Species identification of Bombyx mori and Antheraea pernyi silk via immunology and proteomics

Evidence of the use of silk by bronze age civilization for sacrificial purposes in the Yangtze River basin of China

Silk was the driving force behind the opening of the Silk Road, positioning this material as a global commodity that greatly influenced the progress of human civilization. Due to the natural protein properties of silk, the internal structure and external characteristics of silk cultural relics are irreversibly destroyed during the process of burial or when passed down through the generations until the production information and material components completely disappear, making it difficult to obtain direct archaeological evidence for pinpointing the origin of silk. The sacrificial pits at the Sanxingdui archaeologcal site, located in Guanghan, Sichuan, China, have been found with layers of ash above the layers of artifacts and some bronzes with fabric traces. Among the artifacts, one grid-like ware artifact first appeared in the Bronze Age in China. The two sides of the grid-like ware were grid-like ovals made of bronze material, and inside, there was an oval-shaped complete piece of jade with a bent back. Fabric traces were found on both the jade and bronze surfaces. In order to determine the specific function of fabric at this site, the developed silk fibroin immunoaffinity column (IAC) enrichment technique combined with enzyme-linked immunosorbent assay (ELISA), morphology observation and proteomics were used to identify mineralized fabric material and fabric residues in the ash layer. Silk residues were successfully detected, which confirmed the early use of silk as a material carrier to communicate between Heaven and Earth and provided archaeological evidence for the cultural origins of silk.

Application of ELISA in Cultural Heritage: Recent Advances and Challenges

Organic residue analyses have long been the primary focus and challenge in the fields of scientific archaeology and cultural heritage. Enzyme-linked immunosorbent assay (ELISA) has emerged as a valuable method for detecting organic residues owing to its high sensitivity and specificity. Organic components have been observed within four categories of archaeological artifacts: mortars, adhesives, animal and plant remains, and daily use artifacts. Therefore, in this article, we critically analyzed the advantages and limitations of ELISA in detecting organic residues by tracking its recent application in the abovementioned categories. The current focus of ELISA applications is on the preparation of customized antibodies, development of multicomponent detection methods, and meeting on-site identification demands. Additionally, understanding organic residue degradation mechanisms and the proper handling of archaeological samples are also key factors in these applications. Integration of ELISA with biomolecular science and electrochemistry has allowed the development of comprehensive detection and analyses. In the future, ELISA will be capable of handling more complex and diverse analyses, revealing highly intricate information from archaeological samples.

Molecular Evidence of Structural Changes in Silk Using Unlimited Degradation Mass Spectrometry

Proteomics has important uses in archeological science because it can distinguish species, reveal the evolution of paleontology, and provide biological evidence of historical events. However, this technique still has full potential in the study of silk aging mechanisms. In this work, we propose a strategy combining unlimited degradation with mass-spectrometry-based proteomics techniques, which interpret protein fragmentation propensity and secondary structure changes by detecting content changes of specific peptide groups in complex proteomes. This approach was employed to study the conformational changes in silk microscopic crystals after heat treatment. Combining conventional mechanics and crystallographic characterization, a thermal aging degradation mechanism model was proposed. At the same time, it explained the interesting problem that the crystallinity remained unchanged, but the mechanical properties decreased significantly. Focusing on the unlimited degradation process, this method will be widely applicable to the study of silk and wool aging processes and regenerated silk fibroin.

Effect of cocooning conditions on the structure, carbon and nitrogen isotope ratios of silks

The stable isotope technique provides the possibility to trace ancient textiles because the technique is associated with advantages such as trace indication, fast detection, and accurate results. Since different cocooning conditions may impact cocoons even under identical habitats, it is important to investigate the effects of different cocooning temperatures and humidity on the isotope incorporation values in the cocoons. In this study, silk fibers were reeled under different conditions of temperature and humidity, followed by analysis of the secondary structure of cocoon proteins and isotope incorporation patterns. We found that the deviations in carbon isotope values of silk under different cocooning conditions could reach up to 0.76‰, while the deviation in carbon isotope values at different locations of a single silk was 2.75‰. Further, during the cocooning process, depletion of the 13C-isotope at different locations of the silk fibers was observed, reducing the δ13C values. We proposed that the changes in carbon isotopes in silk were related to the content of sericin and silk fibroin in silk. Finally, we did not observe a significant difference in isotope ratios in degummed cocoons. In summary, the 13C isotope was enriched in sericin, whereas 15N was enriched in fibroin, and these findings provide basic information for tracing the provenance of silks.

Species identification of silks by protein mass spectrometry reveals evidence of wild silk use in antiquity

Silk has been a luxurious commodity throughout modern human history and sericulture has played an important role in ancient global trade as well as technological and cultural developments. Archaeological findings suggest that prior to domestication of the mulberry silkworm (Bombyxmori) silks were obtained from a range of silk-producing moth species with regional specificity. However, investigating the origins of sericulture is difficult as classification of silks by species-type has proved technically challenging. We therefore investigated a range of methods for solubilising modern and archaeological silks and developed a mass spectrometry-based proteomics method that was able to successfully differentiate modern Bombyx,Antheraea, and Samia-produced silks down to the species level. We subsequently analysed archaeological silk materials excavated from the ancient city of Palmyra. Solubilisation behaviour and proteomic analysis provided evidence that the Palmyra silks were constructed from wild silk derived from Antheraeamylitta, the Indian Tasar silkworm. We believe this is the first species-level biochemical evidence that supports archaeological theories about the production and trade of Indian wild silks in antiquity.

Rapid Enrichment and Detection of Silk Residues from Tombs by Double-Antibody Sandwich ELISA Based on Immunomagnetic Beads

The extraction and identification of silk residues in tombs is of great significance for studying the distribution and spread of early silk. However, the complex organic matter in the tomb hinders the accurate identification of silk. In this study, a double-antibody sandwich enzyme-linked immunosorbent assay (ELISA) based on immunomagnetic beads (IMBs) was developed for the rapid enrichment and detection of silk residues. The double-antibody sandwich ELISA method established by pairing the IMBs prepared by the silk fibroin monoclonal antibody SF-3 and the silk fibroin monoclonal-labeled antibody bio-SF-1 had the highest detection sensitivity, with a linear detection range of 10 to 10⁴ ng mL^-1 and a detection limit of 5.12 ng mL^-1. This method was excellent in the extraction and analysis of silk residues from archaeological imprints and soil samples and successfully identified silk residues in samples at the final stage of silk degradation (physical invisible silk). The proteomics analysis results demonstrated the feasibility and practicability of this method.

SGID: a comprehensive and interactive database of the silkworm

Although the domestic silkworm (Bombyx mori) is an important model and economic animal, there is a lack of comprehensive database for this organism. Here, we developed the silkworm genome informatics database (SGID). It aims to bring together all silkworm-related biological data and provide an interactive platform for gene inquiry and analysis. The function annotation in SGID is thorough and covers 98% of the silkworm genes. The annotation details include function description, Gene Ontology, Kyoto Encyclopedia of Genes and Genomes pathway, subcellular location, transmembrane topology, protein secondary/tertiary structure, homologous group and transcription factor. SGID provides genome-scale visualization of population genetics test results based on high-depth resequencing data of 158 silkworm samples. It also provides interactive analysis tools of transcriptomic and epigenomic data from 79 NCBI BioProjects. SGID will be extremely useful to silkworm research in the future.