CDK12 phosphorylates 4E-BP1 to enable mTORC1-dependent translation and mitotic genome stability.

The RNA polymerase II (RNAPII) C-terminal domain kinase, CDK12, regulates genome stability, expression of DNA repair genes, and cancer cell resistance to chemotherapy and immunotherapy. In addition to its role in mRNA biosynthesis of DNA repair genes, we show here that CDK12 phosphorylates the mRNA 5' cap-binding repressor, 4E-BP1, to promote translation of mTORC1-dependent mRNAs. In particular, we found that phosphorylation of 4E-BP1 by mTORC1 (T37 and T46) facilitates subsequent CDK12 phosphorylation at two Ser-Pro sites (S65 and T70) that control the exchange of 4E-BP1 with eIF4G at the 5' cap of CHK1 and other target mRNAs. RNA immunoprecipitation coupled with deep sequencing (RIP-seq) revealed that CDK12 regulates release of 4E-BP1, and binding of eIF4G, to many mTORC1 target mRNAs, including those needed for MYC transformation. Genome-wide ribosome profiling (Ribo-seq) further identified specific CDK12 "translation-only" target mRNAs, including many mTORC1 target mRNAs as well as many subunits of mitotic and centromere/centrosome complexes. Accordingly, confocal imaging analyses revealed severe chromosome misalignment, bridging, and segregation defects in cells deprived of CDK12 or CCNK. We conclude that the nuclear RNAPII-CTD kinase CDK12 cooperates with mTORC1, and controls a specialized translation network that is essential for mitotic chromosome stability.

Light-Triggerable and Gate-Tunable Negative Differential Resistance in Small Molecules Heterojunction.

Negative differential resistance (NDR), a phenomenon in which the current decreases when the applied voltage is increased, is attracting attention as a unique electrical property. Here, we propose a broad spectral photo/gate cotunable channel switching NDR (CS-NDR) device. The proposed CS-NDR device has superior linear gate-tunable NDR behavior and highly reproducible properties compared to the previously reported NDR devices, as the fundamental mechanism of the CS-NDR device is directly related to a charge transport channel switching by the linear increase of the applied drain voltage. We also experimentally demonstrate that the photoinduced NDR behavior of the CS-NDR device was derived from the grain boundaries of dinaphtho[2;3-b:2',3'-f]-thieno[3,2-b]thiophene. Furthermore, this work produces a 9 × 9 CS-NDR device array composed of 81 devices, providing the reproducibility and uniformity of the CS-NDR device. Finally, we successfully demonstrate the detection of text images with 81 CS-NDR devices using the proposed photo/gate cotunable NDR behavior.

Detection of anaerobic and aerobic bacteria from commercial tattoo and permanent makeup inks.

Tattooing and use of permanent makeup (PMU) have dramatically increased over the last decade, with a concomitant increase in ink-related infections. Studies have shown evidence that commercial tattoo and PMU inks are frequently contaminated with pathogenic microorganisms. Considering that tattoo inks are placed into the dermal layer of the skin where anaerobic bacteria can thrive and cause infections in low-oxygen environments, the prevalence of anaerobic and aerobic bacteria should be assessed in tattoo and PMU inks. In this study, we tested 75 tattoo and PMU inks using the analytical methods described in the FDA Bacteriological Analytical Manual Chapter 23 for the detection of both aerobic and anaerobic bacterial contamination, followed by 16S rRNA gene sequencing for microbial identification. Of 75 ink samples, we found 26 contaminated samples with 34 bacterial isolates taxonomically classified into 14 genera and 22 species. Among the 34 bacterial isolates, 19 were identified as possibly pathogenic bacterial strains. Two species, namely Cutibacterium acnes (four strains) and Staphylococcus epidermidis (two strains) were isolated under anaerobic conditions. Two possibly pathogenic bacterial strains, Staphylococcus saprophyticus and C. acnes, were isolated together from the same ink samples (n = 2), indicating that tattoo and PMU inks can contain both aerobic (S. saprophyticus) and anaerobic bacteria (C. acnes). No significant association was found between sterility claims on the ink label and the absence of bacterial contamination. The results indicate that tattoo and PMU inks can also contain anaerobic bacteria. IMPORTANCE: The rising popularity of tattooing and permanent makeup (PMU) has led to increased reports of ink-related infections. This study is the first to investigate the presence of both aerobic and anaerobic bacteria in commercial tattoo and PMU inks under aerobic and anaerobic conditions. Our findings reveal that unopened and sealed tattoo inks can harbor anaerobic bacteria, known to thrive in low-oxygen environments, such as the dermal layer of the skin, alongside aerobic bacteria. This suggests that contaminated tattoo inks could be a source of infection from both types of bacteria. The results emphasize the importance of monitoring these products for both aerobic and anaerobic bacteria, including possibly pathogenic microorganisms.

Ebastine impairs metastatic spread in triple-negative breast cancer by targeting focal adhesion kinase.

We sought to investigate the utility of ebastine (EBA), a second-generation antihistamine with potent anti-metastatic properties, in the context of breast cancer stem cell (BCSC)-suppression in triple-negative breast cancer (TNBC). EBA binds to the tyrosine kinase domain of focal adhesion kinase (FAK), blocking phosphorylation at the Y397 and Y576/577 residues. FAK-mediated JAK2/STAT3 and MEK/ERK signaling was attenuated after EBA challenge in vitro and in vivo. EBA treatment induced apoptosis and a sharp decline in the expression of the BCSC markers ALDH1, CD44 and CD49f, suggesting that EBA targets BCSC-like cell populations while reducing tumor bulk. EBA administration significantly impeded BCSC-enriched tumor burden, angiogenesis and distant metastasis while reducing MMP-2/-9 levels in circulating blood in vivo. Our findings suggest that EBA may represent an effective therapeutic for the simultaneous targeting of JAK2/STAT3 and MEK/ERK for the treatment of molecularly heterogeneous TNBC with divergent profiles. Further investigation of EBA as an anti-metastatic agent for the treatment of TNBC is warranted.

Nanoscale Channel Gate-Tunable Diodes Obtained by Asymmetric Contact and Adhesion Lithography on Fluoropolymers.

Adhesion lithography offers to fabrication of coplanar asymmetric nanogap electrodes with a low-cost and facile process. In this study, a gate-tunable diode with coplanar asymmetric nanogap is fabricated using adhesion lithography. A fluoropolymer material is introduced to the adhesion lithography process to ensure a manufacturing patterning process yield as high as 96.7%. The asymmetric electrodes formed a built-in potential, leading to rectifying behavior. The coplanar electrode structure allowed the use of a gate electrode in vertical contact with the channel, resulting in gate-tunable diode characteristics. The nanoscale channel induced a high current density (3.38 × 10-7  A∙cm-1 ), providing a high rectification ratio (1.67 × 105  A∙A-1 ). This rectifier diode is confirmed to operate with pulsed input signals and suggests the gate-tunability of nanogap diodes.

New Surgical Approach for Secondary Intraocular Lens Implantation Using an Artificial Bag with Optic Capture in Patients with Intraocular Lens Dislocation.

PURPOSE: We present a newly developed approach to secondary intraocular lens (IOL) implantation, which uses an artificial bag with optic capture (i.e., ABC technique) in patients with IOL dislocation. METHODS: This is a retrospective, noncomparative, and interventional case series that reveals the results of secondary IOL implantation using an artificial bag with optic capture in four cases of IOL dislocation. All patients underwent the abovementioned surgery and were followed up for at least 6 months. RESULTS: The best-corrected visual acuity of patients ranged from 20/30 to 20/20. The IOL of all patients showed no tilting or decentration with normal intraocular pressure. CONCLUSION: We believe that this method produces satisfactory results and will be especially beneficial to retinal surgeons for the management of patients with IOL dislocation.

Four-flanged polypropylene optic piercing technique for scleral fixation of multifocal intraocular lens.

BACKGROUND: To evaluate the feasibility of creating flanges using an optic piercing technique with a 6 - 0 polypropylene monofilament for scleral fixation of dislocated one-piece diffractive multifocal intraocular lenses (IOLs). STUDY DESIGN: Experimental study and case series. SUBJECTS: Optical bench test and eyes with IOL dislocation. METHODS: Two separate 6 - 0 polypropylenes were penetrated twice at the opposite peripheral optic of the TECNIS Synergy IOL (Johnson & Johnson Vision). The root mean square of the modulation transfer function (MTFRMS), at between + 1.00 and - 4.00 D of defocus, was measured in the TECNIS Synergy IOL both with and without optic piercing in the optical bench study. This case series included three eyes from two patients who underwent scleral-fixation of multifocal IOLs using the four-flanged polypropylene optic piercing technique. The postoperative corrected distance visual acuity (CDVA) at 4 m, the uncorrected near visual acuity (UNVA) at 40 cm, and IOL centration were evaluated. RESULTS: The optical bench test showed no differences in MTFRMS values measured in the TECNIS Synergy IOL, either with or without optic piercing at all defocuses. In all three case series, the postoperative CDVA at 4 m was 20/20 and UNVA at 40 cm was J1. Postoperative anterior segment photographs showed good centration of IOLs in all cases. CONCLUSION: The four-flanged polypropylene optic piercing technique for multifocal IOL scleral fixation can provide excellent clinical outcomes and IOL stability after surgery without diminishing the performance of the multifocal IOLs.

ß-Escin overcomes trastuzumab resistance in HER2-positive breast cancer by targeting cancer stem-like features.

BACKGROUND: The emergence of de novo or intrinsic trastuzumab resistance is exceedingly high in breast cancer that is HER2 positive and correlates with an abundant cancer stem cell (CSC)-like population. We sought to examine the capacity of ß-escin, an anti-inflammatory drug, to address trastuzumab resistance in HER2-positive breast cancer cells. METHODS: The effect of ß-escin on trastuzumab-resistant and -sensitive cell lines in vitro was evaluated for apoptosis, expression of HER2 family members, and impact on CSC-like properties. An in vivo model of trastuzumab-resistant JIMT-1 was used to examine the efficacy and toxicity of ß-escin. RESULTS: ß-escin induced mitochondrial-mediated apoptosis accompanied by reactive oxygen species (ROS) production and increased active p18Bax fragmentation, leading to caspase-3/-7 activation. Attenuation of CSC-related features by ß-escin challenge was accompanied by marked reductions in CD44high/CD24low stem-like cells and aldehyde dehydrogenase 1 (ALDH1) activity as well as hindrance of mammosphere formation. ß-escin administration also significantly retarded tumor growth and angiogenesis in a trastuzumab-resistant JIMT-1 xenograft model via downregulation of CSC-associated markers and intracellular domain HER2. Importantly, ß-escin selectively inhibited malignant cells and was less toxic to normal mammary cells, and no toxic effects were found in liver and kidney function in animals. CONCLUSIONS: Taken together, our findings highlight ß-escin as a promising candidate for the treatment of trastuzumab-resistant HER2-positive breast cancers.

Scleral fixation of subluxated or dislocated multifocal and multifocal toric intraocular lenses.

PURPOSE: To evaluate the feasibility of scleral fixation of subluxated or dislocated multifocal/multifocal toric intraocular lenses (IOLs) to rescue the IOL and restore both near and far vision. METHOD: A total of 18 eyes of 17 patients who underwent transscleral or intrascleral fixation of subluxated or dislocated multifocal or multifocal toric IOLs at 2.5 mm posterior to the limbus were enrolled. Preoperative uncorrected distance visual acuity (UDVA) and postoperative UDVA values were compared in this retrospective cross-sectional study. The postoperative corrected distance visual acuity (CDVA), uncorrected near visual acuity (UNVA) at 40 cm, residual sphere, cylinder, spherical equivalent, and IOL centration were evaluated. RESULTS: The mean follow-up period was 4.0 ± 5.0 months. The mean preoperative UDVA was 0.73 ± 0.71 logMAR and the postoperative UDVA was 0.05 ± 0.10 logMAR, which was significantly improved relative to the preoperative UDVA. The mean postoperative CDVA was 0.00 ± 0.00 logMAR and the mean postoperative UNVA at 40 cm was 0.05 ± 0.07 logMAR. The mean postoperative residual sphere, cylinder, and spherical equivalent values were - 0.21 ± 0.41 D, - 0.29 ± 0.26 CD, and - 0.33 ± 0.39 D, respectively. Postoperative anterior segment photographs showed good centration of optics in all cases of single-piece foldable multifocal IOLs but a slight inferior decentration in one case of a three-piece multifocal IOL. CONCLUSION: Scleral fixation of subluxated or dislocated multifocal and multifocal toric IOLs could be one of the treatment options to rescue subluxated or dislocated multifocal IOLs and restore both near and far vision.

Bilateral posterior scleritis after sequential bilateral cataract surgery: a case report.

BACKGROUND: Posterior scleritis is a rare, inflammatory ophthalmic disease, leading to severe visual impairment if untreated. Posterior scleritis occurring after surgery, unrelated to systemic inflammatory diseases, is even rarer. This report discusses a case of bilateral posterior scleritis, after cataract surgery in both the eyes, treated with high-dose steroids. CASE PRESENTATION: A 55-year-old man, who had undergone bilateral sequential cataract surgery one week before, presented with sudden loss of vision and ocular pain in both eyes. The patient had no systemic diseases or neurological symptoms. Serous retinal detachment of the macula with optic disc swelling was observed on fundus examination in both the eyes, and bilateral thickening of choroid and sclera was seen in ultrasonography. Under diagnosis of bilateral posterior scleritis due to the increased signal of sclera in both the eyes on magnetic resonance imaging, high-dose steroid therapy was performed. After treatment, improvement in visual acuity and retinal detachment were observed, and thereafter, it has been maintained without relapse. CONCLUSIONS: With high-dose steroid therapy, we successfully treated a rare case of bilateral posterior scleritis following cataract surgery in both eyes. To our knowledge, this is the first report on posterior scleritis occurring after surgery, unrelated to systemic inflammatory diseases.

The Role of Nuclear Factor of Activated T Cells 5 in Hyperosmotic Stress-Exposed Human Lens Epithelial Cells.

We investigated the role of nuclear factor of activated T cells 5 (NFAT5) under hyperosmotic conditions in human lens epithelial cells (HLECs). Hyperosmotic stress decreased the viability of human lens epithelial B-3 cells and significantly increased NFAT5 expression. Hyperosmotic stress-induced cell death occurred to a greater extent in NFAT5-knockout (KO) cells than in NFAT5 wild-type (NFAT5 WT) cells. Bcl-2 and Bcl-xl expression was down-regulated in NFAT5 WT cells and NFAT5 KO cells under hyperosmotic stress. Pre-treatment with a necroptosis inhibitor (necrostatin-1) significantly blocked hyperosmotic stress-induced death of NFAT5 KO cells, but not of NFAT5 WT cells. The phosphorylation levels of receptor-interacting protein kinase 1 (RIP1) and RIP3, which indicate the occurrence of necroptosis, were up-regulated in NFAT5 KO cells, suggesting that death of these cells is predominantly related to the necroptosis pathway. This finding is the first to report that necroptosis occurs when lens epithelial cells are exposed to hyperosmolar conditions, and that NFAT5 is involved in this process.

Phylogenetically diverse bacteria isolated from tattoo inks, an azo dye-rich environment, decolorize a wide range of azo dyes.

PURPOSE: There has been an interest in the microbial azo dye degradation as an optional method for the treatment of azo dye-containing wastes. Tattoo ink is an extremely unique azo dye-rich environment, which have never been explored in terms of microorganisms capable of degrading azo dyes. Previously, we isolated 81 phylogenetically diverse bacteria, belonging to 18 genera and 52 species, contaminated in tattoo inks. In this study, we investigated if these bacteria, which can survive in the azo dye-rich environment, have an ability to degrade azo dyes. METHODS: We conducted a two-step azo dye degradation (or decolorization) assay. In step 1, a high-throughput degradability assay was done for 79 bacterial isolates using Methyl Red and Orange II. In step 2, a further degradation assay was done for 10 selected bacteria with a representative of 11 azo dyes, including 3 commercial tattoo ink azo dyes. Degradation of azo dyes were calculated from measuring optical absorbance of soluble dyes at specific wavelengths. RESULTS: The initial high-throughput azo dye assay (step 1) showed that 79 isolates had a complete or partial degradation of azo dyes; > 90% of Methyl Red and Orange II were degraded within 24 h, by 74 and 20 isolates, respectively. A further evaluation of azo dye degradability for 10 selected isolates in step 2 showed that the isolates, belonging to Bacillus, Brevibacillus, Paenibacillus, and Pseudomonas, exhibited an excellent decolorization ability for a wide range of azo dyes. CONCLUSIONS: This study showed that phylogenetically diverse bacteria, isolated from azo dye-rich tattoo inks, is able to degrade a diverse range of azo dyes, including 3 azo dyes used in commercial tattoo inks. Some of the strains would be good candidates for future studies to provide a systematic understanding of azo dye degradation mechanisms.

CYPminer: an automated cytochrome P450 identification, classification, and data analysis tool for genome data sets across kingdoms.

BACKGROUND: Cytochrome P450 monooxygenases (termed CYPs or P450s) are hemoproteins ubiquitously found across all kingdoms, playing a central role in intracellular metabolism, especially in metabolism of drugs and xenobiotics. The explosive growth of genome sequencing brings a new set of challenges and issues for researchers, such as a systematic investigation of CYPs across all kingdoms in terms of identification, classification, and pan-CYPome analyses. Such investigation requires an automated tool that can handle an enormous amount of sequencing data in a timely manner. RESULTS: CYPminer was developed in the Python language to facilitate rapid, comprehensive analysis of CYPs from genomes of all kingdoms. CYPminer consists of two procedures i) to generate the Genome-CYP Matrix (GCM) that lists all occurrences of CYPs across the genomes, and ii) to perform analyses and visualization of the GCM, including pan-CYPomes (pan- and core-CYPome), CYP co-occurrence networks, CYP clouds, and genome clustering data. The performance of CYPminer was evaluated with three datasets from fungal and bacterial genome sequences. CONCLUSIONS: CYPminer completes CYP analyses for large-scale genomes from all kingdoms, which allows systematic genome annotation and comparative insights for CYPs. CYPminer also can be extended and adapted easily for broader usage.

Aqueous humor and serum 25-Hydroxyvitamin D levels in patients with cataracts.

BACKGROUND: Serum 25-hydroxyvitamin D (25 (OH) D) levels are associated with various pathologic ocular conditions. Few studies have assessed 25 (OH) D concentrations in non-serum specimens, and none to date has assessed 25 (OH) D concentrations in human aqueous humor and their association with ocular diseases. This study investigated the possible correlations between 25 (OH) D concentrations in aqueous humor and serum and whether vitamin D concentrations in aqueous humor were associated with cataract. METHODS: This study prospectively enrolled 136 patients, including 87 with senile cataract and 49 with diabetic cataract, who underwent cataract surgery from January to November 2017. 25 (OH) D was measured in aqueous humor and serum specimens collected from all patients, and their correlation was analyzed statistically. Clinical and laboratory data, including the results of ophthalmologic examinations, were compared in the two groups of cataract patients. RESULTS: No correlation was observed between 25 (OH) D concentrations in aqueous humor and serum (P = 0.381). 25 (OH) D concentrations in aqueous humor were significantly higher in patients with diabetic than senile cataract (P = 0.006). Multivariate logistic regression analysis showed that the adjusted odds ratio for diabetic cataract for the highest compared with the lowest quartile of 25 (OH) D concentration in aqueous humor was 4.36 ng/ml (95% confidence interval [CI]: 1.33-14.34 ng/ml; P = 0.015). Multivariate linear regression analysis showed that 25(OH) D concentration in aqueous humor was 2.68 ng/ml (95% CI: 0.34-5.01 ng/ml; P = 0.025) higher in patients with diabetic than senile cataract. CONCLUSIONS: 25(OH) D concentrations in aqueous humor and serum did not correlate with each other. Higher 25(OH) D level in aqueous humor was associated with diabetic cataract. These findings suggest that studies of vitamin D levels in patients with ocular conditions should include measurements of vitamin D levels in aqueous humor.

Metformin protects against retinal cell death in diabetic mice.

Retinal degeneration is an early feature of diabetic retinopathy, the major cause of blindness in the developed world. Here we investigated how the widely used antidiabetic drug metformin reduces retinal injury in diabetic mice. Metformin was orally administered to control mice or mice with streptozotocin-induced diabetes. Western blot analysis showed that levels of O-linked ß-N-acetylglucosamine (O-GlcNAc) transferase (OGT) and other related proteins such as carbohydrate-responsive element-binding protein (ChREBP) and thioredoxin-interacting protein (TXNIP) were significantly increased, and nuclear factor kappaB (NF-κB) and poly (ADP-ribose) polymerase (PARP) were activated in the diabetic retinas or retinal pigment epithelial (RPE) cells exposed to high glucose compared to controls. More importantly, RPE cells exposed to high glucose and treated with thiamet-G had higher levels of those proteins, demonstrating the role of elevated O-GlcNAcylation. Double immunofluorescence analysis revealed increased co-localization of terminal deoxynucleotide transferase-mediated dUTP nick-end labelling (TUNEL)-positive ganglion cells and OGT, ChREBP, TXNIP, or NF-κB in diabetic retinas compared to control retinas. Co-immunoprecipitation analysis showed that interaction between OGT and ChREBP or NF-κB was increased in diabetic retinas compared to control retinas, and this was accompanied by more cell death. Notably, metformin attenuated the increases in protein levels; reduced co-localization of TUNEL-positive ganglion cells and OGT, ChREBP, TXNIP, or NF-κB; and reduced interaction between OGT and ChREBP or NF-κB. Our results indicate that OGT inhibition might be one of the mechanisms by which metformin decreases retinal cell death.

Ascorbic acid concentrations in aqueous humor after systemic vitamin C supplementation in patients with cataract: pilot study.

BACKGROUND: To measure ascorbic acid concentration in aqueous humor of patients with cataract after oral or intravenous vitamin C supplementation. METHODS: Forty-two eyes of 42 patients with senile cataract who underwent uncomplicated cataract surgery were enrolled. Patients (n = 14 each) were administered oral vitamin C (2 g), intravenous vitamin C (20 g) or no treatment (control group) on the day before surgery. Samples of aqueous humor (0.1 cm3) were obtained by anterior chamber aspiration at the beginning of surgery and stored at -80 °C. Ascorbic acid concentration in aqueous humor was measured by high-pressure liquid chromatography. RESULTS: The mean age at surgery was 62.5 years, with no difference among the three groups. The mean ± standard deviation concentrations of ascorbic acid in aqueous humor in the control and oral and intravenous vitamin C groups were 1347 ± 331 µmol/L, 1859 ± 408 µmol/L and 2387 ± 445 µmol/L, respectively. Ascorbic acid concentration was significantly lower in the control than in the oral (P < 0.01) and intravenous (P < 0.001) vitamin C groups and was significantly higher in the intravenous than in the oral vitamin C group (P < 0.05). CONCLUSIONS: Ascorbic acid concentration in aqueous humor is increased by systemic vitamin C supplementation, with intravenous administration being more effective than oral administration.

Comparative functional pan-genome analyses to build connections between genomic dynamics and phenotypic evolution in polycyclic aromatic hydrocarbon metabolism in the genus Mycobacterium.

BACKGROUND: The bacterial genus Mycobacterium is of great interest in the medical and biotechnological fields. Despite a flood of genome sequencing and functional genomics data, significant gaps in knowledge between genome and phenome seriously hinder efforts toward the treatment of mycobacterial diseases and practical biotechnological applications. In this study, we propose the use of systematic, comparative functional pan-genomic analysis to build connections between genomic dynamics and phenotypic evolution in polycyclic aromatic hydrocarbon (PAH) metabolism in the genus Mycobacterium. RESULTS: Phylogenetic, phenotypic, and genomic information for 27 completely genome-sequenced mycobacteria was systematically integrated to reconstruct a mycobacterial phenotype network (MPN) with a pan-genomic concept at a network level. In the MPN, mycobacterial phenotypes show typical scale-free relationships. PAH degradation is an isolated phenotype with the lowest connection degree, consistent with phylogenetic and environmental isolation of PAH degraders. A series of functional pan-genomic analyses provide conserved and unique types of genomic evidence for strong epistatic and pleiotropic impacts on evolutionary trajectories of the PAH-degrading phenotype. Under strong natural selection, the detailed gene gain/loss patterns from horizontal gene transfer (HGT)/deletion events hypothesize a plausible evolutionary path, an epistasis-based birth and pleiotropy-dependent death, for PAH metabolism in the genus Mycobacterium. This study generated a practical mycobacterial compendium of phenotypic and genomic changes, focusing on the PAH-degrading phenotype, with a pan-genomic perspective of the evolutionary events and the environmental challenges. CONCLUSIONS: Our findings suggest that when selection acts on PAH metabolism, only a small fraction of possible trajectories is likely to be observed, owing mainly to a combination of the ambiguous phenotypic effects of PAHs and the corresponding pleiotropy- and epistasis-dependent evolutionary adaptation. Evolutionary constraints on the selection of trajectories, like those seen in PAH-degrading phenotypes, are likely to apply to the evolution of other phenotypes in the genus Mycobacterium.

Dynamic Response of Mycobacterium vanbaalenii PYR-1 to BP Deepwater Horizon Crude Oil.

We investigated the response of the hydrocarbon-degrading Mycobacterium vanbaalenii PYR-1 to crude oil from the BP Deepwater Horizon (DWH) spill, using substrate depletion, genomic, and proteome analyses. M. vanbaalenii PYR-1 cultures were incubated with BP DWH crude oil, and proteomes and degradation of alkanes and polycyclic aromatic hydrocarbons (PAHs) were analyzed at four time points over 30 days. Gas chromatography-mass spectrometry (GC-MS) analysis showed a chain length-dependent pattern of alkane degradation, with C12 and C13 being degraded at the highest rate, although alkanes up to C28 were degraded. Whereas phenanthrene and pyrene were completely degraded, a significantly smaller amount of fluoranthene was degraded. Proteome analysis identified 3,948 proteins, with 876 and 1,859 proteins up- and downregulated, respectively. We observed dynamic changes in protein expression during BP crude oil incubation, including transcriptional factors and transporters potentially involved in adaptation to crude oil. The proteome also provided a molecular basis for the metabolism of the aliphatic and aromatic hydrocarbon components in the BP DWH crude oil, which included upregulation of AlkB alkane hydroxylase and an expression pattern of PAH-metabolizing enzymes different from those in previous proteome expression studies of strain PYR-1 incubated with pure or mixed PAHs, particularly the ring-hydroxylating oxygenase (RHO) responsible for the initial oxidation of aromatic hydrocarbons. Based on these results, a comprehensive cellular response of M. vanbaalenii PYR-1 to BP crude oil was proposed. This study increases our fundamental understanding of the impact of crude oil on the cellular response of bacteria and provides data needed for development of practical bioremediation applications.

Aralia elata prevents neuronal death by downregulating tonicity response element binding protein in diabetic retinopathy.

BACKGROUND/AIMS: The present study addresses the role of tonicity response element binding protein (TonEBP) in retinal ganglion cell (RGC) death in diabetic retinopathy and the impact of Aralia elata extract on the TonEBP/RGC interaction. METHODS: Diabetes was induced in C57BL/6 mice by intraperitoneal injection of streptozotocin (STZ). Control mice received phosphate-buffered saline. After five injections of STZ or saline buffer, A. elata extract was administered by daily oral tube feeding for 7 weeks. All mice were killed at 2 months after the last injection of STZ or saline and the extent of cell death together with the protein expression levels of TonEBP, aldose reductase (AR) and nuclear factor-kappa B (NF-κB) were examined. RESULTS: Terminal deoxynucleotidyl transferase-mediated dUTP nick end labeling (TUNEL)-positive signals were colocalized with TonEBP-immunoreactive RGCs. The apoptotic cell death of RGCs and the expression levels of TonEBP, AR and NF-κB were significantly increased in the retinas of diabetic mice compared with controls at 2 months after the induction of diabetes. However, these changes were effectively blocked by the administration of A. elata extract. CONCLUSIONS: These results indicate that A. elata prevents diabetes-induced RGC apoptosis and downregulates TonEBP expression. Therefore, A. elata extract may have therapeutic potential to prevent diabetes-induced retinal neurodegeneration in diabetic retinopathy.

Pleiotropic and epistatic behavior of a ring-hydroxylating oxygenase system in the polycyclic aromatic hydrocarbon metabolic network from Mycobacterium vanbaalenii PYR-1.

Despite the considerable knowledge of bacterial high-molecular-weight (HMW) polycyclic aromatic hydrocarbon (PAH) metabolism, the key enzyme(s) and its pleiotropic and epistatic behavior(s) responsible for low-molecular-weight (LMW) PAHs in HMW PAH-metabolic networks remain poorly understood. In this study, a phenotype-based strategy, coupled with a spray plate method, selected a Mycobacterium vanbaalenii PYR-1 mutant (6G11) that degrades HMW PAHs but not LMW PAHs. Sequence analysis determined that the mutant was defective in pdoA2, encoding an aromatic ring-hydroxylating oxygenase (RHO). A series of metabolic comparisons using high-performance liquid chromatography (HPLC) analysis revealed that the mutant had a lower rate of degradation of fluorene, anthracene, and pyrene. Unlike the wild type, the mutant did not produce a color change in culture media containing fluorene, phenanthrene, and fluoranthene. An Escherichia coli expression experiment confirmed the ability of the Pdo system to oxidize biphenyl, the LMW PAHs naphthalene, phenanthrene, anthracene, and fluorene, and the HMW PAHs pyrene, fluoranthene, and benzo[a]pyrene, with the highest enzymatic activity directed toward three-ring PAHs. Structure analysis and PAH substrate docking simulations of the Pdo substrate-binding pocket rationalized the experimentally observed metabolic versatility on a molecular scale. Using information obtained in this study and from previous work, we constructed an RHO-centric functional map, allowing pleiotropic and epistatic enzymatic explanation of PAH metabolism. Taking the findings together, the Pdo system is an RHO system with the pleiotropic responsibility of LMW PAH-centric hydroxylation, and its epistatic functional contribution is also crucial for the metabolic quality and quantity of the PAH-MN.