Microscopic mechanism study of the rheological behavior of non-Newtonian fluids based on dissipative particle dynamics.

Non-Newtonian fluid rheological properties are a hot research topic for realizing intelligent applications. In order to investigate the microscopic mechanism and structural evolution process of the nonlinear rheological behavior of non-Newtonian fluids, this paper systematically investigates two continuous nonlinear rheological behaviors of non-Newtonian fluids, namely shear-thickening and shear-thinning rheological properties, using a non-Newtonian fluid system composed of polyethylene glycol (PEG) mixed with nano-silica (Nano-SiO2) by a dissipative particle dynamics (DPD) method. It is shown that at low shear rates, the molecular chains of PEG in the fluid are stretched due to shear flow and the molecular structure is transformed into an ordered state; and the effective hydrodynamic radius of Nano-SiO2 beads decreases, which makes the translational friction coefficient of the beads decrease and the system mobility increases, exhibiting shear-thinning behavior. When the shear rate exceeds the critical value, the contact and collision probability between Nano-SiO2 beads in the non-Newtonian fluid increases; a large number of silicon hydroxyl groups exist on the surface of Nano-SiO2, which form a large number of hydrogen bonds when they are close to each other and constrain the particle separation, resulting in a large aggregation of Nano-SiO2 beads, leading to an increase in the effective kinetic radius of Nano-SiO2 beads and an increase in the coefficient of translational friction, forming a blockage of the fluid system and exhibiting a shear-thickening behavior. Our study provides insights for understanding the rheological behavior of non-Newtonian fluids from a microscopic perspective, and contributes to the intelligent application of non-Newtonian fluids.

Adaptive VMD-K-SVD-Based Rolling Bearing Fault Signal Enhancement Study.

To address the challenges associated with nonlinearity, non-stationarity, susceptibility to redundant noise interference, and the difficulty in extracting fault feature signals from rolling bearing signals, this study introduces a novel combined approach. The proposed method utilizes the variational mode decomposition (VMD) and K-singular value decomposition (K-SVD) algorithms to effectively denoise and enhance the collected rolling bearing signals. Initially, the VMD method is employed to separate the overall noise into intrinsic mode functions (IMFs), reducing the noise content within each IMF. To optimize the mode component, K, and the penalty factor, α, in VMD, an improved arithmetic optimization algorithm (IAOA) is employed. This ensures the selection of optimal parameters and the decomposition of the signal into a set of IMFs, forming the original dictionary. Subsequently, the signals are decomposed into multiple IMFs using VMD, and an original dictionary is constructed based on these IMFs. K-SVD is then applied to the original dictionary to further reduce the noise in each IMF, resulting in a denoised and enhanced signal. To validate the efficacy of the proposed method, rolling bearing signals collected from Case Western Reserve University (CWRU) and thrust bearing test rigs were utilized. The experimental results demonstrate the feasibility and effectiveness of the proposed approach in denoising and enhancing the rolling bearing signals.

Correction: Amelioration of autism-like social deficits by targeting histone methyltransferases EHMT1/2 in Shank3-deficient mice.

A correction to this paper has been published and can be accessed via a link at the top of the paper.

Amelioration of autism-like social deficits by targeting histone methyltransferases EHMT1/2 in Shank3-deficient mice.

Many of the genes disrupted in autism are identified as histone-modifying enzymes and chromatin remodelers, most prominently those that mediate histone methylation/demethylation. However, the role of histone methylation enzymes in the pathophysiology and treatment of autism remains unknown. To address this, we used mouse models of haploinsufficiency of the Shank3 gene (a highly penetrant monogenic autism risk factor), which exhibits prominent autism-like social deficits. We found that histone methyltransferases EHMT1 and EHMT2, as well as histone lysine 9 dimethylation (specifically catalyzed by EHMT1/2), were selectively increased in the prefrontal cortex (PFC) of Shank3-deficient mice and autistic human postmortem brains. Treatment with the EHMT1/2 inhibitor UNC0642 or knockdown of EHMT1/2 in PFC induced a robust rescue of autism-like social deficits in Shank3-deficient mice, and restored NMDAR-mediated synaptic function. Activity-regulated cytoskeleton-associated protein (Arc) was identified as one of the causal factors underlying the rescuing effects of UNC0642 on NMDAR function and social behaviors in Shank3-deficient mice. UNC0642 treatment also restored a large set of genes involved in neural signaling in PFC of Shank3-deficient mice. These results suggest that targeting histone methylation enzymes to adjust gene expression and ameliorate synaptic defects could be a potential therapeutic strategy for autism.

Insight into the combinatorial transcriptional regulation on α-amylase gene in animal groups with different dietary nutrient content.

Gene expression is generally regulated by multiple transcription factors (TFs). Despite previous findings of individual TFs regulating pancreatic α-amylase gene expression, the combinatorial transcriptional regulation is not fully understood. To gain insight into multiple TF regulation for pancreatic α-amylase gene, we employed a function conservation approach to predict interacting TFs regulating pancreatic α-amylase gene for 3 dietary animal groups. To this end, we have identified 77, 25, and 118 interacting TFs for herbivore, omnivore, and carnivore, respectively. Computational modeling of TF regulatory networks demonstrated that known pancreas-specific TFs (e.g. GR, NFAT, and PR) may play important roles in recruiting non pancreas-specific TFs to the TF-TF interaction networks, offering specificity and flexibility for controlling pancreatic α-amylase gene expression in different dietary animal groups. The findings from this study indicate that combinatorial transcriptional regulation could be a critical component controlling pancreatic α-amylase gene expression.

An albumin-bound drug conjugate of paclitaxel and indoleamine-2,3-dioxygenase inhibitor for enhanced cancer chemo-immunotherapy.

Despite the promising target of immunosuppressive enzyme indoleamine-2,3-dioxygenase (IDO) for cancer immunotherapy, IDO blockade monotherapy does not show significant benefit to cancer patients in the clinic. Recent research has focused on the combinatorial therapy of the IDO inhibitor and the immune checkpoint blockade or chemotherapy. Here, we synthesize a drug conjugate methyltryptophan-paclitaxel (MP) by linking the IDO inhibitor, D-1-methyltryptophan (D-1MT), to the chemotherapeutic agent, paclitaxel (PTX), through an ester bond. MP exhibits a similar tubulin-stabilizing effect to PTX. Like PTX, MP binds to human serum albumin to form albumin-bound MP nanoparticles (MP NPs) with a particle size of ∼115 nm in diameter. MP NPs significantly improve the tumor concentration of D-1MT due to the hydrolysis of MP in tumors. The codelivery of PTX and D-1MT offered by MP NPs in tumors significantly enhances the anti-tumor effect compared with the albumin-bound PTX NPs. Immune cell phenotyping reveals that MP NPs ameliorate the immune environment through increasing the number of the effector CD8+ T cells, and decreasing the population of regulatory T cells and granulocyte-like myeloid-derived suppressor cells. These results prove that the design of the twin drug from the IDO inhibitor and PTX synergizes the anti-tumor effect and shows promise in clinical translation.

Bioengineered Noncoding RNAs Selectively Change Cellular miRNome Profiles for Cancer Therapy.

Noncoding RNAs (ncRNAs) produced in live cells may better reflect intracellular ncRNAs for research and therapy. Attempts were made to produce biologic ncRNAs, but at low yield or success rate. Here we first report a new ncRNA bioengineering technology using more stable ncRNA carrier (nCAR) containing a pre-miR-34a derivative identified by rational design and experimental validation. This approach offered a remarkable higher level expression (40%-80% of total RNAs) of recombinant ncRNAs in bacteria and gave an 80% success rate (33 of 42 ncRNAs). New FPLC and spin-column based methods were also developed for large- and small-scale purification of milligrams and micrograms of recombinant ncRNAs from half liter and milliliters of bacterial culture, respectively. We then used two bioengineered nCAR/miRNAs to demonstrate the selective release of target miRNAs into human cells, which were revealed to be Dicer dependent (miR-34a-5p) or independent (miR-124a-3p), and subsequent changes of miRNome and transcriptome profiles. miRNA enrichment analyses of altered transcriptome confirmed the specificity of nCAR/miRNAs in target gene regulation. Furthermore, nCAR assembled miR-34a-5p and miR-124-3p were active in suppressing human lung carcinoma cell proliferation through modulation of target gene expression (e.g., cMET and CDK6 for miR-34a-5p; STAT3 and ABCC4 for miR-124-3p). In addition, bioengineered miRNA molecules were effective in controlling metastatic lung xenograft progression, as demonstrated by live animal and ex vivo lung tissue bioluminescent imaging as well as histopathological examination. This novel ncRNA bioengineering platform can be easily adapted to produce various ncRNA molecules, and biologic ncRNAs hold the promise as new cancer therapeutics.

Onecut1 and Onecut2 redundantly regulate early retinal cell fates during development.

Previously, we have shown that Onecut1 (Oc1) and Onecut2 (Oc2) are expressed in retinal progenitor cells, developing retinal ganglion cells (RGCs), and horizontal cells (HCs). However, in Oc1-null mice, we only observed an 80% reduction in HCs, but no defects in other cell types. We postulated that the lack of defects in other cell types in Oc1-null retinas was a result of redundancy with Oc2. To test this theory, we have generated Oc2-null mice and now show that their retinas also only have defects in HCs, with a 50% reduction in their numbers. However, when both Oc1 and Oc2 are knocked out, the retinas exhibit more profound defects in the development of all early retinal cell types, including completely failed genesis of HCs, compromised generation of cones, reduced production (by 30%) of RGCs, and absence of starburst amacrine cells. Cone subtype diversification and RGC subtype composition also were affected in the double-null retina. Using RNA-Seq expression profiling, we have identified downstream genes of Oc1 and Oc2, which not only confirms the redundancy between the two factors and renders a molecular explanation for the defects in the double-null retinas, but also shows that the onecut factors suppress the production of the late cell type, rods, indicating that the two factors contribute to the competence of retinal progenitor cells for the early retinal cell fates. Our results provide insight into how onecut factors regulate the creation of cellular diversity in the retina and, by extension, in the central nervous system in general.

Wild-type and IL10-null mice have differential colonic epithelial gene expression responses to dietary supplementation with synbiotic Bifidobacterium animalis subspecies lactis and inulin.

Prebiotic plus probiotic (synbiotic) supplementations promote fermentation and have shown anti-inflammatory activity in colonic epithelium. However, in many instances, patients with inflammatory bowel disease (IBD) have demonstrated adverse effects after prebiotic supplementation at a dose well tolerated by normal individuals. To test the hypothesis that the host inflammation affects the colonic epithelial response to increased fermentation, the gene expression of colonic epithelium was analyzed. In a 1-way experimental design to test the effect of supplements in wild-type mice using the standard diet formulated by the American Institute of Nutrition (AIN-93G) as the control diet, fermentable fiber inulin (5%) in the absence or presence of the probiotic Bifidobacterium animalis subspecies lactis (Bb12) (10(8) CFU/kg diet) showed limited effects on gene expression as determined by whole-genome microarray. Bb12 supplementation alone was known not to increase fermentation and here instead significantly upregulated genes in nucleic acid metabolic processes. The effects of the synbiotic diet were then determined in mice exposed to LPS-induced inflammation in a 2-way experimental design testing the effect of diet and LPS. The microarray and quantitative reverse transcription-polymerase chain reaction analyses on the wild-type mice revealed that LPS-induced changes in the colonic epithelium were 4- to 10-fold less in the synbiotic diet group compared with the control diet group. Unlike the wild-type mice, anti-inflammatory cytokine interleukin 10 (IL10)-null mice (susceptible to IBD) given the synbiotic diet, compared with those given the control diet, had 3- to 40-fold increased expression of inflammation-related genes such as Cxcl1 (chemokine C-X-C motif ligand 1) and S100a9 (S100 calcium binding protein A9) in the absence and presence of LPS exposure. These contrasting intestinal epithelial responses to increased fermentation in wild-type and IL10-null mice are similar to the difference between healthy human individuals and those with IBD, suggesting that the host disease/genetic background should be considered before prebiotic/probiotic supplementation.

Metalloproteinases and their associated genes contribute to the functional integrity and noise-induced damage in the cochlear sensory epithelium.

Matrix metalloproteinases (MMPs) and their related gene products regulate essential cellular functions. An imbalance in MMPs has been implicated in various neurological disorders, including traumatic injuries. Here, we report a role for MMPs and their related gene products in the modulation of cochlear responses to acoustic trauma in rats. The normal cochlea was shown to be enriched in MMP enzymatic activity, and this activity was reduced in a time-dependent manner after traumatic noise injury. The analysis of gene expression by RNA sequencing and qRT-PCR revealed the differential expression of MMPs and their related genes between functionally specialized regions of the sensory epithelium. The expression of these genes was dynamically regulated between the acute and chronic phases of noise-induced hearing loss. Moreover, noise-induced expression changes in two endogenous MMP inhibitors, Timp1 and Timp2, in sensory cells were dependent on the stage of nuclear condensation, suggesting a specific role for MMP activity in sensory cell apoptosis. A short-term application of doxycycline, a broad-spectrum inhibitor of MMPs, before noise exposure reduced noise-induced hearing loss and sensory cell death. In contrast, a 7 d treatment compromised hearing sensitivity and potentiated noise-induced hearing loss. This detrimental effect of the long-term inhibition of MMPs on noise-induced hearing loss was further confirmed using targeted Mmp7 knock-out mice. Together, these observations suggest that MMPs and their related genes participate in the regulation of cochlear responses to acoustic overstimulation and that the modulation of MMP activity can serve as a novel therapeutic target for the reduction of noise-induced cochlear damage.

Small nucleolar RNA-derived microRNA hsa-miR-1291 modulates cellular drug disposition through direct targeting of ABC transporter ABCC1.

Multidrug resistance-associated protein 1 (MRP1/ABCC1) is an important membrane transporter that contributes to cellular disposition of many endobiotic and xenobiotic agents, and it can also confer multidrug resistance. This study aimed to investigate the role of human noncoding microRNA-1291 (hsa-miR-1291) in regulation of ABCC1 and drug disposition. Bioinformatics analyses indicated that hsa-miR-1291, localized within the small nucleolar RNA H/ACA box 34 (SNORA34), might target ABCC1 3'-untranslated region (3'UTR). Using splinted ligation small RNA detection method, we found that SNORA34 was processed into hsa-miR-1291 in human pancreatic carcinoma PANC-1 cells. Luciferase reporter assays showed that ABCC1 3'-UTR-luciferase activity was decreased by 20% in cells transfected with hsa-miR-1291 expression plasmid, and increased by 40% in cells transfected with hsa-miR-1291 antagomir. Furthermore, immunoblot study revealed that ABCC1 protein expression was sharply reduced in hsa-miR-1291-stably transfected PANC-1 cells, which was attenuated by hsa-miR-1291 antagomir. The change of ABCC1 protein expression was associated with an alternation in mRNA expression. In addition, hsa-miR-1291-directed downregulation of ABCC1 led to a greater intracellular drug accumulation and sensitized the cells to doxorubicin. Together, our results indicate that hsa-miR-1291 is derived from SNORA34 and modulates cellular drug disposition and chemosensitivity through regulation of ABCC1 expression. These findings shall improve the understanding of microRNA-controlled epigenetic regulatory mechanisms underlying multidrug resistance and interindividual variability in pharmacokinetics.

Study on the Effect of Metal Mesh on Pulsed Eddy-Current Testing of Corrosion under Insulation Using an Early-Phase Signal Feature.

Corrosion under insulation (CUI) is a major threat to the structural integrity of insulated pipes and vessels. Pulsed eddy-current testing (PECT) is well known in the industry for detecting CUI, but its readings can be easily influenced by nearby conductive objects, including the insulation supporting metal mesh. As a sequel to our previous study, this paper focuses on the surface distribution of eddy currents at the time of the turning off of the driving voltage instead of examining the overall process of eddy current diffusion. Based on the fact that CUI takes place on the outside of the insulated specimen, the probe footprint was calculated only on the specimen surface. The corrosion depth was regarded as an increment to the probe lift-off, whose information was carried in the early PECT signal. Finite element simulations were performed to facilitate the calculation of the probe footprint and predict the signal behavior. The peak value, which appeared in the early phase of the differential PECT signal, was found to be well correlated with the corrosion depth. Further studies revealed that the mild steel mesh could result in the enlargement of the probe footprint and a decrease in the change rate of the peak value in relation to the corrosion depth. Finally, experiments were conducted to verify the simulation results. The presented findings are consistent with the previously reported results and provide a potential alternative to evaluate CUI in specific scenarios where the insulation has a fixed and uniform thickness.

Essential Role of XBP1 in Maintaining Photoreceptor Synaptic Integrity in Early Diabetic Retinopathy.

Purpose: Diabetic retinopathy (DR) is a leading cause of blindness in working-age adults characterized by retinal dysfunction and neurovascular degeneration. We previously reported that deletion of X-box binding protein 1 (XBP1) leads to accelerated retinal neurodegeneration in diabetes; however, the mechanisms remain elusive. The goal of this study is to determine the role of XBP1 in the regulation of photoreceptor synaptic integrity in early DR. Methods: Diabetes was induced by streptozotocin in retina-specific XBP1 conditional knockout (cKO) or wild-type (WT) mice to generate diabetic cKO (cKO/DM) or WT/DM mice for comparison with nondiabetic cKO (cKO/NDM) and WT/NDM mice. Retinal morphology, structure, and function were assessed by immunohistochemistry, optical coherence tomography, and electroretinogram (ERG) after 3 months of diabetes. The synapses between photoreceptors and bipolar cells were examined by confocal microscopy, and synaptic integrity was quantified using the QUANTOS algorithm. Results: We found a thinning of the outer nuclear layer and a decline in the b-wave amplitude in dark- and light-adapted ERG in cKO/DM mice compared to all other groups. In line with these changes, cKO mice showed increased loss of synaptic integrity compared to WT mice, regardless of diabetes status. In searching for candidate molecules responsible for the loss of photoreceptor synaptic integrity in diabetic and XBP1-deficient retinas, we found decreased mRNA and protein levels of DLG4/PSD-95 in cKO/DM retina compared to WT/DM. Conclusions: These findings suggest that XBP1 is a crucial regulator in maintaining synaptic integrity and retinal function, possibly through regulation of synaptic scaffold proteins.

Experimental Study on Chemical-Mechanical Synergistic Preparation for Cemented Carbide Insert Cutting Edge.

Typical edge defects in the edge region of a new cemented carbide insert without edge preparation include burrs, poor surface quality, micro-breakages, and irregularities along the edge. To address the problems in new cemented carbide inserts without edge preparations, a chemical-mechanical synergistic preparation (CMSP) method for the cemented carbide insert cutting edge was proposed. Firstly, the CMSP device for the insert cutting edge was constructed. Then, the polishing slurry of the CMSP for the insert cutting edge was optimized using the Taguchi method combined with a grey relation analysis and fuzzy inference. Finally, orthogonal experiments, the Taguchi method, and analysis of variance (ANOVA) were used to investigate the effect of the polishing plate's rotational speed, swing angle, and input frequency of the controller on the edge preparation process, and the parameters were optimized. The results showed that the best parameter combination for the polishing slurry for the cemented carbide inserts was the mass concentration of the abrasive particle of 10 wt%, the mass concentration of the oxidant of 10 wt%, the mass concentration of the dispersant of 2 wt%, and the pH of 8. The CMSP process parameter combination for the linear edge had the polishing plate's rotational speed of 90 rpm, the swing angle of 6°, and the input frequency of the controller of 5000 Hz. The optimum CMSP process parameter combination for the circular edge had the polishing plate's rotational speed of 90 rpm, the swing angle of 6°, and the input frequency of the controller of 7000 Hz. The polishing plate's rotational speed had the most significant impact on the edge preparation process, followed by the swing angle, and the effect of the input frequency of the controller was the smallest. This study demonstrated that CMSP is a potential way to treat the cemented carbide insert cutting edge in a tool enterprise.

Genomic insights of protein arginine methyltransferase Hmt1 binding reveals novel regulatory functions.

BACKGROUND: Protein arginine methylation is a post-translational modification involved in important biological processes such as transcription and RNA processing. This modification is catalyzed by both type I and II protein arginine methyltransferases (PRMTs). One of the most conserved type I PRMTs is PRMT1, the homolog of which is Hmt1 in Saccharomyces cerevisiae. Hmt1 has been shown to play a role in various gene expression steps, such as promoting the dynamics of messenger ribonucleoprotein particle (mRNP) biogenesis, pre-mRNA splicing, and silencing of chromatin. To determine the full extent of Hmt1's involvement during gene expression, we carried out a genome-wide location analysis for Hmt1. RESULTS: A comprehensive genome-wide binding profile for Hmt1 was obtained by ChIP-chip using NimbleGen high-resolution tiling microarrays. Of the approximately 1000 Hmt1-binding sites found, the majority fall within or proximal to an ORF. Different occupancy patterns of Hmt1 across genes with different transcriptional rates were found. Interestingly, Hmt1 occupancy is found at a number of other genomic features such as tRNA and snoRNA genes, thereby implicating a regulatory role in the biogenesis of these non-coding RNAs. RNA hybridization analysis shows that Hmt1 loss-of-function mutants display higher steady-state tRNA abundance relative to the wild-type. Co-immunoprecipitation studies demonstrate that Hmt1 interacts with the TFIIIB component Bdp1, suggesting a mechanism for Hmt1 in modulating RNA Pol III transcription to regulate tRNA production. CONCLUSIONS: The genome-wide binding profile of Hmt1 reveals multiple potential new roles for Hmt1 in the control of eukaryotic gene expression, especially in the realm of non-coding RNAs. The data obtained here will provide an important blueprint for future mechanistic studies on the described occupancy relationship for genomic features bound by Hmt1.

miRdSNP: a database of disease-associated SNPs and microRNA target sites on 3'UTRs of human genes.

BACKGROUND: Single nucleotide polymorphisms (SNPs) can lead to the susceptibility and onset of diseases through their effects on gene expression at the posttranscriptional level. Recent findings indicate that SNPs could create, destroy, or modify the efficiency of miRNA binding to the 3'UTR of a gene, resulting in gene dysregulation. With the rapidly growing number of published disease-associated SNPs (dSNPs), there is a strong need for resources specifically recording dSNPs on the 3'UTRs and their nucleotide distance from miRNA target sites. We present here miRdSNP, a database incorporating three important areas of dSNPs, miRNA target sites, and diseases. DESCRIPTION: miRdSNP provides a unique database of dSNPs on the 3'UTRs of human genes manually curated from PubMed. The current release includes 786 dSNP-disease associations for 630 unique dSNPs and 204 disease types. miRdSNP annotates genes with experimentally confirmed targeting by miRNAs and indexes miRNA target sites predicted by TargetScan and PicTar as well as potential miRNA target sites newly generated by dSNPs. A robust web interface and search tools are provided for studying the proximity of miRNA binding sites to dSNPs in relation to human diseases. Searches can be dynamically filtered by gene name, miRBase ID, target prediction algorithm, disease, and any nucleotide distance between dSNPs and miRNA target sites. Results can be viewed at the sequence level showing the annotated locations for miRNA target sites and dSNPs on the entire 3'UTR sequences. The integration of dSNPs with the UCSC Genome browser is also supported. CONCLUSION: miRdSNP provides a comprehensive data source of dSNPs and robust tools for exploring their distance from miRNA target sites on the 3'UTRs of human genes. miRdSNP enables researchers to further explore the molecular mechanism of gene dysregulation for dSNPs at posttranscriptional level. miRdSNP is freely available on the web at http://mirdsnp.ccr.buffalo.edu.

Cutaneomucosal venous malformations are linked to the TIE2 mutation in a large Chinese family.

Mutations in TIE2/TEK gene have been identified as the major cause for cutaneomucosal venous malformations (VMCM) that were previously reported to occur in Caucasian families. We report here for the first time a Chinese VMCM family of 19 affected individuals in five generations with multiple vascular lesions on their oral mucosa and extremities. Histological analyses showed that the lesions comprised of irregular vascular spaces with a continuous layer of endothelial cells and variable smooth muscle cells. Although these VMCM characters were consistent with those in Caucasian families, difference was observed in hyperplastic SMC layer and vascular walls. Haplotype analyses and DNA sequencing indicated that both the mutation-associated haplotype and a R849W (c.2545C>T) change of the TIE2 gene cosegregated perfectly with the VMCM phenotype. This result suggested that, like those in Caucasian families, the R849W mutation in TIE2 could be one of the major causes for VMCM in Asian families.

Anti-diabetic effects of a series of vanadium dipicolinate complexes in rats with streptozotocin-induced diabetes.

The effects of oral treatment of rats with streptozotocin-induced diabetes with a range of vanadium dipicolinate complexes (Vdipic) and derivatives are reviewed. Structure-reactivity relationships are explored aiming to correlate properties such as stability, to their insulin-enhancing effects. Three types of modifications are investigated; first, substitutions on the aromatic ring, second, coordination of a hydroxylamido group to the vanadium, and third, changes in the oxidation state of the vanadium ion. These studies allowed us to address the importance of coordination chemistry, and redox chemistry, as modes of action. Dipicolinate was originally chosen as a ligand because the dipicolinatooxovanadium(V) complex (V5dipic), is a potent inhibitor of phosphatases. The effect of vanadium oxidation state (3, 4 or 5), on the insulin-enhancing properties was studied in both the Vdipic and VdipicCl series. Effects on blood glucose, body weight, serum lipids, alkaline phosphatase and aspartate transaminase were selectively monitored. Statistically distinct differences in activity were found, however, the trends observed were not the same in the Vdipic and VdipicCl series. Interperitoneal administration of the Vdipic series was used to compare the effect of administration mode. Correlations were observed for blood vanadium and plasma glucose levels after V5dipic treatment, but not after treatment with corresponding V4dipic and V3dipic complexes. Modifications of the aromatic ring structure with chloride, amine or hydroxyl groups had limited effects. Global gene expression was measured using Affymetrix oligonucleotide chips. All diabetic animals treated with hydroxyl substituted V5dipic (V5dipicOH) and some diabetic rats treated with vanadyl sulfate had normalized hyperlipidemia yet uncontrolled hyperglycemia and showed abnormal gene expression patterns. In contrast to the normal gene expression profiles previously reported for some diabetic rats treated with vanadyl sulfate, where both hyperlipidemia and hyperglycemia were normalized. Modification of the metal, changing the coordination chemistry to form a hydroxylamine ternary complex, had the most influence on the anti-diabetic action. Vanadium absorption into serum was determined by atomic absorption spectroscopy for selected vanadium complexes. Only diabetic rats treated with the ternary V5dipicOH hydroxylamine complex showed statistically significant increases in accumulation of vanadium into serum compared to diabetic rats treated with vanadyl sulfate. The chemistry and physical properties of the Vdipic complexes correlated with their anti-diabetic properties. Here, we propose that compound stability and ability to interact with cellular redox reactions are key components for the insulin-enhancing activity of vanadium compounds. Specifically, we found that the most overall effective anti-diabetic Vdipic compounds were obtained when the compound administered had an increased coordination number in the vanadium complex.

The Influence of 3'UTRs on MicroRNA Function Inferred from Human SNP Data.

MicroRNAs (miRNAs) regulate gene expression posttranscriptionally. Although previous efforts have demonstrated the functional importance of target sites on miRNAs, little is known about the influence of the rest of 3' untranslated regions (3'UTRs) of target genes on microRNA function. We conducted a genome-wide study and found that the entire 3'UTR sequences could also play important roles on miRNA function in addition to miRNA target sites. This was evidenced by the fact that human single nucleotide polymorphisms (SNPs) on both seed target region and the rest of 3'UTRs of miRNA target genes were under significantly stronger negative selection, when compared to non-miRNA target genes. We also discovered that the flanking nucleotides on both sides of miRNA target sites were subject to moderate strong selection. A local sequence region of ~67 nucleotides with symmetric structure is herein defined. Additionally, from gene expression analysis, we found that SNPs and miRNA target sites on target sequences may interactively affect gene expression.

Single cell transcriptomics reveals lineage trajectory of retinal ganglion cells in wild-type and Atoh7-null retinas.

Atoh7 has been believed to be essential for establishing the retinal ganglion cell (RGC) lineage, and Pou4f2 and Isl1 are known to regulate RGC specification and differentiation. Here we report our further study of the roles of these transcription factors. Using bulk RNA-seq, we identify genes regulated by the three transcription factors, which expand our understanding of the scope of downstream events. Using scRNA-seq on wild-type and mutant retinal cells, we reveal a transitional cell state of retinal progenitor cells (RPCs) co-marked by Atoh7 and other genes for different lineages and shared by all early retinal lineages. We further discover the unexpected emergence of the RGC lineage in the absence of Atoh7. We conclude that competence of RPCs for different retinal fates is defined by lineage-specific genes co-expressed in the transitional state and that Atoh7 defines the RGC competence and collaborates with other factors to shepherd transitional RPCs to the RGC lineage.