Characterization of Vitellogenin and Vitellogenin Receptor of Conopomorpha sinensis Bradley and Their Responses to Sublethal Concentrations of Insecticide

Conopomorpha sinensis Bradley is the dominant borer pest of Litchi chinesis and Euphoria longan. Current management of C. sinensis relies upon insecticide application to adult moths. In addition to the direct mortality induced by insecticides, a sublethal dose of insecticides also affects growth, survival, and reproduction in the exposed insects. Vitellogenin (Vg) and vitellogenin receptor (VgR) are normally identified as essential reproduction-related proteins in insects. In this study, we characterized these two genes from C. sinensis, and investigated their differential responses to sublethal concentrations of insecticide. Cloned CsVg and CsVgR consist of 5391 and 5424-bp open reading frames, which encode proteins of 1796 and 1807 amino acid residues, respectively. The CsVg protein contains the typical vitellogenin, DUF1943 and VWFD domains as other reported lepidopteran Vgs. The CsVgR was characterized as a typical low density lipoprotein receptor with two highly conserved LBD and EGF precursor domains, one hydrophobic transmembrane domain, one cytoplasmic domain, and 13 putative N-glycosylation sites. We next assessed the sublethal effect of four major insecticides on egg-laying in C. sinensis. The toxicity against C. sinensis varied among the insecticides tested, with LC50 values ranging from 0.23 ppm for chlorpyrifos to 20.00 ppm for β-cypermethrin, among which emamectin benzoate (EB) showed a significant negative impact on egg-laying, survival rate, ovarian development, and mating rate of C. sinensis at LC30 doses. Further investigation showed that the transcriptional level of CsVg and CsVgR were impaired in different way at 24, 48, and 72 h after EB exposure, and this result was in agreement with the diminished egg-laying of C. sinensis in the sublethal concentration EB-treated group. A repressed transcription level of CsVgR was observed at 48 h after treatment, suggesting that EB elicits a delayed response in the abundance of CsVgR. These results established different roles of CsVg and CsVgR in response to the sublethal effect of insecticides. CsVg might be a better parameter than CsVgR for assessing the effect of sublethal insecticides on reproduction in C. sinensis

Yeast Golden Gate: Standardized Assembly of S. cerevisiae Transcriptional Units

BBF RFC 88 describes a new standard for the assembly of basic Saccharomyces cerevisiae transcriptional units (TUs) consisting of a promoter/5’untranslated region (UTR), open reading frame (ORF), and 3’UTR/terminator. Note that we use the term “promoter” here to refer to both the promoter and the 5’ UTR, which we currently define as a single part. Future iterations of this standard will incorporate subdivision of currently defined parts e.g. into promoter and 5’ UTR. The standard makes use of the type IIS restriction enzyme BsaI to generate standardized and user­‐defined ‘signature overhangs’, thus enabling directional and seamless TU assembly. RFC88 is supported by the Yeast Standardized Collection of Parts for Expression (SCoPE), a repository of subcloned and sequence verified parts compatible with this assembly standard. The Yeast SCoPE is currently populated by a large number of S. cerevisiae promoters and terminators that facilitate expression and characterization of non­‐native ORFs

Chinese Open Instruction Generalist: A Preliminary Release

Instruction tuning is widely recognized as a key technique for building generalist language models, which has attracted the attention of researchers and the public with the release of InstructGPT~\citep{ouyang2022training} and ChatGPT\footnote{\url{https://chat.openai.com/}}. Despite impressive progress in English-oriented large-scale language models (LLMs), it is still under-explored whether English-based foundation LLMs can perform similarly on multilingual tasks compared to English tasks with well-designed instruction tuning and how we can construct the corpora needed for the tuning. To remedy this gap, we propose the project as an attempt to create a Chinese instruction dataset by various methods adapted to the intrinsic characteristics of 4 sub-tasks. We collect around 200k Chinese instruction tuning samples, which have been manually checked to guarantee high quality. We also summarize the existing English and Chinese instruction corpora and briefly describe some potential applications of the newly constructed Chinese instruction corpora. The resulting \textbf{C}hinese \textbf{O}pen \textbf{I}nstruction \textbf{G}eneralist (\textbf{COIG}) corpora are available in Huggingface\footnote{\url{https://huggingface.co/datasets/BAAI/COIG}} and Github\footnote{\url{https://github.com/FlagOpen/FlagInstruct}}, and will be continuously updated

Transatmospheric ileal stoma manometry can be applied for the early detection of stoma outlet obstruction

BackgroundStoma outlet obstruction (SOO) is a common complication of diverting ileostomy and usually detected at the advanced stage when the intestine is obviously obstructed. The objective of this study is to explore the efficacy of transatmospheric ileal stoma manometry (TISM) in early detection of SOO before the manifestation of intestinal obstruction.MethodsA single-center prospective study was performed in patients scheduled to undergo reversal ileostomy and laparoscopic anterior rectal resection and diverting ileostomy in Second Affiliated Hospital of Zhejiang University School of Medicine from 1st July 2022 to 31st December 2022. The stoma pressure was measured by TISM at different time points.ResultsThe mean stoma pressure of the 30 patients before reversal ileostomy was 5.21 cmH2O which was considered as normal standard of stoma pressure, and ranged from 1.2 to 8.56 cmH2O. After excluding two patients with anastomotic leakage, a total of 38 patients who were subjected to laparoscopic anterior rectal resection and diverting ileostomy were further included in this study. The incidence of anastomotic leakage was 5% and that of SOO was 12.5%. The mean postoperative obstruction time was 5.2 (3-7) days and the mean time from elevated stoma pressure to diagnosed as SOO was 2.8 (2-4) days in the five patients who developed SOO. The pressure measured at the third stoma manometry time point (second day after return of gut function) (10.23 vs. 6.04 cmH2O, p<0.001) and the postoperative hospital stay (10 vs. 8.49 days, p=0.028) showed significantly difference between the SOO and non-SOO groups. The pressures measured at the first time point (before return of gut function) (4 vs. 4.49 cmH2O, p=0.585), the second time point (the day of return of gut function) (6.8 vs. 5.62 cmH2O, p=0.123), and the fourth time point (discharge day) (5.88 vs. 5.9 cmH2O, p=0.933) showed no significant difference in both groups.ConclusionTISM can be utilized for early detection of SOO and can be incorporated as a novel diagnostic method together with abdominal CT scan to realize the goal of ERAS

Progress in the study of aging marker criteria in human populations

The use of human aging markers, which are physiological, biochemical and molecular indicators of structural or functional degeneration associated with aging, is the fundamental basis of individualized aging assessments. Identifying methods for selecting markers has become a primary and vital aspect of aging research. However, there is no clear consensus or uniform principle on the criteria for screening aging markers. Therefore, we combine previous research from our center and summarize the criteria for screening aging markers in previous population studies, which are discussed in three aspects: functional perspective, operational implementation perspective and methodological perspective. Finally, an evaluation framework has been established, and the criteria are categorized into three levels based on their importance, which can help assess the extent to which a candidate biomarker may be feasible, valid, and useful for a specific use context

YeastFab:the design and construction of standard biological parts for metabolic engineering in Saccharomyces cerevisiae

It is a routine task in metabolic engineering to introduce multicomponent pathways into a heterologous host for production of metabolites. However, this process sometimes may take weeks to months due to the lack of standardized genetic tools. Here, we present a method for the design and construction of biological parts based on the native genes and regulatory elements in Saccharomyces cerevisiae. We have developed highly efficient protocols (termed YeastFab Assembly) to synthesize these genetic elements as standardized biological parts, which can be used to assemble transcriptional units in a single-tube reaction. In addition, standardized characterization assays are developed using reporter constructs to calibrate the function of promoters. Furthermore, the assembled transcription units can be either assayed individually or applied to construct multi-gene metabolic pathways, which targets a genomic locus or a receiving plasmid effectively, through a simple in vitro reaction. Finally, using β-carotene biosynthesis pathway as an example, we demonstrate that our method allows us not only to construct and test a metabolic pathway in several days, but also to optimize the production through combinatorial assembly of a pathway using hundreds of regulatory biological parts

The Crystal Structure and RNA-Binding of an Orthomyxovirus Nucleoprotein

Genome packaging for viruses with segmented genomes is often a complex problem. This is particularly true for influenza viruses and other orthomyxoviruses, whose genome consists of multiple negative-sense RNAs encapsidated as ribonucleoprotein (RNP) complexes. To better understand the structural features of orthomyxovirus RNPs that allow them to be packaged, we determined the crystal structure of the nucleoprotein (NP) of a fish orthomyxovirus, the infectious salmon anemia virus (ISAV) (genus Isavirus). As the major protein component of the RNPs, ISAV-NP possesses a bi-lobular structure similar to the influenza virus NP. Because both RNA-free and RNA-bound ISAV NP forms stable dimers in solution, we were able to measure the NP RNA binding affinity as well as the stoichiometry using recombinant proteins and synthetic oligos. Our RNA binding analysis revealed that each ISAV-NP binds ,12 nts of RNA, shorter than the 24ﾖ28 nts originally estimated for the influenza A virus NP based on population average. The 12-nt stoichiometry was further confirmed by results from electron microscopy and dynamic light scattering. Considering that RNPs of ISAV and the influenza viruses have similar morphologies and dimensions, our findings suggest that NP-free RNA may exist on orthomyxovirus RNPs, and selective RNP packaging may be accomplished through direct RNA-RNA interactions

Modeling Structure-Function Relationships in Synthetic DNA Sequences using Attribute Grammars

Recognizing that certain biological functions can be associated with specific DNA sequences has led various fields of biology to adopt the notion of the genetic part. This concept provides a finer level of granularity than the traditional notion of the gene. However, a method of formally relating how a set of parts relates to a function has not yet emerged. Synthetic biology both demands such a formalism and provides an ideal setting for testing hypotheses about relationships between DNA sequences and phenotypes beyond the gene-centric methods used in genetics. Attribute grammars are used in computer science to translate the text of a program source code into the computational operations it represents. By associating attributes with parts, modifying the value of these attributes using rules that describe the structure of DNA sequences, and using a multi-pass compilation process, it is possible to translate DNA sequences into molecular interaction network models. These capabilities are illustrated by simple example grammars expressing how gene expression rates are dependent upon single or multiple parts. The translation process is validated by systematically generating, translating, and simulating the phenotype of all the sequences in the design space generated by a small library of genetic parts. Attribute grammars represent a flexible framework connecting parts with models of biological function. They will be instrumental for building mathematical models of libraries of genetic constructs synthesized to characterize the function of genetic parts. This formalism is also expected to provide a solid foundation for the development of computer assisted design applications for synthetic biology