Temporal Structures in Electron Spectra and Charge Sign Effects in Galactic Cosmic Rays

We present the precision measurements of 11 years of daily cosmic electron fluxes in the rigidity interval from 1.00 to 41.9 GV based on 2.0×10^{8} electrons collected with the Alpha Magnetic Spectrometer (AMS) aboard the International Space Station. The electron fluxes exhibit variations on multiple timescales. Recurrent electron flux variations with periods of 27 days, 13.5 days, and 9 days are observed. We find that the electron fluxes show distinctly different time variations from the proton fluxes. Remarkably, a hysteresis between the electron flux and the proton flux is observed with a significance of greater than 6σ at rigidities below 8.5 GV. Furthermore, significant structures in the electron-proton hysteresis are observed corresponding to sharp structures in both fluxes. This continuous daily electron data provide unique input to the understanding of the charge sign dependence of cosmic rays over an 11-year solar cycle.

[A case of malignant peritoneal mesothelioma]

Malignant mesothelioma is a highly malignant disease that most often occurs in the pleural cavity, followed by the peritoneum and pericardium. Malignant peritoneal mesothelioma (MPM) accounts for 10%-15% of all mesothelioma. The most important risk factor for MPM is exposure to asbestos. MPM has no specific clinical symptoms, imaging and histopathology are critical for the diagnosis. There are currently no generally accepted guidelines for curative treatment of MPM. The patient mainly presented with abdominal pain, abdominal distension and discomfort. Due to extensive omentum metastasis, no further surgical treatment was performed. Pemetrexed combined with cisplatin chemotherapy was given for 2 cycles, and the patient is still alive.

A 2-Stage Root Analog Implant with Compact Structure, Uniform Roughness, and High Accuracy

Immediate implant placement has the advantages of shortening the operation time, reducing the treatment cycle and cost. At present, this technology has been used widely, but the indications of immediate implantation are still limited. Here, a novel type of root analog implant (RAI) was manufactured by selective laser melting technology to address the limitation. Under optimized condition, RAIs were printed with the internal density of 99.73% and the uniform surface roughness of 11 μm (Sa). Besides, the deviation between RAI specimen and design models is controlled within 0.15 mm after optimizing scanning parameters. The substrate printed could promote human bone marrow stromal cell proliferation, spreading, and osteogenic differentiation. The bone-implant contact (BIC, 75% ± 7%) and bone volume/total volume (BV/TV, 74% ± 7%) of RAIs were significantly higher than that of conventional implants (BIC, 66% ± 5%; BV/TV, 62% ± 5%) in in vivo experiments. Further, customized abutments were designed for the RAIs, improving the masticatory ability of the beagle dogs after crown restoration. This study aims to design a personalized 2-stage RAI with compact structure and uniform roughness, in order to achieve better fracture resistance, initial osseointegration efficiency, and dispersed stress in immediate implantation. It provides a certain guiding value for standardizing the manufacture and clinical application of RAI in immediate implantation.

First-in-human, phase I study of AK109, an anti-VEGFR2 antibody in patients with advanced or metastatic solid tumors

BACKGROUND

Vascular endothelial growth factor receptor 2 (VEGFR2) plays a key role in antiangiogenesis which has been an essential strategy for cancer treatment. We report the first-in-human study of AK109, a novel anti-VEGFR2 monoclonal antibody, to characterize the safety profile and pharmacokinetics/pharmacodynamics (PK/PD) properties, and explore the preliminary antitumor efficacy in patients with solid tumors.

PATIENTS AND METHODS

This was a multicenter, open-label, phase I study, including dose escalation and dose expansion (NCT04547205). Patients with advanced cancers were treated 2 and 3 weekly with escalating doses of AK109. A 3 + 3 design was used to determine the maximum tolerated dose. Blood was sampled for PK/PD analysis. The primary endpoint was safety and recommended phase II dose (RP2D).

RESULTS

A total of 40 patients were enrolled. No dose-limiting toxicity was observed. However, 38 patients reported treatment-related adverse events (TRAEs); grade ≥3 TRAEs occurred in 10 patients. The most common TRAEs were proteinuria (n = 24, 60%), hypertension (n = 13, 32.5%), increased aspartate transaminase (n = 11, 27.5%), thrombopenia (n = 10, 25%), and anemia (n = 10, 25%). A total of 28 patients (70%) reported adverse events of special interest (AESIs). The most common AESIs were proteinuria (60%), hypertension (32.5%), and hemorrhage (32.5%), mainly including gum bleeding and urethrorrhagia. AK109 exhibited an approximately linear PK exposure with dose escalation at 2-12 mg/kg. PD analyses showed rapid target engagement. Among the 40 patients, 4 achieved partial response and 21 achieved stable disease with an objective response rate of 10% and a disease control rate of 62.5%. Based on the safety profile, the PK/PD profile, and preliminary antitumor activities, 12 mg/kg Q2W and 15 mg/kg Q3W were selected as RP2D.

CONCLUSIONS

AK109 showed manageable safety profile and promising antitumor activity, supporting further clinical development in a large population.

[Association between urinary arsenic level and serum testosterone in Chinese men aged 18 to 79 years]

Objective: To investigate the association between the urinary arsenic level and serum total testosterone in Chinese men aged 18 to 79 years. Methods: A total of 5 048 male participants aged 18 to 79 years were recruited from the China National Human Biomonitoring (CNHBM) from 2017 to 2018. Questionnaires and physical examinations were used to collect information on demographic characteristics, lifestyle, food intake frequency and health status. Venous blood and urine samples were collected to detect the level of serum total testosterone, urine arsenic and urine creatinine. Participants were divided into three groups (low, middle, and high) based on the tertiles of creatinine-adjusted urine arsenic concentration. Weighted multiple linear regression was fitted to analyze the association of urinary arsenic with serum total testosterone. Results: The weighted average age of 5 048 Chinese men was (46.72±0.40) years. Geometric mean concentration (95%CI) of urinary arsenic, creatinine-adjusted urine arsenic and serum testosterone was 22.46 (20.08, 25.12) μg/L, 19.36 (16.92, 22.15) μg/L and 18.13 (17.42, 18.85) nmol/L, respectively. After controlling for covariates, compared with the low-level urinary arsenic group, the testosterone level of the participants in the middle-level group and the high-level group decreased gradually. The percentile ratio (95%CI) was -5.17% (-13.14%, 3.54%) and -10.33% (-15.68%, -4.63). The subgroup analysis showed that the association between the urinary arsenic level and testosterone level was more obvious in the group with BMI<24 kg/m² group (P_interaction<0.05). Conclusion: There is a negative association between the urinary arsenic level and serum total testosterone in Chinese men aged 18-79 years.

Measurement of Sequential ϒ Suppression in Au+Au Collisions at sqrt[s_{NN}]=200 GeV with the STAR Experiment

We report on measurements of sequential ϒ suppression in Au+Au collisions at sqrt[s_{NN}]=200  GeV with the STAR detector at the Relativistic Heavy Ion Collider (RHIC) through both the dielectron and dimuon decay channels. In the 0%-60% centrality class, the nuclear modification factors (R_{AA}), which quantify the level of yield suppression in heavy-ion collisions compared to p+p collisions, for ϒ(1S) and ϒ(2S) are 0.40±0.03(stat)±0.03(sys)±0.09(norm) and 0.26±0.08(stat)±0.02(sys)±0.06(norm), respectively, while the upper limit of the ϒ(3S) R_{AA} is 0.17 at a 95% confidence level. This provides experimental evidence that the ϒ(3S) is significantly more suppressed than the ϒ(1S) at RHIC. The level of suppression for ϒ(1S) is comparable to that observed at the much higher collision energy at the Large Hadron Collider. These results point to the creation of a medium at RHIC whose temperature is sufficiently high to strongly suppress excited ϒ states.

Beam Energy Dependence of Fifth- and Sixth-Order Net-Proton Number Fluctuations in Au+Au Collisions at RHIC

We report the beam energy and collision centrality dependence of fifth and sixth order cumulants (C_{5}, C_{6}) and factorial cumulants (κ_{5}, κ_{6}) of net-proton and proton number distributions, from center-of-mass energy (sqrt[s_{NN}]) 3 GeV to 200 GeV Au+Au collisions at RHIC. Cumulant ratios of net-proton (taken as proxy for net-baryon) distributions generally follow the hierarchy expected from QCD thermodynamics, except for the case of collisions at 3 GeV. The measured values of C_{6}/C_{2} for 0%-40% centrality collisions show progressively negative trend with decreasing energy, while it is positive for the lowest energy studied. These observed negative signs are consistent with QCD calculations (for baryon chemical potential, μ_{B}≤110  MeV) which contains the crossover transition range. In addition, for energies above 7.7 GeV, the measured proton κ_{n}, within uncertainties, does not support the two-component (Poisson+binomial) shape of proton number distributions that would be expected from a first-order phase transition. Taken in combination, the hyperorder proton number fluctuations suggest that the structure of QCD matter at high baryon density, μ_{B}∼750  MeV at sqrt[s_{NN}]=3  GeV is starkly different from those at vanishing μ_{B}∼24  MeV at sqrt[s_{NN}]=200  GeV and higher collision energies.

[Observational study on peripapillary hyper-reflective ovoid mass-like structures in children and adolescents with myopia]

Objective: To investigate the correlation of peripapillary hyper-reflective ovoid mass-like structures (PHOMS) in children and adolescents with myopia and its correlation factors. Methods: It was a cross-sectional study. From September 2021 to January 2022, myopic children and adolescents aged 6-16 years treated in Wuhan Central Hospital and Renmin Hospital of Wuhan University with a myopic spherical equivalent (SE) ≥0.5 D were consecutively included. All patients underwent best corrected visual acuity, refraction, intraocular pressure, slit lamp microscope, axial length, fundus photography and enhanced depth imaging optical coherence tomography (EDI-OCT) examination. EDI-OCT optic disc parameter measurements included diameter, degree of tilt and shift and PHOMS height. The patients were divided into PHOMS group and non-PHOMS group according to the presence or absence of PHOMS. According to the height of PHOMS, the patients were further divided into 3 subgroups: large (>400 μm), medium (200-400 μm) and small (<200 μm). The optic disc characteristics of the PHOMS group and the non-PHOMS group and each subgroup were observed, and the correlation factors of PHOMS were analyzed. Mann-Whitney U test, Kruskal-Wallis test, chi-square test, Logistic regression analysis and Kendall's tau-b correlation coefficient were used. Results: A total of 108 patients (108 eyes) were included, including 46 males (46 eyes) and 62 females (62 eyes). There were 70 eyes (64.8%) in the PHOMS group and 38 eyes (35.2%) in the non-PHOMS group. Small PHOMS can only be detected by EDI-OCT, while medium to large PHOMS showed blurred optic disc boundaries on fundoscopy images. Univariate Logistic regression analysis showed that PHOMS was associated with age (OR=1.36, 95%CI: 1.13-1.65, P=0.001) and myopic SE (OR=4.57, 95%CI: 2.51-8.32, P<0.001), axial length (OR=2.28, 95%CI: 1.37-3.82, P=0.002), optic disc tilt (OR=3.44, 95%CI: 2.09-5.66, P<0.001), optic disc shift (OR=0.95, 95%CI: 0.93-0.98, P<0.001) and optic disc diameter (OR=0.75, 95%CI: 0.58-0.95, P=0.019). Multivariate Logistic regression analysis showed that the higher the myopic SE (OR=3.01, 95%CI: 1.27-7.17, P=0.013) and the greater the tilt of the optic disc (OR=4.06,95%CI:1.99-8.29,P<0.001), the higher the risk of PHOMS. Kendall's tau-b correlation coefficient analysis showed that the height of PHOMS was negatively correlated with optic disc shift (r=-0.31, P<0.001). Conclusions: PHOMS can be found in a subset of myopic children. The fundus manifestations of PHOMS of different heights are slightly different. The large myopic SE and great optic disc tilt are risk factors of PHOMS, and their magnitudes correlate with the border tissue angle.

Integrating genome-wide association studies and population genomics analysis reveals the genetic architecture of growth and backfat traits in pigs

Growth and fat deposition are complex traits, which can affect economical income in the pig industry. Due to the intensive artificial selection, a significant genetic improvement has been observed for growth and fat deposition in pigs. Here, we first investigated genomic-wide association studies (GWAS) and population genomics (e.g., selection signature) to explore the genetic basis of such complex traits in two Large White pig lines (n = 3,727) with the GeneSeek GGP Porcine HD array (n = 50,915 SNPs). Ten genetic variants were identified to be associated with growth and fatness traits in two Large White pig lines from different genetic backgrounds by performing both within-population GWAS and cross-population GWAS analyses. These ten significant loci represented eight candidate genes, i.e., NRG4, BATF3, IRS2, ANO1, ANO9, RNF152, KCNQ5, and EYA2. One of them, ANO1 gene was simultaneously identified for both two lines in BF100 trait. Compared to single-population GWAS, cross-population GWAS was less effective for identifying SNPs with population-specific effect, but more powerful for detecting SNPs with population-shared effects. We further detected genomic regions specifically selected in each of two populations, but did not observe a significant enrichment for the heritability of growth and backfat traits in such regions. In summary, the candidate genes will provide an insight into the understanding of the genetic architecture of growth-related traits and backfat thickness, and may have a potential use in the genomic breeding programs in pigs.

[Association of lead exposure with stunting and underweight among children aged 3-5 years in China]

Objective: To evaluate the association of lead exposure with stunting and underweight among children aged 3-5 years in China. Methods: Data was collected from China National Human Biomonitoring (CNHBM) between January 2017 and December 2018. A total of 3 554 children aged 3-5 years were included. Demographic characteristic, lifestyle and nutritional status were collected through questionnaires. Height and weight were measured by standardized method. Stunting and underweight status were determined by calculating height for age Z-score and weight for age Z-score. Blood and urine samples were collected to detect the concentrations of blood lead, urinary lead and urinary creatinine. Children were stratified into 4 groups (Q₁ to Q₄) by quartiles of blood lead level and corrected urinary lead level, respectively. Complex sampling logistic regression models were applied to evaluate the association of the blood lead level, urinary lead level with stunting and underweight. Results: Among 3 554 children, the age was (4.09±1.06) years, of which 1 779 (80.64%) were female and 1 948 (55.84%) were urban residents. The prevalence of stunting and wasting was 7.34% and 2.96%, respectively. The M (Q₁, Q₃) for blood lead levels and urinary lead levels in children was 17.49 (12.80, 24.71) μg/L, 1.20 (0.61, 2.14) μg/g Cr, respectively. After adjusting for confounding factors, compared with the lowest blood lead concentration group Q₁, the risk of stunting gradually increased in the Q₃ and Q₄ group (P_trend=0.010), with OR (95%CI) values of 1.40 (0.80-2.46) and 1.80 (1.07-3.04), respectively. Compared with the lowest urinary lead concentration group Q₁, the risk of stunting still increased in the Q₃ and Q₄ group (P_trend=0.012), with OR (95%CI) values of 1.69 (1.01-2.84) and 1.79 (1.05-3.06), respectively. The correlation between the lead exposure and underweight was not statistically significant (P>0.05). Conclusion: Lead exposure is positively associated with the risk of stunting among children aged 3-5 years in China.

[Association of body mass index and waist circumference with frailty among people aged 80 years and older in Chinese]

Objective: To examine the association of body mass index (BMI) and waist circumference (WC) with frailty among oldest-old adults in China. Methods: A total of 7 987 people aged 80 years and older (oldest-old) who participated in the Chinese Longitudinal Healthy Longevity Survey (CLHLS) in 2017-2018 were included. Information on demographic characteristics, behavior pattern, diet, activities of daily living, cognitive function, health status, disease condition were collected by questionnaire and physical examination. Generalized linear mixed model and restricted cubic splines (RCS) were used to analyze the association of BMI and WC with frailty. Results: The mean age of all participants was 91.7 years, and their mean BMI and WC were (21.3±3.5) kg/m² and (82.9±10.5) cm, respectively. The proportion of male was 42.3% (3 377/7 987), and the proportion of people with frailty was 33.7% (2 664/7 987). After controlling confounding factors, compared with T₂ (19.1-22.1 kg/m²) of BMI, the OR (95%CI) of the female T₁ (<19.1 kg/m²) and T₃ (≥22.2 kg/m²) group was 1.39 (1.17-1.65) and 1.27 (1.07-1.52), respectively. Compared with T₂ (77-85 cm) of WC, the OR (95%CI) of female T₁ (<77 cm) and T₃ (≥86 cm) group was 1.20 (1.01-1.42) and 1.10 (0.93-1.31), respectively. The results of multiple linear regression model with restrictive cubic spline showed that there was a non-linear association of BMI and WC with frailty in female. Conclusion: There is a U-shaped association of BMI and WC with frailty in female participants.

[Mediation effect of inflammatory biomarkers on the association between blood lead levels and blood pressure changes in Chinese adults]

Objective: To investigate the role of inflammatory biomarkers in the relationship between blood lead levels and blood pressure changes. Methods: A total of 9 910 people aged 18-79 years who participated in the China National Human Biomonitoring in 2017-2018 were included in this study. A self-made questionnaire was used to collect demographic characteristics, lifestyle and other information, and the data including height, weight and blood pressure were determined through physical examination. Blood and urinary samples were collected for the detection of blood lead and cadmium levels, urinary arsenic levels, white blood cells, neutrophils, lymphocytes, and hypersensitive C-reactive protein (hs-CRP). Weighted linear regression models were used to evaluate the associations between blood lead, inflammatory biomarkers and blood pressure. Mediation analysis was performed to investigate the role of inflammation in the relationship between blood lead levels and blood pressure changes. Results: The median (Q₁, Q₃) age of all participants was 45.4 (33.8, 58.4)years, including 4 984 males accounting for 50.3%. Multivariate logistic regression model analysis showed that after adjusting for age, gender, residence area, BMI, education level, smoking and drinking status, family history of hypertension, consumption frequency of rice, vegetables, and red meat, fasting blood glucose, total cholesterol, triglycerides, blood cadmium and urinary arsenic levels, there was a positive association between blood lead levels, inflammatory biomarkers and blood pressure (P<0.05). Each 2.71 μg/L (log-transformed) increase of the lead was associated with a 2.05 (95%CI: 0.58, 3.53) mmHg elevation in systolic blood pressure (SBP), 2.24 (95%CI: 1.34, 3.14) mmHg elevation in diastolic blood pressure (DBP), 0.25 (95%CI: 0.05, 0.46) mg/L elevation in hs-CRP, 0.16 (95%CI: 0.03, 0.29)×10⁹/L elevation in white blood cells, and 0.11 (95%CI: 0.02, 0.21)×10⁹/L elevation in lymphocytes, respectively. Mediation analysis showed that the levels of hs-CRP significantly mediated the association of blood lead with SBP, with a proportion about 3.88% (95%CI: 0.45%, 7.32%). The analysis also found that the levels of hs-CRP and neutrophils significantly mediated the association of blood lead with SBP, with a proportion about 4.10% (95%CI: 1.11%, 7.10%) and 2.42% (95%CI: 0.07%, 4.76%), respectively. Conclusion: This study suggests that inflammatory biomarkers could significantly mediate the association of blood lead levels and blood pressure changes.

GWAS of Reproductive Traits in Large White Pigs on Chip and Imputed Whole-Genome Sequencing Data

Total number born (TNB), number of stillborn (NSB), and gestation length (GL) are economically important traits in pig production, and disentangling the molecular mechanisms associated with traits can provide valuable insights into their genetic structure. Genotype imputation can be used as a practical tool to improve the marker density of single-nucleotide polymorphism (SNP) chips based on sequence data, thereby dramatically improving the power of genome-wide association studies (GWAS). In this study, we applied Beagle software to impute the 50 K chip data to the whole-genome sequencing (WGS) data with average imputation accuracy (R2) of 0.876. The target pigs, 2655 Large White pigs introduced from Canadian and French lines, were genotyped by a GeneSeek Porcine 50K chip. The 30 Large White reference pigs were the key ancestral individuals sequenced by whole-genome resequencing. To avoid population stratification, we identified genetic variants associated with reproductive traits by performing within-population GWAS and cross-population meta-analyses with data before and after imputation. Finally, several genes were detected and regarded as potential candidate genes for each of the traits: for the TNB trait: NOTCH2, KLF3, PLXDC2, NDUFV1, TLR10, CDC14A, EPC2, ORC4, ACVR2A, and GSC; for the NSB trait: NUB1, TGFBR3, ZDHHC14, FGF14, BAIAP2L1, EVI5, TAF1B, and BCAR3; for the GL trait: PPP2R2B, AMBP, MALRD1, HOXA11, and BICC1. In conclusion, expanding the size of the reference population and finding an optimal imputation strategy to ensure that more loci are obtained for GWAS under high imputation accuracy will contribute to the identification of causal mutations in pig breeding.

Integrative Analysis of Liver Metabolomics and Transcriptomics Reveals Oxidative Stress in Piglets with Intrauterine Growth Restriction

The correlation between oxidative stress and liver metabolic dysfunction in piglets with intrauterine growth restriction (IUGR) remains limited. Therefore, the objective of the present study was to investigate potential mechanisms of metabolic characteristics induced by oxidative stress in the livers of IUGR piglets using metabolomic and transcriptomic analysis. Analysis of the phenotypic characteristics showed that the liver weight of the intrauterine growth restriction piglets was significantly lower than that of normal birth weight piglets. Intrauterine growth restriction piglets exhibited disordered hepatic cord arrangement and vacuolization as well as excessive lipid accumulation in hepatocytes. In addition, the activities of antioxidant enzymes were significantly decreased in the liver of the intrauterine growth restriction piglets, whereas the level of the lipid peroxidation marker MDA was significantly increased. Finally, our findings revealed that intrauterine growth restriction piglets were involved in a variety of metabolic abnormalities, including mitochondrial dysfunction, imbalance of fatty acid composition, disruption to sources of one-carbon unit supply, and abnormal galactose conversion, which may be responsible for oxidative stress in the liver. In summary, these data provided a detailed theoretical reference for revealing the hepatic metabolic characteristics of intrauterine growth restriction piglets.

[Improvement effect of Lycium barbarum polysaccharide on the intestinal flora of pregnant rats and their offspring under chronic stress]

Objective: To understand the improvement effect of Lycium barbarum polysaccharide (LBP) on the intestinal flora of mother mice during pregnancy and their offspring who experienced chronic stress, and provide new ideas for improving the effect of stress on the intestinal tract. Methods: From July to October 2019, 24 SPF-grade female SD rats were selected and divided into control group, stress group, and stress+LBP group, with 8 rats in each group. A chronic unpredictable mild stimulation model during pregnancy was established (21 days) , and 40 mg/kg LBP solution was administered by gavage on the 8th day of stress. Venous blood from the medial canthus of the female mice was collected on the 1st day before stress and on the 1st, 7th, 14th and 21st days, respectively. Cortisol was measured and corticosterone concentration was calculated. The fresh feces of famale mice after stress and 20-day postnatal offspring mice were collected, and Illumina Miseq sequencing technology, alpha diversity and community composition were used to analyze the diversity and structure of intestinal flora. Results: On the 7th and 14th days of stress, the plasma corticosterone concentration of female mice in the stress group and stress+LBP group was higher than that in the control group (P<0.05) . In the Alpha diversity of female mice, the Ace index of the stress group was lower than that of the control group (P<0.05) . The analysis of intestinal flora structure showed that at the species level, the proportions of Lachnospiraceae and Lactobacillus in the stress+LBP group were higher than those in the stress group and control group. At the order level, the proportion of Clostridiales in the stress+LBP group was higher than that in the stress group and lower than that in the control group, while the proportion of Lactobacillales was higher than that in the stress group and control group. In the Alpha diversity of the offspring group, the Shannon index, Ace index and Chao index of the stress+LBP offspring group were higher than those of the stress offspring group (P<0.05) . The proportion of Lactobacillus in the stress+LBP offspring group was higher than that in the control offspring group and stress offspring group, and the proportions of Lachnospiraceae and Ruminococcaceae in the stress+LBP offspring group were higher than those in the stress offspring group, the proportion of Bacteroidales in the stress+LBP offspring group was lower than that in the stress offspring group, and the proportion of Clostridiales in the stress+LBP offspring group was higher than that in the stress and control offspring groups. Conclusion: The intervention of LBP may improve the changes in the intestinal flora diversity, abundance and flora structure of mother mice and offspring caused by pregnancy stress, thereby maintaining the balance of intestinal flora.

Progress in Genomic Mating in Domestic Animals

Simple Summary

Since animal domestication, breeders have been selecting candidates for breeding based on phenotypic performance. Estimating breeding values through the best linear unbiased prediction method represents a revolutionary shift in animal breeding. On this basis, selection and mating are utilized to improve the production level of animals. The application of genomic selection has once again revolutionized animal breeding methods. However, although this kind of truncated selection based on breeding values can significantly improve genetic gain, the genetic relationship between individuals with a high breeding value is usually closed, and the probability of being co-selected is greater, which will lead to a rapid increase in the rate of inbreeding in the population. Reduced genetic variation is not conducive to long-term sustainable breeding, so a trade-off between genetic gain and inbreeding is required. Genomic mating is the use of candidate individuals’ genomic information to implement optimized breeding and mating, which can effectively control the rate of inbreeding in the population and achieve long-term and sustainable genetic gain. It is more suitable for modern animal breeding, especially for conservation and genetic improvement of local domestic animal breeds.

Abstract

Selection is a continuous process that can influence the distribution of target traits in a population. From the perspective of breeding, elite individuals are selected for breeding, which is called truncated selection. With the introduction and application of the best linear unbiased prediction (BLUP) method, breeders began to use pedigree-based estimated breeding values (EBV) to select candidates for the genetic improvement of complex traits. Although truncated selection based on EBV can significantly improve the genetic progress, the genetic relationships between individuals with a high breeding value are usually closed, and the probability of being co-selected is greater, which will lead to a rapid increase in the level of inbreeding in the population. Reduced genetic variation is not conducive to long-term sustainable breeding, so a trade-off between genetic progress and inbreeding is required. As livestock and poultry breeding enters the genomic era, using genomic information to obtain optimal mating plans has formally been proposed by Akdemir et al., a method called genomic mating (GM). GM is more accurate and reliable than using pedigree information. Moreover, it can effectively control the inbreeding level of the population and achieve long-term and sustainable genetic gain. Hence, GM is more suitable for modern animal breeding, especially for local livestock and poultry breed conservation and genetic improvement. This review mainly summarized the principle of genomic mating, the methodology and usage of genomic mating, and the progress of its application in livestock and poultry.

Comparison of amino acid digestibility and its additivity determined with slaughter or cecectomy method for yellow-feather chicken

The objective of this experiment was to compare the slaughter and cecectomy methods to determine amino acid (AA) digestibility of corn and soybean meal and their additivity in a corn-soybean meal diet. A completely randomized design was adopted to determine endogenous AA losses (EAAL) and AA digestibility in each of corn, soybean meal, and a corn-soybean meal diet using either slaughter or cecectomy methods. Each treatment contained 6 replicates with 3 chickens per replicate. The endogenous loss (EL) of histidine and glycine was lower and the EL of methionine and phenylalanine was greater when determined by slaughter vs. cecectomy (P < 0.05). The EL of arginine, isoleucine, leucine, lysine, methionine, phenylalanine, valine, alanine, aspartic acid, glutamic acid, and serine determined by slaughter were 1.2 to 3.2 times of those from cecectomy. The standard error (SE) of EL of 14 AA (excluding histidine and glycine) obtained by slaughter method was 2.1 to 9.6 times of those by cecectomy method. The apparent and standardized digestibility was not affected by methods for most AA except apparent digestibility of methionine, phenylalanine and glycine, and standardized digestibility of glycine in corn. The apparent and standardized digestibility of most AA except apparent digestibility of glycine and standardized digestibility of lysine, cysteine and glycine were less for slaughter versus cecectomy methods in soybean meal (P < 0.05). Using slaughter method resulted in reduced apparent digestibility of 15 AA (except glycine) and reduced standardized digestibility of 7 AA (arginine, isoleucine, leucine, valine, aspartic acid, glutamic acid, and proline) relative to cecectomy method (P < 0.05), but the standardized digestibility of glycine was greater when determined by slaughter vs. cecectomy methods in corn-soybean meal diet (P < 0.05). The mean value of SE of 16 AA digestibility in slaughter method was 2.9 times of that by cecectomy method. The apparent digestibility of 2 and 9 of 16 AA and the standardized digestibility of 15 and 7 of 16 AA were additive when using slaughter and cecectomy determinations, respectively. In conclusion, compared to the slaughter method, cecectomy method had less SE and EAAL but greater apparent digestibility of methionine and phenylalanine in corn, and the apparent digestibility of 15 AA (except glycine) in soybean meal and corn-soybean meal diet. Additivity in apparent and standardized AA digestibility was more inconsistent when determined with slaughter vs. cecectomy methods. These findings suggest that the cecectomy method is more suitable than the slaughter method to determine the digestibility of AA.

Enzymatic Synthesis of the Unnatural Nucleotide 2'-Deoxyisoguanosine 5'-Monophosphate

Naturally occurring DNA contains four canonical bases, forming two Watson-Crick base pairs (adenine-thymine, guanine-cytosine). Efforts over the past decades have led to the development of several unnatural base pairs, enabling the synthesis of unnatural DNA with an expanded genetic alphabet. The engineering of organisms capable of de novo biosynthesis of unnatural DNA would have significant technological and philosophical implications, but remains a challenge. Here we report the enzymatic conversion of 2'-deoxyxanthosine 5'-monophosphate (dXMP) into deoxyisoguanosine monophosphate (dBMP), a precursor of the unnatural isoguanine-isocytosine base pair. The reaction is catalyzed by the bacteriophage enzyme PurZ and bacterial PurB, and is a key addition to the toolbox for de novo biosynthesis of unnatural DNA.

[Measuring laryngotracheal stenosis by extracting centerline based on CT 3D reconstruction]

Objective: To compare the accuracy of the centerline extracted based on CT 3D reconstruction and conventional CT 3D reconstruction in measuring the length and degree of laryngotracheal stenosis. Methods: A retrospective analysis was performed on 35 patients with laryngotracheal stenosis (including 19 cases without tracheotomy and 16 cases with tracheotomy) treated in the Department of Otorhinolaryngology Head and Neck Surgery of the First Affiliated Hospital of Guangxi Medical University from March 2006 to March 2016, including 20 males and 15 females, whose ages ranged from 1 to 73 years, with a median age of 40.5 years. And CT data of 20 normal subjects were included in the same period, including 10 males and 10 females, whose ages ranged from 20 to 63 years, with a median age of 37.0 years. The continuous cross-sectional area of the airway perpendicular to the centerline was obtained by Mimics software. The area was compared with the discontinuous cross-sectional areas reconstructed by conventional CT 3D reconstruction software advantage workstation, also the length of cervical trachea, the length of stenosis, and the minimum airway area were compared. Multi-factor linear stepwise regression method was used to analyze the factors influencing the measuring difference between the two methods. Three patients with laryngotracheal stenosis were selected, and the measured stenosis length was compared with the surgical specimens to evaluate the accuracy of the two methods. SPSS 26.0 software was used for statistical analysis. Results: In normal people, the areas of thyroid cartilage notch, glottis, inferio thyroid cartilage margin, inferio cricoid cartilage margin, and suprasternal notch planes measured by Mimics centerline method were smaller than those measured by conventional CT 3D reconstruction (t _{thyroid cartilage notch}=4.685, t_glottis=3.791, t_{lower thyroid cartilage margin}=5.621, t_{lower cricoid cartilage margin}=6.312, t_{suprasternal notch plane}=6.436, P<0.05). And the airway length measured by Mimics centerline method from the inferior thyroid cartilage to the superior sternal notch was longer (t=9.79, P<0.001). In laryngotracheal stenosis, in the non-tracheotomy group, the minimum airway area measured by Mimics centerline method was smaller and the stenosis length was longer than those measured by the conventional CT 3D reconstruction, and the difference was statistically significant (t_{minimum airway area}=2.562, t_{stenosis length}=5.240, P<0.05). In the tracheotomy group, the stenosis length measured by Mimics centerline method was longer than that measured by conventional CT 3D reconstruction, and the difference was statistically significant (t_{stenosis length}=2.854, P<0.05). Multi-factor linear regression analysis showed that different CT thickness had a statistically significant effect on the difference in the length of stenosis measured by the two methods (b=-5.370, t=-3.306, P=0.004), and different tracheal forward angle had a statistically significant effect on the difference in the minimum airway area measured by the two methods (b=-0.419, t=-2.208, P=0.04). The difference between the measured length of the Mimics centerline method and the intraoperative specimens was less than 0.5 mm. Conclusion: The centerline extracted based on CT 3D reconstruction can precisely reflect the laryngotracheal morphology and measure laryngotracheal stenosis more accurately.

Genome-wide association study revealed ABCD4 on SSC7 and GREB1L and MIB1 on SSC6 as crucial candidate genes for rib number in Beijing Black pigs

As one of the few animals with variation in the number of rib pairs (RIB), the pig is a good model to study the mechanism of RIB regulation. Quantitative trait loci (QTL) for porcine RIB are present on Sus scrofa chromosome 7 (SSC7). Although several candidate genes exist in this QTL region on SSC7, the causal gene has yet to be verified. Beijing Black pig with 14-17 RIB is a good population for candidate gene mining and 1104 individuals were genotyped using the Illumina Porcine 50K BeadChip. A total of 14 SNPs from 95.49 to 97.78 Mb on SSC7 showed genome-wide significant association with RIB. On SSC7, a locuszoom plot using pairwise linkage disequilibrium displayed the narrowest linkage region encompassing only two genes, ABCD4 and VRTN. In mice, a transcriptome expression profile was obtained using three embryos at E9.5 (the critical period for rib formation). ABCD4 was highly expressed, but no expression of VRTN was detected. On SSC6, there were four genome-wide significant SNPs from 106.42 to 106.92 Mb associated with RIB. GREB1L and MIB1, in this region, were regarded as novel candidate genes. These results revealed a crucial candidate causal gene on SSC7 and novel genes on SSC6 for rib number and provided interesting new insights into its genetic basis.