 did not recover the phenotypes for PCD and normal growth. In addition, the transiently overexpressed m3875 regulated the transcriptional levels of N. benthamiana orthologs of CNGCs (cyclic nucleotide-gated channels), BI-1 (Bax-inhibitor 1), and WRKY33 that are involved in plant defense mechanisms. To our knowledge, m3875 is the first PCD suppressor identified from CLas. Studying the function of this protein provides insight as to how CLas attenuates the host immune responses to proliferate and cause Huanglongbing disease in citrus plants.

‘Candidatus Liberibacter asiaticus’ (CLas) is one of the causal agents of citrus Huanglongbing (HLB), a bacterial disease of citrus trees that greatly reduces fruit yield and quality. CLas strains produce an array of currently uncharacterized Sec-dependent secretory proteins. In this study, the conserved chromosomally encoded protein CLIBASIA_03875 was identified as a novel Sec-dependent secreted protein. We show that CLIBASIA_03875 contains a putative Sec- secretion signal peptide (SP), a 29 amino acid residue located at the N-terminus, with a mature protein (m3875) of 22 amino acids found to localize in multiple subcellular components of the leaf epidermal cells of Nicotiana benthamiana. When overexpressed via a Potato virus X (PVX)-based expression vector in N. benthamiana, m3875 suppressed programmed cell death (PCD) and the H2O2 accumulation triggered by the pro-apoptotic mouse protein BAX and the Phytophthora infestans elicitin INF1. Overexpression also resulted in a phenotype of dwarfing, leaf deformation and mosaics, suggesting that m3875 has roles in plant immune response, growth, and development. Substitution mutagenesis of the charged amino acid (D7, R9, R11, and K22) with alanine within m3875 did not recover the phenotypes for PCD and normal growth. In addition, the transiently overexpressed m3875 regulated the transcriptional levels of N. benthamiana orthologs of CNGCs (cyclic nucleotide-gated channels), BI-1 (Bax-inhibitor 1), and WRKY33 that are involved in plant defense mechanisms. To our knowledge, m3875 is the first PCD suppressor identified from CLas. Studying the function of this protein provides insight as to how CLas attenuates the host immune responses to proliferate and cause Huanglongbing disease in citrus plants.

Background Bringing free-living animals into captivity subjects them to the stress of both capture and captivity, leading to the alteration of normal physiological processes and behaviors through activation of the hypothalamic–pituitary–adrenal axis. In free-living birds, although elevated plasma corticosterone (CORT) is an important adaptation regulating physiological and behavioral responses during the process of capture and captivity stress, little information is currently available on the effects of such stress on plasma metabolite levels. Methods We examined the effects of immediate capture and 24-h captivity on body mass, body condition, plasma CORT, and metabolite levels including glucose (Glu), triglyceride (TG), total cholesterol (TC), uric acid (UA), in breeding Eurasian Tree Sparrows (Passer montanus). Results CORT and Glu levels were increased significantly by the stress of capture, whereas TC and UA levels decreased. Body mass, body condition declined notably after 24 h in captivity, but CORT, Glu, and UA levels increased. Furthermore, male sparrows had lower TG levels after both capture and captivity than those of females. The relationships between plasma CORT and metabolite levels varied between sexes. Conclusions Our results revealed that the metabolic status of Eurasian Tree Sparrows could be dramatically altered by capture and captivity. Monitoring the dynamic effects of both capture and captivity on plasma CORT, metabolite levels in a free-living bird contributes to a better understanding of the stress-induced pathways involved in sex-dependent energy mobilization.

Additional file 1: Table S1. Multiple post hoc comparisons of differences in mean plasma corticosterone (CORT), glucose (Glu), triglyceride (TG), total cholesterol (TC), uric acid (UA), levels of Eurasian Tree Sparrows (Passer montanus) measured 3, 30 and 60Â min after capture, and after 24Â h in captivity.

Table S2. The primers used for RT-qPCR validation. (DOCX 17 kb)

Figure S4. Gene ontology (GO) enrichment analysis of differentially expressed genes (DEGs) of Xac29â 1 wild-type strain compared with hfq mutant. Up, up-regulation; Down, own-regulation. (PPTX 63 kb)

Figure S3. hfq mutations impair resistance to pH in Xanthomonas axonpodis pv. citri (repeat experiment). Xac29–1, Xac29–1Δhfq and Xac29–1Δhfq-C, were grown on nutrient broth (NB) agar plates with pH 5.0, pH 7.0, or pH 9.0. (PPTX 801 kb)

Figure S2. The pathogenicity test of Xac29â 1 strain, hfq mutant and complementary strain by wound infection on detached citrus leaves. Each test was repeated at least three times. (PPTX 116 kb)