Biomedical subjects

Fei Pan

Publications and source records attributed to Fei Pan.

7 recordsLinked to original sources

PubMed2026

Efficient CRISPR/Cas-SF01 genome editing tools with high editing efficiency in allotetraploid oilseed rape.

CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats)-Cas9 has been widely utilized for plant genome editing, but the protospacer adjacent motif (PAM) requirement limits its editing scope. CRISPR/Cas12i3 belongs to the type-VI Cas system that has gained extensive attention due to its smaller size and less restricted canonical TTN PAM sequence. In this study, we explored the newly developed Cas-SF01 system (Cas12i3 variant) for genome editing in oilseed rape. We established an efficient protoplast transformation system in oilseed rape to compare editing efficiency between Cas-SF01 and Cas9. Cas-SF01 shows cleavage activities at the tested 5'-TTN-3' PAM sites with editing outcomes sharing considerable similarities with the CRISPR-Cas9 system in protoplast. Cas-SF01 also induces high efficiency mutagenesis for multiple target sites in stable transformed oilseed rape lines, generating mutants with multilocular silique and male sterile phenotypes. Furthermore, Cas-SF01-derived cytosine base editors (CBEs) were developed to produce targeted C-to-T base edits. Compared to SpCas9, Cas-SF01 has an expanded PAM range and effectively recognizes TTN PAMs, which has substantially broadened the scope of editable sites within the rapeseed genome. No mutations were identified at the putative off-target sites among the edited plants. This study developed a robust, first-of-its-kind Cas12 system in the allotetraploid Brassica napus, expanding the scope of editing and enriching genome-editing toolkits for biological research and genetic improvement.

Brassica napus↗

PubMed2006

Integrative Array Analyzer: a software package for analysis of cross-platform and cross-species microarray data.

The rapid accumulation of microarray data translates into an urgent need for tools to perform integrative microarray analysis. Integrative Array Analyzer is a comprehensive analysis and visualization software toolkit, which aims to facilitate the reuse of the large amount of cross-platform and cross-species microarray data. It is composed of the data preprocess module, the co-expression analysis module, the differential expression analysis module, the functional and transcriptional annotation module and the graph visualization module.

Algorithms↗

PubMed2006

Evaluation of a two-stage neural model of glaucomatous defect: an approach to reduce test-retest variability.

PURPOSE: The purpose of this study is to model perimetric defect and variability and identify stimulus conditions that can reduce variability while retaining good ability to detect glaucomatous defects. METHODS: The two-stage neural model of Swanson et al. was extended to explore relations among perimetric defect, response variability, and heterogeneous glaucomatous ganglion cell damage. Predictions of the model were evaluated by testing patients with glaucoma using a standard luminance increment 0.43 degrees in diameter and two innovative stimuli designed to tap cortical mechanisms tuned to low spatial frequencies. The innovative stimuli were a luminance-modulated Gabor stimulus (0.5 c/deg) and circular equiluminant red-green chromatic stimuli whose sizes were close to normal Ricco's areas for the chromatic mechanism. Seventeen patients with glaucoma were each tested twice within a 2-week period. Sensitivities were measured at eight locations at eccentricities from 10 degrees to 21 degrees selected in terms of the retinal nerve fiber bundle patterns. Defect depth and response (test-retest) variability were compared for the innovative stimuli and the standard stimulus. RESULTS: The model predicted that response variability in defective areas would be lower for our innovative stimuli than for the conventional perimetric stimulus with similar defect depths if detection of the chromatic and Gabor stimuli was mediated by spatial mechanisms tuned to low spatial frequencies. Experimental data were consistent with these predictions. Depth of defect was similar for all three stimuli (F = 1.67, p > 0.19). Mean response variability was lower for the chromatic stimulus than for the other stimuli (F = 5.58, p < 0.005) and was lower for the Gabor stimulus than for the standard stimulus in areas with more severe defects (t = 2.68, p < 0.005). Variability increased with defect depth for the standard and Gabor stimuli (p < 0.005) but not for the chromatic stimulus (slope less than zero). CONCLUSIONS: Use of large perimetric stimuli detected by cortical mechanisms tuned to low spatial frequencies can make it possible to lower response variability without comprising the ability to detect glaucomatous defect.

Color Perception↗

PubMed2004

Inactivation of the mycobacterial rhamnosyltransferase, which is needed for the formation of the arabinogalactan-peptidoglycan linker, leads to irreversible loss of viability.

Temperature-sensitive mutant 2-20/32 of Mycobacterium smegmatis mc(2)155 was isolated and genetically complemented with a Mycobacterium tuberculosis H37Rv DNA fragment that contained a single open reading frame. This open reading frame is designated Rv3265c in the M. tuberculosis H37Rv genome. Rv3265c shows homology to the Escherichia coli gene wbbL, which encodes a dTDP-Rha:alpha-D-GlcNAc-pyrophosphate polyprenol, alpha-3-L-rhamnosyltransferase. In E. coli this enzyme is involved in O-antigen synthesis, but in mycobacteria it is required for the rhamnosyl-containing linker unit responsible for the attachment of the cell wall polymer mycolyl-arabinogalactan to the peptidoglycan. The M. tuberculosis wbbL homologue, encoded by Rv3265c, was shown to be capable of restoring an E. coli K12 strain containing an insertionally inactivated wbbL to O-antigen positive. Likewise, the E. coli wbbL gene allowed 2-20/32 to grow at higher non-permissive temperatures. The rhamnosyltransferase activity of M. tuberculosis WbbL was demonstrated in 2-20/32 as was the loss of this transferase activity in 2-20/32 at elevated temperatures. The wbbL of the temperature-sensitive mutant contained a single-base change that converted what was a proline in mc(2)155 to a serine residue. Exposure of 2-20/32 to higher non-permissive temperatures resulted in bacteria that could not be recovered at the lower permissive temperatures.

Bacterial Proteins↗

PubMed2004

Comprehensive vertical sample-based KNN/LSVM classification for gene expression analysis.

Classification analysis of microarray gene expression data has been widely used to uncover biological features and to distinguish closely related cell types that often appear in the diagnosis of cancer. However, the number of dimensions of gene expression data is often very high, e.g., in the hundreds or thousands. Accurate and efficient classification of such high-dimensional data remains a contemporary challenge. In this paper, we propose a comprehensive vertical sample-based KNN/LSVM classification approach with weights optimized by genetic algorithms for high-dimensional data. Experiments on common gene expression datasets demonstrated that our approach can achieve high accuracy and efficiency at the same time. The improvement of speed is mainly related to the vertical data representation, P-tree,Patents are pending on the P-tree technology. This work is partially supported by GSA Grant ACT#:K96130308. and its optimized logical algebra. The high accuracy is due to the combination of a KNN majority voting approach and a local support vector machine approach that makes optimal decisions at the local level. As a result, our approach could be a powerful tool for high-dimensional gene expression data analysis.

Algorithms↗

PubMed2004

Perimetric defects and ganglion cell damage: interpreting linear relations using a two-stage neural model.

PURPOSE: To better understand the relations between glaucomatous perimetric defects and ganglion cell damage, a neural model was developed to interpret empiric findings on linear relations between perimetric defects and measures of ganglion cell loss. METHODS: A two-stage model computed responses of ganglion cell mosaics (first stage), then computed perimetric sensitivity in terms of processing by spatial filters (second stage) that pool the ganglion cell responses. Cell death and dysfunction were introduced in a local patch of the first-stage ganglion cell mosaic, and perimetric defect depth was computed for the corresponding region of the visual field. Calculations were performed for both sparse and dense ganglion cell mosaics and for spatial filters with peak frequencies from 0.5 to 4.0 cyc/deg. RESULTS: The model yielded nonlinear functions for perimetric defect depth in decibel versus the percentage of ganglion cell damage, but functions for lower spatial frequencies became linear when perimetric defect was expressed as a percentage of normal. The relations between perimetric defects and percentage of ganglion cell loss were determined primarily by spatial tuning of the second-stage spatial filters. For averaging sensitivities across different visual field locations, linear units (arithmetic mean) can more closely approximate mean ganglion cell loss than decibel units (geometric mean). Fits to data from experimental glaucoma required ganglion cell dysfunction in addition to ganglion cell loss. CONCLUSIONS: Pooling by second-stage spatial filters can account for empiric findings of linear relations between perimetric defects and measures of ganglion cell loss.

Glaucoma↗

PubMed2002

Formation of dTDP-rhamnose is essential for growth of mycobacteria.

It was determined that the dTDP-rhamnose synthesis gene, rmlD, could be inactivated in Mycobacterium smegmatis only in the presence of a rescue plasmid carrying functional rmlD. Hence, dTDP-rhamnose biosynthesis is essential for the growth of mycobacteria and the targeting of dTDP-rhamnose synthesis for new tuberculosis drugs is supported.

Carbohydrate Dehydrogenases↗