On-capillary alkylation micro-reactor: a facile strategy for proteo-metabolome profiling in the same single cells.

Single-cell multi-omics analysis can provide comprehensive insights to study cell-to-cell heterogeneity in normal and disease physiology. However, due to the lack of amplification technique, the measurement of proteome and metabolome in the same cell is challenging. Herein, a novel on-capillary alkylation micro-reactor (OCAM) was developed to achieve proteo-metabolome profiling in the same single cells, by which proteins were first covalently bound to an iodoacetic acid functionalized open-tubular capillary micro-reactor via sulfhydryl alkylation reaction, and metabolites were rapidly eluted, followed by on-column digestion of captured proteins. Compared with existing methods for low-input proteome sample preparation, OCAM exhibited improved efficiency, anti-interference ability and recovery, enabling the identification of an average of 1509 protein groups in single HeLa cells. This strategy was applied to single-cell proteo-metabolome analysis of mouse oocytes at different stages, 3457 protein groups and 171 metabolites were identified in single oocytes, which is the deepest coverage of proteome and metabolome from single mouse oocytes to date, achieving complementary characterization of metabolic patterns during oocyte maturation.

Telomere-to-telomere pear (Pyrus pyrifolia) reference genome reveals segmental and whole genome duplication driving genome evolution.

Previously released pear genomes contain a plethora of gaps and unanchored genetic regions. Here, we report a telomere-to-telomere (T2T) gap-free genome for the red-skinned pear, 'Yunhong No. 1' (YH1; Pyrus pyrifolia), which is mainly cultivated in Yunnan Province (southwest China), the pear's primary region of origin. The YH1 genome is 501.20 Mb long with a contig N50 length of 29.26 Mb. All 17 chromosomes were assembled to the T2T level with 34 characterized telomeres. The 17 centromeres were predicted and mainly consist of centromeric-specific monomers (CEN198) and long terminal repeat (LTR) Gypsy elements (≥74.73%). By filling all unclosed gaps, the integrity of YH1 is markedly improved over previous P. pyrifolia genomes ('Cuiguan' and 'Nijisseiki'). A total of 1531 segmental duplication (SD) driven duplicated genes were identified and enriched in stress response pathways. Intrachromosomal SDs drove the expansion of disease resistance genes, suggesting the potential of SDs in adaptive pear evolution. A large proportion of duplicated gene pairs exhibit dosage effects or sub-/neo-functionalization, which may affect agronomic traits like stone cell content, sugar content, and fruit skin russet. Furthermore, as core regulators of anthocyanin biosynthesis, we found that MYB10 and MYB114 underwent various gene duplication events. Multiple copies of MYB10 and MYB114 displayed obvious dosage effects, indicating role differentiation in the formation of red-skinned pear fruit. In summary, the T2T gap-free pear genome provides invaluable resources for genome evolution and functional genomics.

High-Sensitivity Detection toward SARS-CoV-2 S1 Glycoprotein by Parallel Reaction Monitoring Mass Spectrometry.

The outbreak of coronavirus disease 2019 (COVID-19) has overwhelmed the global economy and human well-being. On account of the sharp increase in test demand, there is a need for an accurate and alternative diagnosis method for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). In this study, with the aim to specifically identify the trace SARS-CoV-2 S1 glycoprotein, we developed a high-sensitivity and high-selectivity diagnostic method based on the targeted parallel reaction monitoring (PRM) assay of eight selected peptides. This study emphasizes the outstanding detection sensitivity of 0.01 pg of the SARS-CoV-2 S1 glycoprotein even in the interference of other structural proteins, which to our knowledge is the current minimum limit of detection for the SARS-CoV-2 S1 glycoprotein. This technology could further identify 0.01 pg of the SARS-CoV-2 S1 glycoprotein in a spike pseudovirus, revealing its practical effectiveness. All our preliminary results throw light on the capability of the mass spectrometry-based targeted PRM assay to identify SARS-CoV-2 as a practicable orthogonal diagnostic tool. Furthermore, this technology could be extended to other pathogens (e.g., MERS-CoV S1 protein or SARS-CoV S1 protein) by quickly adjusting the targeted peptides of MS data acquisition. In summary, this strategy is universal and flexible and could be quickly adjusted to detect and discriminate different mutants and pathogens.

Phylogenetic analyses of 41 Y-STRs and machine learning-based haplogroup prediction in the Qingdao Han population from Shandong province, Eastern China.

BACKGROUND: Known for its rich history and culture, Qingdao is a typical symbol of Chinese maritime culture. Its unique genetic landscape has aroused interest among geneticists and forensic scientists. However, the genetic landscape of Qingdao has never been uncovered. AIM: This investigation intends to provide light on Qingdao's paternal genetic diversity and its evolutionary connections to other Han subgroups. SUBJECTS AND METHODS: The genetic polymorphisms of 41 Y-chromosomal short tandem repeat (STR) loci in the Qingdao Han were investigated using SureID® PathFinder Plus Kit. Phylogenetic studies were performed using genotype data from 52 East Asian groups at 23 common Y-STR loci. A multidimensional scaling plot and cladogram were constructed. Linear Discriminant Analysis (LDA) was carried out for predicting categories among the Han people. The k-nearest neighbour (kNN) algorithm was utilised to designate Y-SNP haplogroups for each haplotype. RESULTS: The Qingdao Han were genetically far from the Tibeto-Burman populations and close with the Han people from northern China. LDA indicated a deep integration among the present-day Han people. By the kNN model, the predicted O2a2 and O2a1 were shown to be the predominant Y-SNP haplogroups. CONCLUSIONS: This study would be helpful for reconstructing the patrilineal history in China and establishing a more comprehensive Y-STR database.

Transcription factor PyHY5 binds to the promoters of PyWD40 and PyMYB10 and regulates its expression in red pear 'Yunhongli No. 1'.

'Yunhongli No. 1' is a rare and well-colored red pear (Pyrus pyrifolia) germplasm resource, and is popular in the market due to its bright red color and high quality. Light induces the expression of transportation factor genes MYB10, WD40, and HY5, which then activate the expression of critical genes in the anthocyanin biosynthesis pathway to promote the synthesis and accumulation of anthocyanin, thus giving the red coloration. Protein HY5 is considered to be a key regulator for induction of anthocyanin biosynthesis. The MYB10 genes physically interact with HY5 to positively regulate anthocyanin biosynthesis in Arabidopsis, apple, and pear by binding to G-box motifs. However, how these transcription factors are regulated by sunlight remains unclear in 'Yunhongli No. 1'. In this study, the transcription factor PyHY5 was cloned, and subcellular localization assay showed that PyHY5 was distributed in the nucleus. The DNA fragments of PyHY5 had a typical BRLZ domain of the bZIP family, and then were aligned against the promoter sequences of PyMYB10 and PyWD40. Electrophoretic mobility shift and transient expression assays showed that PyHY5 could directly recognize and bind to the G-box motifs in the promoters of PyMYB10 and PyWD40, and so boosted transcriptional activation by co-expression. The results demonstrated that PyHY5 binding to G-box motifs of the promoters of PyMYB10 and PyWD40, enhanced its expression, and then promoted accumulation of anthocyanin in red 'Yunhongli No. 1'.

Characterization of the complete chloroplast genome of Pyrus pyrifolia 'Yunhongli No. 1'.

'Yunhongli No. 1' is a rare and well-colored red pear (Pyrus pyrifolia) germplasm resource, and is popular in the market due to its bright red color and high quality. This study used Illumina high-throughput sequencing technologies for red pear 'Yunhongli No. 1' of chloroplast genome sequencing and analysis. The genome features of P. pyrifolia 'Yunhongli No. 1' and the phylogenetic relationships were reported and established. The complete chloroplast genome is 160,113 bp in length, consisting of a pair of inverse duplication regions 26,386 bp, a large single-copy region 88,052 bp, and a small single-copy region 19,214 bp. The entire genome contains 80 messenger RNA (mRNA) genes, 30 transfer RNA (tRNA) genes, and 4 ribosomal RNA (rRNA) genes. The phylogenetic tree of 15 Rosaceae species revealed red pear 'Yunhongli No. 1' is more closely related to Pyrus communis × P. pyrifolia 'Greensis.'

Complete Genome Sequence of Vibrio mediterranei 117-T6, a Potentially Pathogenic Bacterium Isolated from the Conchocelis of Pyropia spp.

Vibrio mediterranei is a Gram-negative bacterium of the family Vibrionaceae. Vibrio mediterranei strain 117-T6 was pathogenic to Pyropia yezoensis, a red seaweed cultivated in China, by causing death to its conchocelis. Here, we report the complete genome sequence of Vibrio mediterranei 117-T6.