Biomedical subjects

Qiang He

Publications and source records attributed to Qiang He.

At least 19 recordsLinked to original sources

PubMed2026

Pan-genome-based resequencing of 2,320 accessions reveals structural variations and accelerates breeding advances in cultivated peanut.

The cultivated peanut is a crucial global legume crop that is essential for food security and nutrition, particularly in developing regions. However, its limited genetic variation hampers breeding progress and yield improvement. Here we constructed a graph-based pan-genome for peanut, incorporating 14 genomes that represent all 6 peanut varieties. Using this pan-genome, we genotyped 2,320 accessions, covering 88.03% of ICRISAT and 59.21% of USDA core germplasm, enriching valuable resources for genomic studies and breeding. We cataloged genomic structural variations and investigated the role of homoeologous exchanges in population divergence. Through our pan-genome approach, we overcame the challenges of genotyping posed by homoeologous exchanges and identified key genes associated with flowering and dwarfism in peanut. By integrating superior haplotypes and germplasm resources guided by the pan-genome, we further developed high-yield dwarf lines. This work provides essential genomic resources to accelerate functional gene discovery and modern peanut breeding.

Journal Article↗

PubMed2026

Genomic and genetic dissection underlying seedling drought resilience in oats.

Drought threatens global crop yields, and common oat, a vital nutritional source for food and feed, is particularly constrained in the semi‑arid regions where it is widely cultivated. Here, we report two high-quality genome assemblies for drought-resilient (Borris37) and drought-sensitive (XymC06) oat accessions with distinct seedling survival rates and genome sizes of 10.92 Gb and 10.96 Gb, and construct comprehensive landscapes of insertion‑deletions (InDels) and structural variants (SVs). Integrating population-level genomic, transcriptomic and phenotypic (seedling survival rate), we demonstrate that InDels and SVs underpin divergent drought resilience and identify 52 candidate genes associated with drought resistance whose expression is significantly modulated by these variants. Borris37 accumulates 36 favorable alleles of these genes. An InDel in the AsNF-YB3 promoter enhances binding to AsARF1, upregulating AsNF‑YB3 under drought, and overexpression of AsNF‑YB3 reduces ROS accumulation. Our findings provide resources and targets for drought‑resistance breeding in oat, thereby supporting global food security.

Drought Resistance↗

PubMed2025

Genomic insights into karyotype evolution and adaptive mechanisms in Polygonaceae species.

Polygonaceae, with ecological versatility and global distribution, is an ideal system for investigating plant adaptation. However, the genomic mechanisms underlying its karyotype evolution and environmental resilience remain unclear. We herein present chromosome-level genomes of 11 species from 10 Polygonaceae genera. Our analyses reveal that Gypsy retrotransposons are key drivers of genome size variations in Polygonaceae. We reconstructed a Polygonaceae ancestral karyotype comprising 28 proto-chromosomes and elucidated evolutionary trajectories via extensive chromosomal rearrangements. Furthermore, we constructed a cross-genus super pan-genome for Polygonaceae, identifying 80,055 gene families, of which 9,845 (12.30%) are core gene families. Private genes are found to contribute significantly to interspecific differences in adaptability. Notably, gene copy number variations are identified as a critical factor influencing adaptations to diverse niches involving species-specific increases in metabolic pathways. This study provides a genomic framework for Polygonaceae karyotype plasticity and adaptive innovation, offering insights into plant evolution under environmental challenges.

Karyotype↗

PubMed2007

Hydrolysis characterization of phospholipid monolayers catalyzed by different phospholipases at the air-water interface.

Combination of some newly developed microscopic and spectroscopic techniques with conventional Langmuir monolayer method can provide more quantitative information with the molecular orientation and reorganization process of spread amphiphilic molecules at the air/water interface. These techniques are extended to investigate the hydrolysis process of spreading lipid monolayer catalyzed by different enzymes, phospholipases A2, C and D, respectively. Synchrotron X-ray diffraction and infrared reflection absorption spectroscopy are able directly to give the structural information of the assembled monolayer, interfacial activity of amphiphiles and their components at the interface. Microscopic technique such as Brewster angle microscopy (BAM), fluorescence microscopy (FM) can be used to trace the morphological changes dynamically as the spreading lipid monolayer is hydrolyzed at the air/water interface. We summary here some latest progress in this filed and give a brief review over the hydrolysis features of phospholipid monolayer catalyzed by different enzymes. It is attempted to establish a model of membrane hydrolysis process in order to better understand the mechanism of membrane metabolism and signal transduction in a living system.

Air↗

PubMed2007

Thermosensitive copolymer networks modify gold nanoparticles for nanocomposite entrapment.

The core-shell gold nanoparticles and copolymer of N-isopropylacrylamide (NIPAM) and N,N'-methylenebisacrylamide (MBAA) hybrids (Au@copolymer) were fabricated through surface-initiated atom-transfer radical polymerization (ATRP) on the surface of gold nanoparticles in 2-propanol/water mixed solvents. The surface of citrate-stabilized gold nanoparticles was first modified by a disulfide initiator for ATRP. The slight cross-linking polymerization between NIPAM and MBAA occurred on the gold surface and resulted in the formation of core-shell Au@copolymer nanostructures that were characterized by TEM, and FTIR and UV-visible spectroscopy. Such synthesized Au@copolymer hybrids possess clearly thermosensitive properties and exhibit "inspire" and "expire" water behavior in response to temperature changes in aqueous solution. Because of this property, we enable to trap and encapsulate smaller nanoparticles by using the free space of the copolymer-network scaffold anchored at the gold surface.

Gold↗

PubMed2006

Biodegradability of tannin-containing wastewater from leather industry.

Tannins occur commonly in the wastewaters from forestry, plant medicine, paper and leather industries. The treatment of this kind of wastewaters, including settling and biodegradation, is usually difficult because tannins are highly soluble in water and would inhibit the growth of microorganisms in activated sludge. The objective of this study is to investigate biodegradability of tannin-containing wastewaters, so as to characterize the pollution properties of such wastewaters and provide a reference for their biological treatment in wastewater treatment plants. The research was typified by using the wastewater collected from vegetable tanning process in leather industry. A model was developed to describe the activated sludge process, and the biodegradation kinetics of vegetable tanning wastewater (VET wastewater) was studied. It was found that the biodegradability of tannin-containing wastewater varies heavily with the content of tannins in wastewater. The biodegradation of VET wastewater with tannin content around 4,900 mg/l occurred inefficiently due to the inhibition of tannins to the activated sludge process, and only 34.7% of biodegradation extent was reached in 14 days of incubation. The optimal biodegradability of VET wastewater was observed when its tannin content was diluted to 490 mg/l, where the COD and tannin removals reached 51.3% and 45.1% respectively in 6 days. Hence, it is suggested that a proper control of tannin content is necessary to achieve an effective biodegradation of tannin-containing wastewaters in wastewater treatment plants.

Kinetics↗

PubMed2006

Synthesis of PNIPAM-co-MBAA copolymer nanotubes with composite control.

We report the preparation of copolymer, poly(N-isopropylacrylamide)-co-(N,N'-methylenebisacrylamide) (PNIPAM-co-MBAA) nanotubes with different composite ratios through surface-initiated atom transfer radical polymerization using a porous anodic aluminum oxide membrane as a template. It is found that the tubular wall strongly depends on the monomer concentration. The composite-induced changes in dimension and shape of nanotubes, especially the wall thickness, were studied by scanning electron microscopy, transmission electron microscopy, atom force microscopy, FT-IR, and gel permeation chromatography. The PNIPAM-co-MBAA nanotubes exhibit a high flexibility and stability.

Journal Article↗

PubMed2006

Evolutionary identification of a subtype specific functional site in the ligand binding domain of steroid receptors.

Nuclear receptors are ubiquitous eukaryotic ligand-activated transcription factors that modulate gene expression through varied interactions. However, the highly conserved functional sites known today seem insufficient to explain receptor specific recruitment of different coactivator and corepressor proteins and regulation of transcription. To search for new receptor-subtype specific functional sites, we applied difference evolutionary trace (difference ET) analysis to the ligand binding domain of steroid receptors, a subgroup of the nuclear receptor (NR) family. This computational approach identified a new functional site located on a surface opposite to currently known protein-protein interaction sites and distinct from the ligand binding pocket. Strikingly, the literature shows that in vivo variations at residues in the new site are linked to androgen resistance and leukemia, and our own targeted mutations to this site lower but do not eradicate transcriptional activation by estrogen receptor alpha (ERalpha), with reduced ligand binding affinity and SRC-1 interaction. Thus, these data demonstrate that this evolutionary important surface can function as an allosteric site that modulates some but not all receptor binding interactions. Evolutionary analysis further shows that this allosteric regulatory site is shared among all NRs from groups 2 (HNF4-like) and 4 (NGFIB-like), suggesting a role among many nuclear receptors. Its concave structure, hydrophobic composition, and residue variability among nuclear receptors further suggest that it would be amenable for specific drug design. This highlights the power of evolutionary information for the identification of new functional sites even in a protein family as well studied as NRs.

Allosteric Site↗

PubMed2006

Human serum albumin supported lipid patterns for the targeted recognition of microspheres coated by membrane based on ss-DNA hybridization.

Human serum albumin (HSA) patterns have been successfully fabricated for the deposition of lipid bilayer, 1,2-dimyristoyl-sglycerophosphate (DMPA), by making use of the micro-contact printing (microCP) technique and liposome fusion. Confocal laser scanning microscopy (CLSM) results indicate that lipid bilayer has been assembled in HSA patterns with a good stability. Such well-defined lipid patterns formed on HSA surface create possibility to incorporate specific components like channels or receptors for specific recognition. In view of this, microspheres coated with lipid membranes were immobilized in HSA-supported lipid patterns via the hybridization of complementary ss-DNAs. This procedure enables to transfer solid materials to a soft surface through a specific recognition.

DNA, Single-Stranded↗

PubMed2006

Assembly of nanotubes of poly(4-vinylpyridine) and poly(acrylic acid) through hydrogen bonding.

Nanotubes of poly(4-vinylpyridine) (PVP) and poly(acrylic acid) (PAA) were fabricated by hydrogen bonding based on layer-by-layer (LbL) assembly. The uniform and flexible tubular structures were characterized by scanning electron microscopy (SEM) and transmission electron microscopy (TEM). FTIR and X-ray photoelectron spectroscopy (XPS) measurements confirm the formation of hydrogen bonds in the assembled nanotubes. PAA can be released from the assembled PAA/PVP nanotubes in a basic aqueous solution to give the walls of the tubes a porous structure. Such assembled nanotubes can be considered as carriers for catalysts or drugs, especially in aqueous solution against capillary force.

Acrylic Resins↗

PubMed2006

Fabrication of fluorescent nanotubes based on layer-by-layer assembly via covalent bond.

A pressure-filter-template approach was employed to prepare fluorescent nanotubes of polyethyleneimine (PEI) and 3,4,9,10-perylenetetracarboxylicdianhydride (PTCDA) through covalent combination in the porous of alumina template based on the layer-by-layer (LbL) assembly technique. Scanning electron microscopy (SEM) and transmission electron microscopy (TEM) images exhibited a tubular structure of the obtained samples. The wall thickness of the nanotubes is well controlled by varying the assembled cycle number, which is detected by UV-visible spectroscopy. Fourier transform infrared (FT-IR) spectroscopy confirmed the formation of covalent bonds between PEI and PTCDA in nanotubes.

Journal Article↗

PubMed2006

Fabrication of protein nanotubes based on layer-by-layer assembly.

Nanotubes of cytochrome C (cyto-c) with glutaraldehyde (GA) or PSS based on the layer-by-layer (LbL) assembly through covalent binding and electrostatic adsorption have been fabricated. The combination of the template method and the LbL method for fabrication of nanotubes exhibits low cost, simplicity, and versatility. The tubular morphology of the assembled glutaraldehyde and cytochrome C film was demonstrated by scanning electron microscopy (SEM) and transmission electron microscopy (TEM) measurements. The components of the tubes were determined by energy-dispersive X- ray spectra (EDAX). It is found that the assembled tubes keep the proteins' biochemical activity and electronic activity by cyclic voltammograms. The measurements of ultraviolet spectra and circular dichroism (CD) on the assembled nanotubes confirmed the cyto-c existence in the tubes.

Absorption↗

PubMed2006

Modulation of biological regulatory networks during nephrogenesis.

Mesenchymal-to-epithelial transition is an important biological event during the course of renal cell differentiation as condensing mesenchyme gives rise to tubuloepithelial structures. Wilms' tumor suppressor gene (Wt1) has been identified as a master regulator of the complex genetic events that mediate mesenchymal transdifferentiation. Evidence is summarized here showing that the tightly regulated series of genetic and biochemical events during nephrogenesis is disrupted by superactivation of aryl hydrocarbon receptor (Ahr) by benzo(a)pyrene (BaP), a ubiquitous polycyclic aromatic hydrocarbon and renal carcinogen (Falahatpisheh and Ramos, 2003). Nephron formation is inhibited by BaP, a response that involves inhibition of metanephric cell differentiation and shifts in the relative abundance of Wt1 splice variants. A systems biology paradigm that combined approaches from genomics, transcriptomics, and bioinformatics revealed that the global response of murine metanephric cultures to BaP involves downregulation of Ahr and disruption of downstream targets of Wt1. Discrete networks of genetic regulation were resolved using Boolean idealizations and included genes involved in renal cell differentiation and metabolic control. This work has established a role for Ahr in renal cell differentiation and kidney development and resolved putative molecular interactions between Ahr and Wt1.

Animals↗

PubMed2006

The potential of wattle tannin extracts for fine use.

As a contribution to the fine use of wattle tannin, four fractions, purified tannin (Tp), ether extracts (Te), ethyl acetate extracts (Ta) and water fraction (Tw), were obtained by the methods of precipitation and liquid-liquid extraction of commercial wattle tannin. The number average molecular weights (M(n)) of Tp, Te, Ta and Tw were determined as 2660, 440, 980 and 2050 Da, respectively. The biological activities including protein precipitation, enzyme inhibition and antibacterial potency of each fraction were studied and compared. The results indicated that the molecular weight of each fraction is directly associated with its biological activities. The fraction of Tw showed the strongest capacity to precipitate protein and Ta showed the strongest capacity to inhibit enzyme activities, while Ta and Te showed better antibacterial potency.

Anti-Bacterial Agents↗

PubMed2006

Energetic consequences of nitrite stress in Desulfovibrio vulgaris Hildenborough, inferred from global transcriptional analysis.

Many of the proteins that are candidates for bioenergetic pathways involved with sulfate respiration in Desulfovibrio spp. have been studied, but complete pathways and overall cell physiology remain to be resolved for many environmentally relevant conditions. In order to understand the metabolism of these microorganisms under adverse environmental conditions for improved bioremediation efforts, Desulfovibrio vulgaris Hildenborough was used as a model organism to study stress response to nitrite, an important intermediate in the nitrogen cycle. Previous physiological studies demonstrated that growth was inhibited by nitrite and that nitrite reduction was observed to be the primary mechanism of detoxification. Global transcriptional profiling with whole-genome microarrays revealed coordinated cascades of responses to nitrite in pathways of energy metabolism, nitrogen metabolism, oxidative stress response, and iron homeostasis. In agreement with previous observations, nitrite-stressed cells showed a decrease in the expression of genes encoding sulfate reduction functions in addition to respiratory oxidative phosphorylation and ATP synthase activity. Consequently, the stressed cells had decreased expression of the genes encoding ATP-dependent amino acid transporters and proteins involved in translation. Other genes up-regulated in response to nitrite include the genes in the Fur regulon, which is suggested to be involved in iron homeostasis, and genes in the Per regulon, which is predicted to be responsible for oxidative stress response.

Desulfovibrio vulgaris↗

PubMed2006

Salt stress in Desulfovibrio vulgaris Hildenborough: an integrated genomics approach.

The ability of Desulfovibrio vulgaris Hildenborough to reduce, and therefore contain, toxic and radioactive metal waste has made all factors that affect the physiology of this organism of great interest. Increased salinity is an important and frequent fluctuation faced by D. vulgaris in its natural habitat. In liquid culture, exposure to excess salt resulted in striking elongation of D. vulgaris cells. Using data from transcriptomics, proteomics, metabolite assays, phospholipid fatty acid profiling, and electron microscopy, we used a systems approach to explore the effects of excess NaCl on D. vulgaris. In this study we demonstrated that import of osmoprotectants, such as glycine betaine and ectoine, is the primary mechanism used by D. vulgaris to counter hyperionic stress. Several efflux systems were also highly up-regulated, as was the ATP synthesis pathway. Increases in the levels of both RNA and DNA helicases suggested that salt stress affected the stability of nucleic acid base pairing. An overall increase in the level of branched fatty acids indicated that there were changes in cell wall fluidity. The immediate response to salt stress included up-regulation of chemotaxis genes, although flagellar biosynthesis was down-regulated. Other down-regulated systems included lactate uptake permeases and ABC transport systems. The results of an extensive NaCl stress analysis were compared with microarray data from a KCl stress analysis, and unlike many other bacteria, D. vulgaris responded similarly to the two stresses. Integration of data from multiple methods allowed us to develop a conceptual model for the salt stress response in D. vulgaris that can be compared to those in other microorganisms.

Bacterial Proteins↗

PubMed2006

Self-assembled molecular pattern by chemical lithography and interfacial chemical reactions.

The fabrication of lipid-modified molecular patterns by Chemical Lithography combined with interfacial chemical reactions is reported. In this method, self-assembled monolayers (SAMs) of 4'-nitro-1,1'-biphenyl-4-thiol (NBT) were structured by Chemical Lithography which produced cross-linked 4'-amino-1,1'-biphenyl-4-thiol (cABT) monolayers within a nitro-terminated (NBT) matrix. The terminal amino groups in the cABT monolayer were diazotized to create diazo cations, and the lipid monolayer with negative charge was assembled on the diazo regions by electrostatic attraction. Under the exposure of UV light, the photoreaction occurs. The diazonium groups interacting with the lipid headgroups via electrostatic attraction decompose and release N2 which leads to the lipid monolayer covalently attaching to the cABT region. The presence of phosphorus in X-ray photoelectron spectra (XPS) reveals the binding of the phospholipid layer to the cABT surface. Atomic force microscopy (AFM) images display that lipid-modified molecular patterns with different sizes and shapes and with a thickness of ca. 2.5 nm have been formed. The resulting lipid-modified molecular patterns are considered to be a first step towards obtaining stable biointerfacing patterns and studying biomolecular recognition.

Membranes, Artificial↗

PubMed2006

Fabrication of polyethyleneimine and poly(styrene-alt-maleic anhydride) nanotubes through covalent bond.

Nanotubes of Polyethyleneimine (PEI) and Poly(styrene-alt-maleic anhydride) (PSMA) based on the layer-by-layer (LbL) technique and template method through covalent bond have been fabricated. The combination of LbL assembly and the template method can well control the length, wall thickness, outside, and inner diameters of the resulting nanotubes. The formation of covalent between PEI and PSMA enables the nanotubes with a good mechanical stability. The uniform tubular structure has been characterized by scanning electron microscopy (SEM) and transmission Electron Microscopy (TEM). Fourier transform infrared (FT-IR) and X-ray photoelectron spectroscopy (XPS) measurements confirms the formation of covalent bond in the assembled nanotubes.

Binding Sites↗