Several models combined with ultrasound techniques to predict breast muscle weight in broilers

The weight of breast muscle (WBM) is a highly monitored indicator in broiler breeding that can be obtained after slaughtering. Currently, due to the lack of accurate in vivo phenotypes for both genomic and phenotypic selection, genetic gains in WBM fall short of initial expectations. In this study, 1,006 market-age (42 d) broilers from 3 generations over 2 yr were randomly selected, and the breast width (BW), fossil bone length (FBL), breast muscle thickness (BMT), and live weight (LW) were measured exactly in vivo. Eight models, including multiple linear regression (MLR), ridge regression (RR), least absolute shrinkage and selection operator (LASSO), and elastic net (EN), were fitted to explore the best regression relationships between breast muscle weight and these indicators. Support vector machine (SVM) methods with both linear kernels and radial kernels were used to fit the models, while 2 decision tree-based machine learning algorithms, random forest (RF), and extreme gradient boosting (XGBoost), were used to establish the prediction model. The predictive effects of different combinations of independent variables were compared, leading to the conclusion that the EN model achieves the best predictive power when all 4 live features are used as inputs and is slightly better than the other models (R2 = 0.7696). This method could be applied in practical production and breeding work, leading to substantial cost savings and enhancements in the breeding process.

MAK: a machine learning framework improved genomic prediction via multi-target ensemble regressor chains and automatic selection of assistant traits

Incorporating the genotypic and phenotypic of the correlated traits into the multi-trait model can significantly improve the prediction accuracy of the target trait in animal and plant breeding, as well as human genetics. However, in most cases, the phenotypic information of the correlated and target trait of the individual to be evaluated was null simultaneously, particularly for the newborn. Therefore, we propose a machine learning framework, MAK, to improve the prediction accuracy of the target trait by constructing the multi-target ensemble regression chains and selecting the assistant trait automatically, which predicted the genomic estimated breeding values of the target trait using genotypic information only. The prediction ability of MAK was significantly more robust than the genomic best linear unbiased prediction, BayesB, BayesRR and the multi trait Bayesian method in the four real animal and plant datasets, and the computational efficiency of MAK was roughly 100 times faster than BayesB and BayesRR.

Incorporating genome-wide and transcriptome-wide association studies to identify genetic elements of longissimus dorsi muscle in Huaxi cattle

Locating the genetic variation of important livestock and poultry economic traits is essential for genetic improvement in breeding programs. Identifying the candidate genes for the productive ability of Huaxi cattle was one crucial element for practical breeding. Based on the genotype and phenotype data of 1,478 individuals and the RNA-seq data of 120 individuals contained in 1,478 individuals, we implemented genome-wide association studies (GWAS), transcriptome-wide association studies (TWAS), and Fisher's combined test (FCT) to identify the candidate genes for the carcass trait, the weight of longissimus dorsi muscle (LDM). The results indicated that GWAS, TWAS, and FCT identified seven candidate genes for LDM altogether: PENK was located by GWAS and FCT, PPAT was located by TWAS and FCT, and XKR4, MTMR3, FGFRL1, DHRS4, and LAP3 were only located by one of the methods. After functional analysis of these candidate genes and referring to the reported studies, we found that they were mainly functional in the progress of the development of the body and the growth of muscle cells. Combining advanced breeding techniques such as gene editing with our study will significantly accelerate the genetic improvement for the future breeding of Huaxi cattle.

Improving Genomic Prediction with Machine Learning Incorporating TPE for Hyperparameters Optimization

Depending on excellent prediction ability, machine learning has been considered the most powerful implement to analyze high-throughput sequencing genome data. However, the sophisticated process of tuning hyperparameters tremendously impedes the wider application of machine learning in animal and plant breeding programs. Therefore, we integrated an automatic tuning hyperparameters algorithm, tree-structured Parzen estimator (TPE), with machine learning to simplify the process of using machine learning for genomic prediction. In this study, we applied TPE to optimize the hyperparameters of Kernel ridge regression (KRR) and support vector regression (SVR). To evaluate the performance of TPE, we compared the prediction accuracy of KRR-TPE and SVR-TPE with the genomic best linear unbiased prediction (GBLUP) and KRR-RS, KRR-Grid, SVR-RS, and SVR-Grid, which tuned the hyperparameters of KRR and SVR by using random search (RS) and grid search (Gird) in a simulation dataset and the real datasets. The results indicated that KRR-TPE achieved the most powerful prediction ability considering all populations and was the most convenient. Especially for the Chinese Simmental beef cattle and Loblolly pine populations, the prediction accuracy of KRR-TPE had an 8.73% and 6.08% average improvement compared with GBLUP, respectively. Our study will greatly promote the application of machine learning in GP and further accelerate breeding progress.

Incorporating kernelized multi-omics data improves the accuracy of genomic prediction

Background

Genomic selection (GS) has revolutionized animal and plant breeding after the first implementation via early selection before measuring phenotypes. Besides genome, transcriptome and metabolome information are increasingly considered new sources for GS. Difficulties in building the model with multi-omics data for GS and the limit of specimen availability have both delayed the progress of investigating multi-omics.

Results

We utilized the Cosine kernel to map genomic and transcriptomic data as \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$${n}\times {n}$$\end{document}n×n symmetric matrix (G matrix and T matrix), combined with the best linear unbiased prediction (BLUP) for GS. Here, we defined five kernel-based prediction models: genomic BLUP (GBLUP), transcriptome-BLUP (TBLUP), multi-omics BLUP (MBLUP, \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$\boldsymbol M=\mathrm{ratio}\times\boldsymbol G+(1-\mathrm{ratio})\times\boldsymbol T$$\end{document}M=ratio×G+(1-ratio)×T), multi-omics single-step BLUP (mssBLUP), and weighted multi-omics single-step BLUP (wmssBLUP) to integrate transcribed individuals and genotyped resource population. The predictive accuracy evaluations in four traits of the Chinese Simmental beef cattle population showed that (1) MBLUP was far preferred to GBLUP (ratio = 1.0), (2) the prediction accuracy of wmssBLUP and mssBLUP had 4.18% and 3.37% average improvement over GBLUP, (3) We also found the accuracy of wmssBLUP increased with the growing proportion of transcribed cattle in the whole resource population.

Conclusions

We concluded that the inclusion of transcriptome data in GS had the potential to improve accuracy. Moreover, wmssBLUP is accepted to be a promising alternative for the present situation in which plenty of individuals are genotyped when fewer are transcribed.

Supplementary Information

The online version contains supplementary material available at 10.1186/s40104-022-00756-6.

Integrating genomics and transcriptomics to identify candidate genes for subcutaneous fat deposition in beef cattle

Fat deposition is a complex economic trait regulated by polygenic genetic basis and environmental factors. Therefore, integrating multi-omics data to uncover its internal regulatory mechanism has attracted extensive attention. Here, we performed genomics and transcriptomics analysis to detect candidates affecting subcutaneous fat (SCF) deposition in beef cattle. The association of 770K SNPs with the backfat thickness captured nine significant SNPs within or near 11 genes. Additionally, 13 overlapping genes regarding fat deposition were determined via the analysis of differentially expressed genes and weighted gene co-expression network analysis (WGCNA). We then calculated the correlations of these genes with BFT and constructed their interaction network. Finally, seven biomarkers including ACACA, SCD, FASN, ACOX1, ELOVL5, HACD2, and HSD17B12 were screened. Notably, ACACA, identified by the integration of genomics and transcriptomics, was more likely to exert profound effects on SCF deposition. These findings provided novel insights into the regulation mechanism underlying bovine fat accumulation.

PacBio Single-Molecule Long-Read Sequencing Provides New Light on the Complexity of Full-Length Transcripts in Cattle

Cattle (Bos taurus) is one of the most widely distributed livestock species in the world, and provides us with high-quality milk and meat which have a huge impact on the quality of human life. Therefore, accurate and complete transcriptome and genome annotation are of great value to the research of cattle breeding. In this study, we used error-corrected PacBio single-molecule real-time (SMRT) data to perform whole-transcriptome profiling in cattle. Then, 22.5 Gb of subreads was generated, including 381,423 circular consensus sequences (CCSs), among which 276,295 full-length non-chimeric (FLNC) sequences were identified. After correction by Illumina short reads, we obtained 22,353 error-corrected isoforms. A total of 305 alternative splicing (AS) events and 3,795 alternative polyadenylation (APA) sites were detected by transcriptome structural analysis. Furthermore, we identified 457 novel genes, 120 putative transcription factors (TFs), and 569 novel long non-coding RNAs (lncRNAs). Taken together, this research improves our understanding and provides new insights into the complexity of full-length transcripts in cattle.

KCRR: a nonlinear machine learning with a modified genomic similarity matrix improved the genomic prediction efficiency

Nowadays, advances in high-throughput sequencing benefit the increasing application of genomic prediction (GP) in breeding programs. In this research, we designed a Cosine kernel-based KRR named KCRR to perform GP. This paper assessed the prediction accuracies of 12 traits with various heritability and genetic architectures from four populations using the genomic best linear unbiased prediction (GBLUP), BayesB, support vector regression (SVR), and KCRR. On the whole, KCRR performed stably for all traits of multiple species, indicating that the hypothesis of KCRR had the potential to be adapted to a wide range of genetic architectures. Moreover, we defined a modified genomic similarity matrix named Cosine similarity matrix (CS matrix). The results indicated that the accuracies between GBLUP_kinship and GBLUP_CS almost unanimously for all traits, but the computing efficiency has increased by an average of 20 times. Our research will be a significant promising strategy in future GP.

A Stacking Ensemble Learning Framework for Genomic Prediction

Machine learning (ML) is perhaps the most useful tool for the interpretation of large genomic datasets. However, the performance of a single machine learning method in genomic selection (GS) is currently unsatisfactory. To improve the genomic predictions, we constructed a stacking ensemble learning framework (SELF), integrating three machine learning methods, to predict genomic estimated breeding values (GEBVs). The present study evaluated the prediction ability of SELF by analyzing three real datasets, with different genetic architecture; comparing the prediction accuracy of SELF, base learners, genomic best linear unbiased prediction (GBLUP) and BayesB. For each trait, SELF performed better than base learners, which included support vector regression (SVR), kernel ridge regression (KRR) and elastic net (ENET). The prediction accuracy of SELF was, on average, 7.70% higher than GBLUP in three datasets. Except for the milk fat percentage (MFP) traits, of the German Holstein dairy cattle dataset, SELF was more robust than BayesB in all remaining traits. Therefore, we believed that SEFL has the potential to be promoted to estimate GEBVs in other animals and plants.

Encapsulation of bacterial cells in cytoprotective ZIF-90 crystals as living composites

Exploiting metal-organic frameworks (MOFs) as selectively permeable shelters for encapsulating engineered cells to form hybrid living materials has attracted increasing attention in recent years. Optimizing the synthesis process to improve encapsulation efficiency (EE) is critical for further technological development and applications. Here, using ZIF-90 and genetically engineered Escherichia coli (E. coli) as a demo, we fabricated E. coli@ZIF-90 living composites in which E. coli cells were encapsulated in ZIF-90 crystals. We illustrated that ZIF-90 could serve as a protective porous cage for cells to shield against toxic bactericides including benzaldehyde, cinnamaldehyde, and kanamycin. Notably, the E. coli cells remained alive and could self-reproduce after removing the ZIF-90 crystal cages in ethylenediaminetetraacetic acid, suggesting a feasible route for protecting and prolonging the lifespan of bacterial cells. Moreover, an aqueous multiple-step deposition approach was developed to improve EE of the E. coli@ZIF-90 composites: the EE increased to 61.9 ± 5.2%, in contrast with the efficiency of the traditional method (21.3 ± 4.4%) prepared with PBS buffer. In short, we develop a simple yet viable strategy to manufacture MOF-based living hybrid materials that promise new applications across diverse fields.

Genome-Wide Association Analysis of Growth Curve Parameters in Chinese Simmental Beef Cattle

The objective of the present study was to perform a genome-wide association study (GWAS) for growth curve parameters using nonlinear models that fit original weight-age records. In this study, data from 808 Chinese Simmental beef cattle that were weighed at 0, 6, 12, and 18 months of age were used to fit the growth curve. The Gompertz model showed the highest coefficient of determination (R² = 0.954). The parameters' mature body weight (A), time-scale parameter (b), and maturity rate (K) were treated as phenotypes for single-trait GWAS and multi-trait GWAS. In total, 9, 49, and 7 significant SNPs associated with A, b, and K were identified by single-trait GWAS; 22 significant single nucleotide polymorphisms (SNPs) were identified by multi-trait GWAS. Among them, we observed several candidate genes, including PLIN3, KCNS3, TMCO1, PRKAG3, ANGPTL2, IGF-1, SHISA9, and STK3, which were previously reported to associate with growth and development. Further research for these candidate genes may be useful for exploring the full genetic architecture underlying growth and development traits in livestock.

Application of ensemble learning to genomic selection in chinese simmental beef cattle

Genomic selection (GS) using the whole-genome molecular makers to predict genomic estimated breeding values (GEBVs) is revolutionizing the livestock and plant breeding. Seeking out novel strategies with higher prediction accuracy for GS has been the ultimate goal of breeders. With the rapid development of artificial intelligence, machine learning algorithms were applied to estimate the GEBVs increasingly. Although some machine learning methods have better performance in phenotype prediction, there is still considerable room for improvement. In this study, we applied an ensemble-learning algorithm, Adaboost.RT, which integrated support vector regression (SVR), kernel ridge regression (KRR) and random forest (RF), to predict genomic breeding values of three economic traits (carcass weight, live weight, and eye muscle area) in Chinese Simmental beef cattle. Predictive accuracy measured as the Pearson correlation between the corrected phenotypes and predicted GEBVs. Moreover, we compared the reliability of SVR, KRR, RF, Adaboost.RT and GBLUP methods. The result showed that machine learning methods outperformed GBLUP, and the average improvement of four machine learning methods over the GBLUP was 12.8%, 14.9%, 5.4% and 14.4%, respectively. Among the four machine learning methods, the reliability of Adaboost.RT was comparable to KRR with higher stability. We therefore believe that the Adaboost.RT algorithm is a reliable and efficient method for GS.

Multiple association analysis of loci and candidate genes that regulate body size at three growth stages in Simmental beef cattle

Background

Body size traits as one of the main breeding selection criteria was widely used to monitor cattle growth and to evaluate the selection response. In this study, body size was defined as body height (BH), body length (BL), hip height (HH), heart size (HS), abdominal size (AS), and cannon bone size (CS). We performed genome-wide association studies (GWAS) of these traits over the course of three growth stages (6, 12 and 18 months after birth) using three statistical models, single-trait GWAS, multi-trait GWAS and LONG-GWAS. The Illumina Bovine HD 770 K BeadChip was used to identify genomic single nucleotide polymorphisms (SNPs) in 1217 individuals.

Results

In total, 19, 29, and 10 significant SNPs were identified by the three models, respectively. Among these, 21 genes were promising candidate genes, including SOX2, SNRPD1, RASGEF1B, EFNA5, PTBP1, SNX9, SV2C, PKDCC, SYNDIG1, AKR1E2, and PRIM2 identified by single-trait analysis; SLC37A1, LAP3, PCDH7, MANEA, and LHCGR identified by multi-trait analysis; and P2RY1, MPZL1, LINGO2, CMIP, and WSCD1 identified by LONG-GWAS.

Conclusions

Multiple association analysis was performed for six growth traits at each growth stage. These findings offer valuable insights for the further investigation of potential genetic mechanism of growth traits in Simmental beef cattle.

Genome-wide association studies using binned genotypes

Linear mixed models (LMM) that tests trait association one marker at a time have been the most popular methods for genome-wide association studies. However, this approach has potential pitfalls: over conservativeness after Bonferroni correction, ignorance of linkage disequilibrium (LD) between neighboring markers, and power reduction due to overfitting SNP effects. So, multiple locus models that can simultaneously estimate and test all markers in the genome are more appropriate. Based on the multiple locus models, we proposed a bin model that combines markers into bins based on their LD relationships. A bin is treated as a new synthetic marker and we detect the associations between bins and traits. Since the number of bins can be substantially smaller than the number of markers, a penalized multiple regression method can be adopted by fitting all bins to a single model. We developed an innovative method to bin the neighboring markers and used the least absolute shrinkage and selection operator (LASSO) method. We compared BIN-Lasso with SNP-Lasso and Q + K-LMM in a simulation experiment, and showed that the new method is more powerful with less Type I error than the other two methods. We also applied the bin model to a Chinese Simmental beef cattle population for bone weight association study. The new method identified more significant associations than the classical LMM. The bin model is a new dimension reduction technique that takes advantage of biological information (i.e., LD). The new method will be a significant breakthrough in associative genomics in the big data era.

Genome-wide association study reveals candidate genes associated with body measurement traits in Chinese Wagyu beef cattle

We performed a genome-wide association study to identify candidate genes for body measurement traits in 463 Wagyu beef cattle typed with the Illumina Bovine HD 770K SNP array. At the genome-wide level, we detected 18, five and one SNPs associated with hip height, body height and body length respectively. In total, these SNPs are within or near 11 genes, six of which (PENK, XKR4, IMPAD1, PLAG1, CCND2 and SNTG1) have been reported previously and five of which (CSMD3, LAP3, SYN3, FAM19A5 and TIMP3) are novel candidate genes that we found to be associated with body measurement traits. Further exploration of these candidate genes will facilitate genetic improvement in Chinese Wagyu beef cattle.

Genome-wide association study identifies loci and candidate genes for internal organ weights in Simmental beef cattle

Cattle internal organs as accessible raw materials have a long history of being widely used in beef processing, feed and pharmaceutical industry. These traits not only are of economic interest to breeders, but they are intrinsically linked to many valuable traits, such as growth, health, and productivity. Using the Illumina Bovine HD 770K SNP array, we performed a genome-wide association study for heart weight, liver weight, spleen weight, lung weight, and kidney weight in 1,217 Simmental cattle. In our research, 38 significant single nucleotide polymorphisms (SNPs) ( P < 1.49 × 10−6) were identified for five internal organ weight traits. These SNPs are within or near 13 genes, and some of them have been reported previously, including NDUFAF4, LCORL, BT.94996, SLIT2, FAM184B, LAP3, BBS12, MECOM, CD300LF, HSD17B3, TLR4, MXI1, and MB21D2. In addition, we detected four haplotype blocks on BTA6 containing 18 significant SNPs associated with spleen weight. Our results offer worthy insights into understanding the genetic mechanisms of internal organs' development, with potential application in breeding programs of Simmental beef cattle.

A Practical Anodic and Cathodic Curve Intersection Model to Understand Multiple Corrosion Potentials of Fe-Based Glassy Alloys in OH- Contained Solutions

A practical anodic and cathodic curve intersection model, which consisted of an apparent anodic curve and an imaginary cathodic line, was proposed to explain multiple corrosion potentials occurred in potentiodynamic polarization curves of Fe-based glassy alloys in alkaline solution. The apparent anodic curve was selected from the measured anodic curves. The imaginary cathodic line was obtained by linearly fitting the differences of anodic curves and can be moved evenly or rotated to predict the number and value of corrosion potentials.

Multiplex Quantitative PCR Assays for the Detection and Quantification of the Six Major Non-O157 Escherichia coli Serogroups in Cattle Feces

Shiga toxin-producing Escherichia coli (STEC) serogroups O26, O45, O103, O111, O121, and O145, called non-O157 STEC, are important foodborne pathogens. Cattle, a major reservoir, harbor the organisms in the hindgut and shed them in the feces. Although limited data exist on fecal shedding, concentrations of non-O157 STEC in feces have not been reported. The objectives of our study were (i) to develop and validate two multiplex quantitative PCR (mqPCR) assays, targeting O-antigen genes of O26, O103, and O111 (mqPCR-1) and O45, O121, and O145 (mqPCR-2); (ii) to utilize the two assays, together with a previously developed four-plex qPCR assay (mqPCR-3) targeting the O157 antigen and three virulence genes (stx1, stx2, and eae), to quantify seven serogroups and three virulence genes in cattle feces; and (iii) to compare the three mqPCR assays to a 10-plex conventional PCR (cPCR) targeting seven serogroups and three virulence genes and culture methods to detect seven E. coli serogroups in cattle feces. The two mqPCR assays (1 and 2) were shown to be specific to the target genes, and the detection limits were 4 and 2 log CFU/g of pure culture-spiked fecal samples, before and after enrichment, respectively. A total of 576 fecal samples collected from a feedlot were enriched in E. coli broth and were subjected to quantification (before enrichment) and detection (after enrichment). Of the 576 fecal samples subjected, before enrichment, to three mqPCR assays for quantification, 175 (30.4%) were quantifiable (≥4 log CFU/g) for at least one of the seven serogroups, with O157 being the most common serogroup. The three mqPCR assays detected higher proportions of postenriched fecal samples (P > 0.01) as positive for one or more serogroups compared with cPCR and culture methods. This is the first study to assess the applicability of qPCR assays to detect and quantify six non-O157 serogroups in cattle feces and to generate data on fecal concentration of the six serogroups.

Involvement of RB kinases and phosphatases in life and death decisions

Previously we found that retinoblastoma protein (RB) became dephosphorylated in an early stage of DNA damage-induced, p53-independent apoptosis. Here, we report that both RB dephosphorylation and apoptosis are regulated by relative levels of RB kinases (cyclin-dependent kinases, or cdks) and phosphatases. Treatment of human Jurkat T cells with roscovitine, a potent and selective synthetic inhibitor of several cdks, rapidly induced RB dephosphorylation, which was followed by induction of apoptosis-associated internucleosomal DNA fragmentation. The roscovitine treatment did not increase levels of the endogenous cdk inhibitor proteins p16(Ink4a), p27(kip1) and p21(Waf1), supporting the idea that the observed RB dephosphorylation was due to a direct inhibition of cdk activities by roscovitine. Treatment with a protein kinase C inhibitor (sphingosine or staurosporine), which leads to suppression of several cdk kinase activities, also induced cellular RB dephosphorylation and apoptosis. Finally, roscovitine- or sphingosine-induced RB dephosphorylation was blocked by a specific inhibitor of protein-serine/threonine phosphatases (calyculin A or okadaic acid). Therefore, RB phosphorylation status and cellular fate are regulated by the ratio of RB kinases to RB phosphatases.

Effects of liraglutide (NN2211), a long-acting GLP-1 analogue, on glycaemic control and bodyweight in subjects with Type 2 diabetes

AIMS

Liraglutide (NN2211) is a long-acting GLP-1 analogue, with a pharmacokinetic profile suitable for once-daily administration. This multicentre, double-blind, parallel-group, double-dummy study explored the dose-response relationship of liraglutide effects on bodyweight and glycaemic control in subjects with Type 2 diabetes.

METHODS

Subjects (BMI 27-42 kg/m(2)) with Type 2 diabetes who were previously treated with an OAD (oral anti-diabetic drug) monotherapy (69% with metformin), and had HbA(1c) < or = 10% were enrolled. After a 4-week metformin run-in period, 210 subjects (27-73 years, 60% female) were randomised to receive liraglutide (0.045-0.75 mg) once daily or continued on metformin 1000 mg b.d. for 12 weeks.

RESULTS

Mean baseline values for the six treatment groups ranged from 6.8 to 7.5% for HbA(1c), and 8.06-9.44 mmol/l (145-170 mg/dl) for fasting plasma glucose. After 12-week treatment, a weight change of -0.05 to -1.9% was observed for the six treatment groups. Mean HbA(1c) changes from baseline for 0.045, 0.225, 0.45, 0.6, 0.75 mg liraglutide and metformin were +1.28%, +0.86%, +0.22%, +0.16%, +0.30% and +0.09%, respectively. No significant differences in HbA(1c) were observed between liraglutide and metformin groups at the three highest liraglutide dose levels (0.45, 0.6 and 0.75 mg). The lowest two liraglutide doses (0.045 mg and 0.225 mg) were not sufficient to maintain the fasting plasma glucose values achieved by metformin. No major hypoglycaemic episodes were reported. Episodes of nausea and/or vomiting were reported by 11 patients (6.3%) receiving liraglutide and three (8.8%) receiving metformin.

CONCLUSIONS

Once-daily liraglutide improved glycaemic control and weight, in a comparable degree to metformin. Liraglutide appeared to be safe and generally well tolerated. Higher doses of liraglutide merit study in future clinical trials.

Cell surface expression and turnover of the alpha-subunit of the epithelial sodium channel

The renal epithelial cell line A6, derived from Xenopus laevis, expresses epithelial Na(+) channels (ENaCs) and serves as a model system to study hormonal regulation and turnover of ENaCs. Our previous studies suggest that the alpha-subunit of Xenopus ENaC (alpha-xENaC) is detectable as 150- and 180-kDa polypeptides, putative immature and mature alpha-subunit heterodimers. The 150- and 180-kDa alpha-xENaC were present in distinct fractions after sedimentation of A6 cell lysate through a sucrose density gradient. Two anti-alpha-xENaC antibodies directed against distinct domains demonstrated that only 180-kDa alpha-xENaC was expressed at the apical cell surface. The half-life of cell surface-expressed alpha-xENaC was 24-30 h, suggesting that once ENaC matures and is expressed at the plasma membrane, its turnover is similar to that reported for mature cystic fibrosis transmembrane conductance regulator. No significant changes in apical surface expression of alpha-xENaC were observed after treatment of A6 cells with aldosterone for 24 h, despite a 5.3-fold increase in short-circuit current. This lack of change in surface expression is consistent with previous observations in A6 cells and suggests that aldosterone regulates ENaC gating and increases channel open probability.

[The numerical simulation of the dynamic stress field from impacting head]

In order to study the mechanism of impact injury to the head, we have simulated the development of the stress field by using the numerical simulation method. The process of the head having been impacted vertically by an impactor can be described as a 2D problem, and the reactions of the head subjected to impacted force can be simulated and analyzed by the method based on the finite difference method (FDM). The model is subjected to applied force by an impactor with the initial velocity of 25 m/s (90 km/h). The pre-processing for the model is done on the microcomputer software. Once imported to the software, the nodes and elements are generated and material characteristics are assigned. The results demonstrate that the high resolution computer graphics can provide the dynamic distribution of the stress field, which can clearly show how the stress is developed, and how many its value is. The results are helpful to understanding the mechanism of impact injury to head.

Modification of the amino terminus of a class II epitope confers resistance to degradation by CD13 on dendritic cells and enhances presentation to T cells

Dendritic cells and human B cell lines were compared for ability to present synthetic peptides corresponding to residues 145-159 and 188-203 of human Ig kappa-chains to peptide-specific mouse T cell hybridomas restricted by HLA-DR4Dw4. B cell lines presented both peptides, but dendritic cells could only efficiently present the latter epitope. In this paper, we show that dendritic cells degrade the 145-159 peptide, removing four residues from the amino terminus. Binding of the peptide to the class II restriction element is not required for this process. The degradation product is resistant to further cleavage, accumulates in the culture supernatant, and does not bind to HLA-DR4Dw4 or stimulate T cell reactivity. Cleavage can be blocked with bestatin, but not with other protease inhibitors tested, or by a mAb directed against aminopeptidase N (CD13). Addition of an acetyl group to the amino terminus of peptide 145-159 also blocks degradation, and allows dendritic cells to present the peptide to specific T cells with greatly increased efficiency. These results demonstrate that CD13 on dendritic cells is able to selectively and efficiently degrade exogenously provided peptide Ags, in a process that can be blocked by addition of an acetyl group to the amino terminus of the peptide. Modification of the amino terminus of peptide epitopes susceptible to degradation may prove to be useful as a general strategy for enhancing their immunogenicity.

Proteasome inhibition leads to significant reduction of Bcr-Abl expression and subsequent induction of apoptosis in K562 human chronic myelogenous leukemia cells

The chimeric oncogene bcr-abl is detected in virtually every case of chronic myelogenous leukemia. It has been shown that cells (such as K562) expressing Bcr-Abl/p210, a protein tyrosine kinase, not only undergo cellular transformation but also demonstrate multiple drug resistance. Recent studies also demonstrate that the proteasome is involved in the survival signaling pathway(s). In the current study, we tested the hypothesis that the proteasome might play a role in regulating Bcr-Abl function. We have demonstrated by using a variety of inhibitors that inhibition of the proteasome, but not of the cysteine protease, activity is able to activate the apoptotic cell death program in K562 cells. Proteasome inhibition-induced apoptosis is demonstrated by condensation and fragmentation of nuclei, appearance of an apoptotic population with sub-G1 DNA content, the internucleosomal fragmentation of DNA, and cleavage of poly(ADP-ribose) polymerase, and can be blocked by a specific caspase-3-like tetrapeptide inhibitor. Western blot analysis with specific antibodies to c-Abl and Bcr proteins show that treatment of K562 cells with a proteasome inhibitor results in significant reduction of Bcr-Abl protein expression, which occurs several hours before the onset of apoptotic execution. Levels of c-Abl/p145 and Bcr/p160 proteins, however, remain essentially unaltered at that time. Furthermore, reduced Bcr-Abl expression is reflected in significantly attenuated Bcr-Abl-mediated protein tyrosine phosphorylation. Taken together, these results indicate that proteasome inhibition is sufficient to inactivate Bcr-Abl function and subsequently activate the apoptotic death program in cells that are resistant to apoptosis induced by chemotherapy.

Novel dipeptidyl proteasome inhibitors overcome Bcl-2 protective function and selectively accumulate the cyclin-dependent kinase inhibitor p27 and induce apoptosis in transformed, but not normal, human fibroblasts

It has been suggested that overexpression of the Bcl-2 oncoprotein in human cancer cells contributes to their resistance to apoptosis induced by chemotherapy. We report here that a novel dipeptidyl proteasome inhibitor, CEP1612, at low concentrations rapidly induces apoptosis in human Jurkat T cells overexpressing Bcl-2 and also in all human prostate, breast, tongue and brain tumor cell lines we have tested to date, without exception. In contrast, etoposide, a standard anticancer drug, fails to kill these cells when employed under the same conditions. The apoptosis-inducing abilities of CEP1612 and its analogous compounds match precisely their order for inhibition of the proteasome chymotrypsin-like activity. CEP1612-induced apoptosis is p53-independent, inhibitable by a tetrapeptide caspase inhibitor, and associated with accumulation of the cyclin-dependent kinase inhibitors p21 and p27. Furthermore, CEP1612 selectively accumulates p27 and induces apoptosis in simian virus 40-transformed, but not the parental normal, human fibroblasts. Proteasome inhibitors such as those investigated herein might therefore have potential use as novel anticancer drugs.

[Studies of antitumor and chemopreventive agents against neoplasm: synthesis of coumarin 3-glyoxal derivatives and relationship between structure and antimutagenic activity]

It has been shown that alpha-glyoxal and its derivatives possess antivirus and antitumor activities. Eighteen new coumarin 3-glyoxal derivatives were synthesized in our laboratory. The fragmentation pattern of MS and the characteristic signals of 1HNMR of these compounds have also been studied. In pharmacological test in vitro most of these analogues showed antimutagenic activities, among them, compound 9 exhibited very strong antimutagenic activity and eight compounds showed strong effects. The struture-activity relationship and the possible active substructure responsible for the activity of these compounds were discussed. As expected, coumarin 3-glyoxals showed higher antimutagenic activities than their 3-acetyl coumarin counterparts. We also found that alkylation or esterification of 7-hydroxy were favorable to their activities.

p53-independent dephosphorylation and cleavage of retinoblastoma protein during tamoxifen-induced apoptosis in human breast carcinoma cells

We have investigated several molecular events that occur during the process of tamoxifen-induced apoptosis in human breast carcinoma cells. We show that the treatment of either MCF-7 (containing wild-type p53) or MDA-MB-231 cells (containing mutant p53) with tamoxifen resulted in apoptotic nuclear changes and an increase in the pre-G1 apoptotic population. This was accompanied by activation of the caspase enzymes, as evidenced by specific cleavage of poly(ADP-ribose) polymerase and retinoblastoma (RB) protein. The RB protein was cleaved at both an interior and carboxyl terminus cleavage site. In addition, dephosphorylation of RB was found at an early stage of tamoxifen-induced apoptosis in both cell lines. However, neither induction of p53 in MCF-7 cells nor induction of p21 in either cell line was detected, suggesting that tamoxifen-induced RB dephosphorylation and apoptosis are independent of the p53/p21 pathway. We also observed an increase in levels of the pro-apoptotic Bax protein, the inhibitory cytokine TGF-beta1 and the transcription factor c-Myc in tamoxifen-treated MDA-MB-231 cells, suggesting the possible involvement of these proteins during apoptosis in this system.

RB and apoptotic cell death

Homeostasis of cell numbers is achieved by balancing the proliferative and death states of cells. Proper regulation in a cell requires an accurate coordination between these two processes. Indeed, dysregulation of cell cycle progression is essential for the initiation of apoptosis. Retinoblastoma protein (RB) is an important tumor suppressor and a cell cycle regulator. Most recent studies suggest that RB also plays a regulatory role in the process of apoptosis. During the onset of apoptosis, the hyperphosphorylated form of RB (p120/hyper) is converted to a hypophosphorylated form (p115/hypo), which is mediated by a specific protein-serine/ threonine phosphatase activity. Accompanied by the internucleosomal fragmentation of DNA, the newly formed p115/hypo/RB is immediately cleaved by a protease that has properties of the caspase family. During apoptosis, RB is also cleaved in its carboxyl terminus by a caspase-3-like activity. By contrast, the unphosphorylated form of RB (p110/unphos) remains uncleaved during apoptosis. Further studies suggest that p110/unphos/RB functions as an inhibitor of apoptosis. Therefore, regulation of the RB proteolytic activities and consequent RB levels is important for the determination of cellular fate.

Bcl-2- and CrmA-inhibitable dephosphorylation and cleavage of retinoblastoma protein during etoposide-induced apoptosis

Cell numbers are regulated by a balance between proliferation and apoptosis (programmed cell death). Recent evidence suggests that proteins regulating cell proliferation also mediate apoptosis. Therefore, cellular fate might be determined by cross talk between regulators of cell cycle progression and apoptosis. Previously, we had found that during DNA damage-induced apoptosis, retinoblastoma protein (RB), an important G1/S regulator and tumor suppressor, became dephosphorylated and then immediately cleaved into p48 and p68 fragments. Here, we report that expression of the Bcl-2 oncoprotein, an inhibitor of caspases (interleukin 1 -converting enzyme-like proteases), blocked RB dephosphorylation, RB cleavage and apoptosis in etoposide-treated human Jurkat T cells. In addition, expression of the cowpox virus CrmA protein, a direct inhibitor of caspases, also inhibited both RB changes and apoptosis. Taken together, our findings demonstrate important roles for caspases in the processes of etoposide-induced RB dephosphorylation, RB proteolysis and apoptosis.

Characterization of interior cleavage of retinoblastoma protein in apoptosis

Previously we reported that at the onset of apoptotic execution, retinoblastoma protein (RB) was cleaved in its interior region, resulting in production of two major fragments, p48 and p68, and that the RB interior cleavage was mediated by a caspase-like activity. Here, we further characterized the RB interior cleavage process in human leukemia cells treated with the anticancer agent etoposide. We found that the RB interior cleavage activity was much more sensitive to two specific tetrapeptide caspase inhibitors, YVAD-CMK and DEVD-FMK, than the poly(ADP-ribose) polymerase cleavage activity, suggesting that two distinct caspases are involved in these processes. Several Asp residues are located in amino acids 341-421 of RB protein, and cleavage of any one of these sites by a caspase would generate a p48, which contains the amino terminus, and a p68 fragment, which contains the A/B pocket and the carboxyl terminus. This hypothesis was supported by the fact that the p48 and p68 fragments had selective binding affinity to different RB antibodies and that the p48 was found only in the low-salt-extracted cytoplasmic fraction, while the p68 was only in the nuclear fraction, of the apoptotic cells. However, the nuclear binding partner of the p68 RB fragment is not the transcription factor E2F-1 since a specific E2F-1 antibody coimmunoprecipitated only the unphosphorylated form of RB, but not the p68 fragment. Lastly, we confirmed that RB also underwent dephosphorylation and carboxyl terminal cleavage during apoptosis, as we and others reported previously.

A prospective evaluation of alcohol-assisted versus mechanical epithelial removal before photorefractive keratectomy

OBJECTIVE

The purpose of the study is to compare alcohol-assisted versus mechanical debridement of the corneal epithelium before photorefractive keratectomy (PRK) for low-to-moderate myopia.

DESIGN

A prospective study was performed on a group of consecutive patients operated on at the Massachusetts Eye and Ear Infirmary from February to April 1996 and followed for 6 months.

PARTICIPANTS

Eighty patients (eyes) were divided in 2 groups: 40 alcohol and 40 mechanical.

INTERVENTION

The patients underwent PRK for myopia (-1.5 to -7.5 diopters) with a Summit Apex excimer laser. The corneal epithelium was removed either with 20% ethanol or with a scalpel blade.

MAIN OUTCOME MEASURES

The two groups were compared for epithelial removal time, epithelial defect size at the end of surgery, and rate of re-epithelialization. Uncorrected visual acuity (UCVA), refractive outcome, best-corrected visual acuity (BCVA), and subjective haze were measured at 4 days and at 1, 3, and 6 months. In an additional short-term study, 40 patients (20 alcohol, 20 mechanical) had intraoperative pachymetry performed.

RESULTS

Alcohol-assisted de-epithelialization was faster than mechanical debridement (107 [+/-20.6 standard deviation] versus 141 [+/-30.5] seconds [P < 0.0001]) and led to a more circumscribed and reproducible epithelial defect at the end of surgery (87,739 [+/-11,852] versus 103,518 [+/-33,942] square pixels [t test, P = 0.04; f test, P = 0.001]). At 4 days, 95% of the alcohol-treated patients had healed compared with 78% of the mechanically scraped patients (Fisher's exact test, P = 0.04). The alcohol group had a better UCVA at 4 days (logarithm of the minimum angle of resolution UCVA 0.36 [+/-0.22] versus 0.51 [+/-0.26]) and at 1 month (0.14 [+/-0.17] versus 0.22 [+/-0.16] [Mann-Whitney U test, P = 0.02 and P = 0.03]) but equalized at 3 months (0.10 [+/-0.14] versus 0.13 [+/-0.16]) and at 6 months (0.11 [+/-0.15] versus 0.14 [+/-0.13] [Mann-Whitney U test, P = 0.23 and P = 0.34]). There was a trend toward less subjective haze in the alcohol-treated patients over the course of the study (area under the curve, 71.9 [+/-35.3] versus 87.9 [+/-33.8] [Mann-Whitney U test, P = 0.07]). The difference from target was equivalent in both groups at 6 months (-0.22 [+/-0.58] diopter in the alcohol group and -0.43 [+/-0.52] diopter in the mechanical group [t test, P = 0.14; f test, P = 0.57]). There were no differences in intraoperative pachymetry, corneal uniformity index as calculated from the corneal topography, and loss of BCVA between the two groups.

CONCLUSIONS

Twenty percent ethanol is a simple, safe, and effective alternative to mechanical scraping before PRK and appears to be associated with a quicker visual rehabilitation.

Fas stimulation induces RB dephosphorylation and proteolysis that is blocked by inhibitors of the ICE protease family

Fas antigen is a member of the tumor necrosis factor/nerve growth factor receptor family. Stimulation of Fas by Fas ligand or agonistic antibodies results in the activation of interleukin-1 beta converting enzyme-like (ICE-like) proteases, and proteolytic cleavage of poly(ADP-ribose) polymerase (PARP). Ultimately, Fas activation leads to apoptotic cell death. The importance of PARP cleavage to the death process remains unclear. We have hypothesized that the cleavage of other cellular substrates may be important for Fas-mediated apoptosis. Here we show that stimulation of Fas results in significant alterations of retinoblastoma protein (RB). Treatment of Jurkat cells, a human leukemic T cell line, with anti-Fas induces dephosphorylation of RB, followed by proteolytic cleavage. These events precede internucleosomal DNA fragmentation. Dephosphorylation and cleavage of RB are inhibited by a specific tetrapeptide inhibitor of ICE-like proteases or by expression of cowpox virus CrmA protein or the Bcl-2 oncoprotein. Inhibition of these RB changes correlates with inhibition of apoptosis. We propose that cleavage of RB may represent an important step in the pathway of Fas-mediated apoptotic cell death.

Failure to activate interleukin 1beta-converting enzyme-like proteases and to cleave retinoblastoma protein in drug-resistant cells

We previously found that retinoblastoma (RB) is cleaved at the initiation of apoptotic execution. Here we report that when an HL-60 cell line resistant to cytosine arabinoside (Ara-C) was exposed to this anticancer drug, neither RB cleavage nor apoptosis was detected. Consistent with that, processing of interleukin 1beta-converting enzyme (ICE) and CPP32 (an ICE-like protease) was also prevented in these cells. In contrast, treatment of the HL-60-Ara-C-resistant cells with etoposide induced all of these apoptotic events. Furthermore, the etoposide-induced RB cleavage was inhibited by a specific tetrapeptide ICE-like inhibitor. Our results demonstrate that activation of the RB cleavage enzyme, an ICE-like protease, is required for overcoming drug resistance.

Cleavage of retinoblastoma protein during apoptosis: an interleukin 1 beta-converting enzyme-like protease as candidate

We had found that in an early stage of DNA damage-induced, p53-independent apoptosis, retinoblastoma (RB) protein is hypophosphorylated to a p115 form by an activated serine/threonine phosphatase. Here, we report that accompanying the internucleosomal fragmentation of DNA, the newly formed p115/hypo/RB was immediately cleaved into at least two fragments, p68 and p48. The RB cleavage activity possessed properties of interleukin 1 beta-converting enzyme family. Addition of a specific tetrapeptide interleukin 1 beta-converting enzyme inhibitor prevented cleavage of p115/hypo/RB and early apoptotic cells from undergoing further apoptosis. We suggest that activation of the RB phosphatase and protease may be involved in mediating the two physiological stages of apoptosis, commitment and execution, respectively.

[Studies of chemopreventive agents against neoplasma: synthesis of 3-acetyl coumarin derivatives and relationship between antimutagenic activity and structure]

Twenty-five 3-acetylcoumarin derivatives were synthesized among which twenty-two were not reported before. Antimutagenic activity screen in vitro has shown that some of these compounds have various activities. The structure and activity relationship for 5-, 7-, 8-substituents has been studied. Pharmacological data showed that: the substituent on position 8 has important effect on its activity. When there is only a hydroxy group on position 7, its activity is the highest among those with other substituents, but when a methyl is on position 8, the order of the activity is reversed. Other trends have also been found which provided some clues for further structural modification.

Induction of a retinoblastoma phosphatase activity by anticancer drugs accompanies p53-independent G1 arrest and apoptosis

DNA-damaging agents induce accumulation of the tumor suppressor and G1 checkpoint protein p53, leading cells to either growth arrest in G1 or apoptosis (programmed cell death). The p53-dependent G1 arrest involves induction of p21 (also called WAF1/CIP1/SDI1), which prevents cyclin kinase-mediated phosphorylation of retinoblastoma protein (RB). Recent studies suggest a p53-independent G1 checkpoint as well; however, little is known about its molecular mechanisms. We report that induction of a protein-serine/threonine phosphatase activity by DNA damage signals is at least one of the mechanisms responsible for p53-independent, RB-mediated G1 arrest and consequent apoptosis. When two p53-null human leukemic cell lines (HL-60 and U-937) were treated with a variety of anticancer agents, RB became hypophosphorylated, accompanied with G1 arrest. This was followed immediately (in less than 30 min) by apoptosis, as determined by the accumulation of pre-G1 apoptotic cells and the internucleosomal fragmentation of DNA. Addition of calyculin A or okadaic acid (specific serine/threonine phosphatase inhibitors) or zinc chloride (apoptosis inhibitor) prevented the G1 arrest- and apoptosis-specific RB dephosphorylation. The levels of cyclin E- and cyclin A-associated kinase activities remained high during RB dephosphorylation, supporting the involvement of a chemotherapy-induced serine/threonine phosphatase(s) rather than p21. Furthermore, the induced phosphatase activity coimmunoprecipitated with the hyperphosphorylated RB and was active in a cell-free system that reproduced the growth arrest- and apoptosis-specific RB dephosphorylation, which was inhibitable by calyculin A but not zinc. We propose that the RB phosphatase(s) might be one of the p53-independent G1 checkpoint regulators.

Activation of cyclin E-dependent kinase by DNA-damage signals during apoptosis

Preexposure of HL-60 cells to a DNA-damaging agent, cytosine arabinoside (Ara-C), dramatically induced the levels of H1 kinase activities associated with cyclin E (CycE-H1K) but not cyclin A. This induction was cell cycle-independent and accompanied by loss of cell viability, a late event in apoptosis. When an Ara-C-resistant variant of HL-60 cells were treated with Ara-C at a low concentration, neither CycE-H1K nor apoptosis were observed. Both events were induced in the resistant cells but only after treatment with Ara-C at a much higher concentration for a longer period. The DNA-damage-induced CycE-H1K is proposed to be involved in a late apoptosis checkpoint.