Understanding monogenic Parkinson's disease at a global scale

Until recently, about three-quarters of all monogenic Parkinson's disease (PD) studies were performed in European/White ancestry, thereby severely limiting our insights into genotype-phenotype relationships at global scale. The first systematic approach to embrace monogenic PD worldwide, The Michael J. Fox Foundation Global Monogenic PD (MJFF GMPD) Project, contacted authors of publications reporting individuals carrying pathogenic variants in known PD-causing genes. In contrast, the Global Parkinson's Genetics Program's (GP2) Monogenic Network took a different approach by targeting PD centers not yet represented in the medical literature. Here, we describe combining both efforts in a "merger project" resulting in a global monogenic PD cohort with build-up of a sustainable infrastructure to identify the multi-ancestry spectrum of monogenic PD and enable studies of factors modifying penetrance and expression of monogenic PD. This effort demonstrates the value of future research based on team science approaches to generate comprehensive and globally relevant results.

GenoTools: An Open-Source Python Package for Efficient Genotype Data Quality Control and Analysis

GenoTools, a Python package, streamlines population genetics research by integrating ancestry estimation, quality control (QC), and genome-wide association studies (GWAS) capabilities into efficient pipelines. By tracking samples, variants, and quality-specific measures throughout fully customizable pipelines, users can easily manage genetics data for large and small studies. GenoTools' "Ancestry" module renders highly accurate predictions, allowing for high-quality ancestry-specific studies, and enables custom ancestry model training and serialization, specified to the user's genotyping or sequencing platform. As the genotype processing engine that powers several large initiatives including the NIH's Center for Alzheimer's and Related Dementias (CARD) and the Global Parkinson's Genetics Program (GP2). GenoTools was used to process and analyze the UK Biobank and major Alzheimer's Disease (AD) and Parkinson's Disease (PD) datasets with over 400,000 genotypes from arrays and 5000 sequences and has led to novel discoveries in diverse populations. It has provided replicable ancestry predictions, implemented rigorous QC, and conducted genetic ancestry-specific GWAS to identify systematic errors or biases through a single command. GenoTools is a customizable tool that enables users to efficiently analyze and scale genotype data with reproducible and scalable ancestry, QC, and GWAS pipelines.

Identification of genetic risk loci and causal insights associated with Parkinson's disease in African and African admixed populations: a genome-wide association study

BACKGROUND

An understanding of the genetic mechanisms underlying diseases in ancestrally diverse populations is an important step towards development of targeted treatments. Research in African and African admixed populations can enable mapping of complex traits, because of their genetic diversity, extensive population substructure, and distinct linkage disequilibrium patterns. We aimed to do a comprehensive genome-wide assessment in African and African admixed individuals to better understand the genetic architecture of Parkinson's disease in these underserved populations.

METHODS

We performed a genome-wide association study (GWAS) in people of African and African admixed ancestry with and without Parkinson's disease. Individuals were included from several cohorts that were available as a part of the Global Parkinson's Genetics Program, the International Parkinson's Disease Genomics Consortium Africa, and 23andMe. A diagnosis of Parkinson's disease was confirmed clinically by a movement disorder specialist for every individual in each cohort, except for 23andMe, in which it was self-reported based on clinical diagnosis. We characterised ancestry-specific risk, differential haplotype structure and admixture, coding and structural genetic variation, and enzymatic activity.

FINDINGS

We included 197 918 individuals (1488 cases and 196 430 controls) in our genome-wide analysis. We identified a novel common risk factor for Parkinson's disease (overall meta-analysis odds ratio for risk of Parkinson's disease 1·58 [95% CI 1·37-1·80], p=2·397 × 10-14) and age at onset at the GBA1 locus, rs3115534-G (age at onset β=-2·00 [SE=0·57], p=0·0005, for African ancestry; and β=-4·15 [0·58], p=0·015, for African admixed ancestry), which was rare in non-African or non-African admixed populations. Downstream short-read and long-read whole-genome sequencing analyses did not reveal any coding or structural variant underlying the GWAS signal. The identified signal seems to be associated with decreased glucocerebrosidase activity.

INTERPRETATION

Our study identified a novel genetic risk factor in GBA1 in people of African ancestry, which has not been seen in European populations, and it could be a major mechanistic basis of Parkinson's disease in African populations. This population-specific variant exerts substantial risk on Parkinson's disease as compared with common variation identified through GWAS and it was found to be present in 39% of the cases assessed in this study. This finding highlights the importance of understanding ancestry-specific genetic risk in complex diseases, a particularly crucial point as the Parkinson's disease field moves towards targeted treatments in clinical trials. The distinctive genetics of African populations highlights the need for equitable inclusion of ancestrally diverse groups in future trials, which will be a valuable step towards gaining insights into novel genetic determinants underlying the causes of Parkinson's disease. This finding opens new avenues towards RNA-based and other therapeutic strategies aimed at reducing lifetime risk of Parkinson's disease.

FUNDING

The Global Parkinson's Genetics Program, which is funded by the Aligning Science Across Parkinson's initiative, and The Michael J Fox Foundation for Parkinson's Research.

Elucidating causative gene variants in hereditary Parkinson's disease in the Global Parkinson's Genetics Program (GP2)

The Monogenic Network of the Global Parkinson's Genetics Program (GP2) aims to create an efficient infrastructure to accelerate the identification of novel genetic causes of Parkinson's disease (PD) and to improve our understanding of already identified genetic causes, such as reduced penetrance and variable clinical expressivity of known disease-causing variants. We aim to perform short- and long-read whole-genome sequencing for up to 10,000 patients with parkinsonism. Important features of this project are global involvement and focusing on historically underrepresented populations.

Genome-wide Association Identifies Novel Etiological Insights Associated with Parkinson's Disease in African and African Admixed Populations

Background

Understanding the genetic mechanisms underlying diseases in ancestrally diverse populations is a critical step towards the realization of the global application of precision medicine. The African and African admixed populations enable mapping of complex traits given their greater levels of genetic diversity, extensive population substructure, and distinct linkage disequilibrium patterns.

Methods

Here we perform a comprehensive genome-wide assessment of Parkinson's disease (PD) in 197,918 individuals (1,488 cases; 196,430 controls) of African and African admixed ancestry, characterizing population-specific risk, differential haplotype structure and admixture, coding and structural genetic variation and polygenic risk profiling.

Findings

We identified a novel common risk factor for PD and age at onset at the GBA1 locus (risk, rs3115534-G; OR=1.58, 95% CI = 1.37 - 1.80, P=2.397E-14; age at onset, BETA =-2.004, SE =0.57, P = 0.0005), that was found to be rare in non-African/African admixed populations. Downstream short- and long-read whole genome sequencing analyses did not reveal any coding or structural variant underlying the GWAS signal. However, we identified that this signal mediates PD risk via expression quantitative trait locus (eQTL) mechanisms. While previously identified GBA1 associated disease risk variants are coding mutations, here we suggest a novel functional mechanism consistent with a trend in decreasing glucocerebrosidase activity levels. Given the high population frequency of the underlying signal and the phenotypic characteristics of the homozygous carriers, we hypothesize that this variant may not cause Gaucher disease. Additionally, the prevalence of Gaucher's disease in Africa is low.

Interpretation

The present study identifies a novel African-ancestry genetic risk factor in GBA1 as a major mechanistic basis of PD in the African and African admixed populations. This striking result contrasts to previous work in Northern European populations, both in terms of mechanism and attributable risk. This finding highlights the importance of understanding population-specific genetic risk in complex diseases, a particularly crucial point as the field moves toward precision medicine in PD clinical trials and while recognizing the need for equitable inclusion of ancestrally diverse groups in such trials. Given the distinctive genetics of these underrepresented populations, their inclusion represents a valuable step towards insights into novel genetic determinants underlying PD etiology. This opens new avenues towards RNA-based and other therapeutic strategies aimed at reducing lifetime risk.

Research in Context

Evidence Before this Study

Our current understanding of Parkinson's disease (PD) is disproportionately based on studying populations of European ancestry, leading to a significant gap in our knowledge about the genetics, clinical characteristics, and pathophysiology in underrepresented populations. This is particularly notable in individuals of African and African admixed ancestries. Over the last two decades, we have witnessed a revolution in the research area of complex genetic diseases. In the PD field, large-scale genome-wide association studies in the European, Asian, and Latin American populations have identified multiple risk loci associated with disease. These include 78 loci and 90 independent signals associated with PD risk in the European population, nine replicated loci and two novel population-specific signals in the Asian population, and a total of 11 novel loci recently nominated through multi-ancestry GWAS efforts.Nevertheless, the African and African admixed populations remain completely unexplored in the context of PD genetics.

Added Value of this Study

To address the lack of diversity in our research field, this study aimed to conduct the first genome-wide assessment of PD genetics in the African and African admixed populations. Here, we identified a genetic risk factor linked to PD etiology, dissected African-specific differences in risk and age at onset, characterized known genetic risk factors, and highlighted the utility of the African and African admixed risk haplotype substructure for future fine-mapping efforts. We identified a novel disease mechanism via expression changes consistent with decreased GBA1 activity levels. Future large scale single cell expression studies should investigate the neuronal populations in which expression differences are most prominent. This novel mechanism may hold promise for future efficient RNA-based therapeutic strategies such as antisense oligonucleotides or short interfering RNAs aimed at preventing and decreasing disease risk. We envisage that these data generated under the umbrella of the Global Parkinson's Genetics Program (GP2) will shed light on the molecular mechanisms involved in the disease process and might pave the way for future clinical trials and therapeutic interventions. This work represents a valuable resource in an underserved population, supporting pioneering research within GP2 and beyond. Deciphering causal and genetic risk factors in all these ancestries will help determine whether interventions, potential targets for disease modifying treatment, and prevention strategies that are being studied in the European populations are relevant to the African and African admixed populations.

Implications of all the Available Evidence

We nominate a novel signal impacting GBA1 as the major genetic risk factor for PD in the African and African admixed populations. The present study could inform future GBA1 clinical trials, improving patient stratification. In this regard, genetic testing can help to design trials likely to provide meaningful and actionable answers. It is our hope that these findings may ultimately have clinical utility for this underrepresented population.

[Clinicopathological features of early gastric cancer after Helicobacter pylori eradication]

Objective: To investigate the clinicopathological features of early gastric cancers after Helicobacter pylori (H. pylori) eradication. Methods: The clinical data of 26 cases of gastric cancer that were diagnosed after H. pylori eradication and 45 cases without H. pylori eradication in the 989 Hospital of the Joint Logistics Support Force of the People's Liberation Army (the former 152 Hospital), Pingdingshan, China from 2013 to 2021 were collected. The histological, immunophenotypic and clinical characteristics of the two groups were compared, and discussed with review of the related literature. Results: Among the gastric cancer patients with H. pylori eradication, there were 20 males and 6 females with a median age of 65 years (range 53 to 77 years). The cancer involved the upper part of the stomach in 12 cases, the middle part of the stomach in 4 cases, and the lower part of the stomach in 10 cases. The median diameter of the tumors was 12 mm (range 4-29 mm). According to the Paris Classification, 4 cases were 0-Ⅱa, 4 cases were 0-Ⅱb, 18 cases were 0-Ⅱc. White light endoscopy showed that the lesions were reddish to yellowish. The lesion boundary was clear in 12 cases and was unclear or gastritis-like changes in 14 cases, while the irregular microvascular structure and microsurface structure, as well as the relatively visible spinous boundary, were visible under narrow-band imaging. There were 20 cases of well-differentiated tubular adenocarcinoma, 4 cases of highly to moderately differentiated tubular adenocarcinoma, and 2 cases of well-differentiated tubular adenocarcinoma with papillary adenocarcinoma. Compared with gastric cancers without H. pylori eradication, gastric cancers diagnosed after H. pylori eradication was associated with lower nucleus-cytoplasm ratio (<50%), normal epithelial coverage on the cancer surface, mild atypical epithelial coverage on the cancer surface, elongation of non-cancerous glands in the cancer tissue and subepithelial progression of cancerous glands were higher (P<0.05). The cellular immunophenotypes were gastric type in 6 cases, intestinal type in 4 cases and gastrointestinal mixed type in 16 cases. Conclusions: The early gastric cancers diagnosed after H. pylori eradication are more subtle clinically and mostly well-differentiated tubular adenocarcinoma. The important morphological features of gastric cancer diagnosed after H. pylori eradication are decreased cytological atypia and overlying normal epithelium or mildly atypical epithelium of the cancer. Understanding and recognizing these morphological features are helpful to make correct endoscopic and pathological diagnoses.

Structural variant-based pangenome construction has low sensitivity to variability of haplotype-resolved bovine assemblies

Advantages of pangenomes over linear reference assemblies for genome research have recently been established. However, potential effects of sequence platform and assembly approach, or of combining assemblies created by different approaches, on pangenome construction have not been investigated. Here we generate haplotype-resolved assemblies from the offspring of three bovine trios representing increasing levels of heterozygosity that each demonstrate a substantial improvement in contiguity, completeness, and accuracy over the current Bos taurus reference genome. Diploid coverage as low as 20x for HiFi or 60x for ONT is sufficient to produce two haplotype-resolved assemblies meeting standards set by the Vertebrate Genomes Project. Structural variant-based pangenomes created from the haplotype-resolved assemblies demonstrate significant consensus regardless of sequence platform, assembler algorithm, or coverage. Inspecting pangenome topologies identifies 90 thousand structural variants including 931 overlapping with coding sequences; this approach reveals variants affecting QRICH2, PRDM9, HSPA1A, TAS2R46, and GC that have potential to affect phenotype.

A 1-bp deletion in bovine QRICH2 causes low sperm count and immotile sperm with multiple morphological abnormalities

Background

Semen quality and insemination success are monitored in artificial insemination bulls to ensure high male fertility rates. Only ejaculates that fulfill minimum quality requirements are processed and eventually used for artificial inseminations. We examined 70,990 ejaculates from 1343 Brown Swiss bulls to identify bulls from which all ejaculates were rejected due to low semen quality. This procedure identified a bull that produced 12 ejaculates with an aberrantly small number of sperm (0.2 ± 0.2 × 109 sperm per mL) which were mostly immotile due to multiple morphological abnormalities.

Results

The genome of this bull was sequenced at a 12× coverage to investigate a possible genetic cause. Comparing the sequence variant genotypes of this bull with those from 397 fertile bulls revealed a 1-bp deletion in the coding sequence of the QRICH2 gene which encodes the glutamine rich 2 protein, as a compelling candidate causal variant. This 1-bp deletion causes a frameshift in translation and a premature termination codon (ENSBTAP00000018337.1:p.Cys1644AlafsTer52). The analysis of testis transcriptomes from 76 bulls showed that the transcript with the premature termination codon is subject to nonsense-mediated mRNA decay. The 1-bp deletion resides in a 675-kb haplotype that includes 181 single nucleotide polymorphisms (SNPs) from the Illumina BovineHD Bead chip. This haplotype segregates at a frequency of 5% in the Brown Swiss cattle population. Our analysis also identified another bull that carried the 1-bp deletion in the homozygous state. Semen analyses from the second bull confirmed low sperm concentration and immotile sperm with multiple morphological abnormalities that primarily affect the sperm flagellum and, to a lesser extent, the sperm head.

Conclusions

A recessive loss-of-function allele of the bovine QRICH2 gene likely causes low sperm concentration and immotile sperm with multiple morphological abnormalities. Routine sperm analyses unambiguously identify homozygous bulls for this allele. A direct gene test can be implemented to monitor the frequency of the undesired allele in cattle populations.

Infertility due to defective sperm flagella caused by an intronic deletion in DNAH17 that perturbs splicing

Artificial insemination in pig (Sus scrofa domesticus) breeding involves the evaluation of the semen quality of breeding boars. Ejaculates that fulfill predefined quality requirements are processed, diluted and used for inseminations. Within short time, eight Swiss Large White boars producing immotile sperm that had multiple morphological abnormalities of the sperm flagella were noticed at a semen collection center. The eight boars were inbred on a common ancestor suggesting that the novel sperm flagella defect is a recessive trait. Transmission electron microscopy cross-sections revealed that the immotile sperm had disorganized flagellar axonemes. Haplotype-based association testing involving microarray-derived genotypes at 41,094 SNPs of six affected and 100 fertile boars yielded strong association (P = 4.22 × 10-15) at chromosome 12. Autozygosity mapping enabled us to pinpoint the causal mutation on a 1.11 Mb haplotype located between 3,473,632 and 4,587,759 bp. The haplotype carries an intronic 13-bp deletion (Chr12:3,556,401-3,556,414 bp) that is compatible with recessive inheritance. The 13-bp deletion excises the polypyrimidine tract upstream exon 56 of DNAH17 (XM_021066525.1: c.8510-17_8510-5del) encoding dynein axonemal heavy chain 17. Transcriptome analysis of the testis of two affected boars revealed that the loss of the polypyrimidine tract causes exon skipping which results in the in-frame loss of 89 amino acids from DNAH17. Disruption of DNAH17 impairs the assembly of the flagellar axoneme and manifests in multiple morphological abnormalities of the sperm flagella. Direct gene testing may now be implemented to monitor the defective allele in the Swiss Large White population and prevent the frequent manifestation of a sterilizing sperm tail disorder in breeding boars.

Activation of cryptic splicing in bovine WDR19 is associated with reduced semen quality and male fertility

Cattle are ideally suited to investigate the genetics of male reproduction, because semen quality and fertility are recorded for all ejaculates of artificial insemination bulls. We analysed 26,090 ejaculates of 794 Brown Swiss bulls to assess ejaculate volume, sperm concentration, sperm motility, sperm head and tail anomalies and insemination success. The heritability of the six semen traits was between 0 and 0.26. Genome-wide association testing on 607,511 SNPs revealed a QTL on bovine chromosome 6 that was associated with sperm motility (P = 2.5 x 10⁻²⁷), head (P = 2.0 x 10⁻⁴⁴) and tail anomalies (P = 7.2 x 10⁻⁴⁹) and insemination success (P = 9.9 x 10⁻¹³). The QTL harbors a recessive allele that compromises semen quality and male fertility. We replicated the effect of the QTL on fertility (P = 7.1 x 10⁻³²) in an independent cohort of 2481 Brown Swiss bulls. The analysis of whole-genome sequencing data revealed that a synonymous variant (BTA6:58373887C>T, rs474302732) in WDR19 encoding WD repeat-containing protein 19 was in linkage disequilibrium with the fertility-associated haplotype. WD repeat-containing protein 19 is a constituent of the intraflagellar transport complex that is essential for the physiological function of motile cilia and flagella. Bioinformatic and transcription analyses revealed that the BTA6:58373887 T-allele activates a cryptic exonic splice site that eliminates three evolutionarily conserved amino acids from WDR19. Western blot analysis demonstrated that the BTA6:58373887 T-allele decreases protein expression. We make the remarkable observation that, in spite of negative effects on semen quality and bull fertility, the BTA6:58373887 T-allele has a frequency of 24% in the Brown Swiss population. Our findings are the first to uncover a variant that is associated with quantitative variation in semen quality and male fertility in cattle.

In cattle farming, artificial insemination is the most common method of breeding. To ensure high fertilization rates, ejaculate quality and insemination success are closely monitored in artificial insemination bulls. We analyse semen quality, insemination success and microarray-called genotypes at more than 600,000 genome-wide SNP markers of 794 bulls to identify a recessive allele that compromises semen quality. We take advantage of whole-genome sequencing to pinpoint a variant in the coding sequence of WDR19 encoding WD repeat-containing protein 19 that activates a novel exonic splice site. Our results indicate that cryptic splicing in WDR19 is associated with reduced male reproductive performance. This is the first report of a variant that contributes to quantitative variation in bovine semen quality.

Multi-trait meta-analyses reveal 25 quantitative trait loci for economically important traits in Brown Swiss cattle

Background

Little is known about the genetic architecture of economically important traits in Brown Swiss cattle because only few genome-wide association studies (GWAS) have been carried out in this breed. Moreover, most GWAS have been performed for single traits, thus not providing detailed insights into potentially existing pleiotropic effects of trait-associated loci.

Results

To compile a comprehensive catalogue of large-effect quantitative trait loci (QTL) segregating in Brown Swiss cattle, we carried out association tests between partially imputed genotypes at 598,016 SNPs and daughter-derived phenotypes for more than 50 economically important traits, including milk production, growth and carcass quality, body conformation, reproduction and calving traits in 4578 artificial insemination bulls from two cohorts of Brown Swiss cattle (Austrian-German and Swiss populations). Across-cohort multi-trait meta-analyses of the results from the single-trait GWAS revealed 25 quantitative trait loci (QTL; P < 8.36 × 10^− 8) for economically relevant traits on 17 Bos taurus autosomes (BTA). Evidence of pleiotropy was detected at five QTL located on BTA5, 6, 17, 21 and 25. Of these, two QTL at BTA6:90,486,780 and BTA25:1,455,150 affect a diverse range of economically important traits, including traits related to body conformation, calving, longevity and milking speed. Furthermore, the QTL at BTA6:90,486,780 seems to be a target of ongoing selection as evidenced by an integrated haplotype score of 2.49 and significant changes in allele frequency over the past 25 years, whereas either no or only weak evidence of selection was detected at all other QTL.

Conclusions

Our findings provide a comprehensive overview of QTL segregating in Brown Swiss cattle. Detected QTL explain between 2 and 10% of the variation in the estimated breeding values and thus may be considered as the most important QTL segregating in the Brown Swiss cattle breed. Multi-trait association testing boosts the power to detect pleiotropic QTL and assesses the full spectrum of phenotypes that are affected by trait-associated variants.

Electronic supplementary material

The online version of this article (10.1186/s12864-019-6066-6) contains supplementary material, which is available to authorized users.

Genome-wide association study for αS1- and αS2-casein phosphorylation in Dutch Holstein Friesian

Phosphorylation of caseins (CN) is a crucial post-translational modification that allows caseins to form colloid particles known as casein micelles. Both α_S1- and α_S2-CN show varying degrees of phosphorylation (isoforms) in cow milk and were suggested to be more relevant for stabilizing internal micellar structure than β- and κ-CN. However, little is known about the genetic background of individual α_S2-CN phosphorylation isoforms and the phosphorylation degrees of α_S1- and α_S2-CN (α_S1-CN PD and α_S2-CN PD), defined as the proportion of isoforms with higher degrees of phosphorylation in total α_S1- and α_S2-CN, respectively. We aimed to identify genomic regions associated with these traits using 50K single nucleotide polymorphisms for 1,857 Dutch Holstein Friesian cows. A total of 10 quantitative trait loci (QTL) regions were identified for all studied traits on 10 Bos taurus autosomes (BTA1, 2, 6, 9, 11, 14, 15, 18, 24, and 28). Regions associated with multiple traits were found on BTA1, 6, 11, and 14. We showed 2 QTL regions on BTA1, one affecting α_S2-CN production and the other harboring the SLC37A1 gene, which encodes a phosphorus antiporter and affects α_S1- and α_S2-CN PD. The QTL on BTA6 harbors the casein gene cluster and affects individual α_S2-CN phosphorylation isoforms. The QTL on BTA11 harbors the PAEP gene that encodes for β-lactoglobulin and affects relative concentrations of α_S2-CN-10P and α_S2-CN-11P as well as α_S1-CN PD and α_S2-CN PD. The QTL on BTA14 harbors the DGAT1 gene and affects relative concentrations of α_S2-CN-10P and α_S2-CN-11P as well as α_S1-CN PD and α_S2-CN PD. Our results suggest that effects of identified genomic regions on phosphorylation of α_S1- and α_S2-CN are related to changes in milk synthesis and phosphorus secretion in milk. The actual roles of SLC37A1, PAEP, and DGAT1 in α_S1- and α_S2-CN phosphorylation in Dutch Holstein Friesian require further investigation.

[Analysis of occupational chronic carbon disulfide poisoning: a study of 372 cases]

Objective: To investigate the clinical features of occupational chronic carbon disulfide(CS(2)) poisoning. Methods: A total of 372 patients with occupational chronic CS(2) poisoning were selected from a chemical fiber factory, and their clinical features were summarized and analyzed. Results: Major clinical manifestations of the 372 patients with occupational chronic CS(2) poisoning included sleep disorders, dizziness, headache, and numbness of limbs, and the detection rates of these manifestations were 84.7%, 84.4%, 79.8%, and 72.8%, respectively. Electroneuromyography showed peripheral nerve injuries. Conclusion: Occupational chronic CS(2) poisoning can affect the central and peripheral nervous system.

Elliptically bent crystal x-ray spectrometer for time-resolved laser plasma experiments

Measuring time-resolved spectra is crucial in inertial confinement fusion and radiation source development experiments. An elliptically bent crystal spectrometer is designed to measure X-rays in the range of 2.5-11.0 keV, which was achieved using four different lattice spacings of 0.8512, 0.6687, 0.4246, and 0.2749 nm with spectral resolution E/δE of ∼500. The X-rays emitted from a source at one focus of the ellipse undergo Bragg reflection off a crystal and pass through the second focus of the ellipse to a streak camera slit with 18-mm length and 80-μm width to generate a time-resolved spectrum. An alignment method for the time-resolved spectrometer was developed with the straight line connecting the centers of the two small holes on the fabricated substrate being the axis of the ellipse, thus allowing the spacing between the source and the elliptical crystal to be tuned to couple with the streak camera. The time-resolved spectrometer's performance was experimentally tested at the Shenguang II laser facility. The results indicate that its performance is close to that predicted theoretically.

Genetic parameters for αS1-casein and αS2-casein phosphorylation isoforms in Dutch Holstein Friesian

Relative concentrations of α_S1-casein and α_S2-casein (α_S1-CN and α_S2-CN) phosphorylation isoforms vary considerably among milk of individual cows. We estimated heritabilities for α_S2-CN phosphorylation isoforms, determined by capillary zone electrophoresis from 1,857 morning milk samples, and genetic correlations among α_S2-CN phosphorylation isoforms in Dutch Holstein Friesian. To investigate if phosphorylation of α_S1-CN and α_S2-CN are due to the same genetic mechanism, we also estimated genetic correlations between α_S1-CN and α_S2-CN phosphorylation isoforms as well as the genetic correlations between the phosphorylation degrees (PD) of α_S1-CN and α_S2-CN defined as the proportion of isoforms with higher degrees of phosphorylation in total α_S1-CN and α_S2-CN, respectively. The intra-herd heritabilities for the relative concentrations of α_S2-CN phosphorylation isoforms were high and ranged from 0.54 for α_S2-CN-10P to 0.89 for α_S2-CN-12P. Furthermore, the high intra-herd heritabilities of α_S1-CN PD and α_S2-CN PD imply a strong genetic control of the phosphorylation process, which is independent of casein production. The genetic correlations between α_S2-CN phosphorylation isoforms are positive and moderate to high (0.33-0.90). Furthermore, the strong positive genetic correlation (0.94) between α_S1-CN PD and α_S2-CN PD suggests that the phosphorylation processes of α_S1-CN and α_S2-CN are related. This study shows the possibility of breeding for specific α_S1-CN and α_S2-CN phosphorylation isoforms, and relations between the phosphorylation degrees of α_S1-CN and α_S2-CN and technological properties of milk need to be further investigated to identify potential benefits for the dairy industry.

A pinhole camera for ultrahigh-intensity laser plasma experiments

A pinhole camera is an important instrument for the detection of radiation in laser plasmas. It can monitor the laser focus directly and assist in the analysis of the experimental data. However, conventional pinhole cameras are difficult to use when the target is irradiated by an ultrahigh-power laser because of the high background of hard X-ray emission generated in the laser/target region. Therefore, an improved pinhole camera has been developed that uses a grazing-incidence mirror that enables soft X-ray imaging while avoiding the effect of hard X-ray from hot dense plasmas.

Genetic and nongenetic factors contributing to differences in αS-casein phosphorylation isoforms and other major milk proteins

Relative concentrations of α_S-casein (α_S-CN) phosphorylation isoforms vary considerably among milk of individual cows. We aimed to explore to what extent genetic and other factors contribute to the variation in relative concentrations of α_S-CN phosphorylation isoforms and the phosphorylation degree of α_S-CN defined as the proportion of isoforms with higher degrees of phosphorylation. We also investigated the associations of genetic variants of milk proteins and casein haplotypes with relative concentrations of α_S-CN phosphorylation isoforms and with the phosphorylation degree of α_S-CN in French Montbéliarde cattle from the cheese production area of Franche-Comté. Detailed milk protein composition was determined by liquid chromatography coupled with electrospray ionization mass spectrometry from 531 test-day morning milk samples. Parity, lactation stage, and genetic variation of cows contributed to the phenotypic variation in relative concentrations of individual α_S-CN phosphorylation isoforms and in the phosphorylation degree of α_S-CN. As lactation progressed, we observed a significant increase for relative concentrations of α_S-CN isoforms with higher degrees of phosphorylation (α_S1-CN-9P, α_S2-CN-13P, and α_S2-CN-14P) as well as for the phosphorylation degree of both α_S1-CN and α_S2-CN. Furthermore, the β-CN I variant was associated with a greater proportion of isoforms with lower degrees of phosphorylation (α_S1-CN-8P, α_S2-CN-10P, and α_S2-CN-11P); the β-CN B variant was associated with a greater proportion of isoforms with higher degrees of phosphorylation (α_S1-CN-9P, α_S2-CN-12P to α_S2-CN-14P). The heritability estimates were low to moderate for relative concentrations of α_S2-CN phosphorylation isoforms (0.07 to 0.32), high for relative concentrations of α_S1-CN-8P (0.84) and α_S1-CN-9P (0.56), and moderate for phosphorylation degrees of α_S1-CN (0.37) and α_S2-CN (0.23). Future studies investigating relations between the phosphorylation degree of α_S-CN and technological properties of milk will be beneficial for the dairy industry.

[A clinical study of serum protein markers in patients with 1-bromopropane poisoning]

Objective: To investigate the changes in protein expression in patients with 1-bromopropane (1-BP) poisoning using high-throughput proteomic technique and to screen out protein markers. Methods: Serum samples were collected from 3 patients with 1-BP poisoning and 15 controls. The label-free proteomic tech-nique was used for the quantitation and identification of proteins expressed in these samples, and the results were compared between the patients with 1-BP poisoning and the control population. The bioinformatics tools were used to analyze the function of differentially expressed proteins. Results: Compared with the control popula-tion, the patients with 1-BP poisoning had >2-fold upregulation of 38 proteins and >2-fold downregulation of 68 proteins. The differentially expressed proteins were mainly involved in immune response, signal transduction, and stress response. Conclusion: The proteins screened out may be potential protein markers for 1-BP poison-ing, which provides reliable and precise methods and thoughts for the diagnosis of 1-BP poisoning.

[The research of proteome profiling change of 1-bromopropane poisoning cases]

Objective: This study was mainly focused on styudy on he proteome profile change between exposure to 1-Bromopropane (1-BP) and 1-BP poisoning. Methods: The samples of serums from exposure to 1-BP and 1-BP poisoning were collected and analyzed through Label free proteome technology platform. The differently expressed proteins between the two groups were quantified and identified, followed by function analysis by bioinformatics. Results: 127 proteins over 2 fold-change were selected, in which 39 proteins were up-regulated and 88 proteins were down-regulated. These different-ly expressed proteins were mainly involved in the process of enzyme active regulation, inflammatory reaction, protein modification, stress response, coagulation, transport. Conclusion: The differently expressed proteins provided the potential protein biomarkers for the early diagnosis of 1-BP poisoning and was beneficial for clinical diagnosis of 1-BP and understanding of the mechanism of 1-BP poisoning.

The relationships among bovine αS-casein phosphorylation isoforms suggest different phosphorylation pathways

Casein (CN) phosphorylation is an important posttranslational modification and is one of the key factors responsible for constructing and stabilizing casein micelles. Variation in phosphorylation degree of αS-CN is of great interest because it is suggested to affect milk technological properties. This study aimed to investigate the variation in phosphorylation degree of αS-CN among milk of individual cows and to explore relationships among different phosphorylation isoforms of αS-CN. For this purpose, we analyzed morning milk samples from 529 French Montbéliarde cows using liquid chromatography coupled with electrospray ionization mass spectrometry. We detected 3 new phosphorylation isoforms: αS2-CN-9P, αS2-CN-14P, and αS2-CN-15P in bovine milk, in addition to the known isoforms αS1-CN-8P, αS1-CN-9P, αS2-CN-10P, αS2-CN-11P, αS2-CN-12P, and αS2-CN-13P. The relative concentrations of each αS-CN phosphorylation isoform varied considerably among individual cows. Furthermore, the phenotypic correlations and hierarchical clustering suggest at least 2 regulatory systems for phosphorylation of αS-CN: one responsible for isoforms with lower levels of phosphorylation (αS1-CN-8P, αS2-CN-10P, and αS2-CN-11P), and another responsible for isoforms with higher levels of phosphorylation (αS1-CN-9P, αS2-CN-12P, αS2-CN-13P, and αS2-CN-14P). Identifying all phosphorylation sites of αS2-CN and investigating the genetic background of different αS2-CN phosphorylation isoforms may provide further insight into the phosphorylation mechanism of caseins.

G-CSF-mobilized peripheral blood mononuclear cells from diabetic patients augment neovascularization in ischemic limbs but with impaired capability

BACKGROUND

Autologous transplantation of mobilized peripheral blood mononuclear cells (M-PBMNCs) is a novel approach to improve critical limb ischemia (CLI) in diabetes. However, endothelial progenitor cells (EPCs) from diabetes are dysfunctional and impaired in ischemia-induced neovascularization.

OBJECTIVE

This study aimed to confirm the compromised efficiency of diabetic M-PBMNCs in therapeutic neovascularization, and to determine the underlying mechanisms of this impairment.

METHODS

Diabetic M-PBMNCs from 17 diabetic patients or healthy controls, or phosphate-buffered saline (PBS) were injected into the ischemic limbs of streptozotocin-induced diabetic nude mice. The limb blood perfusion, ambulatory score, ischemia damage, capillary/fiber ratio, arteriole density, collateral vessel formation, and pericytes recruitment were evaluated between these three groups. Non-invasive real time image and histopathology were used to detect the in vivo role of transplanted M-PBMNCs. Proliferation and adhesion of EPCs were assayed. In vitro vascular network incorporation and matrigel plug assay were used to test the pro-neovascularization role of M-PBMNCs.

RESULTS

Transplantation of diabetic M-PBMNCs also improved neovascularization, but to a lesser extent from that observed with non-diabetic ones. This was associated with the impairment of diabetic M-PBMNCs capacity to differentiate into EPCs, to incorporate into vessel-like tubules in vitro, to participate in vascular-like structure formation in a subcutaneous matrigel plug, and to stimulate the recruitment of pericytes/smooth muscle cells. In addition, there was impairment in vasculogenesis, which was related to the reduced adhesion ability of EPCs from diabetic M-PBMNCs.

CONCLUSIONS

Diabetes reduced the capacity of M-PBMNCs to augment neovascularization in ischemia.

The transcription factor E2F: a crucial switch in the control of homeostasis and tumorigenesis

The transcription factor E2F plays a crucial role in governing cell proliferation through manipulation of the expression of many genes required for cell cycle progression. As studies are exploring in depth, E2F has grown into a multimember family and has been required for the regulation of a large number of genes involved in various cellular processes. The expanding E2F membership and biological function provide us some new insights relating to the evolution of E2F. One of them is to understand the exact mechanisms by which E2F executes in these different cellular processes during ontogenesis. This review summarizes recent advances in this field, with an emphasis on a notion that E2F acts as a molecular switch in the control of both normal cell and tumor development.

ATM induction insufficiency in a radiosensitive breast-cancer patient

The ataxia telangiectasia (A-T) gene (ATM) is a dominant breast cancer gene with tumour suppressor activity. ATM also regulates cellular sensitivity to ionising radiation (IR) presumably through its role as a facilitator of DNA repair. In normal cells and tissues the ATM protein is rapidly induced by IR to threshold/maximum levels. The kinase function of the ATM protein is also rapidly activated in response to IR. The fact that women carriers of ATM mutations can have an increased risk of developing breast cancer and that many sporadic breast tumours have reduced levels of the ATM protein broadens the scope of ATM's tumour suppressor within the breast. This report describes the downregulation of ATM protein levels in a radiosensitive breast cancer patient. Postinduction ATM levels were up to tenfold lower in the patient's fresh tissues compared to normal controls. These results might indicate a much broader role for ATM anomalies in breast cancer aetiology.

[Experimental study on effect of xinfeng capsule in treating rats' adjuvant arthritis on ultrastructure of synoviocyte and splenic lymphocyte]

OBJECTIVE

To observe the effect of Xinfeng capsule (XFC) on the ultrastructure of synoviocyte and splenic lymphocyte in rat adjuvant arthritis (AA) model.

METHODS

Sixty rats were randomly divided into normal control group, model group, XFC group and Tripterygium wilfordii polycoside (TP) group, 15 in each. Complete adjuvant 0.1 ml was injected into right posterior metatarsus of rats subcutaneously to induce inflammation, except that in the normal control. The ultrastructural change including mitochondria swelling, vacuolation and ridge pathologic change of synoviocyte and splenic lymphocyte was observed by transmission electron microscopy (TEM). The mitochondria lesion rate (MLR) of each group was then calculated.

RESULTS

The swelling degree of right posterior metatarsus in XFC and TP group obviously lowered after treatment (P < 0.05). MLR of synoviocyte in the XFC group and the TP group after treatment was also obviously lower than that in the model group (P < 0.05). MLR of splenic lymphocyte in the XFC group reduced markedly (P < 0.05) after treatment, while in the TP group, the change was insignificant (P > 0.05). In comparison with TP group, the reduction of both MLR of synoviocyte and splenic lymphocyte after treatment in the XFC group was more significant (P < 0.05).

CONCLUSION

XFC could lower the degree of swelling in AA rats like TP did, but XFC could improve ultrastructural change of rat's synovicocyte and splenic lymphocyte better than that of TP, which was likely the morphological basis of XFC's therapeutical effect.

Pressure dependence of the melting temperature of rare-gas solids

According to Lindemann's law and the Debye model and with the assumption that the volume derivative [Formula: see text] of the Grüineisen parameter [Formula: see text] is a constant depending on the material, we present a new expression for the analysis of the experimental data for the melting temperature of solids under a high pressure. The test on rare-gas solids (Ne, Ar, Kr and Xe) shows that the calculated results are in good agreement with the corresponding experimental data.