Biomedical subjects

Jindong Li

Publications and source records attributed to Jindong Li.

5 recordsLinked to original sources

PubMed2026

Natural variation in GmSOP5 regulates seed oil and protein content during soybean domestication.

Seed oil content, protein content, and yield are agronomically important, correlated traits that determine the economic value of soybean (Glycine max). However, improving seed quality and yield simultaneously is challenging because gains in one breeding target often compromise the other, and the genetic basis of this trade-off is poorly understood. Here, we performed a genome-wide association study of 429 diverse soybean accessions and identified Seed Oil and Protein 5 (SOP5), which encodes a kinesin protein, as a key locus associated with seed oil and protein content. Knockout and overexpression experiments demonstrated that GmSOP5 positively affects seed oil content and 100-seed weight and negatively influences seed protein content. GmSOP5 is located in a selective sweep region, and the domestication-related GmSOP5H1 allele is nearly fixed in cultivated soybean, contributing to increased seed size, weight, and oil content and reduced protein content. Field trials demonstrated that neither loss-of-function GmSOP5-edited mutants, which have increased seed protein content, nor GmSOP5-overexpression lines, which have increased seed oil content, differed significantly in yield from wild-type plants, because changes in plant architecture were offset by changes in seed weight. Our results shed light on soybean domestication and suggest how pleiotropy can be harnessed in breeding to enhance seed quality without compromising yield.

GWAS↗

PubMed2026

NanoSSL: attention mechanism-based self-supervised learning method for protein identification using nanopores.

MOTIVATION: Nanopores are cutting-edge interdisciplinary tools that can analyze biomolecules at the single-molecule level for many applications, e.g. DNA sequencing. Efforts are underway to extend nanopores to proteomics, including the development of machine learning algorithms for protein sequencing and identification. However, single-molecule data are intrinsically noisy and hard to process. Moreover, the development and performance of machine learning for nanopore is jeopardized by data scarcity. Self-supervised learning is an emerging method that may yield advantages in nanopore scenarios. RESULTS: We propose and experimentally validate Nanopore analysis using Self-Supervised Learning (NanoSSL), a generative self-supervised learning framework based on attention mechanisms for the identification of protein signals from nanopores. Leveraging a two-step approach consisting of self-supervised pre-training and supervised fine-tuning, NanoSSL learns useful feature representations from empirical data to facilitate downstream classification tasks. Inspired by the concept of fragmentation in conventional protein sequencing technologies, during pretraining each translocation event is split into multiple non-overlapping fragments of equal size, some of which are randomly masked and reconstructed using a masked autoencoder. Learning the feature representations of the reconstructed nanopore events facilitates molecular identification in fine-tuning. In this study, we retested a publicly available nanopore multiplexed protein sensing dataset for model iteration, and subsequently measured Alzheimer's disease biomarker Aβ1-42 using homemade solid-state nanopores. Empirical results indicated NanoSSL achieved an unprecedented performance across four metrics: accuracy, precision, recall, and F1 score, when classifying two mutated Aβ1-42, E22G and G37R. The self-supervised learning and attention mechanism were verified as the source of performance gains. AVAILABILITY AND IMPLEMENTATION: The main program is available at https://doi.org/10.5281/zenodo.17172822.

Nanopores↗

PubMed2006

XIAP is related to the chemoresistance and inhibited its expression by RNA interference sensitize pancreatic carcinoma cells to chemotherapeutics.

OBJECTIVES: To explore the exact role does the x-linked inhibitor of apoptosis (XIAP) play in chemoresistance of pancreatic carcinoma cell and the cell sensitivity to chemotherapeutic drugs changed after XIAP is inhibited by RNA interference (RNAi). METHODS: Pancreatic carcinoma cell line SW1990 was exposed to 5-fluorouracil (5-fu) with the concentrations of 1.0 and 10 mug/mL to increase the expression of XIAP. Then 4 RNAi plasmid vectors against XIAP were designed and constructed, then transfected into SW1990. Repressive effect was evaluated by reverse transcriptase polymerase chain reaction and Western blot; 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide and flow cytometry were performed to determine cell sensitivity to 5-fu and gemcitabine; furthermore, apoptosis is confirmed by Hoechst 33258 stain. RESULTS: XIAP of SW1990 can be up-regulated with the chemoresistance increasing 1.5- and 4-fold after 10 and 30 days induced by 5-fu. Two of the 4 vectors can inhibit the expression of XIAP protein more than 60%. The cells apoptosis index induced by 5-fu and gemcitabine increased greatly after XIAP is inhibited by the RNAi plasmid vectors. CONCLUSIONS: XIAP is one of the most important factors in the pancreatic carcinoma chemoresistance, and inhibition of XIAP in pancreatic carcinoma can enhance the cancer sensitivity to chemotherapeutic drugs.

Apoptosis↗

PubMed2005

A micro-chemiluminescence determination of cyanide in whole blood.

A reactant volume self-controlled micro-device was presented and applied to the flow injection chemiluminescence (CL) for determination of cyanide in whole blood. A mini distiller was fabricated for cyanide extraction from the blood samples with the extraction efficiencies of cyanide > or = 98%. A fluidic control platform with air driving was fabricated. The described system showed the features of easy fabrication, undiluted sample injection, safe analysis operation, and suitability for automatic cyanide analysis. The calibration curve showed linearity in the cyanide concentration range of 5.0 x 10(-7) to 5.0 x 10(-5) mol l(-1) with the detection limits (3sigma) of 2.3 x 10(-7) mol l(-1). CL peak-height precision was 1.9% R.S.D. (n = 11) at the 1.0 x 10(-6) mol l(-1) cyanide level. The new devices were applied to the analysis of cyanide in rabbit whole blood samples and the results agreed well with those obtained from official method.

Animals↗

PubMed2002

[T(1) carcinoma of the lung: characteristics of lymph node metastasis and its clinical significance].

OBJECTIVE: To investigate the frequency, distribution and features of lymph node metastasis in T(1) carcinoma of the lung, and to provide evidence for lymph node dissection. METHODS: Two hundred and fifteen patients with T(1) carcinoma of the lung underwent R2 surgery plus extended dissection of hilar, interlobular and mediastinal lymph nodes according to the mapping system developed by Naruke. RESULTS: 1 674 groups of lymph nodes were dissected. The metastatic rates of N(1) and N(2) were 11% and 6% respectively. Lymph node metastatic rates in carcinoma of the lung with maximum diameters less than 1.5 cm and between 1.6 cm approximately 3.0 cm were 5% and 8% respectively. N(1) and N(2) metastasis was not found in squamous cell carcinoma of the lung with a maximum diameter less than 1.5 cm. N(2) metastatic rates were 5% in squamous cell carcinoma 23% in adenocarcinoma and 3/9 in small cell carcinoma, the difference being significant (P < 0.01). 3/4 squamous cell carcinoma invaded only one group of N(2) nodes, but over 3 groups of lymph nodes were positive in 40% of adenocarcinoma. Saltatory metastasis accounted for 41% of N(2) metastasis. Fourteen percent of N(2)-positive tumors in upper lobes metastasized to the lower mediastinum, whereas 60% of N(2)-positive cancers in lower lobes invaded the upper mediastinum. CONCLUSIONS: The frequency of lymph node metastasis increases with the growth of tumors. Metastasis in adenocarcinoma occurs more frequently than in squamous cell carcinoma, but most common in small cell carcinoma. Tumors at any site can metastasize to the distant mediastinum. Except for squamous cell carcinoma with maximum diameter less than 1.5 cm which are likely to be cured without lymph node dissection, other types of T(1) carcinoma of the lung need extended lymph node dissection.

Adult↗