Integration of cloud-based molecular networking and docking for enhanced umami peptide screening from Pixian douban.

This study presents an innovative cloud-based approach, using Pixian Douban, a well-known Chinese fermented seasoning, as a case study, to improve the identification of umami peptides and explore their interactions with the T1R1/T1R3 receptor. A feature-based molecular networking method was utilized to rapidly identify a total of eighteen peptides, including seven previously unrecorded ones. Notably, the umami threshold of QIVK in an aqueous solution was determined to be 0.3215 mmol/L, surpassing the majority of peptides reported in the past three years. Molecular docking analysis further revealed the strong binding of QIVK to T1R3 receptor residues through hydrogen bonds, as well as interactions via salt bridges and electrostatic attractions. As a result, this research significantly contributes to the efficient screening of umami peptides and the elucidation of the molecular basis of umami sensory perception in complex food systems.

Vector solitonic pulses excitation in microresonators via free carrier effects.

We numerically investigate the excitation of vector solitonic pulse with orthogonally polarized components via free-carrier effects in microresonators with normal group velocity dispersion (GVD). The dynamics of single, dual and oscillated vector pulses are unveiled under turn-key excitation with a single frequency-fixed CW laser source. Parameter spaces associated with detuning, polarization angle, interval between the pumped orthogonal resonances and pump amplitude have been revealed. Different vector pulse states can also be observed exploiting the traditional pump scanning scheme. Simultaneous and independent excitation regimes are identified due to varying interval of the orthogonal pump modes. The nonlinear coupling between two modes contributes to the distortion of the vector pulses' profile. The free-carrier effects and the pump polarization angle provide additional degrees of freedom for efficiently controlling the properties of the vector solitonic microcombs. Moreover, the crucial thermal dynamics in microcavities is discussed and weak thermal effects are found to be favorable for delayed vector pulse formation. These findings reveal complex excitation mechanism of solitonic structures and could provide novel routes for microcomb generation.

Assembling a Heterobimetallic Actinide Metal-Organic Framework by a Reaction-Induced Preorganization Strategy.

Periodically arranging coordination-distinct actinides into one crystalline architecture is intriguing but of great synthetic challenge. We report a rare example of a heterobimetallic actinide metal-organic framework (An-MOF) by a unique reaction-induced preorganization strategy. A thorium MOF (SCU-16) with the largest unit cell among all Th-MOFs was prepared as the precursor, then the uranyl was precisely embedded into the MOF precursor under oxidation condition. Single crystal of the resulting thorium-uranium MOF (SCU-16-U) shows that a uranyl-specific site was in situ induced by the formate-to-carbonate oxidation reaction. The heterobimetallic SCU-16-U exhibits multifunction catalysis properties derived from two distinct actinides. The strategy proposed here offers a new avenue to create mixed-actinide functional material with unique architecture and versatile functionality.

Metabolite fingerprinting of the ripening process in Pixian douban using a feature-based molecular network and metabolomics analysis.

The unique flavor of Pixian douban (PXDB) is widely acknowledged to be associated with its maturation process. However, there is limited knowledge about the non-volatile metabolites that contribute to this flavor. To bridge this gap, this study employed a metabolomics approach and a feature-based molecular network (FBMN) analysis to investigate the non-volatile metabolite fingerprints of PXDB during its two-year maturation process. Specifically, the FBMN tool was utilized to annotate the flavonoid, amide derivatives, and lipid components of PXDB for the first time. Subsequently, the MolNetEnhancer tool was employed to complement the FBMN annotation and identify eight substructural components. Finally, metabolomics analysis was carried out to identify 45 key metabolites involved in flavor formation across 10 major metabolic pathways (p < 0.05). Overall, the findings of this study have significantly expanded our understanding of the non-volatile metabolite fingerprinting and flavor formation mechanisms.

Forensic characteristics and genetic substructure analysis of the Handan Han population, Northern China.

We analysed the forensic characteristics and substructure of the Handan Han population based on 36 Y-STR (short tandem repeat) and Y-SNP (single nucleotide polymorphism) markers. The two most dominant haplogroups in Handan Han, O2a2b1a1a1-F8 (17.95%) and O2a2b1a2a1a (21.51%), and their abundant downstream branches, reflected the strong expansion of the precursor of the Hans in Handan. The present results enrich the forensic database and explore the genetic relationships between Handan Han and other neighbouring and/or linguistically close populations, which suggests that the current concise overview of the Han intricate substructure remains oversimplified.

[Research progress of anterior cruciate ligament reconstruction with over-the-top technique].

Objective: To review the research progress regarding the over-the-top technique for anterior cruciate ligament (ACL) reconstruction. Methods: The relevant literature on ACL reconstruction using the over-the-top technique was analyzed for its evolution, clinical application, advantages, and limitations. Results: Over-the-top technique for ACL reconstruction is a combined intra- and extra-articular technique. Because it avoids drilling the femoral tunnel, its advantages are mainly highlighted in the protection of the femur. Therefore, it is widely used in children and adolescents with epiphyseal occlusion and in patients with revision reconstruction. In addition, significant improvements in postoperative joint stability, functional scores, and return to exercise rates are found in long-term follow-up studies of patients with primary ACL reconstruction and combined anterolateral tenodesis. However, the technique also has some limitations, such as poor stability of knee flexion after operation, high requirement for graft length, and easy impact of graft in the intercondylar fossa. Conclusion: The current research results show the effectiveness and safety of the over-the-top technique for primary and revision ACL reconstruction, with the advantages of wide application, simple operation, and quick recovery; however, more researches are needed to further optimize the selection of grafts and femoral condyle management problems, and to clarify the long-term effectiveness.

Strategies to mitigate the on- and off-target toxicities of recombinant immunotoxins: an antibody engineering perspective.

Targeted cancer therapies using immunotoxins have achieved remarkable efficacy in hematological malignancies. However, the clinical development of immunotoxins is also faced with many challenges like anti-drug antibodies and dose-limiting toxicity issues. Such a poor efficacy or safety ratio is also the major hurdle in the research and development of antibody-drug conjugates. From an antibody engineering perspective, various strategies were summarized or proposed to tackle the notorious on-target off-tumor toxicity issues, including passive strategy (XTENylation of immunotoxins) and active strategies (modulating the affinity and valency of the targeting moiety of immunotoxins, conditionally activating immunotoxins in the tumor microenvironments and reconstituting split toxin to reduce systemic toxicity, etc.). By modulating the functional characteristics of the targeting moiety and the toxic moiety of immunotoxins, selective tumor targeting can be augmented while sparing the healthy cells in normal tissues expressing the same target of interest. If successful, the improved therapeutic index will likely help to address the dose-limiting toxicities commonly observed in the clinical trials of various immunotoxins.

[Relative molecular mass distribution and monosaccharide composition of polysaccharides in Polygonatum kingianum var.grandifolium].

Polygonatum kingianum var.grandifolium, different from most Polygonatum species in biological characteristics, sprouts and blooms in spring and autumn, respectively, and it is evergreen in winter.It is difficult to learn from the patterns of other Polygonatum plants because the chemical composition in P.kingianum var.grandifolium changes with phenology, which consequently restricts the production of high-quality medicinal and eatable substances.Samples of P.kingianum var.grandifolium in different months and ages collected from Xiushan, Chongqing were analyzed for polysaccharide content, polysaccharide relative molecular mass, and mono-saccharide composition by anthrone-sulfuric acid colorimetric assay, high-performance gel-permeation chromatography, and trimethylsilane(TMS) derivatization prior to GC-MS.The results showed that the polysaccharide content and composition in the rhizome of P.kingianum var.grandifolium were closely related to the growth period.New shoot sprouting promoted the accumulation of polysaccharides, and flowering and fruiting consumed polysaccharides.The highest polysaccharide content was found in April, reaching 134.04 mg·g~(-1).Polysaccharides in P.kingianum var.grandifolium were divided into five fractions according to the weight-average M_W, i.e., P1(2.02×10~7), P2(5.09×10~6), P3(1.37×10~6), P4(4.73×10~5), and P5(5.11×10~3), and P5 had the highest content.In terms of monosaccharide composition, polysaccharides were mainly composed of fructose, glucose, galactose, mannose, xylose, and arabinose with the average molar ratio of 1.31∶1.00∶0.90∶0.53∶0.22∶0.21.The results of the study provide a scientific basis for the precise harvesting and resource utilization of P.kingianum var.grandifolium.

Whole mitochondrial genome analysis of the Daur ethnic minority from Hulunbuir in the Inner Mongolia Autonomous Region of China.

BACKGROUND: Mitochondrial DNA (mtDNA) variations are often associated with bioenergetics, disease, and speciation and can be used to track the history of women. Although advances in massively parallel sequencing (MPS) technology have greatly promoted our understanding of the population's history (especially genome-wide data and whole Y chromosome sequencing), the whole mtDNA sequence of many important groups has not been fully studied. In this study, we employed whole mitogenomes of 209 healthy and unrelated individuals from the Daur group, a Mongolic-speaking representative population of the indigenous groups in the Heilongjiang River basin (also known as the Amur River basin). RESULTS: The dataset presented 127 distinct mtDNA haplotypes, resulting in a haplotype diversity of 0.9933. Most of haplotypes were assigned to eastern Eurasian-specific lineages, such as D4 (19.62%), B4 (9.09%), D5 (7.66%) and M7 (4.78%). Population comparisons showed that the Daurians do have certain connections with the ancient populations in the Heilongjiang River basin but the matrilineal genetic composition of the Daur group was also greatly influenced by other non-Mongolic groups from neighboring areas. CONCLUSIONS: Collectively, the whole mtDNA data generated in the present study will augment the existing mtDNA database. Our study provides genetic links between the Daur population and the aborigine peoples from Siberia and the Amur-Ussuri Region. But on the whole, compared with other Mongolic-speaking groups, the modern Daur population is closer to the East Asian ancestry group.

[Polygonati Rhizoma: a crop with potential of being consumed as food and medicine].

As revealed by the investigation on the name change, biological characteristics, artificial cultivation, and edible history of Polygonatum kingianum var. grandifolium, it was described as a variation pattern of P. kingianum in the Chinese version of Flora of China(1978) and as a variant of P. kingianum in the revised English version of the Flora of China(2000). P. kingianum var. grandifolium, long been consumed as food by local folks, has been widely cultivated in its natural distribution area and circulated as Polygonati Rhizoma in the market. The important biological properties of P. kingianum var. grandifolium make it possess a great potential of being consumed as both medicine and food. The shoots of P. kingianum var. grandifolium sprout immediately out of the ground after seed germination and a new seedling will be formed at the same year, implying that its seedling cultivation period is at least two years shorter than that of P. cyrtonema. It can sprout more than twice a year, and the adult plants always remain evergreen, thereby obtaining higher biomass. Its rhizome biomass can be more than one time higher than that of P. cyrtonema. With reference to the diploid P. cyrtonema, flow cytometry revealed the polyploid and aneuploid forms in natural populations, which were tall and light-adapted with large underground rhizome. It can grow normally under the forest canopy and in the open field. Furthermore, P. kingianum var. grandifolium has important theoretical values for the study of ploidy variation, bud dormancy mechanism, etc.

Dual origins of the Northwest Chinese Kyrgyz: the admixture of Bronze age Siberian and Medieval Niru'un Mongolian Y chromosomes.

The Kyrgyz are a trans-border ethnic group, mainly living in Kyrgyzstan. Previous genetic investigations of Central Asian populations have repeatedly investigated the Central Asian Kyrgyz. However, from the standpoint of human evolution and genetic diversity, Northwest Chinese Kyrgyz is one of the more poorly studied populations. In this study, we analyzed the non-recombining portion of the Y-chromosome from 298 male Kyrgyz samples from Xinjiang Uygur Autonomous Region in northwestern China, using a high-resolution analysis of 108 biallelic markers and 17 or 24 STRs. First, via a Y-SNP-based PCA plot, Northwest Chinese Kyrgyz tended to cluster with other Kyrgyz population and are located in the West Asian and Central Asian group. Second, we found that the Northwest Chinese Kyrgyz display a high proportion of Y-lineage R1a1a1b2a2a-Z2125, related to Bronze Age Siberian, and followed by Y-lineage C2b1a3a1-F3796, related to Medieval Niru'un Mongols, such as Uissun tribe from Kazakhs. In these two dominant lineages, two unique recent descent clusters have been detected via NETWORK analysis, respectively, but they have nearly the same TMRCA ages (about 13th-14th centuries). This finding once again shows that the expansions of Mongol Empire had a striking effect on the Central Asian gene pool.

Forensic application of a novel MPS-based panel (90 STRs and 100 SNPs) in a non-exclusion parentage case with three autosomal STRs incompatibilities.

In kinship tests, the investigating of the forensic STRs usually provides decisive information to resolve relationship cases. We describe a parentage case with 3 genetic incompatibilities (D6S1043, D18S51 and D2S1338) between the child and alleged parent. With 90 STR loci and 100 SNP loci, the massively parallel sequencing (MPS)-based genotyping results support the certainty of parentage, and the mismatched alleles were considered to be mutations. MPS can provide additional allele sequence structures that can be used to infer the origins of the mutations. SNPs as supplementary markers can provide effective information to give an unequivocal statement of the parentage.

Polygonati Rhizoma: a crop with potential of being consumed as food and medicine / 中国中药杂志

As revealed by the investigation on the name change, biological characteristics, artificial cultivation, and edible history of Polygonatum kingianum var. grandifolium, it was described as a variation pattern of P. kingianum in the Chinese version of Flora of China(1978) and as a variant of P. kingianum in the revised English version of the Flora of China(2000). P. kingianum var. grandifolium, long been consumed as food by local folks, has been widely cultivated in its natural distribution area and circulated as Polygonati Rhizoma in the market. The important biological properties of P. kingianum var. grandifolium make it possess a great potential of being consumed as both medicine and food. The shoots of P. kingianum var. grandifolium sprout immediately out of the ground after seed germination and a new seedling will be formed at the same year, implying that its seedling cultivation period is at least two years shorter than that of P. cyrtonema. It can sprout more than twice a year, and the adult plants always remain evergreen, thereby obtaining higher biomass. Its rhizome biomass can be more than one time higher than that of P. cyrtonema. With reference to the diploid P. cyrtonema, flow cytometry revealed the polyploid and aneuploid forms in natural populations, which were tall and light-adapted with large underground rhizome. It can grow normally under the forest canopy and in the open field. Furthermore, P. kingianum var. grandifolium has important theoretical values for the study of ploidy variation, bud dormancy mechanism, etc.

27 Y-chromosomal STR haplotypic structure for the Chinese Han population from Changchun, Northeastern China.

Y- Changchun is the capital and largest city of Jilin Province in the northeast China. In this study, we genotyped and investigated haplotypes of 27 Y-STR loci in 1037 Changchun Han male individuals using commercially available AmpFlSTR Yfiler® Plus kit. We calculated the Gene diversity (GD) values and haplotype diversity (HD) as important forensic parameters. Furthermore, we observed genetic affinities between Changchun Han with other Northern Han Chinese populations and also Korans in Yanbian in the Multidimensional scaling and phylogenetic tree analysis.

Haplotype analysis of 36 Y-STR loci in a Chinese Han population from Anhui Province, Eastern China.

We analyzed haplotypes for 36 Y chromosomal STRs (Y-STRs), including 27 Yfiler Plus loci and 9 additional STRs (DYS549, DYS643, DYS508, DYS447, DYS596, DYS444, DYS557, and DYS527a/b) in 2018 unrelated Chinese Han individuals from Anhui Province using DNATyperTM 36Y Kit. Phylogenetic analysis was performed to determine the genetic relationship of the Anhui Han population with other neighboring and/or linguistically close populations.

Y-chromosome evidence confirmed the Kerei-Abakh origin of Aksay Kazakhs.

Aksay Kazakhs are the easternmost branch of Kazakhs, residing in Jiuquan city, the forefront of the ancient Silk Road. However, the genetic diversity of Aksay Kazakhs and its relationships with other Kazakhs still lack attention. To clarify this issue, we analyzed the non-recombining portion of the Y-chromosome from 93 Aksay Kazakhs samples, using a high-resolution analysis of 106 biallelic markers and 17 STRs. The lowest haplogroup diversity (0.38) was observed in Aksay Kazakhs among all studied Kazakh populations. The social and cultural traditions of the Kazakhs shaped their current pattern of genetic variation. Aksay Kazakhs tended to migrate with clans and had limited paternal admixture with neighboring populations. Aksay Kazakhs had the highest frequency (80%) of haplogroup C2b1a3a1-F3796 (previous C3*-Star Cluster) among the investigated Eurasian steppe populations, which was now seen as the genetic marker of Kerei clan. Furthermore, NETWORK analysis indicated that Aksay Kazakhs originated from sub-clan Kerei-Abakh in Kazakhstan with DYS448 = 23. TMRCA estimates of three recent descent clusters detected in C2*-M217 (xM48) network, one of which incorporate nearly all of the C2b1a3a1-F3796 Aksay Kazakhs samples, gave the age range of 976-1405 YA for DC1, 1059-1314 YA for DC2, and 1139-1317 YA for DC3, respectively; this is coherent with the 7th to the 11th centuries Altaic-speaking pastoral nomadic population expansion.

Paternal heritage of the Han Chinese in Henan province (Central China): high diversity and evidence of in situ Neolithic expansions.

Background: Due to their long history, complex admixture processes and large population sizes, more research is required to explore the fine genetic structure of Han populations from different geographic locations of China.Aim: To characterise the paternal genetic structure of the Han Chinese in Henan province, which was once the central living region of the ancient Huaxia population, the precursors of the Han Chinese.Subjects and methods: We sequenced Y chromosomes of 60 males from Zhengzhou, Henan Province, and reconstructed a phylogenetic tree for these samples with age estimation.Results: We observed high diversity of paternal lineages in our collection. We found that the in situ Neolithic expansion of the "Major lineages" contributed to a large portion of the paternal gene pool of the Han population in Henan Province. We also detected a large number of "Minor lineages" that diverged in the Palaeolithic Age.Conclusion: We suggest that the high genetic diversity in the paternal gene pool of modern Han populations is mainly attributed to the reservation of a larger number of lineages that diverged in the Palaeolithic Age, while the recent expansion of limited lineages contributed to the majority of the gene pool of modern Han populations. We propose that such a structure is a basal characteristic for the genetic structure of modern Han populations.

Reprogramming of sugar transport pathways in Escherichia coli using a permeabilized SecY protein-translocation channel.

In the initial step of sugar metabolism, sugar-specific transporters play a decisive role in the passage of sugars through plasma membranes into cytoplasm. The SecY complex (SecYEG) in bacteria forms a membrane channel responsible for protein translocation. The present work shows that permeabilized SecY channels can be used as nonspecific sugar transporters in Escherichia coli. SecY with the plug domain deleted allowed the passage of glucose, fructose, mannose, xylose, and arabinose, and, with additional pore-ring mutations, facilitated lactose transport, indicating that sugar passage via permeabilized SecY was independent of sugar stereospecificity. The engineered E. coli showed rapid growth on a wide spectrum of monosaccharides and benefited from the elimination of transport saturation, improvement in sugar tolerance, reduction in competitive inhibition, and prevention of carbon catabolite repression, which are usually encountered with native sugar uptake systems. The SecY channel is widespread in prokaryotes, so other bacteria may also be engineered to utilize this system for sugar uptake. The SecY channel thus provides a unique sugar passageway for future development of robust cell factories for biotechnological applications.

How black tea pigment theaflavin dyes chicken eggs: Binding affinity study of theaflavin with ovalbumin.

Theaflavin (TF), which is the key pigment in black tea, is a health-promoting food component with beneficial effects on humans. However, the interactions by which these effects are transferred and exerted into protein-rich foods are unclear. Here, egg ovalbumin (OVA) was selected as a representative dietary protein to ascertain their binding mechanism. Steady-state, time-resolved fluorescence and isothermal titration calorimetric results showed that TF can interact well with OVA with an affinity magnitude of 104. The noncovalent binding was mainly driven by hydrophobic interaction and hydrogen bonds. Structural analysis displayed that the TF binding pocket significantly overlapped with one of the surrounding specific IgE-binding epitopes, thereby causing a subtle structural adjustment on the secondary conformation of OVA. The biological complexation model that was delineated here will help understand how black tea dyes egg white in tea egg products and for the development of protein-rich carriers in functional foods.