Publications by authors named "Shoujun Xu"

53 Publications

A 4-day-old newborn with an isolated sternal cleft: A rare case and literature review.

Pediatr Pulmonol 2021 Oct 12. Epub 2021 Oct 12.

Department of Medical Imaging, Guangdong Second Provincial General Hospital, Guangzhou, China.

An isolated sternal cleft is an orphan congenital defect of the sternum that presents from birth to adulthood. We report the case of a 4-day-old newborn with an isolated congenital cleft sternum. We also reviewed the related literature and operative options.
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http://dx.doi.org/10.1002/ppul.25677DOI Listing
October 2021

Cadmium-induced changes in composition and co-metabolism of glycerolipids species in wheat root: Glycerolipidomic and transcriptomic approach.

J Hazard Mater 2021 Sep 4;423(Pt B):127115. Epub 2021 Sep 4.

Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan 430070, China; State Environmental Protection Key Laboratory of Soil Health and Green Remediation, Wuhan 430070, China. Electronic address:

Lipids are the structural constituents of cell membranes and play crucial roles in plant adaptation to abiotic stresses. The aim of this study was to use glycerolipidomic and transcriptomic to analyze the changes in lipids metabolism induced by cadmium (Cd) exposure in wheat. The results indicated that Cd stress did not decrease the concentrations of monogalactosyldiacyglycerol (MGDG), phosphatidylcholine (PC), lysophosphatidylcholine (LPC) and phosphatidic acid at 6 h, but decreased digalactosyldoacylglycerol (DGDG), MGDG, PC, phosphatidylethanolamine (PE), phosphatidylglycerol (PG), phosphatidylserine (PS) and LPC concentrations in wheat root at 24 h. Although the concentrations of highly abundant glycerolipids PC and PE were decreased, the ratios of PC/PE increased thus contributing to wheat adaptation to Cd stress. Cd did not reduce the extent of total lipid unsaturation due to the unchanged concentrations of high abundance species of C36:4, C34:2, C34:3 and C36:6 at 6 h, indicative of their roles in resisting Cd stress. The correlation analysis revealed the glycerolipids species experiencing co-metabolism under Cd stress, which is driven by the activated expression of genes related to glycerolipid metabolism, desaturation and oxylipin synthesis. This study gives insights into the changes of glycerolipids induced by Cd and the roles in wheat adaptation to Cd stress.
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http://dx.doi.org/10.1016/j.jhazmat.2021.127115DOI Listing
September 2021

Twice exploration of tRNA +1 frameshifting in an elongation cycle of protein synthesis.

Nucleic Acids Res 2021 Sep;49(17):10046-10060

Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA 19107, USA.

Inducing tRNA +1 frameshifting to read a quadruplet codon has the potential to incorporate a non-natural amino acid into the polypeptide chain. While this strategy is being considered for genome expansion in biotechnology and bioengineering endeavors, a major limitation is a lack of understanding of where the shift occurs in an elongation cycle of protein synthesis. Here, we use the high-efficiency +1-frameshifting SufB2 tRNA, containing an extra nucleotide in the anticodon loop, to address this question. Physical and kinetic measurements of the ribosome reading frame of SufB2 identify twice exploration of +1 frameshifting in one elongation cycle, with the major fraction making the shift during translocation from the aminoacyl-tRNA binding (A) site to the peptidyl-tRNA binding (P) site and the remaining fraction making the shift within the P site upon occupancy of the A site in the +1-frame. We demonstrate that the twice exploration of +1 frameshifting occurs during active protein synthesis and that each exploration is consistent with ribosomal conformational dynamics that permits changes of the reading frame. This work indicates that the ribosome itself is a determinant of changes of the reading frame and reveals a mechanistic parallel of +1 frameshifting with -1 frameshifting.
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http://dx.doi.org/10.1093/nar/gkab734DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8464047PMC
September 2021

Ionomics analysis provides new insights into the co-enrichment of cadmium and zinc in wheat grains.

Ecotoxicol Environ Saf 2021 Oct 10;223:112623. Epub 2021 Aug 10.

Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture, Micro-elements Research Center, College of Resource and Environment, Huazhong Agricultural University, Wuhan 430070, China; State Environmental Protection Key Laboratory of Soil Health and Green Remediation, Wuhan 430070, China. Electronic address:

Cadmium (Cd) is present in many soils and, when enter a food chain, represents a major health threat to humans. The existent large variation in grain Cd content amongst wheat genotypes opens prospects for genetic improvement for reduced Cd uptake in this species. However, selecting low-Cd-accumulating varieties comes with a possible caveat of affecting uptake other essential nutrients. In this work, we screened 134 wheat varieties in 3 various field studies and selected 15 high- and 15 low-Cd accumulating varieties in grains for ionomics analysis. Our results showed that high-Cd accumulating varieties also possessed an ability to accumulate mineral elements of calcium, magnesium, manganese, iron and zinc, while varieties with low Cd content were deficient in many essential nutrients and, especially, zinc (Zn). The above data was confirmed in an independent trail involving another 97 wheat varieties. Thus, selecting plants for high Zn accumulation (as a part of biofortification programs) resulted in an inadvertent increase in accumulation of the toxic Cd in wheat. Vice versa, selecting low Cd-accumulating varieties comes with a danger of reducing their Zn content, with major consequences to food quality and human health. We suggest that the above conundrum can be resolved by understanding the structure-function relations of various transporters isoforms involved in Zn and Cd transport and issue-specific mode of their operation, via cell-based phenotyping followed by molecular breeding.
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http://dx.doi.org/10.1016/j.ecoenv.2021.112623DOI Listing
October 2021

Association of Reduced Tract Integrity with Social Communication Deficits in Preschool Autism Children: A Tract-Based Spatial Statistics Study.

Neuropsychiatr Dis Treat 2021 18;17:2003-2010. Epub 2021 Jun 18.

The Second School of Clinical Medicine, Southern Medical University, Guangzhou, People's Republic of China.

Purpose: To analyze the changes in white matter tracts in preschool children with autism spectrum disorder (ASD), and the correlation between these changes and social communication deficits.

Methods: Diffuse tensor imaging was used to assess white matter integrity using tract-based spatial statistics in a sample of 50 right-handed children with ASD aged 2-6 years vis a reference sample of 46 typically developing children aged 2-6 years. We then correlated these significant different fiber tracts between groups with communication and social interaction scores using the Autism Diagnostic Interview-Revised Assessment (ADI-R) Scale.

Results: We observed decreased fractional anisotropy (FA) in tracts including the left superior longitudinal fasciculus (SLF), the splenium of the corpus callosum (splCC), the left corticospinal tracts, and the left inferior longitudinal fasciculus (ILF) in children with ASD. Specifically, there was reduced white matter integrity of these tracts in the left cerebral hemisphere. In addition, we found that the decreased FA of left SLF and ILF was negatively associated with the ADI-R scores in children with ASD.

Conclusion: The structural integrity of some white matter tracts in the five-level anatomical model for the social communication was reduced. The reduced integrity white matter that we observed primarily in the left cerebral hemisphere may be a neural substrate of social communication deficits in preschool children with ASD, and we speculate that the reduction is associated with the severity of social interaction. The reduced FA of the splCC might be a substantial biomarker for children with ASD.
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http://dx.doi.org/10.2147/NDT.S306596DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8219119PMC
June 2021

Alterations of Regional Homogeneity in Preschool Boys With Autism Spectrum Disorders.

Front Neurosci 2021 22;15:644543. Epub 2021 Mar 22.

Department of Medical Imaging, Guangdong Second Provincial General Hospital, Guangzhou, China.

Objectives: The study was aimed at investigating the alterations of local spontaneous brain activity in preschool boys with autism spectrum disorders (ASD).

Methods: Based on regional homogeneity (ReHo), the acquired resting state functional magnetic resonance imaging (fMRI) data sets, which included 86 boys with ASD and 54 typically developing (TD) boys, were used to detect regional brain activity. Pearson correlation analysis was used to study the relationship between abnormal ReHo value and the Childhood Autism Rating Scale (CARS), Autism Behavior Checklist (ABC), developmental quotient, and age.

Results: In the ASD group, we found increased ReHo in the right calcarine as well as decreased ReHo in the opercular part of the left inferior frontal gyrus, the left middle temporal gyrus, the left angular gyrus, and the right medial orbital frontal cortex ( < 0.05, false discovery rate correction). We did not find a correlation between the results of brain regions and the CARS, ABC, and age.

Conclusions: Our study found spontaneous activity changes in multiple brain regions, especially the visual and language-related areas of ASD, that may help to further understand the clinical characteristics of boys with ASD.
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http://dx.doi.org/10.3389/fnins.2021.644543DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8019812PMC
March 2021

High-Resolution DNA Dual-Rulers Reveal a New Intermediate State in Ribosomal Frameshifting.

Chembiochem 2021 May 25;22(10):1775-1778. Epub 2021 Feb 25.

Department of Biology and Biochemistry, University of Houston, Houston, TX 77204, USA.

Ribosomal frameshifting is an important pathway used by many viruses for protein synthesis that involves mRNA translocation of various numbers of nucleotides. Resolving the mRNA positions with subnucleotide precision will provide critical mechanistic information that is difficult to obtain with current techniques. We report a method of high-resolution DNA rulers with subnucleotide precision and the discovery of new frameshifting intermediate states on mRNA containing a GA G motif. Two intermediate states were observed with the aid of fusidic acid, one at the "0" reading frame and the other near the "-1" reading frame, in contrast to the "-2" and "-1" frameshifting products found in the absence of the antibiotic. We termed the new near-"-1" intermediate the Post(-1*) state because it was shifted by approximately half a nucleotide compared to the normal "-1" reading frame at the 5'-end. This indicates a ribosome conformation that is different from the conventional model of three reading frames. Our work reveals uniquely precise mRNA motions and subtle conformational changes that will complement structural and fluorescence studies.
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http://dx.doi.org/10.1002/cbic.202000863DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8014572PMC
May 2021

Effects of the on Integration Ability of Brain Functions in Children With ADHD.

J Atten Disord 2020 Oct 21:1087054720964561. Epub 2020 Oct 21.

Shenzhen Children's Hospital, Shenzhen, China.

Objective: The present study aimed to examine the effects of on the integration ability of intrinsic brain functions in children with ADHD, and whether the integration ability was associated with working memory (WM).

Methods: A sliding time window method was used to calculate the spatial and temporal concordance among five rs-fMRI regional indices in 55 children with ADHD and 20 healthy controls.

Results: The exhibited significant interaction effects with ADHD diagnosis on the voxel-wise concordance in the right posterior central gyrus, fusiform gyrus and lingual gyrus. Specifically, for children with ADHD, G-carriers showed increased voxel-wise concordance in comparison to TT homozygotes in the right precentral gyrus, superior frontal gyrus, postcentral gyrus, and middle frontal gyrus. The voxel-wise concordance was also found to be related to WM.

Conclusion: Our findings provided a new insight into the neural mechanisms of the brain function of ADHD children.
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http://dx.doi.org/10.1177/1087054720964561DOI Listing
October 2020

Functional connectome-based biomarkers predict chronic codeine-containing cough syrup dependent.

J Psychiatr Res 2020 11 20;130:333-341. Epub 2020 Aug 20.

Department of Medical Imaging, Guangdong Second Provincial General Hospital, Shiliugang Rd, Haizhu District, Guangzhou, 510317, PR China. Electronic address:

Purpose: Codeine-containing cough syrup (CCS) is considered among the most popular drugs of abuse in adolescents worldwide. Accurate prediction and identification of CCS dependent (CCSD) users are crucial. This study aimed to identify a brain-connectome-based predictor of CCSD using a machine learning model based on a ten-fold cross-validation logistic regression (LR) classifier.

Methods: 40 CCSD users and 40 healthy control (HC) subjects underwent functional magnetic resonance imaging to construct weight functional networks. Partial correlation analysis was used to analyze relations between abnormal network metrics and clinical characteristics (BIS total scores, CCS abuse duration, and mean CCS dose) in CCSD. A ten-fold cross-validation LR classifier was used to classify CCSD users and HC subjects.

Results: The CCSD group showed significantly abnormal nodes and connections in the right posterior cingulate, right middle insula, bilateral prefrontal cortex, parietal lobe, temporal lobe, occipital lobe, and cerebellum. Furthermore, higher characteristic path length and lower clustering coefficient (Cp), global efficiency, and local efficiency (Eloc) were observed in the global topologies in CCSD. The abnormal global properties (Cp and Eloc) and node properties of the prefrontal cortex were significantly correlated with clinical characteristics (BIS-11 scores, CCS abuse duration) in CCSD. The LR classifier models demonstrated accuracy, sensitivity, specificity, precision, and AUC of 82.5%, 82.5%, 82.5%, 76.8%, and 82.5%.

Conclusions: These data demonstrate that abnormal functional connectome may be closely linked to clinical characteristics in CCSD. Functional connectome-based biomarkers can be a powerful tool for personalized diagnosis of CCSD in the future.
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http://dx.doi.org/10.1016/j.jpsychires.2020.08.001DOI Listing
November 2020

Antimony symplastic and apoplastic absorption, compartmentation, and xylem translocation in Brassica parachinensis L. under antimonate and antimonite.

Ecotoxicol Environ Saf 2020 Jul 15;197:110621. Epub 2020 Apr 15.

Public Monitoring Center for Agro-Product of Guangdong Academy of Agricultural Sciences, China; Key Laboratory of Testing and Evaluation for Agro-product Safety and Quality (Guangzhou), Ministry of Agriculture and Rural Affairs, China; Hubei Provincial Engineering Laboratory for New-Type Fertilizer, China; Microelement Research Center for Huazhong Agricultural University, China. Electronic address:

Antimony (Sb) excess accumulation in edible parts of crops causes potential risks to human health. However, knowledge about the mechanisms of its accumulation within vegetable plants is still not well known. Here, we investigated the physiological processes of Sb involved in symplastic and apoplastic absorption, compartmentation by roots, and translocation in xylem in Brassica parachinensis L. exposed to antimonate (SbV) and antimonite (SbIII) forms. The results showed that plants treated with SbIII emerged to be more toxic than SbV as proved by the lower biomass and the higher concentrations of malonaldehyde (MDA) and hydrogen peroxide (HO) in plant tissues, especially at high dosages. The Sb concentration showed more in shoots but less in roots treated with SbV than with SbIII. The total Sb accumulation was higher under the SbV treatment than the SbIII treatment, mainly due to the higher accumulation in shoots. Additionally, the Sb concentration in symplastic flow of roots was higher exposed to SbV than SbIII, while no differences were found for the Sb concentration in apoplastic flow between them. Moreover, the Sb concentration in cell walls of roots was higher exposed to SbIII than SbV, especially at high levels. Furthermore, the Sb concentration in xylem was higher exposed to SbV than SbIII, and a greatly positive correlation was observed between the Sb concentrations in xylem and shoots. Overall, these findings revealed that vegetable plants accumulated more SbV than SbIII in edible parts mainly due to xylem translocation rather than root absorption.
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http://dx.doi.org/10.1016/j.ecoenv.2020.110621DOI Listing
July 2020

Abnormal white matter within brain structural networks is associated with high-impulse behaviour in codeine-containing cough syrup dependent users.

Eur Arch Psychiatry Clin Neurosci 2021 Aug 2;271(5):823-833. Epub 2020 Mar 2.

Department of Medical Imaging, Guangdong Second Provincial General Hospital, Shiliugang Rd, Haizhu District, Guangzhou, 510317, People's Republic of China.

Codeine-containing cough syrup (CCS) is considered as one of the most popular drug of dependence among adolescents because of its inexpensiveness and easy availability. However, its relationship with neurobiological effects remains sparsely explored. Herein, we examined how high-impulse behaviours relate to changes in the brain structural networks. Forty codeine-containing cough syrup dependent (CCSD) users and age-, gender-, and number of cigarettes smoked per day -matched forty healthy control (HC) subjects underwent structural brain imaging via MRI. High-impulse behaviour was assessed using the 30-item self-rated Barratt Impulsiveness Scale (BIS-11), and structural networks were constructed using diffusion tensor imaging and AAL-90 template. Between-group topological metrics were compared using nonparametric permutations. Benjamin-Hochberg false discovery rate correction was used to correct for multiple comparisons (P < 0.05). The relationships between abnormal network metrics and clinical characteristics of CCS dependent (BIS-11 total score, CCS- dependent duration and mean dose) were examined by Spearman's correlation. Structural networks of the CCSD group demonstrated lower small-world properties than those of the HC group. Abnormal changes in nodal properties among CCSD users were located mainly in the frontal gyrus, inferior parietal lobe and olfactory cortex. NBS analysis further indicated disrupted structural connections between the frontal gyrus and multiple brain regions. There were significant correlations between abnormal nodal properties of the frontal gyrus and clinical characteristics (BIS-11 total score, CCS dependent duration and mean dose) in the CCSD group. These findings suggest that the high-impulse behavioural expression in CCS addiction is associated with widespread brain regions, particularly within those in the frontal cortex. Aberrant brain regions and disrupted connectivity of structural network may be the bases of neuropathology for underlying symptoms of high-impulse behaviours in CCSD users, which may provide a novel sight to better treat and prevent codeine dependency in adolescents.
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http://dx.doi.org/10.1007/s00406-020-01111-4DOI Listing
August 2021

Ammonium nutrition mitigates cadmium toxicity in rice (Oryza sativa L.) through improving antioxidase system and the glutathione-ascorbate cycle efficiency.

Ecotoxicol Environ Saf 2020 Feb 29;189:110010. Epub 2019 Nov 29.

Public Monitoring Center for Agro-Product of Guangdong Academy of Agricultural Sciences, China; Key Laboratory of Testing and Evaluation for Agro-product Safety and Quality (Guangzhou), Ministry of Agriculture and Rural Affairs, China; Research Center of Trace Elements/College of Resources and Environment for Huazhong Agricultural University, China. Electronic address:

Nitrogen (N) forms not only affect cadmium (Cd) accumulation in plants, but also affect plant resistance to Cd toxicity. However, few researches have been reported underlying the mechanism of the relationship between nitrogen forms and plant resistance under Cd exposure. Here, we explored the mechanism on how different NO/NH ratios affect antioxidase system and the glutathione-ascorbate cycle under five different ratios of NO/NH (1:0, 2:1, 1:1, 1:2, 0:1) and three dosages of Cd exposure (0, 1, 5 μmol L Cd) in rice (Oryza sativa L.). The results showed that high NO and high Cd exposure both significantly inhibited tissue growth of rice plants, and this inhibiting trend was mitigated with increasing NH ratios as proved by the increased biomass and the decreased concentrations of malonaldehyde (MDA) and hydrogen peroxide (HO), as well as the levels of Cd contents in rice tissues. Additionally, high NH ratios elevated the SOD activities in rice tissues, especially at high Cd treatment. However, other two antioxidases (CAT and APX) were insensitive to changes of NO/NH ratios (except the full NO). Furthermore, high NH ratios induced increasing of the efficiency of glutathione-ascorbate cycle (GSH-AsA) under two levels of Cd exposure, as evidenced by increasing concentrations of GSH and AsA and the activities of GR and DHAR in rice tissues. Overall, these results revealed that ammonium nutrition caused an enhancement resistance to Cd stress in rice plants was responsible for increasing of partial antioxidase system and the efficiencies of GSH-AsA cycle.
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http://dx.doi.org/10.1016/j.ecoenv.2019.110010DOI Listing
February 2020

Altered Functional Connectivity in Children With Low-Function Autism Spectrum Disorders.

Front Neurosci 2019 2;13:806. Epub 2019 Aug 2.

The Second School of Clinical Medicine, Southern Medical University, Guangzhou, China.

Neuroimaging studies have shown that autism spectrum disorders (ASDs) may be associated with abnormalities in brain structures and functions at rest as well as during cognitive tasks. However, it remains unclear if functional connectivity (FC) of all brain neural networks is also changed in these subjects. In this study, we acquired functional magnetic resonance imaging scans from 93 children with ASD and 79 matched healthy subjects. Group independent component analysis was executed for all of the participants to estimate FC. One-sample -tests were then performed to obtain the networks for each group. Group differences in the different brain networks were tested using two-sample -tests. Finally, relationships between abnormal FC and clinical variables were investigated with Pearson's correlation analysis. The results from one-sample -tests revealed nine networks with similar spatial patterns in these two groups. When compared with the controls, children with ASD showed increased connectivity in the right dorsolateral superior frontal gyrus and left middle frontal gyrus (MFG) within the occipital pole network. Children with ASD also showed decreased connectivity in the left gyrus rectus, left middle occipital gyrus, right angular gyrus, right MFG and right inferior frontal gyrus (IFG), orbital part within the lateral visual network (LVN), the left IFG, right precuneus, and right angular gyrus within the left frontoparietal (cognition) network. Furthermore, the mean FC values within the LVN showed significant positive correlations with total score of the Childhood Autism Rating Scale. Our findings indicate that abnormal FC extensively exists within some networks in children with ASD. This abnormal FC may constitute a biomarker of ASD. Our results are an important contribution to the study of neuropathophysiological mechanisms in children with ASD.
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http://dx.doi.org/10.3389/fnins.2019.00806DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6688725PMC
August 2019

Dual DNA Rulers to Study the Mechanism of Ribosome Translocation with Single-Nucleotide Resolution.

J Vis Exp 2019 07 8(149). Epub 2019 Jul 8.

Department of Biology and Biochemistry, University of Houston;

The ribosome translocation refers to the ribosomal movement on the mRNA by exactly three nucleotides (nt), which is the central step in protein synthesis. To investigate its mechanism, there are two essential technical requirements. First is single-nt resolution that can resolve normal translocation from frameshifting, during which the ribosome moves by other than 3 nt. The second is the capability to probe both the entrance and exit sides of mRNA in order to elucidate the whole picture of translocation. We report the dual DNA ruler assay that is based on the critical dissociation forces of DNA-mRNA duplexes, obtained by force-induced remnant magnetization spectroscopy (FIRMS).  With 2-4 pN force resolution, the dual ruler assay is sufficient to distinguish different translocation steps. By implementing a long linker on the probing DNAs, they can reach the mRNA on the opposite side of the ribosome, so that the mRNA position can be determined for both sides. Therefore, the dual ruler assay is uniquely suited to investigate the ribosome translocation, and nucleic acid motion in general. We show representative results which indicated a looped mRNA conformation and resolved normal translocation from frameshifting.
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http://dx.doi.org/10.3791/59918DOI Listing
July 2019

Modulation and Visualization of EF-G Power Stroke During Ribosomal Translocation.

Chembiochem 2019 12 20;20(23):2927-2935. Epub 2019 Sep 20.

Department of Biology and Biochemistry, University of Houston, Houston, TX, 77204, USA.

During ribosome translocation, the elongation factor EF-G undergoes large conformational change while maintaining its contact with the moving tRNA. We previously measured a power stroke accompanying EF-G catalysis, which was consistent with structural studies. However, the role of power stroke in translocation fidelity remains unclear. Here, we report quantitative measurements of the power strokes of structurally modified EF-Gs by using two different techniques and reveal the correlation between power stroke and translocation efficiency and fidelity. We discovered that the reduced power stroke only lowered the percentage of translocation but did not introduce translocation error. The established force -structure-function correlation for EF-G indicates that power stroke drives ribosomal translocation, but the mRNA reading frame is probably maintained by ribosome itself. Furthermore, the microscope detection method reported here can be simply implemented for other biochemical applications.
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http://dx.doi.org/10.1002/cbic.201900276DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6888950PMC
December 2019

Probing drug-DNA interactions using super-resolution force spectroscopy.

Appl Phys Lett 2018 Nov 6;113(19):193702. Epub 2018 Nov 6.

Department of Chemistry, University of Houston, Houston, Texas 77204, USA.

Atomic magnetometry and ultrasound, as individual techniques, have been used extensively in various physical, chemical, and biomedical fields. Their combined application, however, has been rare. We report that super-resolution force spectroscopy, which is based on the integration of the two techniques, can find unique biophysical applications in studying drug-DNA interactions. The precisely controlled ultrasound generates acoustic radiation force on the biological systems labeled with magnetic microparticles. A decrease in the magnetic signal, measured by an automated atomic magnetometer, indicates that the acoustic radiation force equals the binding force of the biological system. With 0.5 pN force resolution, we were able to precisely resolve three small molecules binding with two DNA sequences and quantitatively reveal the effect of a single hydrogen bond. Our results indicate that the increases in DNA binding force caused by drug binding correlate with the enthalpy instead of free energy, thus providing an alternative physical parameter for optimizing chemotherapeutic drugs.
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http://dx.doi.org/10.1063/1.5045787DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6219894PMC
November 2018

Dual DNA rulers reveal an 'mRNA looping' intermediate state during ribosome translocation.

RNA Biol 2018 25;15(11):1392-1398. Epub 2018 Oct 25.

b Department of Biology and Biochemistry , University of Houston , Houston , TX , USA.

The precise 3-nucleotide movement of mRNA is critical for translation fidelity. One mRNA translocation error propagates to all of the following codons, which is detrimental to the cell. However, none of the current methods can reveal the mRNA dynamics near the ribosome entry site, which limits the understanding of this important issue. We have developed an assay of dual DNA rulers that provides such capability. By uniquely probing both the 3'- and 5'-ends of mRNA, we observed an antibiotic-trapped intermediate state that is consistent with a ribosomal conformation containing mRNA asymmetric partial displacements at its entry and exit sites. Based on the available ribosome structures and computational simulations, we proposed a 'looped' mRNA conformation, which suggested a stepwise 'inchworm' mechanism for ribosomal translocation. The same 'looped' intermediate state identified with the dual rulers persists with a '-1' frameshifting motif, indicating that the branching point of normal and frameshifting translocations occurs at a later stage of translocation.
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http://dx.doi.org/10.1080/15476286.2018.1536590DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6284597PMC
January 2019

Comparison of foliar silicon and selenium on cadmium absorption, compartmentation, translocation and the antioxidant system in Chinese flowering cabbage.

Ecotoxicol Environ Saf 2018 Dec 26;166:157-164. Epub 2018 Sep 26.

Public Monitoring Center for Agro-Product, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China; Key Laboratory of Testing and Evaluation for Agro-product Safety and Quality, Ministry of Agriculture, Guangzhou 510640, China; Laboratory of Quality and Safety Risk Assessment for Agro-product (Guangzhou), Ministry, Guangzhou 510640, China; Hubei Provincial Engineering Laboratory for New Fertilizers/Research Center of Trace Elements College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China. Electronic address:

Silicon (Si) and selenium (Se) are beneficial for many higher plants when grown on stress conditions. However, the mechanisms underlying the differential effects between foliar Si and Se in alleviation of plant toxicity exposed to cadmium (Cd) stress are remained unclear. In this study, we investigated the discrepant mechanisms of foliar Si and Se on Cd absorption and compartmentation by roots, its translocation in xylem, and the antioxidant system within Chinese flowering cabbage (Brassica campestris L. ssp. chinensis var. utilis) under low and high Cd stress. Results showed that plant growth was significantly enhanced by foliar additions of Si or/and Se according to an increased plant tissue biomass at high Cd exposure. In addition, the foliar coupled addition of Si and Se showed little effects on the concentrations of Si or Se in plant tissues in comparison with the single addition of foliar Si or Se respectively. The foliar Si alone or combined with Se markedly reduced the Cd concentrations in plant shoots under two Cd treatments. This might be explained by the lower Cd concentrations in symplast and apoplast and the higher Cd concentrations in cell walls of plant roots, and the lower Cd concentrations in xylem sap. However, no great changes in these values were observed under the treatments of foliar Se alone. Moreover, the foliar additions of Si or/and Se all increased the antioxidant enzyme activities of SOD, CAT and APX in plant tissues, especially at high Cd dosage. No significant differences in the increasing degrees of these three antioxidant enzymes were found between the foliar Si and Se treatments. However, only the foliar Se alone or combined with Si markedly promoted the antioxidant enzyme activities of GR and DHAR in plant tissues. Our findings demonstrate that the alleviation of Cd toxicity by foliar Si maybe mainly responsible for inhibition of Cd absorption and its translocation to plant shoots, reinforcing its compartmentation into root cell walls, whilst enhancing the antioxidant enzyme system may be employed by foliar Se.
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http://dx.doi.org/10.1016/j.ecoenv.2018.09.085DOI Listing
December 2018

Metabolomics analysis reveals potential mechanisms of tolerance to excess molybdenum in soybean seedlings.

Ecotoxicol Environ Saf 2018 Nov 24;164:589-596. Epub 2018 Aug 24.

Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture, Wuhan 430070, China; Micro-Element Research Center, Huazhong Agricultural University, No. 1, Shizishan Street, Hongshan District, Wuhan 430070, Hubei Province, China. Electronic address:

Most plants exhibit strong tolerance to excess molybdenum (Mo). However, the metabolic profile and tolerance mechanisms of plants in response to excess Mo remain unknown. We comprehensively analyzed changes in the metabolic profiles of leaves and roots in soybean (Glycine max L.) seedlings cultured under normal-Mo and excess-Mo conditions by using ultra performance liquid chromatography (UPLC) combined with MS/MS (mass spectrometry). There were 42 differential metabolites in the roots and 19 differential metabolites in the leaves in response to excess Mo stress. In roots, the organic acids, levels of gluconic acid, D-glucarate and citric acid increased by 107.63-, 4.42- and 2.87-folds after excess Mo exposure. Several hormones (salicylic acid, jasmonic acid) and lipids (PG, MG, DG etc) also increased significantly under excess Mo condition. Metabolites related to ascorbate-glutathione metabolism and flavonoid and isoflavone biosynthesis notably accumulated in roots. Only lipid metabolism and salicylic acid accumulation were induced in leaves under excess Mo stress. It is speculated that organic compounds such as 2-oxoarginine, L-nicotine, gluconic acid, D-glucurate, and citric acid played important roles to chelate Mo and reduce its toxicity. Signaling molecules (JA, SA, and some lipids) and non-enzyme antioxidants such as flavonoids/isoflavones act synergistically to detoxify ROS and contribute to Mo tolerance in soybean seedlings. More metabolic pathways were induced by Mo excess in roots than in leaves, suggesting that roots play more implant role in Mo tolerance.
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http://dx.doi.org/10.1016/j.ecoenv.2018.08.062DOI Listing
November 2018

Super-resolution force spectroscopy reveals ribosomal motion at sub-nucleotide steps.

Chem Commun (Camb) 2018 Jun;54(46):5883-5886

Department of Chemistry, University of Houston, Houston, TX 77204, USA.

Probing biomolecular motion beyond a single nucleotide is technically challenging but fundamentally significant. We have developed super-resolution force spectroscopy (SURFS) with 0.5 pN force resolution and revealed that the ribosome moves by half a nucleotide upon the formation of the pre-translocation complex, which is beyond the resolution of other techniques.
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http://dx.doi.org/10.1039/c8cc02658kDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5989005PMC
June 2018

Specific Detection of Proteins Using Exceptionally Responsive Magnetic Particles.

Anal Chem 2018 06 24;90(11):6749-6756. Epub 2018 May 24.

Sensitivity and specificity are among the most important parameters for viable sensor technologies based on magnetic nanoparticles. In this work, we describe synthetic routes and analytical approaches to improve both aspects. Magnetic iron oxide particles having diameters of 120, 440, and 700 nm were synthesized, and their surfaces were specifically functionalized. The larger particles showed significantly stronger magnetic signals and responses when compared to commercially available magnetic particles (Dynabeads). A force-based detection method was used to distinguish specifically bound particles (via protein interactions) and nonspecifically bound ones (e.g., via physisorption). In addition, an exchange platform, denoted as exchange-induced remnant magnetization (EXIRM), was developed and utilized to detect label-free proteins specifically. Using EXIRM, the 700 nm magnetic particles showed a 7-fold increase in detection sensitivity when compared to the markedly larger commercially available Dynabeads; furthermore, EXIRM exhibited high specificity, even in a 100-fold increase of nontargeted protein. More generally, particle size effects, reaction times, and dynamic ranges are evaluated and discussed herein.
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http://dx.doi.org/10.1021/acs.analchem.8b00593DOI Listing
June 2018

Nitric oxide acts downstream of abscisic acid in molybdenum-induced oxidative tolerance in wheat.

Plant Cell Rep 2018 Apr 16;37(4):599-610. Epub 2018 Jan 16.

Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture, Huazhong Agricultural University, Wuhan, 430070, China.

Key Message: Our study first reveals that Mo mediates oxidative tolerance through ABA signaling. Moreover, NO acts downstream of ABA signaling in Mo-induced oxidative tolerance in wheat under drought stress. Nitric oxide (NO) is related to the improvement of molybdenum (Mo)-induced oxidative tolerance. While the function of Mo in abscisic acid (ABA) synthesis and in mediating oxidative tolerance by the interaction of ABA and NO remain to be studied. The -Mo and +Mo treatment-cultivated wheat was separated and subsequently was pretreated with AO inhibitor, ABA synthesis inhibitor, exogenous ABA, NO scavenger, NO donor or their combinations under polyethylene glycol 6000 (PEG)-stimulated drought stress (PSD). The AO activity and ABA content were increased by Mo in wheat under PSD, however, AO inhibitor decreased AO activity, correspondingly reduced ABA accumulation, suggesting that AO involves in the regulation of Mo-induced ABA synthesis. Mo enhanced activities and expressions of antioxidant enzyme, while these effects of Mo were reversed by AO inhibitor and ABA synthesis inhibitor due to the decrease of ABA content, but regained by exogenous ABA, indicating that Mo induces oxidative tolerance through ABA. Moreover, NO scavenger inhibited activities of antioxidant enzyme caused by Mo and exogenous ABA, but the inhibitions were eliminated by NO donor, indicating that NO is involved in ABA pathway in the regulation of Mo-induced oxidative tolerance in wheat under PSD. Finally, we proposed a scheme for the mechanism of Mo-induced oxidative tolerance.
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http://dx.doi.org/10.1007/s00299-018-2254-0DOI Listing
April 2018

Subcellular distribution of molybdenum, ultrastructural and antioxidative responses in soybean seedlings under excess molybdenum stress.

Plant Physiol Biochem 2018 Feb 5;123:75-80. Epub 2017 Dec 5.

Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture, Wuhan, 430070, China; Micro-element Research Center, Huazhong Agricultural University, Wuhan, 430070, China; Key Laboratory of Environment Remediation and Ecological Health (Zhejiang University), Ministry of Education, Hangzhou, 310058, China. Electronic address:

Some studies have shown that excess molybdenum (Mo) could produce toxic effects on plants. However, little is known about the subcellular distribution of Mo and cell ultrastructure within plants under excess Mo stress. Here, we comprehensively analyzed the changes of Mo distribution in subcellular fractions, cell ultrastructure and antioxidant enzymes in leaves and roots of soybean seedlings in response to excess Mo stress. The results showed that roots exhibited higher Mo accumulation than leaves at the 100 mg L Mo level, about 38.58-, 171.48- and 52.99-fold higher in cell walls, cell organelles and soluble fractions, respectively. Subcellular fractionations of Mo-containing tissues indicated that approximately 90% of Mo was accumulated in the soluble fractions and cell walls of the roots and leaves, and soluble fractions (accumulated 66.3-72.2% Mo) might serve as an effective storage site for excess Mo. Furthermore, excess Mo caused ultrastructural alterations in roots and leaves of soybean seedlings, leading to structural abnormality of chloroplast in leaf cells, plasmolysis, cellular deformity, vacuole enlargement and the swelling of cell wall and cytoplasm in root cells. Meanwhile, under excess Mo stress, the activity of POD, CAT and APX enzymes in roots was 1.43, 2.35 and 1.23 times that under standard Mo condition, while that of SOD and CAT enzymes in leaves was 1.23 and 1.94 times, respectively. This study provided novel insights into the mechanisms of excess Mo toxicity in soybean seedlings.
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http://dx.doi.org/10.1016/j.plaphy.2017.11.023DOI Listing
February 2018

Magnetic Sensing Potential of FeO Nanocubes Exceeds That of FeO Nanospheres.

ACS Omega 2017 Nov 16;2(11):8010-8019. Epub 2017 Nov 16.

Department of Chemistry and Texas Center for Superconductivity, Department of Electrical and Computer Engineering, Department of Chemical and Biomolecular Engineering, and Department of Physics and Texas Center for Superconductivity, University of Houston, 4800 Calhoun Road, Houston, Texas 77204, United States.

This paper highlights the relation between the shape of iron oxide (FeO) particles and their magnetic sensing ability. We synthesized FeO nanocubes and nanospheres having tunable sizes via solvothermal and thermal decomposition synthesis reactions, respectively, to obtain samples in which the volumes and body diagonals/diameters were equivalent. Vibrating sample magnetometry (VSM) data showed that the saturation magnetization () and coercivity of 100-225 nm cubic magnetic nanoparticles (MNPs) were, respectively, 1.4-3.0 and 1.1-8.4 times those of spherical MNPs on a same-volume and same-body diagonal/diameter basis. The Curie temperature for the cubic FeO MNPs for each size was also higher than that of the corresponding spherical MNPs; furthermore, the cubic FeO MNPs were more crystalline than the corresponding spherical MNPs. For applications relying on both higher contact area and enhanced magnetic properties, higher- FeO nanocubes offer distinct advantages over FeO nanospheres of the same-volume or same-body diagonal/diameter. We evaluated the sensing potential of our synthesized MNPs using giant magnetoresistive (GMR) sensing and force-induced remnant magnetization spectroscopy (FIRMS). Preliminary data obtained by GMR sensing confirmed that the nanocubes exhibited a distinct sensitivity advantage over the nanospheres. Similarly, FIRMS data showed that when subjected to the same force at the same initial concentration, a greater number of nanocubes remained bound to the sensor surface because of higher surface contact area. Because greater binding and higher translate to stronger signal and better analytical sensitivity, nanocubes are an attractive alternative to nanospheres in sensing applications.
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http://dx.doi.org/10.1021/acsomega.7b01312DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5709776PMC
November 2017

Biosensing Using Magnetic Particle Detection Techniques.

Sensors (Basel) 2017 Oct 10;17(10). Epub 2017 Oct 10.

Department of Chemistry and the Texas Center for Superconductivity, University of Houston, Houston, TX 77204, USA.

Magnetic particles are widely used as signal labels in a variety of biological sensing applications, such as molecular detection and related strategies that rely on ligand-receptor binding. In this review, we explore the fundamental concepts involved in designing magnetic particles for biosensing applications and the techniques used to detect them. First, we briefly describe the magnetic properties that are important for bio-sensing applications and highlight the associated key parameters (such as the starting materials, size, functionalization methods, and bio-conjugation strategies). Subsequently, we focus on magnetic sensing applications that utilize several types of magnetic detection techniques: spintronic sensors, nuclear magnetic resonance (NMR) sensors, superconducting quantum interference devices (SQUIDs), sensors based on the atomic magnetometer (AM), and others. From the studies reported, we note that the size of the MPs is one of the most important factors in choosing a sensing technique.
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http://dx.doi.org/10.3390/s17102300DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5676660PMC
October 2017

Nitric Oxide Mediates Molybdenum-Induced Antioxidant Defense in Wheat under Drought Stress.

Front Plant Sci 2017 23;8:1085. Epub 2017 Jun 23.

Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture, Huazhong Agricultural UniversityWuhan, China.

Molybdenum (Mo) has been reported to alleviate drought stress by enhancing antioxidant defense in plants, but the underlying mechanism remains unclear. Here, we hypothesized that Mo mediates nitric oxide (NO)-induced antioxidant defense through Mo-enzymes, particularly by nitrate reductase (NR) in wheat under drought stress. The 30-day-old wheat seedlings cultivated in -Mo (0 μM Mo) and +Mo (1 μM Mo) Hoagland solutions were detached and then pretreated with Mo-enzyme inhibitors, NO scavengers, NO donors or their combinations according to demands of complementary experiment under 10% polyethylene glycol 6000 (PEG)-stimulated drought stress (PSD). Mo supplementation increased the activities and transcripts of antioxidant enzymes, decreased HO and MDA contents, and elevated NO production, implying that Mo-induced antioxidant defense may be related to NO signal. Complementary experiment showed that NO production was induced by Mo, while suppressed by Mo-enzyme inhibitors and NO scavengers, but restored by NO donors, suggesting that Mo-induced increase of NO production may be due to the regulation by Mo-enzymes. Further experiment indicated that the increased activities and transcripts of antioxidant enzymes induced by Mo were suppressed by Mo-enzyme inhibitors and NO scavengers, and NO donors could eliminate their suppressing effects. Moreover, Mo application increased NR activity and inhibitors of Mo-enzymes inhibited NR activity in wheat leaves under PSD, suggesting that NR might involve in the regulation of Mo-induced NO production. These results clearly indicate that NO mediates Mo-induced antioxidant defense at least partially through the regulation of NR.
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http://dx.doi.org/10.3389/fpls.2017.01085DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5481953PMC
June 2017

High-Efficiency "-1" and "-2" Ribosomal Frameshiftings Revealed by Force Spectroscopy.

ACS Chem Biol 2017 06 2;12(6):1629-1635. Epub 2017 May 2.

Department of Biology and Biochemistry, ‡Department of Chemistry, University of Houston , Houston, Texas 77204, United States.

Ribosomal frameshifting is a rare but ubiquitous process that is being studied extensively. Meanwhile, frameshifting motifs without any secondary mRNA structures were identified but rarely studied experimentally. We report unambiguous observation of highly efficient "-1" and "-2" frameshiftings on a GAG slippery mRNA without the downstream secondary structure, using force-induced remnant magnetization spectroscopy combined with unique probing schemes. The result represents the first experimental evidence of multiple frameshifting steps. It is also one of the rare reports of the "-2" frameshifting. Our assay removed the ambiguity of transcriptional slippage involvement in other frameshifting assays. Two significant insights for the frameshifting mechanism were revealed. First, EF-G·GTP is indispensable to frameshifting. Although EFG·GDPCP has been shown to prompt translocation before, we found that it could not induce frameshifting. This implies that the GTP hydrolysis is responsible for the codon-anticodon re-pairing in frameshifting, which corroborates our previous mechanical force measurement of EF-G·GTP. Second, translation in all three reading frames of the slippery sequence can be induced by the corresponding in-frame aminoacyl tRNAs. Although A-site tRNA is known to affect the partition between "0" and "-1" frameshifting, it has not been reported that all three reading frames can be translated by their corresponding tRNAs. The in vitro results were confirmed by toe-printing assay and protein sequencing.
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http://dx.doi.org/10.1021/acschembio.7b00028DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5477775PMC
June 2017

Effects of tungsten on uptake, transport and subcellular distribution of molybdenum in oilseed rape at two different molybdenum levels.

Plant Sci 2017 Mar 23;256:87-93. Epub 2016 Dec 23.

Micro-Element Research Center, Huazhong Agricultural University, Wuhan, China; Hubei Provincial Engineering Laboratory for New-Type Fertilizer, Wuhan, China; Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture, China.

Due to the similarities of molybdenum (Mo) with tungsten (W) in the physical structure and chemical properties, studies involving the two elements have mainly examined their competitive relationships. The objectives of this study were to assess the effects of equimolar W on Mo accumulation, transport and subcellular distribution in oilseed rape at two Mo levels with four treatments: Mo (1μmol/L Mo, Low Mo), Mo+W (1μmol/L Mo+1μmol/LW, Low Mo with Low W), Mo (200μmol/L Mo, High Mo) and Mo+W (200μmol/L Mo+200μmol/L Mo, High Mo with high W). The fresh weight and root growth were inhibited by equimolar W at both low and high Mo levels. The Mo concentration and accumulation in root was increased by equimolar W at the low Mo level, but that in the root and shoot was decreased at the high Mo level. Additionally, equimolar W increased the Mo concentrations of xylem and phloem sap at low Mo level, but decreased that of xylem and increased that of phloem sap at the high Mo level. Furthermore, equimolar W decreased the expression of BnMOT1 in roots and leaves at the low Mo level, and only decreased its expression in leaves at the high Mo level. The expression of BnMOT2 was also decreased in root for equimolar W compared with the low Mo level, but increased compared with high Mo level. Moreover, equimolar W increased the proportion of Mo in cell wall fraction in root and that of soluble fraction in leaves when compared with the low Mo level. The results suggest that cell wall and soluble fractions might be responsible for the adaptation of oilseed rape to W stress.
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http://dx.doi.org/10.1016/j.plantsci.2016.12.009DOI Listing
March 2017

Quantitatively Resolving Ligand-Receptor Bonds on Cell Surfaces Using Force-Induced Remnant Magnetization Spectroscopy.

ACS Cent Sci 2016 Feb 5;2(2):75-9. Epub 2016 Feb 5.

Department of Chemistry, University of Houston , Houston, Texas 77204, United States.

Molecule-specific noncovalent bonding on cell surfaces is the foundation for cellular recognition and functioning. A major challenge in probing these bonds is to resolve the specific bonds quantitatively and efficiently from the nonspecific interactions in a complex environment. Using force-induced remnant magnetization spectroscopy (FIRMS), we were able to resolve quantitatively three different interactions for magnetic beads bearing anti-CD4 antibodies with CD4(+) T cell surfaces based upon their binding forces. The binding force of the CD4 antibody-antigen bonds was determined to be 75 ± 3 pN. For comparison, the same bonds were also studied on a functionalized substrate surface, and the binding force was determined to be 90 ± 6 pN. The 15 pN difference revealed by high-resolution FIRMS illustrates the significant impact of the bonding environment. Because the force difference was unaffected by the cell number or the receptor density on the substrate, we attributed it to the possible conformational or local environmental differences of the CD4 antigens between the cell surface and substrate surface. Our results show that the high force resolution and detection efficiency afforded by FIRMS are valuable for studying protein-protein interactions on cell surfaces.
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http://dx.doi.org/10.1021/acscentsci.5b00325DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4827459PMC
February 2016

Quantitatively resolving multivalent interactions on a macroscopic scale using force spectroscopy.

Chem Commun (Camb) 2016 Mar;52(18):3705-8

Department of Chemistry, University of Houston, Houston, TX 77204, USA.

Multivalent interactions remain difficult to be characterized and consequently controlled, particularly on a macroscopic scale. Using force-induced remnant magnetization spectroscopy (FIRMS), we have resolved the single-, double-, and triple-biotin-streptavidin interactions, multivalent DNA interactions and CXCL12-CXCR4 interactions on millimetre-scale surfaces. Our results establish FIRMS as a viable method for systematic resolution and controlled formation of multivalent interactions.
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http://dx.doi.org/10.1039/c5cc10535hDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4767602PMC
March 2016
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