Defining E3 ligase-substrate relationships through multiplex CRISPR screening

Specificity within the ubiquitin-proteasome system is primarily achieved through E3 ubiquitin ligases, but for many E3s their substrates-and in particular the molecular features (degrons) that they recognize-remain largely unknown. Current approaches for assigning E3s to their cognate substrates are tedious and low throughput. Here we developed a multiplex CRISPR screening platform to assign E3 ligases to their cognate substrates at scale. A proof-of-principle multiplex screen successfully performed ~100 CRISPR screens in a single experiment, refining known C-degron pathways and identifying an additional pathway through which Cul2FEM1B targets C-terminal proline. Further, by identifying substrates for Cul1FBXO38, Cul2APPBP2, Cul3GAN, Cul3KLHL8, Cul3KLHL9/13 and Cul3KLHL15, we demonstrate that the approach is compatible with pools of full-length protein substrates of varying stabilities and, when combined with site-saturation mutagenesis, can assign E3 ligases to their cognate degron motifs. Thus, multiplex CRISPR screening will accelerate our understanding of how specificity is achieved within the ubiquitin-proteasome system.

Liquid-like atoms in dense-packed solid glasses

Revealing the microscopic structural and dynamic pictures of glasses is a long-standing challenge for scientists^1,2. Extensive studies on the structure and relaxation dynamics of glasses have constructed the current classical picture^3-5: glasses consist of some 'soft zones' of loosely bound atoms embedded in a tightly bound atomic matrix. Recent experiments have found an additional fast process in the relaxation spectra^6-9, but the underlying physics of this process remains unclear. Here, combining extensive dynamic experiments and computer simulations, we reveal that this fast relaxation is associated with string-like diffusion of liquid-like atoms, which are inherited from the high-temperature liquids. Even at room temperature, some atoms in dense-packed metallic glasses can diffuse just as easily as they would in liquid states, with an experimentally determined viscosity as low as 10⁷ Pa·s. This finding extends our current microscopic picture of glass solids and might help establish the dynamics-property relationship of glasses⁴.

[An investigation on serum antibody level of varicella-zoster virus in healthy population in Beijing]

Objective: To assess the level and trend of varicella-zoster virus (VZV) antibody among healthy population in Beijing in 2017, after the five-year implementation of the two doses varicella vaccination strategy in 2012, and to provide evidence for scientific evaluation of immunization strategy. Methods: A total of 2 144 subjects in ten age groups from 8 districts of Beijing city were recruited in this study using cross-sectional survey based on multi-stage cluster random sampling method. Serum samples were collected and VZV antibody was detected by ELISA. The influencing factors of antibody concentration and positive rate were analyzed and compared with the study in 2012. The antibody concentration and antibody positive rate were analyzed by nonparametric test and χ² test respectively. Results: The ratio of subjects with registered residence in Beijing city to other provinces was 1∶1. The ratio of male to female was 1∶1.08. The median concentration of VZV antibody was 341.4 (78.6, 1 497.8) mIU/ml, and the total antibody positive rate was 71.1% (1 524/2 144). There were significant differences in antibody positive rate (χ²=736.39, P<0.01) and antibody concentration (χ²=740.34, P<0.01) among different age groups. The antibody positive rate generally increased with age (χ²_trend=7.32, P_trend<0.01). Among 862 children under 14 years old, the antibody positive rate of two doses vaccination 72.8% (182/250) was significantly higher than that of one dose vaccination 51.9% (154/297) (χ²=25.14, P<0.01). There was significant difference between 1-4 years old group (χ²=11.71, P<0.01) and 10-14 years old group (χ²=5.95, P=0.02), but not in 5-9 years old group (χ²=3.00, P=0.07). Compared with the study in 2012, the antibody positive rate increased in 5-9 years old group (χ²=14.35, P<0.01) and decreased in 1-4 years old group (χ²=11.51, P=0.01) in 2017. Conclusion: The recommended varicella booster vaccination has significantly improved the VZV antibody level of children in Beijing city. In the future, it is necessary to explore a more optimized two doses varicella vaccination schedule for children in combination with epidemiological evidence.

High-resolution epitope mapping by AllerScan reveals relationships between IgE and IgG repertoires during peanut oral immunotherapy

Peanut allergy can result in life-threatening reactions and is a major public health concern. Oral immunotherapy (OIT) induces desensitization to food allergens through administration of increasing amounts of allergen. To dissect peanut-specific immunoglobulin E (IgE) and IgG responses in subjects undergoing OIT, we have developed AllerScan, a method that leverages phage-display and next-generation sequencing to identify the epitope targets of peanut-specific antibodies. We observe a striking diversification and boosting of the peanut-specific IgG repertoire after OIT and a reduction in pre-existing IgE levels against individual epitopes. High-resolution epitope mapping reveals shared recognition of public epitopes in Ara h 1, 2, 3, and 7. In individual subjects, OIT-induced IgG specificities overlap extensively with IgE and exhibit strikingly similar antibody footprints, suggesting related clonal lineages or convergent evolution of peanut-specific IgE and IgG B cells. Individual differences in epitope recognition identified via AllerScan could inform safer and more effective personalized immunotherapy.

The adaptive immune system is a major driver of selection for tumor suppressor gene inactivation

During tumorigenesis, tumors must evolve to evade the immune system and do so by disrupting the genes involved in antigen processing and presentation or up-regulating inhibitory immune checkpoint genes. We performed in vivo CRISPR screens in syngeneic mouse tumor models to examine requirements for tumorigenesis both with and without adaptive immune selective pressure. In each tumor type tested, we found a marked enrichment for the loss of tumor suppressor genes (TSGs) in the presence of an adaptive immune system relative to immunocompromised mice. Nearly one-third of TSGs showed preferential enrichment, often in a cancer- and tissue-specific manner. These results suggest that clonal selection of recurrent mutations found in cancer is driven largely by the tumor’s requirement to avoid the adaptive immune system.

[Epidemiological characteristics of Chlamydia pneumoniae in cases with acute respiratory infection in Beijing, 2015-2019]

Objective: To analyze the epidemiological characteristics of Chlamydia pneumoniae infection among patients with acute respiratory infection in Beijing from 2015 to 2019. Methods: The epidemiological data of acute respiratory infection patients from 35 sentinel hospitals in Beijing were collected by the respiratory pathogen surveillance system in Beijing. The clinical samples were collected to detect Chlamydia pneumoniae, and the sequence of the VD4 region of the ompA gene in positive samples was analyzed. Results: From January 2015 to December 2019, the overall positive rate of Chlamydia pneumoniae among patients with acute respiratory infection in Beijing was 0.34% (129/37 460). The positive rate of Chlamydia pneumoniae generally increased in March, reaching the peak in May, and started to drop in July, with a duration of about 5-8 months. The epidemic season in different years fluctuated by 1-2 months. The positive monthly rate of Chlamydia pneumoniae was no less than 0.30% in every epidemic season. The positive rate of Chlamydia pneumoniae was the highest in the 5-44 years old group and the highest in 10-14 year-olds. The risk of Chlamydia pneumoniae infection increased with age in patients younger than 25 years old and decreased in those older one aged than 25 years of age. The positive rates in male and female patients were 0.33% (68/20 830) and 0.37% (61/16 528), respectively, and there was no significant difference between the two groups (χ²=0.486, P=0.486). The positive rate of Chlamydia pneumoniae in patients with common pneumonia was higher than that in patients with upper pneumonia and severe pneumonia (χ²=36.797, P<0.01). Other respiratory pathogens were also detected in the Chlamydia pneumoniae samples, and the top four pathogens appeared as Haemophilus influenzae (15 cases), Streptococcus pneumoniae (13 cases), Rhinovirus (8 cases), and Stenotrophomonas maltophilia (7 cases). 101 strains of 129 Chlamydia pneumoniae positive samples were identified as type A by sequencing. Conclusions: The annual epidemic pattern of Chlamydia pneumoniae in Beijing, is unimodal, and the epidemic season generally appears from March to July. The seasonal characteristics of Chlamydia pneumoniae in Beijing can be used for the differential diagnosis of Chlamydia pneumoniae from other respiratory pathogens. Chlamydia pneumoniae is most common in people aged 5-44 years, and the primary genotype is type A. People aged 10-44 years old suffer the highest incidence. If the nucleic acid positive rate of Chlamydia pneumoniae exceeds 0.30% for two consecutive months, the high prevalence period of Chlamydia pneumoniae can be preliminarily expected. Chlamydia pneumoniae infection has a higher probability of progressing to severe pneumonia from general pneumonia.

[Clinical characteristics of patients infected with Chlamydia pneumoniae in Beijing from 2015 to 2019]

Objective: To aralyze the clinical characteristics of Chlamydia pneumoniae infection in Beijing. Methods: Based on Beijing Respiratory Pathogen Surveillance System, acute respiratory infection patients were recruited from 35 different types of sentinel hospitals in Beijing. Their epidemiological and clinical data were systematically collected and clinical specimens were also obtained. Nuclear acid testing was performed for 30 types of respiratory pathogens (including Chlamydia pneumoniae). The identified patients of Chlamydia pneumoniae infection were divided into two groups, the acute upper respiratory tract infection (AURI) group and pneumoniae group. The differences in clinical characteristics, laboratory examination and prognosis were compared by using independent sample t test, Mann-Whitney U test, χ² test or Fisher's exact probability test. Results: A total of 119 patients of Chlamydia pneumoniae infection were included, including 12 patients in the AURI group and 107 patients in pneumoniae group. Chlamydia pneumoniae infection mainly occurred in people aged from 5 to 44 years, accounting for 81.5% (97/119). The three most common clinical symptoms were cough (92.4%, 110/119), fever (88.8%, 95/107), and sputum production (76.5%, 91/119). White blood cell counts increased in 39.3% (46/117) of patients. Neutrophile granulocyte proportion increased in 39.7% (46/116) of patients. Platelet count increased in 36.9% (41/111) of patients. An increase of the creatine kinase MB isoenzyme (CKMB) was observed in 12 pneumonia patients (24.5%, 12/49). Radiological examination showed that 90.6% (87/105) of patients in the pneumoniae group had pulmonary parenchymal changes; the lesion occurred most commonly in the lower right lung lobe (34.3%, 36/105) and the lower left lung lobe (27.6%, 29/105). Although 73.8% (79/107) of patients in the pneumoniae group were hospitalized, no case received intensive care unit or mechanical ventilation. As to outcomes, one patient developed respiratory failure and 6 patients suffered myocardial injury. No death was observed in this study. The median days of hospitalization and course of illness for pneumonia patients M(P₂₅,P₇₅) were 10.0 (7.0, 13.0) days and 18.0 (13.5, 22.0) days, respectively. Conclusion: Generally, Chlamydia pneumoniae infections in Beijing from 2015 to 2019 were mild, and the main clinical manifestations were cough, fever and sputum. However, most patients in the pneumoniae group caused by Chlamydia pneumoniae still required hospitalization but with a better outcome.

Local crystalline order features in disordered packings of monodisperse spheres

A new tetrahedral structure model was developed for disordered sphere packings, including not only regular tetrahedron (T), but also quartoctahedron (Q) and bcc simplex (B), the tetrahedral building blocks in fcc, hcp and bcc crystal structures, respectively. Both geometric frustrated configurations and local configurations associated with crystalline order in disordered packings can be comprehensively characterized. It is found that with increasing packing fraction, the population of T, Q, and B increases. Moreover, the crystal-type local configurations formed by face-adjacent T, Q and B increases as packing fraction increases, which is more prevalent than the geometric frustrated ones formed by face-adjacent T. In addition, as packing fraction increases, the local density of irregular simplexes is found to increase more quickly than regular ones, playing more important roles in the density increase in disordered packings. These structure features are found to be intrinsic in the jammed random sphere packings with different friction coefficients, which is independent of interparticle friction and only determined by the packing fraction. Our findings provide new understanding for the structural nature of disordered packings and the underlying structural basis of the random close packing.

[The prognostic impact of diabetic mellitus and hyperglycemia during DLBCL treatment on patients with diffuse large B-cell lymphoma]

目的

探讨弥漫大B细胞淋巴瘤（DLBCL）患者的临床特征和预后因素，评估合并糖尿病（DM）及治疗过程中发生血糖升高对DLBCL预后的影响。

方法

回顾性收集2009年1月1日至2019年12月31日天津医科大学肿瘤医院及中山大学肿瘤防治中心收治的481例初诊DLBCL患者的临床资料，重点关注其治疗前及治疗中的血糖水平，采用Cox回归风险模型进行单因素分析评估预后影响因素，采用Kaplan-Meier法绘制生存曲线分析血糖异常对DLBCL患者总生存（OS）、无进展生存（PFS）的影响。

结果

82例（17.0％）患者在诊断DLBCL前患DM，88例（18.3％）患者在DLBCL治疗过程中至少发生一次血糖升高。单因素分析显示，年龄、Ann-Arbor分期、IPI评分、是否合并DM与OS、PFS相关（P值均<0.05）。组间比较显示，合并DM组与治疗过程中血糖升高组的OS和PFS均较无血糖异常组差（OS：P值分别为0.001、0.003，PFS：P值均<0.001），合并DM组与治疗过程中血糖升高组相比OS和PFS的差异均无统计学意义（P值分别为0.557、0.463）。化疗期间血糖控制良好组的OS和PFS优于血糖控制差组（OS：P＝0.037，PFS：P＝0.007）。

结论

合并DM是影响DLBCL患者预后的重要因素，治疗过程中血糖升高与DLBCL患者的不良预后相关。

Antibody responses to endemic coronaviruses modulate COVID-19 convalescent plasma functionality

SARS-CoV-2 (CoV2) antibody therapies, including COVID-19 convalescent plasma (CCP), monoclonal antibodies, and hyperimmune globulin, are among the leading treatments for individuals with early COVID-19 infection. The functionality of convalescent plasma varies greatly, but the association of antibody epitope specificities with plasma functionality remains uncharacterized. We assessed antibody functionality and reactivities to peptides across the CoV2 and the 4 endemic human coronavirus (HCoV) genomes in 126 CCP donations. We found strong correlation between plasma functionality and polyclonal antibody targeting of CoV2 spike protein peptides. Antibody reactivity to many HCoV spike peptides also displayed strong correlation with plasma functionality, including pan-coronavirus cross-reactive epitopes located in a conserved region of the fusion peptide. After accounting for antibody cross-reactivity, we identified an association between greater alphacoronavirus NL63 antibody responses and development of highly neutralizing antibodies against CoV2. We also found that plasma preferentially reactive to the CoV2 spike receptor binding domain (RBD), versus the betacoronavirus HKU1 RBD, had higher neutralizing titer. Finally, we developed a 2-peptide serosignature that identifies plasma donations with high anti-spike titer, but that suffer from low neutralizing activity. These results suggest that analysis of coronavirus antibody fine specificities may be useful for selecting desired therapeutics and understanding the complex immune responses elicited by CoV2 infection.

CARM1 Inhibition Enables Immunotherapy of Resistant Tumors by Dual Action on Tumor Cells and T Cells

A number of cancer drugs activate innate immune pathways in tumor cells but unfortunately also compromise antitumor immune function. We discovered that inhibition of CARM1, an epigenetic enzyme and cotranscriptional activator, elicited beneficial antitumor activity in both cytotoxic T cells and tumor cells. In T cells, Carm1 inactivation substantially enhanced their antitumor function and preserved memory-like populations required for sustained antitumor immunity. In tumor cells, Carm1 inactivation induced a potent type 1 interferon response that sensitized resistant tumors to cytotoxic T cells. Substantially increased numbers of dendritic cells, CD8 T cells, and natural killer cells were present in Carm1-deficient tumors, and infiltrating CD8 T cells expressed low levels of exhaustion markers. Targeting of CARM1 with a small molecule elicited potent antitumor immunity and sensitized resistant tumors to checkpoint blockade. Targeting of this cotranscriptional regulator thus offers an opportunity to enhance immune function while simultaneously sensitizing resistant tumor cells to immune attack. SIGNIFICANCE: Resistance to cancer immunotherapy remains a major challenge. Targeting of CARM1 enables immunotherapy of resistant tumors by enhancing T-cell functionality and preserving memory-like T-cell populations within tumors. CARM1 inhibition also sensitizes resistant tumor cells to immune attack by inducing a tumor cell-intrinsic type 1 interferon response.This article is highlighted in the In This Issue feature, p. 1861.

Orbital competition of Mn3+ and V3+ ions in Mn1+x V2-x O4

The structural and magnetic properties of Mn1+x V2-x O4 (0 < x ⩽ 1) have been investigated by the heat capacity, magnetization, x-ray diffraction and neutron diffraction measurements, and a phase diagram of temperature versus composition was built up. For x ⩽ 0.3, a cubic-to-tetragonal (c > a) phase transition was observed. For x > 0.3, the system maintained the tetragonal lattice. Although the collinear and noncollinear magnetic transitions of V3+ ions were obtained in all compositions, the canting angles between the V3+ ions decreased with Mn3+-doping, and the ordering of the Mn3+ ions was only observed as x > 0.4. In order to study the dynamics of the ground state, the first principles simulation was applied to analyze not only the orbital effects of Mn2+, Mn3+, and V3+ ions, but also the related exchange energies.

Antibody responses to endemic coronaviruses modulate COVID-19 convalescent plasma functionality

COVID-19 convalescent plasma, particularly plasma with high-titer SARS-CoV-2 (CoV2) antibodies, has been successfully used for treatment of COVID-19. The functionality of convalescent plasma varies greatly, but the association of antibody epitope specificities with plasma functionality remains uncharacterized. We assessed antibody functionality and reactivities to peptides across the CoV2 and the four endemic human coronavirus (HCoV) genomes in 126 COVID-19 convalescent plasma donations. We found strong correlation between plasma functionality and polyclonal antibody targeting of CoV2 spike protein peptides. Antibody reactivity to many HCoV spike peptides also displayed strong correlation with plasma functionality, including pan-coronavirus cross-reactive epitopes located in a conserved region of the fusion peptide. After accounting for antibody cross-reactivity, we identified an association between greater alphacoronavirus NL63 antibody responses and development of highly neutralizing antibodies to SARS-CoV-2. We also found that plasma preferentially reactive to the CoV2 receptor binding domain (RBD), versus the betacoronavirus HKU1 RBD, had higher neutralizing titer. Finally, we developed a two-peptide serosignature that identifies plasma donations with high anti-S titer but that suffer from low neutralizing activity. These results suggest that analysis of coronavirus antibody fine specificities may be useful for selecting therapeutic plasma with desired functionalities.

Viral epitope profiling of COVID-19 patients reveals cross-reactivity and correlates of severity

Understanding humoral responses to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is critical for improving diagnostics, therapeutics, and vaccines. Deep serological profiling of 232 coronavirus disease 2019 (COVID-19) patients and 190 pre-COVID-19 era controls using VirScan revealed more than 800 epitopes in the SARS-CoV-2 proteome, including 10 epitopes likely recognized by neutralizing antibodies. Preexisting antibodies in controls recognized SARS-CoV-2 ORF1, whereas only COVID-19 patient antibodies primarily recognized spike protein and nucleoprotein. A machine learning model trained on VirScan data predicted SARS-CoV-2 exposure history with 99% sensitivity and 98% specificity; a rapid Luminex-based diagnostic was developed from the most discriminatory SARS-CoV-2 peptides. Individuals with more severe COVID-19 exhibited stronger and broader SARS-CoV-2 responses, weaker antibody responses to prior infections, and higher incidence of cytomegalovirus and herpes simplex virus 1, possibly influenced by demographic covariates. Among hospitalized patients, males produce stronger SARS-CoV-2 antibody responses than females.

[DNA barcoding of 4 species of cheyletid mites based on COI and 18S rRNA gene sequences]

OBJECTIVE

To analyze the sequences of mitochondrial cytochrome C oxidase subunit I gene (COI) and 18S ribosomal RNA gene (18S rRNA), so as to identify the feasible DNA barcodes for 4 species of cheyletid mites and improve the DNA barcoding database for cheyletid mites.

METHODS

Cheyletid mite samples were collected from small-scale flour mills in Fuyang, Wuhu and Tongling cities of Anhui Province from May 2018 to July 2019, extracted and morphologically identified. Then, genomic DNA was extracted from a single cheyletid mite, and the COI and 18S rRNA gene sequences were obtained by PCR amplification, cloning and sequencing. The obtained sequences were aligned using the BLAST software. Multiple sequence alignment was done using the software ClustalX version 1.83 using the known gene sequences from cheyletid mites. The genetic distance was calculated using the software MEGA X, and the phylogenetic tree was created using the maximum likelihood method.

RESULTS

The DNA barcoding results of Cheyletus malaccensis, C. carnifex and Cheletomorpha lepidopterorum were consistent with the morphological identification, while no sequences pertaining to Eucheyletia reticulate were retrieved in the GenBank database. The proportions of A + T were 69.6% and 55.1% in the COI and 18S rRNA sequences of 4 cheyletid mites species, respectively, and the numbers of base substitutions were 137 and 46, respectively. There were 154 to 321 and 58 to 99 inter-species variation loci in the COI and 18S rRNA gene sequences of 4 cheyletid mites species, respectively, and the intra-species genetic distance was all 0.020 or less in the COI and 18S rRNA gene sequences of 4 cheyletid mites species, with inter-species genetic distance of 0.235 to 0.583 and 0.078 to 0.114, respectively. Phylogenetic analysis based on COI and 18S rRNA genes showed that all four species of cheyletid mites were clustered into a branch with a 100% supportive rate, which was consistent with the morphological identification.

CONCLUSIONS

Mitochondrial COI gene is superior to 18S rRNA gene as DNA barcodes for 4 species of cheyletid mites, which is more suitable to be used to investigate the phylogenetic relationship of at genus and species levels.

Observation of High-Frequency Transverse Phonons in Metallic Glasses

Using inelastic neutron scattering and molecular dynamics simulations on a model Zr-Cu-Al metallic glass, we show that transverse phonons persist well into the high-frequency regime, and can be detected at large momentum transfer. Furthermore, the apparent peak width of the transverse phonons was found to follow the static structure factor. The one-to-one correspondence, which was demonstrated for both Zr-Cu-Al metallic glass and a three-dimensional Lennard-Jones model glass, suggests a universal correlation between the phonon dynamics and the underlying disordered structure. This remarkable correlation, not found for longitudinal phonons, underscores the key role that transverse phonons hold for understanding the structure-dynamics relationship in disordered materials.

[Clavien-Dindo classification of complications after complete mesocolic excision in laparoscopic radical resection of right hemicolon cancer and analysis on its influencing factors]

Objective: To investigate the Clavien-Dindo (CD) classification of complications after complete mesocolic excision (CME) in laparoscopic radical resection of right-sided hemicolon cancer and its influencing factors. Methods: A retrospective case-control study was performed. Inclusion criteria: (1) the adenocarcinoma located at colon from cecum to hepatic flexure; (2) laparoscopic right hemicolectomy with CME was completed. Exclusion criteria: (1) patients had severe organ dysfunction before operation; (2) tumor invaded adjacent organs or developed distant organ metastasis; (3) emergency surgery; (4) failure of laparoscopic surgery, and conversion to laparotomy; (5) without complete clinical data. Finally, clinical data of 141 patients in our hospital form March 2015 to February 2019 were retrospectively analyzed. CD grading standard was used to evaluate postoperative complications. Univariate and multivariate logistic regression analyse were used to analyze the factors that might affect the complications. Survival analysis was conducted by grouping the indicators with statistically significant difference in multivariate analysis. Kaplan-Meier method was used to draw the survival curve and log-rank test was used to analyze the difference. Results: Of the 141 patients, 89 were male and 52 were female with mean age of (61.8±11.0) years. All the operations completed successfully. A total of 37 postoperative complications were developed in 26 (18.4%) patients had postoperative 37 cases of complications, mainly including 7 delayed incision healing, 6 diarrhea, and 5 respiratory dysfunction. According to CD classification standard, grade I, II, and IV a complication rates were 40.5% (15/37), 56.8% (21/37), and 2.7% (1/37) respectively. Univariate analysis showed that age ≥ 65 years (χ(2)=4.338, P=0.037), BMI ≥ 28 kg/m(2) (χ(2)=5.971, P=0.015), and preoperative hemoglobin < 100 g/L (χ(2)=3.985, P=0.046) were risk factors of postoperative complications. Multivariate analysis testified that age ≥ 65 years (OR=7.991, 95%CI: 2.203 to 28.983, P=0.002) and body mass index (BMI) ≥ 28 kg/m(2) (OR=4.231, 95%CI: 1.034 to 17.322, P=0.045) were independent risk factors for complications after laparoscopic CME surgery for right-sided hemicolon cancer. All the patients were followed up for median time of 24 (1-48) months. The log-rank test showed that there were no significant differences in the cumulative survival rate between patients of age < 65 years and age ≥ 65 years (χ(2)=0.986, P=0.321), and between those with BMI < 28 kg/m(2) and BMI ≥ 28 kg/m(2) (χ(2)=0.370, P=0.543). Conclusions: The main complications after CME in laparoscopic radical resection of right hemicolon cancer are CD grade I and II. Elderly and obesity are independent risk factor for postoperative complications. Before the operation, reasonable preventive measures should be taken for the elderly and the obese in order to reduce postoperative complications.

Diversified Application of Barcoded PLATO (PLATO-BC) Platform for Identification of Protein Interactions

Proteins usually associate with other molecules physically to execute their functions. Identifying these interactions is important for the functional analysis of proteins. Previously, we reported the parallel analysis of translated ORFs (PLATO) to couple ribosome display of full-length ORFs with affinity enrichment of mRNA/protein/ribosome complexes for the "bait" molecules, followed by the deep sequencing analysis of mRNA. However, the sample processing, from extraction of precipitated mRNA to generation of DNA libraries, includes numerous steps, which is tedious and may cause the loss of materials. Barcoded PLATO (PLATO-BC), an improved platform was further developed to test its application for protein interaction discovery. In this report, we tested the antisera-antigen interaction using serum samples from patients with inclusion body myositis (IBM). Tripartite motif containing 21 (TRIM21) was identified as a potentially new IBM autoantigen. We also expanded the application of PLATO-BC to identify protein interactions for JQ1, single ubiquitin peptide, and NS5 protein of Zika virus. From PLATO-BC analyses, we identified new protein interactions for these "bait" molecules. We demonstrate that Ewing sarcoma breakpoint region 1 (EWSR1) binds to JQ1 and their interactions may interrupt the EWSR1 association with acetylated histone H4. RIO kinase 3 (RIOK3), a newly identified ubiquitin-binding protein, is preferentially associated with K63-ubiquitin chain. We also find that Zika NS5 protein interacts with two previously unreported host proteins, par-3 family cell polarity regulator (PARD3) and chromosome 19 open reading frame 53 (C19orf53), whose attenuated expression benefits the replication of Zika virus. These results further demonstrate that PLATO-BC is capable of identifying novel protein interactions for various types of "bait" molecules.

[A comparative study of induction chemotherapy with or without autologous hematopoietic stem cell transplantation in the treatment of newly diagnosed young medium/high risk diffuse large B cell lymphoma patients]

Objective: To compare the efficacy of induction chemotherapy with or without autologous hematopoietic stem cell transplantation (auto-HSCT) for newly diagnosed young diffuse large B cell lymphoma (DLBCL) patients. Methods: The retrospective study was performed in 90 cases of young patients (≤60 years) with newly diagnosed DLBCL and an age-adjusted International Prognostic Index (aa-IPI) score of 2 or 3. All of them were treated with R-CHOP (32 cases, rituximab combined with CHOP), dose-intensive regimens (DA-EPOCH, Hyper CVAD/MA or ESHAP) combined with or without rituximab (25 cases), and consolidated with up-front auto-HSCT (33 cases), respectively. The efficacy and the potential predictors were evaluated. Results: ①The median age of 90 patients was 43 (18-60) years old. The median follow-up time was 42 (3-110) months. ②The 5-year progression-free survival (PFS) for R-CHOP group, dose-intensive chemotherapy group and auto-HSCT group were (33.5±10.7) %, (55.3±10.1) % and (65.8±13.6) % (P=0.012), the 5-year overall survival (OS) were (49.7±9.0) %, (61.6±10.2) % and (78.6±7.8) % (P=0.035), respectively. There was no significant difference in 5-years PFS and OS between the R-CHOP group and dose-intensive chemotherapy group (P=0.519, P=0.437) compared with that of the dose-intensive chemotherapy group, auto-HSCT group has higher 5-year PFS (P=0.042). ③ When stratified with IPI score, the high-risk group treated with auto-HSCT (26 cases) showed similar 5-years PFS and 5-years OS to those in the low-risk group with chemotherapy alone (12 cases were in R-CHOP group and 8 cases were in dose-intensive chemotherapy group) [5-years PFS were (62.3 ±14.3)%, (58.3 ±18.6)% and (51.4±18.7)%, respectively, P=0.686; 5-years OS were (69.2±13.9)%, (62.5±15.5)% and (58.3±18.6)%, respectively, P=0.592]. ④However, the high-risk group treated with auto-HSCT (26 cases) showed superior 5-years PFS (P=0.002) and 5-years OS (P=0.019) compared to the high-risk group with chemotherapy alone (20 cases were in R-CHOP group and 17 cases were in dose-intensive chemotherapy group) [5-years PFS were (62.3±14.3)%, (41.1±13.5)% and (21.9±11.6)%, respectively; 5-years OS were (69.2±13.9)%, (51.5%±14.0)% and (35.4±13.6)%, respectively]. ⑤In the univariate analysis, as a whole, patients diagnosed with GCB subtype had higher 3-years PFS (P=0.022) and 3-years OS (P=0.037) compared to non-GCB subtype patients; in subgroup analysis, patients diagnosed with GCB subtype had higher 3-years PFS and 3-years OS compared to non-GCB subtype both in R-CHOP group (P=0.030, P=0.041) and dose-intensive chemotherapy group (P=0.044, P=0.047), but not in auto-HSCT group (P=0.199, P=0.093). ⑥In the multivariate analysis, different molecular classification (GCB/non-GCB) was an independent predictor for PFS and OS both in R-CHOP group [HR=0.274 (95% CI 0.094-0.800), P=0.018; HR=0.408 (95% CI 0.164-1.015), P=0.045] and dose-intensive chemotherapy group [HR=0.423 (95% CI 0.043-1.152), P=0.048; HR=5.758 (95% CI 0.882-6.592), P=0.035]. However, there was no significant difference in PFS and OS for auto-HSCT group between GCB/non-GCB patients. Conclusion: Induction chemotherapy followed by up-front auto-HSCT has significant effect on efficacy for young and untreated patients with high risk DLBCL. Combined with induction chemotherapy followed by up-front auto-HSCT could improve the prognosis of non-GCB patients.

[Accuracy analysis of computer assisted navigation for condylectomy via intraoral approach]

OBJECTIVE

To explore the application accuracy of virtual preoperative plan after the condylectomy via intraoral approach under computer assisted surgical navigation, and to analyze the location and cause of the surgical deviation to provide reference for the surgical procedure improvement in the future.

METHODS

In the study, 23 cases with condylar hypertrophy (11 with condylar osteochondroma and 12 with condylar benign hypertrophy) in Department of Oral and Maxilloficial Surgery, Peking University School and Hospital of Atomatology from December 2012 to December 2016 were treated by condylectomy via intraoral approach under computer assisted surgical navigation. The patient's spiral CT data were imported into ProPlan software before operation, and the affected mandibular ramus was reconstructed three-dimensionally. The condylar osteotomy line was designed according to the lesion range, and the preoperative design model was generated and introduced into the BrainLab navigation system. Under the guidance of computer navigation, the intraoral approach was used to complete the condylar resection according to the preoperative design of the osteotomy line. Cranial spiral CT of the craniofacial region was taken within one week after operation. three-dimensional reconstruction of the mandibular ramus at the condylectomy side was performed, and the condylar section was divided into six segments (anterolateral, anterior, anteromedial, posteromedial, posterior, and posterolateral) and the corresponding regional measurement points P1 to P6 were defined. Then the preoperative virtual model and the postoperative actual model were matched by Geomagic studio 12.0 to compare the differences and to analyze the accuracy of the operation.

RESULTS

All the patients had successfully accomplished the operation and obtained satisfactory results. Postoperative CT showed that the condyle lesion was completely resected, and the condylar osteotomy line was basically consistent with the surgical design. No tumor recurrence or temporomandibular joint ankylosis during the follow-up period. The postoperative accuracy analysis of the condylar resection showed that the confidence intervals measured by the six groups of P1 to P6 were (-2.26 mm, -1.89 mm), (-2.30 mm, -1.45 mm), (-3.37 mm, -2.91 mm), (-2.83 mm, -1.75 mm), (-1.13 mm, 0.99 mm), and(-1.17 mm, 0.17 mm), where P3 group was different from the other 5 groups. There was no significant difference between the P5 and P6 groups and the difference between the other four groups was statistically significant.

CONCLUSION

Under the guidance of computer navigation, the intraoral approach can be performed more accurately. The surgical deviation of each part of the osteotomy surface is mainly due to excessive resection. The anterior medial area of the anterior medial condyle represents the most excessive resection. The posterior and posterior lateral measurement points represent the posterior condylar area. The average deviation is not large, but the fluctuation of the deviation value is larger than that of the other four groups. The accuracy of computer-assisted subtotal resection has yet to be improved.

Contrasting Bonding-Interaction-Induced Distinct Relaxation in La65Ni35 and La65Al35 Glass-Forming Alloys

The α and β relaxations are two fundamental processes in glass-forming materials, and quite important for many of the properties. Although intensive studies have found that α and β relaxations can be tuned by changing the constituent elements, the underlying structural basis is still elusive. Here, we explored the effect of two key elements of Al and Ni on distinct β and α relaxations in La₆₅Al₃₅ and La₆₅Ni₃₅ glass-forming alloys via classical and ab initio molecular dynamics simulations combined with dynamical mechanical spectroscopy. Unexpected coupling of relaxation in both β and α relaxation time scales is observed for La and Al atoms in the La₆₅Al₃₅ system, which drastically suppresses the relaxation dynamics. It is revealed that the dynamic coupling of La and Al results from the covalent-like bonding interaction between Al atoms, which connect Al together, forming a network-like structure. The bonding network not only drastically slows down the dynamics of Al but also couples the motion of La and Al together. This finding elucidates the underlying basis of Al and Ni elements for distinct β and α relaxation and sheds light on tuning the formation and properties of metallic glasses by minor alloying.

[MiR-222-3р Regulates the Proliferation and Differentiation of C2C12 Myoblasts by Targeting BTG2]

MiR-222-3р has been implicated in tumor cell proliferation and has an important role in the differentiation and maturation of myogenic cells. However, its role in skeletal myoblast proliferation is still unclear. In this study, we found that miR-222-3р expression increases initially and then decreases during C2C12 myoblast proliferation. Using synthetic miRNA mimics and inhibitors in gain- or loss-of-function experiments, we snowed that miR-222-3р overexpression in C2C12 cells promotes myoblast proliferation and represses myofiber formation, while miR-222-3р downregulation has the opposite effect. Using a prediction program, BTG2 was identified as a possible target gene of miR-222-3р. During myogenesis, miR-222-3р mimics repress BTG2 expression, while miR-222-3р inhibitors promote BTG2 expression. Using dual-luciferase reporter assay, we further demonstrated that miR-222-3р specifically targets BTG2. Additionally, we show that siRNA-mediated downregulation of BTG2 expression in C2C12 myoblasts promotes the proliferation and suppresses differentiation. In conclusion, we provide a novel insight into the mechanism by which miR-222-3р regulates the proliferation and differentiation of C2C12 myoblasts by targeting BTG2. This information contributes to our understanding of the role of miRNAs in skeletal muscle development.

The Eukaryotic Proteome Is Shaped by E3 Ubiquitin Ligases Targeting C-Terminal Degrons

Degrons are minimal elements that mediate the interaction of proteins with degradation machineries to promote proteolysis. Despite their central role in proteostasis, the number of known degrons remains small, and a facile technology to characterize them is lacking. Using a strategy combining global protein stability (GPS) profiling with a synthetic human peptidome, we identify thousands of peptides containing degron activity. Employing CRISPR screening, we establish that the stability of many proteins is regulated through degrons located at their C terminus. We characterize eight Cullin-RING E3 ubiquitin ligase (CRL) complex adaptors that regulate C-terminal degrons, including six CRL2 and two CRL4 complexes, and computationally implicate multiple non-CRLs in end recognition. Proteome analysis revealed that the C termini of eukaryotic proteins are depleted for C-terminal degrons, suggesting an E3-ligase-dependent modulation of proteome composition. Thus, we propose that a series of "C-end rules" operate to govern protein stability and shape the eukaryotic proteome.

Profound Tissue Specificity in Proliferation Control Underlies Cancer Drivers and Aneuploidy Patterns

Genomics has provided a detailed structural description of the cancer genome. Identifying oncogenic drivers that work primarily through dosage changes is a current challenge. Unrestrained proliferation is a critical hallmark of cancer. We constructed modular, barcoded libraries of human open reading frames (ORFs) and performed screens for proliferation regulators in multiple cell types. Approximately 10% of genes regulate proliferation, with most performing in an unexpectedly highly tissue-specific manner. Proliferation drivers in a given cell type showed specific enrichment in somatic copy number changes (SCNAs) from cognate tumors and helped predict aneuploidy patterns in those tumors, implying that tissue-type-specific genetic network architectures underlie SCNA and driver selection in different cancers. In vivo screening confirmed these results. We report a substantial contribution to the catalog of SCNA-associated cancer drivers, identifying 147 amplified and 107 deleted genes as potential drivers, and derive insights about the genetic network architecture of aneuploidy in tumors.

A Role for Mitochondrial Translation in Promotion of Viability in K-Ras Mutant Cells

Activating mutations in the KRAS oncogene are highly prevalent in tumors, especially those of the colon, lung, and pancreas. To better understand the genetic dependencies that K-Ras mutant cells rely upon for their growth, we employed whole-genome CRISPR loss-of-function screens in two isogenic pairs of cell lines. Since loss of essential genes is uniformly toxic in CRISPR-based screens, we also developed a small hairpin RNA (shRNA) library targeting essential genes. These approaches uncovered a large set of proteins whose loss results in the selective reduction of K-Ras mutant cell growth. Pathway analysis revealed that many of these genes function in the mitochondria. For validation, we generated isogenic pairs of cell lines using CRISPR-based genome engineering, which confirmed the dependency of K-Ras mutant cells on these mitochondrial pathways. Finally, we found that mitochondrial inhibitors reduce the growth of K-Ras mutant tumors in vivo, aiding in the advancement of strategies to target K-Ras-driven malignancy.

Structural and dynamical characteristics of flow units in metallic glasses

The metallic glasses (MGs) are conjectured to be heterogeneous—their microscopic structures are embedded with localized, soft and loosely packed atomic regions, which are termed as flow units (FUs). Detailed knowledges on the structure and dynamical features of FUs are essential for understanding the plasticity of MGs. In our study, by performing dynamical tests on MGs in molecular dynamics simulations, we show that mechanical hysteretic loops are formed in the strain-stress curves due to the undergoing plastic events. By analyzing the activated times of each atom in different dynamical tests, we map the exact locations of FUs and the distribution of their activation probability in the initial structure of MGs. More importantly, we demonstrate that the FUs are indeed liquid-like according to the Lindemann criterion of melting.

Machine Learning Approach for Prediction and Understanding of Glass-Forming Ability

The prediction of the glass-forming ability (GFA) by varying the composition of alloys is a challenging problem in glass physics, as well as a problem for industry, with enormous financial ramifications. Although different empirical guides for the prediction of GFA were established over decades, a comprehensive model or approach that is able to deal with as many variables as possible simultaneously for efficiently predicting good glass formers is still highly desirable. Here, by applying the support vector classification method, we develop models for predicting the GFA of binary metallic alloys from random compositions. The effect of different input descriptors on GFA were evaluated, and the best prediction model was selected, which shows that the information related to liquidus temperatures plays a key role in the GFA of alloys. On the basis of this model, good glass formers can be predicted with high efficiency. The prediction efficiency can be further enhanced by improving larger database and refined input descriptor selection. Our findings suggest that machine learning is very powerful and efficient and has great potential for discovering new metallic glasses with good GFA.

Functional genomics reveals that tumors with activating phosphoinositide 3-kinase mutations are dependent on accelerated protein turnover

Davoli et al. identified ribosomal protein translation and proteasomal protein degradation as critical nononcogene dependencies for PI3K-driven tumors. Their results suggest that disruption of protein turnover homeostasis via ribosome or proteasome inhibition may be a novel treatment strategy for PI3K mutant human tumors.

Activating mutations in the phosphoinositide 3-kinase (PI3K) signaling pathway are frequently identified in cancer. To identify pathways that support PI3K oncogenesis, we performed a genome-wide RNAi screen in isogenic cell lines harboring wild-type or mutant PIK3CA to search for PI3K synthetic-lethal (SL) genes. A combined analysis of these results with a meta-analysis of two other large-scale RNAi screening data sets in PI3K mutant cancer cell lines converged on ribosomal protein translation and proteasomal protein degradation as critical nononcogene dependencies for PI3K-driven tumors. Genetic or pharmacologic inhibition of either pathway alone, but not together, selectively killed PI3K mutant tumor cells in an mTOR-dependent manner. The expression of ribosomal and proteasomal components was significantly up-regulated in primary human colorectal tumors harboring PI3K pathway activation. Importantly, a PI3K SL gene signature containing the top hits of the SL genes identified in our meta-analysis robustly predicted overall patient survival in colorectal cancer, especially among patients with tumors with an activated PI3K pathway. These results suggest that disruption of protein turnover homeostasis via ribosome or proteasome inhibition may be a novel treatment strategy for PI3K mutant human tumors.

[Feasibility and effectiveness of percutaneous ventricular septal defect closure under solely guidance of echocardiography]

Objective: To compare the efficacy and safety of percutaneous ventricular septal defect (VSD) closure under solely guidance of echocardiography and fluoroscopy. Methods: The retrospective study was conducted at Fuwai Hospital, between February 2014 and February 2015. The patients were divided into two groups. VSD closure was conducted in 42 patients under solely guidance of echocardiography, and 100 patients who were treated with percutaneous catheter closure under fluoroscopy guidance were selected as a control group. The baseline characteristics, procedural time and complications were recorded and assessed. Results: There were no significant differences in terms of age, gender and pre-operative echocardiographic characteristics (all P>0.05). Percutaneous VSD closure under traditional fluoroscopy guidance was successful in 95 patients (95%). The procedural time was (54.7±12.5) minutes. The symmetrical occluders diameter was (6.9±1.8) mm. Four patients had postoperative residual shunt, one patient developed left bundle branch block, and 6 patients developed new tricuspid regurgitation. Percutaneous VSD closure under only transthoracic echocardiography (TTE) guidance was successful in 39 patients (93%). Because of delivery catheter passage failure through the defect, one case required conversion to perventricular closure via a small transthoracic incision under transesophageal echocardiography (TEE) guidance. The other two cases underwent surgical repair because of residual shunt with more than 2 mm after closure. The procedural time was (40.3±13.2) minutes. The symmetrical occluders diameter was (6.5±1.2) mm. Four patients had postoperative residual shunt that disappeared after 1 month follow-up, and one patient developed right bundle branch block which disappeared 3 days later. During (9.3±3.6) months follow-up, there were no other complications, such as pericardial effusion, occluder malposition, atrioventricular block, aortic valve regurgitation, and aggravating tricuspid regurgitation in each group. However, the total operation time, diameter of VSD occluder, total mild complications, and the equipment cost in the study group were less than that in the control group (P<0.05). Conclusion: Percutaneous VSD closure can be successfully performed under sole guidance of echocardiography with outcomes similar to those achieved with fluoroscopy guidance.

Mechanical Relaxation-to-Rejuvenation Transition in a Zr-based Bulk Metallic Glass

The relaxation of amorphous materials, i.e., aging, would largely endanger their performances in service. Here we report a mechanical relaxation-to-rejuvenation transition of a Zr35Ti30Be27.5Cu7.5 bulk metallic glass (BMG) in elastostatic compression at ambient temperature, thus provide an accessible way to tailor the mechanical properties of amorphous materials. To unravel the structural evolution underlying the observed transition, atomistic simulations parallel with the experimental tests on a typical model glass system Zr60Cu40 were performed, which successfully reproduced and thus upheld the experimentally observed mechanical relaxation-to-rejuvenation transition. The variations of coordination number and atomic volume during the transition are evaluated to indicate a de-mixing tendency of the constituent atoms in the rejuvenation stage. This de-mixing tendency largely explains the difference between mechanical rejuvenation and thermal rejuvenation and reveals a competitive relationship between activation enthalpy and activation entropy in the stress-driven temperature-assisted atomic dynamics of BMG, such as diffusion and plastic deformation etc.

[Clinical possibility of low ligation of inferior mesenteric artery and lymph nodes dissection in laparoscopic low anterior resection]

OBJECTIVE

To investigate the clinical possibility of low ligation of inferior mesenteric artery (IMA) and lymph nodes dissection in laparoscopic low anterior resection.

METHODS

Data was collected retrospectively from 216 patients who underwent laparoscopic low anterior resection in our hospital from June 2011 to January 2015.Patients were divided into control group (132 cases) and observation group (84 cases). The observation group was treated with low ligation of IMA and lymph nodes dissection, and the control group was cured by high ligation of IMA and lymph nodes dissection. We analyzed the operation time, the number of lymph nodes dissection, the number of lymph nodes removed around the root of IMA, the rate of lymph node metastasis around the root of IMA, the incidence of anastomotic leakage and the ventilation time after the operation.

RESULTS

There was no significant difference between the two group in the pre-operative data, operation time, the number of lymph nodes dissection the number of lymph nodes removed around the root of IMA, the rate of lymph node metastasis around the root of IMA and the incidence of anastomotic leakage (P>0.05). The observation group were significantly better than the control group the in the ventilation time after the operation (P<0.05). The follow up time was 12 to 67 months. The median follow up time was 37 months. One patient in observation group died of cardiovascular disease. One patient in control group died of metastatic carcinoma.

CONCLUSION

Detection of low ligation of inferior mesenteric artery and lymph nodes dissection in laparoscopic low anterior resection is safe and practicable, which should be widely applied.

A genetic interaction analysis identifies cancer drivers that modify EGFR dependency

In this study, Liao et al. comprehensively investigated how cancer drivers genetically interact. They searched for modifiers of EGFR dependency by performing CRISPR, shRNA, and expression screens in a NSCLC model, and their data provide strong support for the hypothesis that many cancer drivers can substitute for each other in certain contexts.

A large number of cancer drivers have been identified through tumor sequencing efforts, but how they interact and the degree to which they can substitute for each other have not been systematically explored. To comprehensively investigate how cancer drivers genetically interact, we searched for modifiers of epidermal growth factor receptor (EGFR) dependency by performing CRISPR, shRNA, and expression screens in a non-small cell lung cancer (NSCLC) model. We elucidated a broad spectrum of tumor suppressor genes (TSGs) and oncogenes (OGs) that can genetically modify proliferation and survival of cancer cells when EGFR signaling is altered. These include genes already known to mediate EGFR inhibitor resistance as well as many TSGs not previously connected to EGFR and whose biological functions in tumorigenesis are not well understood. We show that mutation of PBRM1, a subunit of the SWI/SNF complex, attenuates the effects of EGFR inhibition in part by sustaining AKT signaling. We also show that mutation of Capicua (CIC), a transcriptional repressor, suppresses the effects of EGFR inhibition by partially restoring the EGFR-promoted gene expression program, including the sustained expression of Ets transcription factors such as ETV1. Together, our data provide strong support for the hypothesis that many cancer drivers can substitute for each other in certain contexts and broaden our understanding of EGFR regulation.

Effects of atomic interaction stiffness on low-temperature relaxation of amorphous solids

While low-temperature relaxations show significant differences among metallic glasses with different compositions, the underlying mechanism remains mysterious. Using molecular dynamics simulation, low-temperature relaxation of amorphous solids is investigated in model systems with different atomic interaction stiffness. It was found that as the interaction stiffness increases, the low-temperature relaxation is enhanced. The fraction of mobile atoms increases with increasing interaction stiffness, while the length scale of dynamical heterogeneity does not change. The enhanced relaxation may be due to increased dynamical heterogeneity. These findings provide a physical picture for better understanding the origin of low-temperature relaxation dynamics in amorphous solids, and the experimentally observed different β-relaxation behaviors in various metallic glasses.

Developmental methylation pattern regulates porcine GPR120 expression

DNA methylation is an important component of the epigenetic machinery and plays a critical role in transcriptional regulation. It mostly occurs in CpG abundant regions, known as CpG islands (CGIs). G protein-coupled receptor 120 (GPR120) functions as an omega-3 fatty acid receptor and is involved in multiple-biological processes, including lipogenesis. Herein, we show that GPR120 is highly expressed in porcine mature adipose tissue and is positively associated with adipose tissue development (r = 0.86, P < 0.01). We also predicted 5 CGIs across the GPR120 genomic sequence and investigated their methylation status using the MassArray approach. Our results show that these CGIs exhibit significantly different methylation states (P(CGI) < 0.01), and that the DNA methylation of GPR120 5ꞌ-untranslated and first exon regions can negatively regulate its expression levels. This study will aid further investigations on the epigenetic mechanism regulating GPR120 expression.

Effects of muscle fiber type on glycolytic potential and meat quality traits in different Tibetan pig muscles and their association with glycolysis-related gene expression

The myosin heavy chain (MyHC) composition, glycolytic potential, mitochondrial content, and gene expression related to energy metabolism were analyzed in eight muscles from Tibetan pigs, to study how meat quality develops in different muscle tissues. The muscles were classified into three clusters, based on MyHC composition: masseter, trapezius, and latissimus dorsi as 'slow-oxidative-type'; psoas major and semimembranosus as 'intermediate-type'; and longissimus dorsi, obliquus externus abdominis, and semitendinosus as 'fast-glycolytic-type'. The 'slow-oxidative-type' muscles had the highest MyHC I and MyHC IIA content (P < 0.01); 'intermediate-type' muscles, the highest MyHC IIx content (P < 0.01); and 'fast-glycolytic-type' muscles, the highest MyHC IIb content (P < 0.01). The pH values measured in 'slow-oxidative-type' muscles were higher than those in the other clusters were; however, the color of 'fast-glycolytic-type' muscles was palest (P < 0.01). Mitochondrial content increased in the order: fast-glycolytic-type < intermediate-type < slow-oxidative-type. In the 'slow-oxidative-type' muscles, the expression levels of genes related to ATP synthesis were higher, but were lower for those related to glycogen synthesis and glycolysis. Mitochondrial content was significantly positively correlated with MyHC I content, but negatively correlated with MyHC IIb content. MyHC I and mitochondrial content were both negatively correlated with glycolytic potential. Overall, muscles used frequently in exercise had a higher proportion of type I fibers. 'Slow-oxidative-type' muscles, rich in type I fibers with higher mitochondrial and lower glycogen and glucose contents, had a higher ATP synthesis efficiency and lower glycolytic capacity, which contributed to their superior meat quality.

The DNA damage response induces inflammation and senescence by inhibiting autophagy of GATA4

Cellular senescence is a terminal stress-activated program controlled by the p53 and p16(INK4a) tumor suppressor proteins. A striking feature of senescence is the senescence-associated secretory phenotype (SASP), a pro-inflammatory response linked to tumor promotion and aging. We have identified the transcription factor GATA4 as a senescence and SASP regulator. GATA4 is stabilized in cells undergoing senescence and is required for the SASP. Normally, GATA4 is degraded by p62-mediated selective autophagy, but this regulation is suppressed during senescence, thereby stabilizing GATA4. GATA4 in turn activates the transcription factor NF-κB to initiate the SASP and facilitate senescence. GATA4 activation depends on the DNA damage response regulators ATM and ATR, but not on p53 or p16(INK4a). GATA4 accumulates in multiple tissues, including the aging brain, and could contribute to aging and its associated inflammation.

Viral immunology. Comprehensive serological profiling of human populations using a synthetic human virome

The human virome plays important roles in health and immunity. However, current methods for detecting viral infections and antiviral responses have limited throughput and coverage. Here, we present VirScan, a high-throughput method to comprehensively analyze antiviral antibodies using immunoprecipitation and massively parallel DNA sequencing of a bacteriophage library displaying proteome-wide peptides from all human viruses. We assayed over 10(8) antibody-peptide interactions in 569 humans across four continents, nearly doubling the number of previously established viral epitopes. We detected antibodies to an average of 10 viral species per person and 84 species in at least two individuals. Although rates of specific virus exposure were heterogeneous across populations, antibody responses targeted strongly conserved "public epitopes" for each virus, suggesting that they may elicit highly similar antibodies. VirScan is a powerful approach for studying interactions between the virome and the immune system.

Effectiveness of microsatellite and single nucleotide polymorphism markers for parentage analysis in European domestic pigs

Parentage analysis and individual identification are recent, promising methods that have been applied to evolutionary and ecological studies, as well as conservation management. Parental exclusion relying on polymorphic microsatellites has been used worldwide in parentage determination, while the low mutation rate and genotyping error rate of single nucleotide polymorphisms (SNPs) make them another important marker for pedigree tracing. Here, we compared the effectiveness of microsatellites and SNP markers in European pigs. We also measured and presented the minimum and optimal criteria for SNP markers to be used in paternity and identity analysis. Our findings may contribute to the development of techniques for future molecular evolution and conservation studies, as well as breeding programs.

Development-related expression patterns of protein-coding and miRNA genes involved in porcine muscle growth

Muscle growth and development is associated with remarkable changes in protein-coding and microRNA (miRNA) gene expression. To determine the expression patterns of genes and miRNAs related to muscle growth and development, we measured the expression levels of 25 protein-coding and 16 miRNA genes in skeletal and cardiac muscles throughout 5 developmental stages by quantitative reverse transcription-polymerase chain reaction. The Short Time-Series Expression Miner (STEM) software clustering results showed that growth-related genes were downregulated at all developmental stages in both the psoas major and longissimus dorsi muscles, indicating their involvement in early developmental stages. Furthermore, genes related to muscle atrophy, such as forkhead box 1 and muscle ring finger, showed unregulated expression with increasing age, suggesting a decrease in protein synthesis during the later stages of skeletal muscle development. We found that development of the cardiac muscle was a complex process in which growth-related genes were highly expressed during embryonic development, but they did not show uniform postnatal expression patterns. Moreover, the expression level of miR-499, which enhances the expression of the β-myosin heavy chain, was significantly different in the psoas major and longissimus dorsi muscles, suggesting the involvement of miR-499 in the determination of skeletal muscle fiber types. We also performed correlation analyses of messenger RNA and miRNA expression. We found negative relationships between miR-486 and forkhead box 1, and miR-133a and serum response factor at all developmental stages, suggesting that forkhead box 1 and serum response factor are potential targets of miR-486 and miR-133a, respectively.

Evolution of atomic rearrangements in deformation in metallic glasses

Atomic rearrangements induced by shear stress are fundamental for understanding deformation mechanisms in metallic glasses (MGs). Using molecular dynamic simulation, the atomic rearrangements characterized by nonaffine displacements (NADs) and their spatial distribution and evolution with tensile stress in Cu50Zr50 MG were investigated. It was found that in the elastic regime the atomic rearrangements with the largest NADs are relatively homogeneous in space, but exhibit strong spatial correlation, become localized and inhomogeneous, and form large clusters as strain increases, which may facilitate the so-called shear transformation zones. Furthermore, initially they prefer to take place around Cu atoms which have more nonicosahedral configurations. As strain increases, the preference decays and disappears in the plastic regime. The atomic rearrangements with the smallest NADs are preferentially located around Cu atoms, too, but with more icosahedral or icosahedral-like atomic configurations. The preference is maintained in the whole deformation process. In contrast, the atomic rearrangements with moderate NADs distribute homogeneously, and do not show explicit preference or spatial correlation, acting as matrix during deformation. Among the atomic rearrangements with different NADs, those with largest and smallest NADs are nearest neighbors initially, but separating with increasing strain, while those with largest and moderate NADs always avoid to each other. The correlations in the fluctuations of the NADs confirm the long-range strain correlation and the scale-free characteristic of NADs in both elastic and plastic deformation, which suggests a universality of the scaling in the plastic flow in MGs.

Abstract IA28: Haploinsufficiency in cancer

Breast cancer is a collection of diseases with distinct clinical behaviors and underlying genetic causes. We have searched genetically for genes that have cancer relevant phenotypes including genes that alter cellular proliferation, cellular transformation, cell survival, cellular senescence, and genes that are essential for the proliferation of cancer cells. We have approached this by the generation of libraries of shRNAs for loss of function experiments and libraries of ORFs for gain of function experiments. We will discuss these technologies and how they can be applied to the functional dissection of genes important for breast cancer. Using these new technologies we have identified new oncogenes and tumor suppressors. We find that tumor cells selectively delete negative growth regulators and suggest that the deletion of clusters of these genes may drive tumorigenesis by haploinsufficiency. These recurrent deletions also avoid deletion of one copy of many essential genes through haploinsufficiency. We put forward the Cancer Gene Island model that postulates that tumors select for hemizygous loss of islands of gene enriched in negative regulators of proliferation and depleted in essential genes to promote tumor cell proliferation through cumulative haploinsufficiency.

Citation Format: Teresa Davoli, Nicole L. Solimini, Natalya N. Pavlova, Qikai Xu, Kristen Mengwasser, Laura M. Sack, Anthony C. Liang, Michael R. Schlabach, Ji Luo, Anna E. Burrows, Anthony N. Anselmo, Mamie Z. Li, Stephen J. Elledge. Haploinsufficiency in cancer. [abstract]. In: Proceedings of the Third AACR International Conference on Frontiers in Basic Cancer Research; Sep 18-22, 2013; National Harbor, MD. Philadelphia (PA): AACR; Cancer Res 2013;73(19 Suppl):Abstract nr IA28.

Carcass and meat quality traits of four commercial pig crossbreeds in China

We evaluated carcass and meat quality traits of two Chinese native crossbreeds Landrace x Meishan (LM) and Duroc x (Landrace x Meishan) (DLM) and two foreign crossbreeds Duroc x (Landrace x Yorkshire) (DLY) and PIC (an imported five-way crossbreed). One hundred and twenty weaned pigs (half castrated males and half females) were reared and slaughtered at a predestinated slaughter age. The general carcass and meat quality traits were measured and analyzed. The DLY and PIC crosses had significantly heavier live weights (93.39 and 96.33 kg, P < 0.01), significantly higher dressing percentages (80.65 and 79.39%, P < 0.05), significantly bigger loin areas (42.69 and 43.91 cm(2), P < 0.001), and significantly more lean carcasses (65.78 and 66.40%, P < 0.001) than LM and DLM. On the other hand, LM had a significantly lower live weight (70.29 kg, P < 0.01), significantly thicker back fat (3.54 cm, P < 0.001), significantly less lean carcasses (46.82%, P < 0.001), and significantly less ham and breech (26.53%, P < 0.05) than the other crossbreeds. Among meat quality parameters, LM had the highest intramuscular fat content (5.02%, P < 0.001) and the smallest fiber area (3126.45 μm(2), P < 0.01). However, PIC showed the lowest pH(1) (5.82, P < 0.01) and pH(2) (5.63, P < 0.01), the highest drip loss (2.89%, P < 0.01), and the lowest intramuscular fat (1.35%, P < 0.001). We concluded that LM and DLM had good meat quality traits but poorer carcass traits than DLY and PIC; DLY had good carcass and meat quality traits; PIC had good carcass traits, but it had less intramuscular fat, lower pH and higher drip loss.

Methylation-sensitive amplification polymorphism analysis of fat and muscle tissues in pigs

DNA methylation may be involved in regulating the expression of protein-coding genes, resulting in different fat and muscle phenotypes. Using a methylation-sensitive amplified polymorphism approach, we obtained 7423 bands by selective amplification of genomic DNA from six different fat depots and two heterogeneous muscle types from Duroc/Landrace/Yorkshire cross-bred pigs. The degrees of DNA methylation, determined by the percentages of hemi- and fully methylated sites relative to the total number of CCGG sites, were similar in male and female pigs for each specific tissue [χ(2) test; P (two-tailed) > 0.05]. Gender bias was therefore ignored. There were significant differences in the degree of DNA methylation among the eight tissue types [χ(2) test; P(total) (two-tailed) = 0.009]. However, similar degrees of methylation were observed among the six fat depots [χ(2) test; P(fat) (two-tailed) = 0.24 > 0.05]and between the two muscle types [χ(2) test; P(muscle) (two-tailed) = 0.76 > 0.05]. We conclude that the degree of DNA methylation differs between porcine fat and muscle tissue, but that the methylation status of a particular tissue type is similar, despite being deposited at different body sites.