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Wei Shen

Publications and source records attributed to Wei Shen.

At least 19 recordsLinked to original sources
PubMed2026

Genomic and transcriptomic features of HBV integration in treatment-naïve, HBeAg-positive children with chronic HBV infection.

BACKGROUND: Hepatitis B virus (HBV) integration represents a major obstacle to curing HBV; however, the landscape of HBV integration and local immune response to transcriptionally active viral integration in children with chronic HBV infection remain unclear. Herein, we aimed to elucidate this landscape in this population. METHODS: Genomic analyses using a probe-based capture strategy were performed on 18 children and 28 adults with chronic HBV infection. Spatial transcriptomics (ST) was performed on 12 children from our cohort and 3 adults from a public database. FINDINGS: All patients were hepatitis B e antigen (HBeAg)-positive and treatment-naïve. Genomically, children exhibited significantly lower clonal expansion level of HBV-integrated hepatocytes than adults, despite comparable unique breakpoint counts. After adjusting for confounding variables, age was identified as an independent risk factor for total frequency of unique integration breakpoints (b = 3.22, P = 0.005). Spatially, ST revealed that spots with transcriptionally active viral integration exhibited a sparse distribution and accounted for a low proportion of all spots in children. Notably, at these spots, children showed reduced adaptive immune cells (e.g., CD8+ T cells) but increased innate components (myeloid cells, Kupffer cells, activated dendritic cells) and APC co-stimulation, whereas adults exhibited a uniform reduction of immune cell populations. INTERPRETATION: Compared with adults, children exhibit lower clonal expansion of HBV-integrated hepatocytes and distinct immune profiles in response to transcriptionally active viral integration, offering new insights into their differing clinical course. FUNDING: Key Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education).

Humans↗
PubMed2026

Genome-wide association and selective sweep analyses reveal genetic loci for teat number trait in pigs.

Teat number is a key reproductive trait for the commercial pig industry, as an optimum number enhances weaned piglet survival rate. This study aimed to identify single nucleotide polymorphisms (SNPs) and genomic regions that are associated with teat number in the Large White sow. A total of 1000 French Large White sows were used in an analysis of total, left/right, and maximum unilateral teat number. Environmental factor, Spearman correlation, genome-wide association study (GWAS), linkage disequilibrium, and selective sweep analyses were conducted, with validation performed in a population of 1145 Landrace pigs. Genetic statistics showed that this population's teat number had moderate-low genomic heritability (h2 = 0.17-0.21) and weak negative correlation with weaned piglet litter weight. Parity and season affected teat development. GWAS identified 17 candidate SNPs on SSC 4, 7, and 17. Combined with selective sweep analysis, two key regions on SSC 7 were found, with four teat number-related SNPs, annotated to VRTN, DIO2, NRXN3. These candidate genes are associated with thoracic vertebrae development, hormone regulation during the early stage of teat formation, and nervous system development. These five SNPs showed similar results in the Landrace pig validation population; non-mutant homozygotes had 0.25-1.15 more teats than mutant ones in both populations. This study contributes to the identification of key variant loci associated with teat number-related traits in sows, thereby providing reliable molecular markers and a theoretical basis for marker-assisted selection of sow reproductive performance.

Animals↗
PubMed2026

Clinical and genetic characterization of constitutional MLH1 promoter hypermethylation: Implications for Lynch syndrome diagnosis.

PURPOSE: Constitutional MLH1 promoter hypermethylation (CMPH) is a relatively rare cause of Lynch syndrome. While most cases appear to be sporadic, some result from secondary epimutations, mainly caused by germline variants in the MLH1 promoter region. This study describes the clinical phenotype and genetic etiology of CMPH in the largest clinical cohort to date. METHODS: A retrospective analysis was conducted for 422 individuals who underwent clinical CMPH testing. Promoter sequencing was used to identify the underlying variants. Long-read sequencing further characterized MLH1 promoter methylation. RESULTS: CMPH was identified in 15.6% of the study cohort participants. Of these, 63 exhibited clinical features consistent with Lynch syndrome. The most common associated cancers were colorectal cancer, followed by endometrial cancer, breast cancer, and sebaceous neoplasms. Mendelian inheritance of CMPH was observed in 5 families in the study cohort, indicating secondary epimutations. Promoter sequencing identified 8 unique germline variants, including 3 novel variants. Methylation analysis by long-read sequencing revealed mutant allele-specific promoter methylation for these variants. CONCLUSION: Our findings provide the most comprehensive review of the clinical phenotype associated with CMPH and highlight the significant contribution of promoter variants to its etiology. These results underscore the need to include the assessment of constitutional MLH1 promoter methylation for Lynch syndrome diagnosis.

Humans↗
PubMed2025

Aplf/Dna2 variants drive chromosomal fission and accelerate speciation in zokors.

Chromosomal fissions and fusions are common, yet the molecular mechanisms and implications in speciation remain poorly understood. Here, we confirm a fission event in one zokor species through multiple-omics and functional analyses. We traced this event to a mutation in a splicing enhancer of the DNA repair gene Aplf in the fission-bearing species, which caused exon skipping and produced a truncated protein that disrupted DNA repair. An intronic deletion in Dna2, known to facilitate neo-telomere formation when knocked out, reduced gene activity. These variants collectively drove chromosomal fission in this zokor species. The newly formed chromosome became fixed due to carrying essential genes and strong selective pressure. While geographic isolation likely initiated the divergence of this species and the sister one, the fission event and associated decline at the chromosome level in gene flow probably exacerbated the speciation process. Our work elucidates the genetic basis of chromosomal fission and underscores its role in speciation dynamics.

Multiomics↗
PubMed2025

Alternative spliceosomal protein Eftud2 mediated Kif3a exon skipping promotes SHH-subgroup medulloblastoma progression.

Alternative splicing plays a pivotal role in various facets of organogenesis, immune response, and tumorigenesis. Medulloblastoma represents a prevalent childhood brain tumor, with approximately one-third classified as the Sonic Hedgehog (SHH) subgroup. Nevertheless, the contribution of alternative splicing to medulloblastoma oncogenesis remains elusive. This investigation delineated an upregulation of the spliceosomal protein Eftud2 in the SHH-subgroup medulloblastoma mouse model and human medulloblastoma patients. Targeted ablation of Eftud2 in granule precursor cells (GNPs) within the cerebellum prolonged the survival of SHH-subgroup medulloblastoma mice, indicating a putative association between Eftud2 expression and medulloblastoma prognosis. Functional assays unveiled that EFTUD2 depletion in human medulloblastoma cells significantly curtailed cellular proliferation by impeding the activation of the SHH signaling pathway. Through multi-omics sequencing analysis, it was discerned that Eftud2 influences exons 10-11 skipping of Kif3a, a kinesin motor critical for primary cilia formation. Notably, exons 10-11 skipping in Kif3a augmented human medulloblastoma cell proliferation by potentiating the transcriptional activity of Gli2. These findings underscore a robust correlation between Eftud2 and SHH-subgroup medulloblastoma, emphasizing its regulatory role in modulating downstream transcription factors through the alternative splicing of pivotal genes within the SHH signaling pathway, thereby propelling the aggressive proliferation of SHH-subgroup medulloblastoma.

Medulloblastoma↗
PubMed2003

Adipose tissue quantification by imaging methods: a proposed classification.

Recent advances in imaging techniques and understanding of differences in the molecular biology of adipose tissue has rendered classical anatomy obsolete, requiring a new classification of the topography of adipose tissue. Adipose tissue is one of the largest body compartments, yet a classification that defines specific adipose tissue depots based on their anatomic location and related functions is lacking. The absence of an accepted taxonomy poses problems for investigators studying adipose tissue topography and its functional correlates. The aim of this review was to critically examine the literature on imaging of whole body and regional adipose tissue and to create the first systematic classification of adipose tissue topography. Adipose tissue terminology was examined in over 100 original publications. Our analysis revealed inconsistencies in the use of specific definitions, especially for the compartment termed "visceral" adipose tissue. This analysis leads us to propose an updated classification of total body and regional adipose tissue, providing a well-defined basis for correlating imaging studies of specific adipose tissue depots with molecular processes.

Adipose Tissue↗
PubMed2003

Volume estimates by imaging methods: model comparisons with visible woman as the reference.

OBJECTIVE: To compare the accuracy of four volume estimation models to actual tissue and organ volumes measured in the visible woman. METHODS: Actual volumes were calculated from 1-mm-thick visible woman images that were segmented for five major components including subcutaneous and visceral adipose tissue across the 1730 available slices. Four available models resolved to two equations: truncated cone/truncated pyramid vs. two-column/parallel trapezium. Between-slice interval and initial slice were systematically varied when deriving component volumes using the two equations in four regions. RESULTS: For each compartment and each between-slice interval, the means of the two-column model were always the same as the corresponding reference volumes, whereas those of the truncated cone model were smaller than the reference volumes. Similarly, the coefficient variation for the two-column model was always smaller than for the truncated cone model. DISCUSSION: The equation based on the parallel trapezium and the two-column models is more accurate in estimating tissue volumes than the corresponding equation for truncated pyramid and truncated cone models. This finding has important implications for the volume calculations of imaging-based body compartments such as adipose tissue.

Anatomy↗
PubMed2003

The C-terminal tail of Arabidopsis 14-3-3omega functions as an autoinhibitor and may contain a tenth alpha-helix.

The eukaryotic regulatory protein 14-3-3 is involved in many important plant cellular processes including regulation of nitrate assimilation through inhibition of phosphorylated nitrate reductase (pNR) in darkened leaves. Divalent metal cations (Me2+) and some polyamines interact with the loop 8 region of the 14-3-3 proteins and allow them to bind and inhibit pNR in vitro. The role of the highly variant C-terminal regions of the 14-3-3 isoforms in regulation by polycations is not clear. In this study, we carried out structural analyses on the C-terminal tail of the Arabidopsis 14-3-3omega isoform and evaluated its contributions to the inhibition of pNR. Nested C-terminal truncations of the recombinant 14-3-3omega protein revealed that the removal of the C-terminal tail renders the protein partially Mg2+-independent in both pNR binding and inhibition of activity, suggesting that the C-terminus functions as an autoinhibitor. The C-terminus of 14-3-3omega appears to undergo a conformational change in the presence of polycations as demonstrated by its increased trypsin cleavage at Lys-247. C-terminal truncation of 14-3-3omega at Thr-255 increased its interaction with antibodies to the C-terminus of 14-3-3omega in non-denaturing conditions, but not in denaturing conditions, suggesting that the C-terminal tail contains ordered structures that might be disrupted by the truncation. Circular dichroism (CD) analysis of a C-terminal peptide, from Trp-234 to Lys-249, revealed that the C-terminal tail might contain a tenth alpha-helix, in agreement with the in silico predictions. The function of the putative tenth alpha-helix is not clear because substituting two prolyl residues within the predicted helix (E245P/I246P mutant), which prevented the corresponding peptide from adopting a helical conformation, did not affect the inhibition of pNR activity in the presence or absence of Mg2+. We propose that in the absence of polycations, access of target proteins to their binding groove in the 14-3-3 protein is restricted by the C-terminus, which acts as part of a gate that opens with the binding of polycations to loop 8.

14-3-3 Proteins↗
PubMed2003

Percentage body fat ranges associated with metabolic syndrome risk: results based on the third National Health and Nutrition Examination Survey (1988-1994).

BACKGROUND: Increasing attention has focused on the association between body fatness and related metabolic risk factors. The quantitative link between percentage body fat (%BF) and the risk of metabolic syndrome is unknown. OBJECTIVES: The objectives were to determine the risk [odds ratios (ORs)] of metabolic syndrome based on %BF in black and white men and women in the United States and to provide corresponding ranges of %BF associated with a risk equivalent to body mass index (BMI; in kg/m(2)). DESIGN: The subjects were participants in the third National Health and Nutrition Examination Survey and were divided into those with and without the metabolic syndrome. OR equations were derived from logistic regression models for %BF and BMI, with the 25th percentile in the study population as the reference. Ranges were developed by associating %BF with the equivalent risk of metabolic syndrome based on established BMI cutoffs. RESULTS: Four sets (men, women, black, and white) of OR curves were generated for %BF and for BMI by using data from 8259 adults. The ORs for metabolic syndrome were lower in blacks than in whites at any given %BF or BMI. The developed cutoffs for %BF differed between men and women but showed only small race and age effects. A simplified set of sex-specific %BF ranges for the risk of metabolic syndrome were developed. CONCLUSIONS: The risk of metabolic syndrome can be established from measured %BF by using either the developed OR curves or %BF thresholds at traditional BMI cutoffs. This information should prove useful in both clinical and research settings.

Adipose Tissue↗
PubMed2003

Tadalafil has no detrimental effect on human spermatogenesis or reproductive hormones.

PURPOSE: We assessed the effects on spermatogenesis of placebo vs 10 or 20 mg tadalafil administered daily for 6 months to healthy men and men with mild erectile dysfunction. MATERIALS AND METHODS: In 2 studies 421 healthy men or men with mild erectile dysfunction who were 45 years or older and met semen criteria derived from WHO reference values were randomized to 6 months of treatment with placebo (101) or 10 mg tadalafil (103), or to placebo (106) or 20 mg tadalafil (111). Semen samples and serum for reproductive hormones (testosterone, luteinizing hormone and follicle-stimulating hormone) were collected at baseline, after 3 months and at the end of treatment. RESULTS: Tadalafil had no adverse effects on spermatogenesis, as assessed by sperm concentration, sperm count per ejaculate, percent sperm motility, normal morphology or serum reproductive hormones. Tadalafil was well tolerated. Common adverse events were headache, dyspepsia and back pain. CONCLUSIONS: Chronic daily administration of tadalafil at doses of 10 and 20 mg for 6 months had no adverse effects on spermatogenesis or on reproductive hormones in men older than 45 years.

3',5'-Cyclic-GMP Phosphodiesterases↗
PubMed2003

Inhibitive effect of cordyceps sinensis on experimental hepatic fibrosis and its possible mechanism.

AIM: To investigate the inhibitive effect and its possible mechanism of Cordyceps Sinensis (CS) on CCl(4)-plus ethanol-induced hepatic fibrogenesis in experimental rats. METHODS: Rats were randomly allocated into a normal control group, a model control group and a CS group. The latter two groups were administered with CCl(4) and ethanol solution at the beginning of the experiment to induce hepatic fibrosis. The CS group was also treated with CS 10 days after the beginning of CCl(4) and ethanol administration. All control groups were given corresponding placebo at the same time. At the end of the 9th week, rats in each group were humanely sacrificed. Blood and tissue specimens were taken. Biochemical, radioimmunological, immunohistochemical and molecular biological examinations were used to determine the level change of ALT, AST, HA, LN content in serum and TGFbeta(1), PDGF, collagen I and III expression in tissue at either protein or mRNA level or both of them. RESULTS: As compared with the model control group, serum ALT, AST, HA, and LN content levels were markedly dropped in CS group (86.0+/-34.4 vs 224.3+/-178.9, 146.7+/-60.2 vs 272.6+/-130.1, 202.0+/-79.3 vs 316.5+/-94.1 and 50.4+/-3.0 vs 59.7+/-9.8, respectively, P<0.05). Tissue expression of TGFbeta(1) and its mRNA, collagen I mRNA were also markedly decreased (0.2+/-0.14 vs 1.73+/-1.40, 1.68+/-0.47 vs 3.17+/-1.17, 1.10+/-0.84 vs 2.64+/-1.40, respectively, P<0.05). More dramatical drop could be seen in PDGF expression (0.87+/-0.43 vs 1.91+/-0.74, P<0.01). Although there was no statistical significance, it was still strongly suggested that collagen III mRNA expression was also decreased in CS group as compared with model control group (0.36+/-0.27 vs 0.95+/-0.65, P=0.0615). In this experiment, no significant change could be found in PDGF mRNA expression between two groups (0.35+/-0.34 vs 0.70+/-0.46, P>0.05). CONCLUSION: Cordyceps sinensis could inhibit hepatic fibrogenesis derived from chronic liver injury, retard the development of cirrhosis, and notably ameliorate the liver function. Its possible mechanism involves inhibiting TGFbeta(1) expression, and thereby, down regulating PDGF expression, preventing HSC activation and deposition of procollagen I and III.

Animals↗
PubMed2003

[Influence of Cordyceps sinensis on pancreatic islet beta cells in rats with experimental liver fibrogenesis].

OBJECTIVE: To investigate the effect of Cordyceps sinensis (CS) on pancreatic islet B cells of experimental hepatic fibrogenesis rats. METHODS: Rats were randomly allocated into three groups: normal group, model group and CS group. The rats in the latter two groups were administered with CCl(4) solution to induce liver fibrosis, the CS group was also treated with CS 10 days after the beginning of CCl(4) administration. Rats in normal group were sacrificed at the beginning of the experiment, while the rats in the other two groups were sacrificed randomly at the end of the third and sixth weeks. The rats' islets were isolated and cultured in vitro, then the basal insulin level of the islets and the serum level of insulin were determined by radioimmunological assay. RESULTS: It seemed no change that the levels of serum insulin and basal insulin between the model group and the normal group at the third week. But at the sixth week, both insulin levels in the model group were higher than those in the normal group (52.6 mU/L2.5 mU/L vs 23.7 mU/L 2.3 mU/L, q=13.01, p<0.05; 52.94muU/ml 13.12muU/ml vs 35.16muU/ml 5.64muU/ml, q=10.06, p<0.01). No significant change could be seen in the serum levels of insulin between the CS group and the model group at the third and sixth weeks. But the basal insulin levels in the CS group were apparently higher than those in the model group at the third and sixth weeks (156.63muU/ml 6.57muU/ml vs 39.64muU/ml 3.95muU/ml, q=66.94, p<0.001; 140.44muU/ml 38.53muU/ml vs 52.94muU/ml 13.12muU/ml, q=12.98, p<0.01). CONCLUSION: Cordyceps sinensis can increase the basal insulin level of the islets in CCl(4)-induced liver fibrosis rats.

Animals↗
PubMed2003

The impact of incident vertebral and non-vertebral fragility fractures on health-related quality of life in established postmenopausal osteoporosis: results from the teriparatide randomized, placebo-controlled trial in postmenopausal women.

OBJECTIVE: To report the combined impact of both vertebral and non-vertebral fractures on decreased health-related quality of life (HRQOL) in postmenopausal women (mean age 70.7) with osteoporosis who participated in a clinical trial to examine the anti-fracture efficacy of teriparatide [rhPTH(1-34)] injection. METHODS: Patients were randomly assigned to 1 of 3 study arms: placebo, 20 micro g or 40 micro g of teriparatide by daily self-injection. All patients received daily calcium (1000 mg) and vitamin D (400-1200 U) supplements. Patients were followed for a median of 21 months. Incident vertebral fractures were assessed by lateral spinal radiograph. Incident non-vertebral fractures were ascertained by patient self-report and verified by a review of radiological reports. HRQOL was assessed at baseline and annually until study termination using the Osteoporosis Assessment Questionnaire (OPAQ), a validated disease-targeted instrument. RESULTS: Of the 365 women in the HRQOL sub-study, 53 had an incident vertebral or non-vertebral fracture during the study period. Compared to women without incident fractures, women who fractured reported significant declines in physical functioning, emotional status, and symptoms (all p < 0.05). Similarly, when analysis was limited to patients with significant loss in HRQOL, patients with incident fracture accounted for a greater proportion of those patients with decreased physical function, emotional status, and increased symptoms (all p < 0.05). CONCLUSION: Our results confirm and extend previous findings to show that a composite endpoint of incident vertebral and non-vertebral fractures in women with postmenopausal osteoporosis was associated with significant decreases in HRQOL.

Aged↗
PubMed2003

[Establishment of BAC mediated transgenic mice containing 97 kb beta-globin gene cluster].

OBJECTIVE: To delete IL-11 receptor alpha chain gene from the Bacterial Artificial Chromosome (BAC) chimeric DNA by RecA protein mediated homologous recombination method and establish the transgenic mice model containing whole beta-globin gene cluster. METHODS: Two 500 bp homologous sequences (A and B) located at the upstream and downstream of IL-11 receptor alpha chain gene respectively were cloned into the Hind III and Xba I sites of pBV vector, then the 1 kb A + B fragment was recovered from the building vector and inserted into the Sal I site of the shuttle vector pSV-RecA. After transforming the shuttle vector into the competent DH10B E. Coli containing BAC DNA, the IL-11 receptor alpha chain gene was finally deleted from the BAC DNA through chloramphenicol positive selection and fusaic acid negative selection. The new BAC clone was characterized by Pulse Field Gel Electrophoresis (PFGE). Then, we microinjected the linearized and purified BAC DNA into the mouse fertilized eggs and prepared the transgenic mice. RESULTS: By RecA protein mediated homologous recombination method, we deleted the IL-11 receptor alpha chain gene from the BAC DNA containing the complete beta-globin Gene Cluster and established 3 respective transgenic mice lines. CONCLUSION: Human beta-globin gene cluster in the transgenic mice mediated by new BAC expresses in a correct mode and level as compared with previous transgenic mice.

Animals↗
PubMed2002

Field testing of Schistosoma japonicum DNA vaccines in cattle in China.

Vaccines are needed to reduce the zoonotic reservoir of Schistosoma japonicum infection in bovines in China. We have developed two experimental DNA vaccines and have already shown these to be capable of inducing partial protection in water buffalo naturally exposed to the risk of S. japonicum infection in the field. We now report a similar field trial in cattle, the other major bovine reservoir host species in China. Groups of cattle were vaccinated with the VRSj28 vaccine or the VRSj23 vaccine, or, to test whether protection could be enhanced by combination vaccination, with both these DNA vaccines together. After vaccination, the cattle were exposed to natural infection in the field for a period of 54 days. Worm and egg counts carried out at the end of the experiment showed that each of the vaccine groups showed partial resistance, and that combined vaccination was not more effective than vaccination with the individual plasmids.

Animals↗
PubMed2002

Expression of creatine kinase isoenzyme genes during postnatal development of rat brain cerebellum: evidence for transcriptional regulation.

Transcription and accumulation of brain-type creatine kinase (CKB) mRNA and its protein was examined during postnatal development of rat brain cerebellum, the brain region containing highest CKB mRNA in the adult. CKB protein was extremely low at day 1, increased about 10-fold until week 4 and remained constant until week 10. This time course was paralleled by cerebellar CKB mRNA, which was also extremely low at day 1 and increased 5-fold during the first 3 weeks and then remained constant. High levels of CKB protein were also detected in cultured primary cerebellar granular neurons. Nuclear run-on assays directly showed that CKB mRNA accumulation during postnatal cerebellar development was due to increased transcription. When compared with cerebrum and whole brain, cerebellar CKB mRNA accumulation during postnatal development was temporally delayed. Analysis of myocyte enhancer factor (MEF)-2 and Sp1, factors known to initiate or sustain CKB transcription in tissues other than brain, revealed that MEF-2 in cerebellum was low at week 1 but increased 3.5-fold by week 7, while Sp1 remained unchanged. The increase in CKB protein during cerebellar postnatal development was coincident with that of the ubiquitous mitochondrial CK protein and mRNA, indicating that a functional phosphocreatine energy shuttle probably exists for efficient ATP regeneration in the cerebellum. This should be beneficial for the many energy-demanding requirements during cerebellar development, as indicated by the observed temporal co-expression of CKB with myelin basic protein, which is involved in axon myelination by oligodendrocytes.

Animals↗
PubMed2002

Foxa3 (HNF-3gamma) binds to and activates the rat proglucagon gene promoter but is not essential for proglucagon gene expression.

Members of the Forkhead box a (Foxa) transcription factor family are expressed in the liver, pancreatic islets and intestine and both Foxa1 and Foxa2 regulate proglucagon gene transcription. As Foxa proteins exhibit overlapping DNA-binding specificities, we examined the role of Foxa3 [hepatocyte nuclear factor (HNF)-3gamma] in control of proglucagon gene expression. Foxa3 was detected by reverse transcriptase PCR in glucagon-producing cell lines and binds to the rat proglucagon gene G2 promoter element in GLUTag enteroendocrine cells. Although Foxa3 increased rat proglucagon promoter activity in BHK fibroblasts, augmentation of Foxa3 expression did not increase proglucagon promoter activity in GLUTag cells. Furthermore, adenoviral Foxa3 expression did not affect endogenous proglucagon gene expression in islet or intestinal endocrine cell lines. Although Foxa3(-/-) mice exhibit mild hypoglycaemia during a prolonged fast, the levels of proglucagon-derived peptides and proglucagon mRNA transcripts were comparable in tissues from wild-type and Foxa3(-/-) mice. These findings identify Foxa3 as a member of the proglucagon gene G2 element binding-protein family that, unlike Foxa1, is not essential for control of islet or intestinal proglucagon gene expression in vivo.

Animals↗