Runs of homozygosity and selection signature analyses reveal putative genomic regions for artificial selection in layer breeding.

BACKGROUND: The breeding of layers emphasizes the continual selection of egg-related traits, such as egg production, egg quality and eggshell, which enhance their productivity and meet the demand of market. As the breeding process continued, the genomic homozygosity of layers gradually increased, resulting in the emergence of runs of homozygosity (ROH). Therefore, ROH analysis can be used in conjunction with other methods to detect selection signatures and identify candidate genes associated with various important traits in layer breeding. RESULTS: In this study, we generated whole-genome sequencing data from 686 hens in a Rhode Island Red population that had undergone fifteen consecutive generations of intensive artificial selection. We performed a genome-wide ROH analysis and utilized multiple methods to detect signatures of selection. A total of 141,720 ROH segments were discovered in whole population, and most of them (97.35%) were less than 3 Mb in length. Twenty-three ROH islands were identified, and they overlapped with some regions bearing selection signatures, which were detected by the De-correlated composite of multiple signals methods (DCMS). Sixty genes were discovered and functional annotation analysis revealed the possible roles of them in growth, development, immunity and signaling in layers. Additionally, two-tailed analyses including DCMS and ROH for 44 phenotypes of layers were conducted to find out the genomic differences between subgroups of top and bottom 10% phenotype of individuals. Combining the results of GWAS, we observed that regions significantly associated with traits also exhibited selection signatures between the high and low subgroups. We identified a region significantly associated with egg weight near the 25 Mb region of GGA 1, which exhibited selection signatures and has higher genomic homozygosity in the low egg weight subpopulation. This suggests that the region may be play a role in the decline in egg weight. CONCLUSIONS: In summary, through the combined analysis of ROH, selection signatures, and GWAS, we identified several genomic regions that associated with the production traits of layers, providing reference for the study of layer genome.

Rab3B enhances the stabilization of DDX6 to promote lung adenocarcinoma aggressiveness.

BACKGROUND: Liver kinase B1 (LKB1) is frequently mutated in lung adenocarcinoma, and its loss contributes to tumor progression. METHODS: To identify LKB1 downstream genes that promote lung adenocarcinoma aggressiveness, we performed bioinformatical analysis using publicly available datasets. RESULTS: Rab3B was upregulated in LKB1-depleted lung adenocarcinoma cells and suppressed by LKB1 overexpression. CREB protein was enriched at the promoter of Rab3B in lung cancer cells. Silencing of CREB abrogated the upregulation of Rab3B upon LKB1 loss. Immunohistochemistry revealed the elevated expression of Rab3B in lung adenocarcinomas relative to adjacent normal tissues. Upregulation of Rab3B was significantly associated with lymph node metastasis, advanced tumor stage, and reduced overall survival in lung adenocarcinoma patients. Knockdown of Rab3B suppressed and overexpression of Rab3B promoted the proliferation, colony formation, and migration of lung adenocarcinoma cells in vitro. In a mouse xenograft model, Rab3B depletion restrained and Rab3B overexpression augmented the growth of lung adenocarcinoma tumors. Mechanistically, Rab3B interacted with DDX6 and enhanced its protein stability. Ectopic expression of DDX6 significantly promoted the proliferation, colony formation, and migration of lung adenocarcinoma cells. DDX6 knockdown phenocopied the effects of Rab3B depletion on lung adenocarcinoma cells. Additionally, DDX6 overexpression partially rescued the aggressive phenotype of Rab3B-depleted lung adenocarcinoma cells. CONCLUSION: LKB1 deficiency promotes Rab3B upregulation via a CREB-dependent manner. Rab3B interacts with and stabilizes DDX6 protein to accelerate lung adenocarcinoma progression. The Rab3B-DDX6 axis may be potential therapeutic target for lung adenocarcinoma.

Benefits of osimertinib treat a lung adenocarcinoma patient with germline EGFR T790M, somatic EGFR 19-Del, TP53 and PIK3CA mutations.

BACKGROUND: Somatic mutations in the EGFR gene occur in about 50% of non-small cell lung cancers, with the T790M mutation significantly contributing to secondary resistance against EGFR-TKI drugs. However, EGFR T790M germline mutations rarely occur. CASE PRESENTATION: In this study, we report a case of a lung adenocarcinoma family lineage linked to a germline EGFR T790M mutation. The main subject was diagnosed with stage IV lung adenocarcinoma and experienced a 19-month period without disease progression while treated with Osimertinib. We collected both clinicopathological and familial data from a patient with lung adenocarcinoma. Next-generation sequencing of 40 key genes was performed on the proband's tumor tissue. To detect EGFR germline mutations, Sanger sequencing was conducted on peripheral blood mononuclear cells from the proband and his two daughters. Mutations such as EGFR T790M, EGFR 19-Del, TP53, and PIK3CA were identified in the proband's lung cancer tissue. Additionally, germline EGFR T790M mutations were confirmed in the proband and his daughters through sequencing of their peripheral blood samples. CT scans revealed multiple pulmonary nodules in both daughters. CONCLUSIONS: These observations suggest that germline mutations in EGFR T790M could be strongly linked to a familial predisposition to lung cancer.

Real-world applications of the new grading system in lung adenocarcinoma: A study of 907 patients focusing on revealing the relationship between pathologic grade and genetic status.

BACKGROUND: The status of the lung adenocarcinoma (LUAD) grading system and the association between LUAD differentiation, driver genes, and clinicopathological features remain to be elucidated. METHODS: We included patients with invasive non-mucinous LUAD, evaluated their differentiation, and collected available clinicopathological information, gene mutations, and analyzed clinical outcomes. RESULTS: Among the 907 patients with invasive non-mucinous LUAD, 321 (35.4 %) were poorly differentiated, 422 (46.5 %) were moderately differentiated, and 164 (18.1 %) were well differentiated. EGFR mutation was more common in the LUADs accompanied without CGP (complex glandular pattern) than LUADs with CGP (p < 0.001). Correlation analysis between mutations and clinical characteristics showed that EGFR gene mutation (p < 0.001), KRAS gene mutation (p < 0.05), and ALK gene rearrangement (p < 0.001) were significantly related to the degree of tumor differentiation, and the KRAS and ALK gene mutation frequencies were higher in the low-differentiation group than in the high and medium differentiation groups. The EGFR mutation frequency was higher in the well/moderately differentiated adenocarcinoma group. CONCLUSIONS: Our study adds to the evidence regarding the role of the grading system in prognosis. EGFR, KRAS, and ALK are related to the degree of tumor differentiation.

Artificial intelligence in radiotherapy.

Radiotherapy is a discipline closely integrated with computer science. Artificial intelligence (AI) has developed rapidly over the past few years. With the explosive growth of medical big data, AI promises to revolutionize the field of radiotherapy through highly automated workflow, enhanced quality assurance, improved regional balances of expert experiences, and individualized treatment guided by multi-omics. In addition to independent researchers, the increasing number of large databases, biobanks, and open challenges significantly facilitated AI studies on radiation oncology. This article reviews the latest research, clinical applications, and challenges of AI in each part of radiotherapy including image processing, contouring, planning, quality assurance, motion management, and outcome prediction. By summarizing cutting-edge findings and challenges, we aim to inspire researchers to explore more future possibilities and accelerate the arrival of AI radiotherapy.

Comparison of uniform-density, variable-density, and dual-density spiral samplings for multi-shot DWI.

PURPOSE: To compare the performances of uniform-density spiral (UDS), variable-density spiral (VDS), and dual-density spiral (DDS) samplings in multi-shot diffusion imaging, and determine a sampling strategy that balances reliability of shot navigator and overall DWI image quality. THEORY AND METHODS: UDS, VDS, and DDS trajectories were implemented to achieve four-shot diffusion-weighted spiral imaging. First, the static B0 off-resonance effects in UDS, VDS, and DDS acquisitions were analyzed based on a signal model. Then, in vivo experiments were performed to verify the theoretical analyses, and fractional anisotropy (FA) fitting residuals were used to quantitatively assess the quality of spiral diffusion data for tensor estimation. Finally, the SNR performances and g-factor behavior of the three spiral samplings were evaluated using a Monte Carlo-based pseudo multiple replica method. RESULTS: Among the three spiral trajectories with the same readout duration, UDS sampling exhibited the least off-resonance artifacts. This was most evident when the static B0 off-resonance effect was severe. The UDS diffusion images had higher anatomical fidelity and lower FA fitting residuals than the other two counterparts. Furthermore, the four-shot UDS acquisition achieved the best SNR performance in diffusion imaging with 12.11% and 40.85% improvements over the VDS and DDS acquisitions with the same readout duration, respectively. CONCLUSION: UDS sampling is an efficient spiral acquisition scheme for high-resolution diffusion imaging with reliable navigator information. It provides superior off-resonance performance and SNR efficiency over the VDS and DDS samplings for the tested scenarios.

Investigating the effect of substrate binding on the catalytic activity of xylanase.

XynAF1 from Aspergillus fumigatus Z5 is an efficient thermophilic xylanase belonging to glycoside hydrolase family 10 (GH10). The non-catalytic amino acids N179 and R246 in its catalytic center formed one and three intermolecular H-bonds with the substrate in the aglycone region, respectively. Here we purified XynAF1-N179S and XynAF1-R246K, and obtained the protein-product complex structures by X-ray diffraction. The snapshots indicated that mutations at N179 and R246 had decreased the substrate-binding ability in the aglycone region. XynAF1-N179S, XynAF1-R246K, and XynAF1-N179S-R246K lost one, three, and four H-bonds with the substrate in comparison with the wild-type XynAF1, respectively, but this had little influence on the protein structure. As expected, N179S, R246K, and N179S-R246K led to a gradual decrease of substrate affinity of XynAF1. Interestingly, the enzyme assay showed that N179S increased catalytic efficiency, while both R246K and N179S-R246K had decreased catalytic efficiency. KEY POINTS: • The non-catalytic amino acids of XynAF1 could form H-bonds with the substrate. • The protein-product complex structures were obtained by X-ray diffraction. • The enzyme-substrate-binding capacity could affect enzyme catalytic efficiency.

LMP2-mRNA lipid nanoparticle sensitizes EBV-related tumors to anti-PD-1 therapy by reversing T cell exhaustion.

BACKGROUND: Targeting EBV-proteins with mRNA vaccines is a promising way to treat EBV-related tumors like nasopharyngeal carcinoma (NPC). We assume that it may sensitize tumors to immune checkpoint inhibitors. RESULTS: We developed an LMP2-mRNA lipid nanoparticle (C2@mLMP2) that can be delivered to tumor-draining lymph nodes. C2@mLMP2 exhibited high transfection efficiency and lysosomal escape ability and induced an increased proportion of CD8 + central memory T cells and CD8 + effective memory T cells in the spleen of the mice model. A strong synergistic anti-tumor effect of C2@mLMP2 in combination with αPD-1 was observed in tumor-bearing mice. The mechanism was identified to be associated with a reverse of CD8 + T cell exhaustion in the tumor microenvironment. The pathological analysis further proved the safety of the vaccine and the combined therapy. CONCLUSIONS: This is the first study proving the synergistic effect of the EBV-mRNA vaccine and PD-1 inhibitors for EBV-related tumors. This study provides theoretical evidence for further clinical trials that may expand the application scenario and efficacy of immunotherapy in NPC.

Nanobody-armed T cells endow CAR-T cells with cytotoxicity against lymphoma cells.

BACKGROUND: Taking advantage of nanobodies (Nbs) in immunotherapy, we investigated the cytotoxicity of Nb-based chimeric antigen receptor T cells (Nb CAR-T) against lymphoma cells. METHODS: CD19 Nb CAR-T, CD20 Nb CAR-T, and Bispecific Nb CAR-T cells were generated by panning anti-human CD19- and CD20-specific nanobody sequences from a natural Nb-expressing phage display library, integrating Nb genes with a lentiviral cassette that included other CAR elements, and finally transducing T cells that were expanded under an optimization system with the above generated CAR lentivirus. Prepared Nb CAR-T cells were cocultured with tumour cell lines or primary tumour cells for 24 h or 5 days to evaluate their biological function. RESULTS: The nanobodies that we selected from the natural Nb-expressing phage display library had a high affinity and specificity for CD19 and CD20. CD19 Nb CAR-T, CD20 Nb CAR-T and Bispecific Nb CAR-T cells were successfully constructed, and these Nb CAR-T cells could strongly recognize Burkitt lymphoma cell lines (Raji and Daudi), thereby leading to activation, enhanced proliferation, and specific killing of target cells. Furthermore, similar results were obtained when using patient samples as target cells, with a cytotoxicity of approximately 60%. CONCLUSIONS: Nanobody-based CAR-T cells can kill both tumour cell lines and patient-derived tumour cells in vitro, and Nb-based CAR-T cells may be a promising therapeutic strategy in future immunotherapy.

Significantly improving the thermostability of a hyperthermophilic GH10 family xylanase XynAF1 by semi-rational design.

Xylanases have a broad range of applications in industrial biotechnologies, which require the enzymes to resist the high-temperature environments. The majority of xylanases have maximum activity at moderate temperatures, which limited their potential applications in industries. In this study, a thermophilic GH10 family xylanase XynAF1 from the high-temperature composting strain Aspergillus fumigatus Z5 was characterized and engineered to further improve its thermostability. XynAF1 has the optimal reaction temperature of 90 °C. The crystal structure of XynAF1 was obtained by X-ray diffraction after heterologous expression, purification, and crystallization. The high-resolution X-ray crystallographic structure of the protein-product complex was obtained by soaking the apo-state crystal with xylotetraose. Structure analysis indicated that XynAF1 has a rigid skeleton, which helps to maintain the hyperthermophilic characteristic. The homologous structure analysis and the catalytic center mutant construction of XynAF1 indicated the conserved catalytic center contributed to the high optimum catalytic temperature. The amino acids in the surface of xylanase XynAF1 which might influence the enzyme thermostability were identified by the structure analysis. Combining the rational design with the saturation mutation at the high B-value regions, the integrative mutant XynAF1-AC with a 6-fold increase of thermostability was finally obtained. This study efficiently improved the thermostability of a GH10 family xylanase by semi-rational design, which provided a new biocatalyst for high-temperature biotechnological applications. KEY POINTS: • Obtained the crystal structure of GH10 family hyperthermophilic xylanase XynAF1. • Shed light on the understanding of the GH10 family xylanase thermophilic mechanism. • Constructed a 6-fold increased thermostability recombinant xylanase.

MED12 exon 2 and TERT promoter mutations in primary and recurrent breast fibroepithelial lesions.

The genetic alterations in the recurrent breast fibroepithelial tumors are poorly understood. In the present study, we aimed to investigate mediator protein complex subunit 12 (MED12) exon 2 and telomerase reverse transcriptase (TERT) promoter mutations in a series of primary and recurrent fibroepithelial tumors. Sanger sequencing for MED12 exon 2 and TERT promoter was performed in 26 pairs of primary and recurrent fibroepithelial tumors (19 pairs of phyllodes tumors and seven pairs of fibroadenomas). The relationship between the genotypes and clinicopathological variables was also analyzed. MED12 mutation was identified in 19 primary tumors (12 phyllodes tumors and 7 fibroadenomas) and 17 recurrences (14 phyllodes tumors and three fibroadenomas). Most recurrent phyllodes tumors retained the original MED12 variants (17/19). Six recurrent fibroadenomas showed different MED12 variants from their paired primary tumors (6/7). TERT promoter mutation was identified in 13 primary phyllodes tumors (13/19) and 15 recurrent phyllodes tumors (15/19). However, it was only identified in one primary fibroadenoma (1/7). Recurrent phyllodes tumors often retained the original MED12 and TERT promoter mutations, while recurrent fibroadenomas often acquired new MED12 mutations. Our findings suggest that recurrent phyllodes tumors may be "true recurrence," and TERT mutant "benign fibroepithelial tumors" should be treated as phyllodes tumors.

Gene signatures based on therapy responsiveness provide guidance for combined radiotherapy and chemotherapy for lower grade glioma.

For a long time, the guidance for adjuvant chemoradiotherapy for lower grade glioma (LGG) lacks instructions on the application timing and order of radiotherapy (RT) and chemotherapy. We, therefore, aimed to develop indicators to distinguish between the different beneficiaries of RT and chemotherapy, which would provide more accurate guidance for combined chemoradiotherapy. By analysing 942 primary LGG samples from The Cancer Genome Atlas (TCGA) and the Chinese Glioma Genome Atlas (CGGA) databases, we trained and validated two gene signatures (Rscore and Cscore) that independently predicted the responsiveness to RT and chemotherapy (Rscore AUC = 0.84, Cscore AUC = 0.79) and performed better than a previous signature. When the two scores were combined, we divided patients into four groups with different prognosis after adjuvant chemoradiotherapy: RSCS (RT-sensitive and chemotherapy-sensitive), RSCR (RT-sensitive and chemotherapy-resistant), RRCS (RT-resistant and chemotherapy-sensitive) and RRCR (RT-resistant and chemotherapy-resistant). The order and dose of RT and chemotherapy can be adjusted more precisely based on this patient stratification. We further found that the RRCR group exhibited a microenvironment with significantly increased T cell inflammation. In silico analyses predicted that patients in the RRCR group would show a stronger response to checkpoint blockade immunotherapy than other patients.

The exploration of new therapeutic targets for HPV-negative head and neck squamous cell cancer through the construction of a ceRNA network and immune microenvironment analysis.

Previous studies have shown that human papillomavirus (HPV)-negative patients with head and neck squamous cell cancer (HNSCC) suffer from an unsatisfactory prognosis. Long noncoding RNAs (lncRNAs) have been verified to participate in many biological processes, including regulating gene expression as competing endogenous RNAs (ceRNAs), while few studies focused the ceRNA network regulation mechanism in patients with HPV-negative HNSCC tumor. Meanwhile, the immune microenvironment may be critical in the development and prognosis of HPV-negative tumors. Our study aimed to further investigate the pathogenesis and potential biomarkers for the diagnosis, therapy and prognosis of HPV-negative HNSCC through a ceRNA network. Comprehensively analyzing the sequencing data of lncRNAs, microRNAs (miRNAs), and messenger RNAs (mRNAs) in The Cancer Genome Atlas HNSCC dataset, we constructed a differentially expressed ceRNA network containing 131 lncRNAs, 35 miRNAs and 162 mRNAs. Then, survival analysis in the network was cited to explore the prognostic biomarkers. Eight mRNAs, nine lncRNAs, and one miRNA were identified to be associated with prognosis. Neuropilin (NRP) binding function, retinoid X receptor (RXR) binding, and the vascular endothelial growth factor (VEGF) signaling pathway were associated with the enrichment analysis, and they also related to the immune microenvironment. Combined with the analysis of the immune microenvironment differences, we obtained new targeted therapies using an RXR agonist, or a combination of the VEGF monoclonal antibody and an NRP antagonist, which may provide a promising future for HPV-negative HNSCC patients.

Pulmonary peripheral glandular papilloma and mixed squamous cell and glandular papilloma frequently harbour the BRAF V600E mutation.

AIMS: Pulmonary peripheral glandular papilloma (GP) and mixed squamous cell and glandular papilloma (MP) have very similar histological features to pulmonary ciliated muconodular papillary tumour (CMPT)/bronchiolar adenoma (BA). The underlying genetic relationships between GP/MP and CMPT/BA have rarely been characterised. We aimed to reveal the relationship between them. METHODS AND RESULTS: We performed a clinicopathological review and next-generation sequencing (NGS) study of two GPs and five MPs. Histologically, GPs/MPs showed similar cellular and architectural features to CMPTs/BAs, such as bilayered epithelium, bronchiole-associated lesions and skipping (discontinuous) growth pattern. One MP showed partial and inconspicuous endobronchiolar growth and more glandular structures, which was very similar to the appearance of CMPT/BA. BRAF V600E mutation was detected in four papillomas (57.1%, one GP and three MPs). CONCLUSIONS: Overlapping morphological features and comparable mutation profiles support that peripheral GPs/MPs and CMPTs/BAs are on the same disease spectrum. We propose expanding the concept of CMPT/BA and including GP and MP in the CMPT/BA family.

Overexpression of SAPCD2 correlates with proliferation and invasion of colorectal carcinoma cells.

BACKGROUND: Suppressor anaphase-promoting complex domain containing 2 (SAPCD2) is a novel gene playing important roles in the initiation, invasion, and metastasis of several malignancies. However, its role in colorectal carcinoma (CRC) still remains unclear. METHOD: In this study, we investigated the expression and biological function of SAPCD2 in CRC. Immunohistochemistry (IHC) for SAPCD2 was performed in 410 pairs of CRC specimens and corresponding normal epithelial tissues, and in 50 adenoma tissues. Clinical pathological factors were analyzed in relation to the expression of SAPCD2. The biological functions of SAPCD2 in CRC cells and its effect on cell cycle were investigated in vitro and in vivo through gain/loss-of-function approaches. RESULTS: IHC showed that SAPCD2 expression was significantly higher in CRC tissues compared to adenoma and normal epithelium tissues and was correlated with tumor location (p = 0.018). SAPCD2 significantly promoted cell proliferation, migration, and invasion both in vitro and in vivo (p < 0.05). In addition, SAPCD2 knockdown in CRC cells was associated with reduced G1/S transition, while overexpression caused G2/M phase arrest (p < 0.05). CONCLUSIONS: In sum, SAPCD2 is overexpressed in CRC tissues and plays a critical role in CRC progression. Therefore, it might represent a promising therapeutic target for CRC treatment.

Autophagic blockage by bismuth sulfide nanoparticles inhibits migration and invasion of HepG2 cells.

The biological effects of nanoparticles are of great importance for the in-depth understanding of safety issues in biomedical applications. Induction of autophagy is a cellular response after nanoparticle exposure. Bismuth sulfide nanoparticles (Bi2S3 NPs) are often used as a CT contrast agent because of their excellent photoelectric conversion ability. Yet there has been no previous detailed study other than a cell toxicity assessment. In this study, three types of Bi2S3 NPs with different shapes (Bi2S3 nano rods (BSNR), hollow microsphere Bi2S3 NPs (BSHS) and urchin-like hollow microsphere Bi2S3 NPs (ULBSHS)) were used to evaluatecytotoxicity, autophagy induction, cell migration and invasion in human hepatocellular carcinoma cells (HepG2). Results showed that all three Bi2S3 NPs lead to blockage in autophagic flux, causing p62 protein accumulation. The cell death caused by these Bi2S3 NPs is proved to be autophagy related, rather than related to apoptosis. Moreover, Bi2S3 NPs can reduce the migration and invasion in HepG2 cells in an autophagy-dependent manner. ULBSHS is the most cytotoxic among three Bi2S3 NPs and has the best tumor metastasis suppression. These results demonstrated that, even with relatively low toxicity of Bi2S3 NPs, autophagy blockage may still substantially influence cell fate and thus significantly impact their biomedical applications, and that surface topography is a key factor regulating their biological response.

Interleukin-6 production mediated by the IRE1-XBP1 pathway confers radioresistance in human papillomavirus-negative oropharyngeal carcinoma.

Endoplasmic reticulum stress (ERS) plays a key role in the pathogenesis and development of tumors and protects tumor cells from radiation damage and drug-induced stress. We previously demonstrated that EGFR confers radioresistance in human papillomavirus (HPV)-negative human oropharyngeal carcinoma by activating ERS signaling through PERK and IRE1α. In addition, PERK confers radioresistance by activating the inflammatory cytokine NF-κB. However, the effect of IRE1 on radiosensitivity has not yet been fully elucidated. Here, we clarified that IRE1 overexpression was associated with poor outcome in HPV-negative patients treated with radiotherapy (P = 0.0001). In addition, a significantly higher percentage of radioresistant HPV-negative patients than radiosensitive HPV-negative patients exhibited high IRE expression (66.7% vs 27.8%, respectively; P = 0.001). Silencing IRE1 and XBP1 increased DNA double-strand break (DSB) and radiation-induced apoptosis, thereby increasing the radiosensitivity of HPV-negative oropharyngeal carcinoma cells. IRE1-XBP1 silencing also inhibited radiation-induced IL-6 expression at both the RNA and protein levels. The regulatory effect of IRE1-XBP1 silencing on DNA DSB-induced and radiation-induced apoptosis was inhibited by pretreatment with IL-6. These data indicate that IRE1 regulates radioresistance in HPV-negative oropharyngeal carcinoma through IL-6 activation, enhancing X-ray-induced DNA DSB and cell apoptosis.

Improvement of GH10 family xylanase thermostability by introducing of an extra α-helix at the C-terminal.

Xylanase is an important enzyme in industrial applications, which usually require the enzyme to maintain activity in high-temperature condition. In this study, a GH10 family xylanase XynAF0 from a thermophilic composting fungus, Aspergillus fumigatus Z5, was investigated to determine its thermostable mechanism. XynAF0 showed excellent thermostability, which could maintain 50% relative activity after incubation for 1 h at 70 °C. The homologous modeling structure of XynAF0 was constructed and an α-helix composed of poly-threonine has been found in the linker region between the catalytic domain and the carbohydrate-binding module domain. Both the molecular dynamics simulation and the biochemical experiments proved that the α-helix plays an important role in the thermostability of XynAF0. Introducing of this poly-threonine region to the C-terminus of another GH10 family xylanase improved its thermostability. Our results indicated that the poly-threonine α-helix at the C-terminus of the catalytic domain was important for improving the thermophilic of GH10 family xylanases, which provides a new strategy for the thermostability modification of xylanases.

Distortion correction for high-resolution single-shot EPI DTI using a modified field-mapping method.

PURPOSE: The widely used single-shot EPI (SS-EPI) diffusion tensor imaging (DTI) suffers from strong image distortion due to B0 inhomogeneity, especially for high-resolution imaging. Traditional methods such as the field-mapping method and the top-up method have various deficiencies in high-resolution SS-EPI DTI distortion correction. This study aims to propose a robust distortion correction approach, which combines the advantages of traditional methods and overcomes their deficiencies, for high-resolution SS-EPI DTI. METHODS: The proposed correction method is based on the echo planar spectroscopic imaging field-mapping followed by an intensity correction procedure. To evaluate the efficacy of distortion correction, the proposed method was compared with the conventional field-mapping method and the top-up method, using a newly developed quantitative evaluation framework. The correction results were also compared with multi-shot EPI DTI to investigate whether the proposed method can provide high-resolution SS-EPI DTI with high geometric fidelity and high time efficiency. RESULTS: The results show that accurate field-mapping and intensity correction are critical to distortion correction in high-resolution SS-EPI DTI. The proposed method can provide more precise field maps and better correction results than the other two methods (p < 0.0001), and the corrected images show higher geometric fidelity than those from MS-EPI DTI. CONCLUSION: An effective method is proposed to reduce image distortion in high-resolution SS-EPI DTI. It is practical to achieve high-resolution DTI with high time efficiency and high structure accuracy using this method.

Genome-wide association analysis of egg production performance in chickens across the whole laying period.

BACKGROUND: Egg production is the most economically-important trait in layers as it directly influences benefits of the poultry industry. To better understand the genetic architecture of egg production, we measured traits including age at first egg (AFE), weekly egg number (EN) from onset of laying eggs to 80 weeks which was divided into five stage (EN1: from onset of laying eggs to 23 weeks, EN2: from 23 to 37 weeks, EN3: from 37 to 50 weeks, EN4: from 50 to 61 weeks, EN5: from 61 to 80 weeks) based on egg production curve and total egg number across the whole laying period (Total-EN). Then we performed genome-wide association studies (GWAS) in 1078 Rhode Island Red hens using a linear mixed model. RESULTS: Estimates of pedigree and SNP-based genetic parameter showed that AFE and EN1 exhibited high heritability (0.51 ± 0.09, 0.53 ± 0.08), while the h2 for EN in other stages varied from low (0.07 ± 0.04) to moderate (0.24 ± 0.07) magnitude. Subsequently, seven univariate GWAS for AFE and ENs were carried out independently, from which a total of 161 candidate SNPs located on GGA1, GGA2, GGA5, GGA6, GGA9 and GGA24 were identified. Thirteen SNP located on GGA6 were associated with AFE and an interesting gene PRLHR that may affect AFE through regulating oxytocin secretion in chickens. Sixteen genome-wide significant SNPs associated with EN3 were in a strong linkage disequilibrium (LD) region spanning from 117.87 Mb to 118.36 Mb on GGA1 and the most significant SNP (rs315777735) accounted for 3.57% of phenotypic variance. Genes POLA1, PDK3, PRDX4 and APOO identified by annotating sixteen genome-wide significant SNPs can be considered as candidates associated with EN3. Unfortunately, our study did not find any candidate gene for the total egg number. CONCLUSIONS: Findings in our study could provide promising genes and SNP markers to improve egg production performance based on marker-assisted breeding selection, while further functional validation is still needed in other populations.