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Tao Zhou

Publications and source records attributed to Tao Zhou.

At least 19 recordsLinked to original sources
PubMed2026

Transposable Element Dynamics Drive the Genomic Evolution and Phenotypic Diversification of Allotetraploid Common Carp.

An important question in evolutionary biology is how polyploidization generates raw material for phenotypic diversification. Transposable elements (TEs) represent an underestimated source of genetic variation in eukaryotic genomes. By integrating 516 whole-genome resequencing datasets and 236 transcriptomes from common carp (Cyprinus carpio), a representative allotetraploid fish, we constructed the first population-scale landscape of TE insertions in teleosts. TE insertions are widespread in the carp genome and preferentially associated with stress-responsive genes, with DNA transposons as major contributors. Relaxed purifying selection and TE burst events coexist, generating abundant variation for subsequent subspecies differentiation. Compared with a closely related diploid species, carp exhibits more exonic TE insertions and shorter TE-gene distances, and multiple TE superfamilies expanded during tetraploidization. Genome-wide association analyses uncovered intragenic TE variants underlying domesticated traits missed by SNPs, including DNA transposon deletions associated with scale reduction and altered body shape. Notably, lighter-colored individuals harbor homozygous deletions of LTR and DNA transposons within mdfic2, whose knockout in zebrafish reduces pigmentation. Most trait-associated variants reflect lineage-specific loss of ancient TE insertions rather than recent transposition. Overall, these findings highlight the distinct role of TEs in polyploid genome evolution and phenotypic diversification, providing new insights into TE dynamics in vertebrates.

allotetraploidization↗
PubMed2026

Genomic and food-safety evaluation of Staphylococcus chromogenes in Chinese dairy milk.

Non-aureus staphylococci and mammaliicocci (NASM) cause mastitis and may contaminate milk and dairy products. Milk samples (n&#xa0;=&#xa0;1916) from cows with subclinical or clinical mastitis (SCM and CM, respectively) were collected from 28 large-scale (> 500 lactating cows) Chinese dairy farms. Overall, 999 NASM isolates representing 19 species were identified by MALDI-TOF MS and cpn60 sequencing, with Staphylococcuschromogenes, Mammaliicoccus sciuri and Staphylococcus haemolyticus being most prevalent. Antimicrobial resistance (AMR) was determined with disc diffusion; non-susceptible to penicillin was most common (SCM, 30% and CM, 29%) whereas cefoxitin non-susceptible NASM accounted for 8-10% of isolates; among these, 12.5% carried mecA but none carried mecC. Galleria mellonella was used to assess virulence of 78 strains of S. chromogenes, a dominant species; subsequently, 32 strains, representing higher- and lower-virulence in the Galleria model, were selected for whole-genome sequencing and comparative genomics. S. chromogenes isolates from CM had higher virulence (p&#xa0;<&#xa0;0.05) than those from SCM. The 32 genomes comprised 20 sequence types, indicating high genetic diversity. No robust genomic marker of Galleria virulence phenotype was identified in this selected WGS subset. Acquired resistance genes (n&#xa0;=&#xa0;5) were detected, including a first report of fusC in S. chromogenes; the fusC-positive isolate had an elevated fusidic acid MIC (8&#xa0;mg/L). Although S. chromogenes persisted in milk at 4&#xa0;&#xb0;C, pasteurization (64&#xa0;&#xb0;C for 30&#xa0;min) reduced viable counts to below detection. This study provided new insights into the prevalence, AMR, genomic diversity, and dairy-chain relevance of milk-derived NASM, particularly S. chromogenes. However, the genomic findings were based on an intentionally selected WGS subset and should be interpreted as hypothesis-generating rather than population-representative.

Animals↗
PubMed2025

The suprachiasmatic nucleus regulates brown fat thermogenesis in male mice through an adrenergic receptor ADRB3-S100B signaling pathway.

The suprachiasmatic nucleus (SCN), the central circadian pacemaker, orchestrates daily metabolic rhythms, yet its role in substrate selection and thermogenic adaptation under stress remains insufficiently understood. Here, we show that SCN lesioning abolishes the adaptive suppression of brown adipose tissue (BAT) thermogenesis typically observed during time-restricted feeding in subthermoneutral environments (TRF-STE), a paradigm that imposes concurrent nutrient and thermal stress. Contrary to wild-type responses, SCN-lesioned mice maintain elevated BAT thermogenic activity, despite impaired lipolysis, instead shifting toward glucose-driven heat production. This phenotype is accompanied by sustained sympathetic tone and &#x3b2;3-adrenergic receptor (ADRB3) signaling in BAT. Mechanistically, we identify a SCN-regulated ADRB3-S100B signaling axis underlying this metabolic reprogramming. S100B, a nutrient-sensitive calcium-binding protein, is upregulated in BAT following SCN disruption, where it promotes thermogenesis by stimulating brown adipocyte proliferation and suppressing senescence. Functional studies reveal that S100B is both necessary and sufficient for sustaining BAT thermogenesis under TRF-STE. Furthermore, diverse SCN disruption models, including light-induced circadian arrhythmia, N-Methyl-D-aspartic acid (NMDA) excitotoxicity, and Caspase-3-mediated ablation, consistently elevate S100B expression in BAT, reinforcing its role as a convergent effector of SCN-regulated metabolic adaptation. Thus, in intact animal, the SCN restrains the ADRB3-S100B module, gating BAT thermogenic output in accordance with energetic availability. Disruption of SCN output lifts this restraint, unmasking a latent ADRB3-S100B program that preserves thermogenesis when lipid fuel is limited. These findings reveal a previously unrecognized role of the SCN in governing thermogenic flexibility and fuel partitioning, and position the ADRB3-S100B axis as a potential target for mitigating circadian misalignment and metabolic disease.

Animals↗
PubMed2025

Harnessing Landscape Genomics to Evaluate Genomic Vulnerability and Future Climate Resilience in an East Asia Perennial.

In this era of rapid climate change, understanding the adaptive potential of organisms is imperative for buffering biodiversity loss. Genomic forecasting provides invaluable insights into population vulnerability and adaptive potential under diverse climatic conditions, thereby facilitating management interventions and bolstering shaping species-specific germplasm conservation strategies. We primarily employed landscape genomics approaches, leveraging single-nucleotide polymorphisms obtained through whole-genome resequencing of 201 individuals across 43 Rheum palmatum complex populations, to pinpoint adaptive variation and its significance in the context of future climates, delineate seed zones, and establish guidelines for ex situ germplasm conservation. The species complex exhibited strong signatures of local adaptation and differential genomic vulnerabilities across its distribution range, with eastern lineage populations facing significant maladaptation risks under future climate scenarios. Using diverse datasets of putatively adaptive loci and climate change scenarios, we delineated three distinct seed zones within the species' range, estimated varying sample sizes per zone to capture most adaptive diversity, and predicted shifts in seed zone centroids ranging from 48.3 to 359.3&#x2009;km from historical distributions to mitigate climate change impacts. Collectively, our findings underscore the importance of integrating genomic and environmental data to forecast the adaptive trajectory of an East Asian perennial under anticipated climate changes, guide seed zone delineation for germplasm conservation and enhance population resilience. These results provide a blueprint for designing targeted conservation strategies and restoration plans in other imperilled species.

Climate Change↗
PubMed2006

Sno/scaRNAbase: a curated database for small nucleolar RNAs and cajal body-specific RNAs.

Small nucleolar RNAs (snoRNAs) and Cajal body-specific RNAs (scaRNAs) are named for their subcellular localization within nucleoli and Cajal bodies (conserved subnuclear organelles present in the nucleoplasm), respectively. They have been found to play important roles in rRNA, tRNA, snRNAs, and even mRNA modification and processing. All snoRNAs fall in two categories, box C/D snoRNAs and box H/ACA snoRNAs, according to their distinct sequence and secondary structure features. Box C/D snoRNAs and box H/ACA snoRNAs mainly function in guiding 2'-O-ribose methylation and pseudouridilation, respectively. ScaRNAs possess both box C/D snoRNA and box H/ACA snoRNA sequence motif features, but guide snRNA modifications that are transcribed by RNA polymerase II. Here we present a Web-based sno/scaRNA database, called sno/scaRNAbase, to facilitate the sno/scaRNA research in terms of providing a more comprehensive knowledge base. Covering 1979 records derived from 85 organisms for the first time, sno/scaRNAbase is not only dedicated to filling gaps between existing organism-specific sno/scaRNA databases that are focused on different sno/scaRNA aspects, but also provides sno/scaRNA scientists with an opportunity to adopt a unified nomenclature for sno/scaRNAs. Derived from a systematic literature curation and annotation effort, the sno/scaRNAbase provides an easy-to-use gateway to important sno/scaRNA features such as sequence motifs, possible functions, homologues, secondary structures, genomics organization, sno/scaRNA gene's chromosome location, and more. Approximate searches, in addition to accurate and straightforward searches, make the database search more flexible. A BLAST search engine is implemented to enable blast of query sequences against all sno/scaRNAbase sequences. Thus our sno/scaRNAbase serves as a more uniform and friendly platform for sno/scaRNA research. The database is free available at http://gene.fudan.sh.cn/snoRNAbase.nsf.

Base Sequence↗
PubMed2006

Immunological evaluation of SW-HSA conjugate on goats.

Locoweeds cause significant livestock poisoning and economic loss all over the world. The purpose of this study was to investigate the immune effects of locoweed toxin, swainsonine (SW) and human serum albumin (HSA) conjugate (SW-HSA), on goats. Twenty-four Sannon goats were randomly separated into immune control group (eight goats), immune poisoning group I (six goats), immune poisoning group II (six goats) and poisoning control group (four goats). Immune control group, immune poisoning groups I and II were first vaccinated with SW-HSA conjugate. The poisoning control group, immune poisoning groups I and II were then fed with 10.0 g/kg BW/day dry powder of Oxytropis kansuensis Bunge everyday morning. The immune control group was supplied with an alfalfa-based diet. Blood samples of these experimental animals were collected at different time interval. Immunoassay was performed using indirect ELISA and E-rosette technique. The results show that, after second booster immunization: (1) anti-SW antibody level in some goats increased to 2(8), which proves that SW-HSA conjugate can induce experimental animals to produce high-level anti-SW antibody in their bodies; (2) the high-level antibody in their bodies could maintain 30 days, and decreased gradually after poisoning experiment (in our experiment, there was a return of the antibody level on day 21 after poisoning experiment); (3) the decreasing of the E-rosette rate of the immune poisoning group was delayed 14 days, which suggests that SW-HSA could low down the loss of the immunity of the goats; (4) swainsonine concentration in the blood was significantly lower (p<0.01) in the immune poisoning groups than that in the poisoning control group, and there was no significant difference (p>0.01) between the two immune poisoning groups within the poisoning experiment.

Animals↗
PubMed2006

PIAS3 induction of PRB sumoylation represses PRB transactivation by destabilizing its retention in the nucleus.

Progesterone receptor (PR) plays a critical role in cell proliferation and differentiation, and its transcriptional activity is known to be modulated by cofactor proteins. In the present study, we demonstrated that in the presence of progesterone, protein inhibitor of activated STAT-3 (PIAS3) significantly inhibited the PR transcriptional activity and the expression of progesterone-responsive genes. Reduction of endogenous PIAS3 by PIAS3 small-interfering RNA enhanced PR transactivation in a ligand-dependent manner. PIAS3 interacted with PR both in vitro and in vivo and the interaction was enhanced by progesterone. Furthermore, our findings suggested that PIAS3 strongly induced PRB sumoylation at three sites, Lys-7, Lys-388 and Lys-531. In addition, novel roles in PRB nuclear retention and transactivation were identified for these sites. Our data also suggested that PIAS3 was recruited in a largely hormone-dependent manner in response to a progesterone-responsive promoter. Finally, we demonstrated that PIAS3 inhibited the DNA-binding activity of PR and influenced its nuclear export as well as PR transactivation. Taken together, these data strongly suggested that PIAS3 played an important physiological role in PR function.

Animals↗
PubMed2006

Universal scaling behavior of clustering coefficient induced by deactivation mechanism.

We propose a model of network growth that generalizes the deactivation model previously suggested for complex networks. Several topological features of this generalized model, such as the degree distribution and clustering coefficient, have been investigated analytically and by simulations. A scaling behavior of clustering coefficient C approximately 1/M is theoretically obtained, where M refers to the number of active nodes in the network. We discuss the relationship between the recently observed numerical behavior of clustering coefficient in the coauthor and paper citation networks and our theoretical result. It shows that both of them are induced by deactivation mechanism. By introducing a perturbation, the generated network undergoes a transition from large to small world, meanwhile the scaling behavior of C is conserved. It indicates that C approximately 1/M is a universal scaling behavior induced by deactivation mechanism.

Journal Article↗
PubMed2006

Iron binding dendrimers: a novel approach for the treatment of haemochromatosis.

A range of iron binding dendrimers terminated with hexadentate ligands formed from hydroxypyridinone, hydroxypyranone, and catechol moieties have been synthesized in order to investigate their potential as clinically useful iron(III)-selective chelators capable of removing dietary iron from the gastrointestinal tract and preventing the development of iron overload typical of haemochromatosis and thalassaemia intermedia. The iron chelating abilities of these molecules have been characterized by MALDI-TOF mass spectrometry and UV spectrometry. Hydroxypyridinone-terminated dendrimers were found to possess a high affinity and selectivity for iron(III). A hydroxypyridinone-based dendrimer was demonstrated to be highly efficient at reducing the absorption of iron(III) in rat intestine. This family of dendrimers may find an application in the treatment of iron overload.

Animals↗
PubMed2006

3-Hydroxy-2-(5-hydroxypentyl)-4H-chromen-4-one: a bidentate or tridentate iron(III) ligand?

The pK(a) value and iron affinity constants for 3-hydroxy-2-(5-hydroxypentyl)-4H-chromen-4-one 1 have been determined by spectrophotometry using aqueous methanol solutions. The extrapolated affinity constants beta(1), beta(2), and beta(3)( )()for iron(III) in aqueous solution were 9.95, 18.69, and 26.02, respectively, with a corresponding pFe(3+) value of 14.64. Job plot and MS spectra data demonstrated that the 3:1 species is favored at pH 7.0. These results indicate that 1 acts as a bidentate ligand when coordinated to iron(III).

Chlorides↗
PubMed2006

Identification of up-regulated genes after complete spinal cord transection in adult rats.

Spinal cord injury (SCI) initiates a cascade of events and these responses to injury are likely to be mediated and reflected by changes in mRNA concentrations. As a step towards understanding the complex mechanisms underlying repair and regeneration after SCI, the gene expression pattern was examined 4.5 days after complete transection at T8-9 level of rat spinal cord. Improved subtractive hybridization was used to establish a subtracted cDNA library using cDNAs from normal rat spinal cord as driver and cDNAs from injured spinal cord as tester. By expressed sequence tag (EST) sequencing, we obtained 73 EST fragments from this library, representing 40 differentially expressed genes. Among them, 32 were known genes and 8 were novel genes. Functions of all annotated genes were scattered in almost every important field of cell life such as DNA repair, detoxification, mRNA quality control, cell cycle control, and signaling, which reflected the complexity of SCI and regeneration. Then we verified subtraction results with semiquantitative RT-PCR for eight genes. These analyses confirmed, to a large extent, that the subtraction results accurately reflected the molecular changes occurring at 4.5 days post-SCI. The current study identified a number of genes that may shed new light on SCI-related inflammation, neuroprotection, neurite-outgrowth, synaptogenesis, and astrogliosis. In conclusion, the identification of molecular changes using improved subtractive hybridization may lead to a better understanding of molecular mechanisms responsible for repair and regeneration after SCI.

Animals↗
PubMed2006

MDM2 interacts with and downregulates a sarcomeric protein, TCAP.

Recent reports have shown that MDM2 may attenuate hypertrophy of cardiac myocytes. However, mechanism of MDM2 involving in this process is unclear. In this study, we identified a novel specific MDM2-binding protein TCAP by the yeast two-hybrid screen. It was validated by GST pull-down and co-immunoprecipitation assays. Confocal analysis showed that MDM2 and TCAP co-localized in the nucleus, and elevated MDM2 expression could alter the subcellular localization of TCAP. Notably, MDM2 downregulated the protein level of TCAP through the proteasomal pathway, and this downregulation was inhibited by p14(ARF). In addition, our results suggested that the degradation of TCAP by MDM2 was through the ubiquitin-independent pathway. Given that TCAP is a key component involving in the cardiac hypertrophy, the degradation of TCAP by MDM2 might be connected with the roles of MDM2 in cardiac hypertrophy. Further investigation will focus on the biological significance of MDM2-TCAP interaction in cardiac hypertrophy.

Connectin↗
PubMed2006

Direct electrochemistry of hemoglobin in PHEA and its catalysis to H2O2.

Hemoglobin (Hb) was immobilized on glassy carbon (GC) electrode by a kind of synthetic water-soluble polymer, poly-alpha,beta-[N-(2-hydroxyethyl)-L-aspartamide] (PHEA). A pair of well-defined and quasi-reversible cyclic voltammetric peaks was achieved, which reflected the direct electron-transfer of the Fe(III)/Fe(II) couple of Hb. The formal potential (E degrees'), the apparent coverage (Gamma(*)) and the electron-transfer rate constant (k(s)) were calculated by integrating cyclic voltammograms experimental data. Scanning electron microscopy (SEM) demonstrated the morphology of Hb-PHEA film very different from the Hb and PHEA films. Ultraviolet visible (UV-vis) spectroscopy showed Hb in PHEA film remained its secondary structure similar to the native state. In respect that the immobilized protein remained its biocatalytic activity to the reduction of hydrogen peroxide (H(2)O(2)), a kind of mediator-free biosensor for H(2)O(2) could be developed. The apparent Michaelis-Menten constant (K(m)(app)) was estimated to be 18.05 microM. The biosensor exhibited rapid electrochemical response and good stability. Furthermore, uric acid (UA), ascorbic acid (AA) and dopamine (DA) had little interferences with the amperometric signal of H(2)O(2), which provide the perspective of this H(2)O(2) sensor to be used in biological environments.

Biosensing Techniques↗
PubMed2006

Ubc9 interacts with SOX4 and represses its transcriptional activity.

SOX4 is a member of SOX transcriptional factor family that is crucial for many cellular processes. In this study, a yeast two-hybrid screening of human mammary cDNA library identified human ubiquitin-conjugating enzyme 9 (hUbc9) that interacted with SOX4. This interaction was confirmed by GST pull-down in vitro and co-immunoprecipitation assays in vivo. Deletion mapping demonstrated that HMG-box domain of SOX4 is required to mediate the interaction with Ubc9 in yeast. Furthermore, confocal microscopy showed that Ubc9 co-localized with SOX4 in the nucleus. Luciferase assays found that Ubc9 specifically repressed SOX4 transcriptional activity in 293T cells. We further demonstrated that Ubc9 could functionally repress the transcriptional activity of endogenous SOX4 induced by progesterone in T47D cells. The C93S mutant of Ubc9, which abrogates SUMO-1 conjugation activity, did not abolish the ability to repress SOX4 activity. It shows that Ubc9 interacts with SOX4 and represses its transcriptional activity independent of its SUMO-1-conjugating activity.

High Mobility Group Proteins↗
PubMed2006

Efficient routing on complex networks.

We propose a routing strategy to improve the transportation efficiency on complex networks. Instead of using the routing strategy for shortest path, we give a generalized routing algorithm to find the so-called efficient path, which considers the possible congestion in the nodes along actual paths. Since the nodes with the largest degree are very susceptible to traffic congestion, an effective way to improve traffic and control congestion, as our strategy, can be redistributing traffic load in central nodes to other noncentral nodes. Simulation results indicate that the network capability in processing traffic is improved more than 10 times by optimizing the efficient path, which is in good agreement with the analysis.

Journal Article↗
PubMed2006

Better synchronizability predicted by crossed double cycle.

In this Brief Report, we propose a network model named crossed double cycles, which are completely symmetrical and can be considered as the extensions of nearest-neighboring lattices. The synchronizability, measured by eigenratio R, can be sharply enhanced by adjusting the only parameter, the crossed length m. The eigenratio R is shown very sensitive to the average distance L, and the smaller average distance will lead to better synchronizability. Furthermore, we find that, in a wide interval, the eigenratio R approximately obeys a power-law form as R approximately L(1.5).

Journal Article↗
PubMed2006

The effect of atorvastatin on serum myeloperoxidase and CRP levels in patients with acute coronary syndrome.

BACKGROUND: Inflammation is involved in the atherogenesis and pathogenesis of acute coronary syndrome (ACS). As the acute-phase reaction proteins in ACS, myeloperoxidase (MPO) and C-reactive protein (CRP) may play critical roles. Anti-inflammation may be one of benefits of statin drugs in ACS. Studies have showed that statins can suppress serum CRP concentrations. However, whether statins also reduce serum MPO concentrations in patients with ACS is unknown. METHODS: Seventy-eight patients with ACS were randomly separated into Group A and Group B, the patients in Group A receiving conventional therapy, which include no cholesterol-lowering drugs, +atorvastatin (10 mg/day, n=40), the patients in Group B receiving conventional therapy (n=38). The serum concentrations of MPO were measured by enzyme-linked immunosorbent assay (ELISA) and CRP were measured by turbidimetric immunoassay. RESULTS: Serum concentrations of MPO were significantly lower after 1-week therapy in both groups of patients [Group A from 590+/-168 to 496+/-154 microg/l, Group B from 570+/-165 to 521+/-153 microg/l; P<0.01, respectively]. Serum concentrations of CRP also were markedly lower than pretreatment [Group A from 6.56+/-1.87 to 5.14+/-2.07 mg/l; Group B from 6.36+/-1.94 to 5.45+/-1.90 mg/l, P<0.05, respectively]. Compared with conventional therapy alone, atorvastatin significantly further reduced serum MPO [P=0.014] and CRP concentrations [P=0.032]. There were no correlations detected between the reduction of MPO and CRP (r=0.124, P=0.068). CONCLUSIONS: Atorvastatin reduced serum MPO and CRP concentrations in patients with ACS. These effects may explain some clinical benefits of statins in the treatment of these patients.

Acute Disease↗