CT-Derived Deep Learning-Based Quantification of Body Composition Associated with Disease Severity in Chronic Obstructive Pulmonary Disease.

Purpose: Our study aimed to evaluate the association between automated quantified body composition on CT and pulmonary function or quantitative lung features in patients with chronic obstructive pulmonary disease (COPD). Materials and Methods: A total of 290 patients with COPD were enrolled in this study. The volume of muscle and subcutaneous fat, area of muscle and subcutaneous fat at T12, and bone attenuation at T12 were obtained from chest CT using a deep learning-based body segmentation algorithm. Parametric response mapping-derived emphysema (PRMemph), PRM-derived functional small airway disease (PRMfSAD), and airway wall thickness (AWT)-Pi10 were quantitatively assessed. The association between body composition and outcomes was evaluated using Pearson's correlation analysis. Results: The volume and area of muscle and subcutaneous fat were negatively associated with PRMemph and PRMfSAD (p < 0.05). Bone density at T12 was negatively associated with PRMemph (r = -0.1828, p = 0.002). The volume and area of subcutaneous fat and bone density at T12 were positively correlated with AWT-Pi10 (r = 0.1287, p = 0.030; r = 0.1668, p = 0.005; r = 0.1279, p = 0.031). However, muscle volume was negatively correlated with the AWT-Pi10 (r = -0.1966, p = 0.001). Muscle volume was significantly associated with pulmonary function (p < 0.001). Conclusion: Body composition, automatically assessed using chest CT, is associated with the phenotype and severity of COPD.

Hyperpolarized [1-13C]pyruvate Magnetic Resonance Spectroscopy Shows That Agmatine Increased Lactate Production in the Brain of Type 2 Diabetic Mice.

PURPOSE: Type 2 diabetes mellitus (T2DM) is associated with a 2-fold increased risk of developing Alzheimer's disease. In earlier research, agmatine has been demonstrated to alleviate diabetes symptoms and increase cognitive performance. However, it is unclear whether the improvement of cognitive function is attributable to the reduction of diabetic symptoms or its direct influence on brain metabolism. Using hyperpolarized (HP) [1-13C]pyruvate magnetic resonance spectroscopy (MRS), this study intends to evaluate the influence of agmatine on brain metabolism. MATERIALS AND METHODS: ICR mice were fed a high-fat diet and injected with streptozotocin to develop a T2DM animal model. During a 2-week period, T2DM mice were treated with normal saline or 100 mg/kg of agmatine, and brain HP [1-13C]pyruvate MRS was performed. The effect of agmatine on lactate generation and NADH/NAD+ redox state was investigated using C6 and neuro-2a (N2a) cells. RESULTS: As a perfusion marker, the total 13C signals in the brain of T2DM mice (p=0.07) and agmatine-treated mice (p<0.05) were reduced. The conversion constant (Kpl) from [1-13C]pyruvate to [1-13C]lactate was not distinguishable in the brains of T2DM mice but was significantly increased in the brains of agmatine-treated T2DM mice. Treating C6 and N2a cells with agmatine increased NADH/NAD+ratio and lactate generation. CONCLUSION: Agmatine influences the NADH/NAD+ redox state in the brains of T2DM mice, which may be connected with enhanced cognitive performance and increased conversion of HP [1-13C]pyruvate to HP [1-13C]lactate.

CHATogether: a novel digital program to promote Asian American Pacific Islander mental health in response to the COVID-19 pandemic.

BACKGROUND: In response to the COVID-19 pandemic and the associated rise in anti-Asian hate crimes, we developed the Compassionate Home, Action Together program, (CHATogether) to support the mental health of the Asian American and Pacific Islander (AAPI) community. CHATogether is a culturally informed and virtually delivered support program that harnesses the talents of AAPI teens, young adults, parents, and mental health professionals who share a commitment to serve their local communities. METHODS: Our objective was to identify the active components, optimal utilization, potential benefits, and pertinent limitations of the CHATogether program during the 3 years since its inception in 2019. By that time, the program had developed six distinct component arms: interactive theater, mental health education, research, peer support and community outreach, collaboration, and AAPI mentorship. To work towards this objective, we conducted a qualitative study using thematic analysis and an inductive approach based on grounded theory (GT), in which we analyzed anonymized transcripts of four focus groups, comprised of 20 program participants (11 females; 9 males). RESULTS: We developed a model of two overarching domains, each with three underlying themes: I. Individual stressors: (1) Family conflict; (2) Cultural identity; and (3) Pandemic impact; and II. Collective stressors: (1) Stigma related to mental health and illness; (2) Pandemic uncertainty; and (3) Xenophobia and societal polarization. Strengths of the CHATogether program include its role as a conduit toward AAPI connectedness and pride as well as purpose in building community. Through support and mentorship, the program cultivates a unique platform that promotes healing and resiliency in response to pandemic stressors and beyond. CONCLUSIONS: CHATogether creates a safe space for the AAPI community. Through its methods of storytelling and encouraging creativity, CHATogether facilitates the discussion of challenging topics specific to the AAPI community. Given the national mental health crisis that is further being exacerbated by the COVID-19 pandemic, a digital prevention program such as CHATogether holds promise towards providing access to mental health resources and supporting early help-seeking behaviors for individuals in the AAPI community.

Improved Multi-Echo Gradient-Echo-Based Myelin Water Fraction Mapping Using Dimensionality Reduction.

Multi-echo gradient-echo (mGRE)-based myelin water fraction (MWF) mapping is a promising myelin water imaging (MWI) modality but is vulnerable to noise and artifact corruption. The linear dimensionality reduction (LDR) method has recently shown improvements with regard to these challenges. However, the magnitude value based low rank operators have been shown to misestimate the MWF for regions with [Formula: see text] anisotropy. This paper presents a nonlinear dimensionality reduction (NLDR) method to estimate the MWF map better by encouraging nonlinear low dimensionality of mGRE signal sources. Specifically, we implemented a fully connected deep autoencoder to extract the low-dimensional features of complex-valued signals and incorporated a sparse regularization to separate the anomaly sources that do not reside in the low-dimensional manifold. Simulations and in vivo experiments were performed to evaluate the accuracy of the MWF map under various situations. The proposed NLDR-based MWF improves the accuracy of the MWF map over the conventional nonlinear least-squares method and the LDR-based MWF and maintains robustness against noise and artifact corruption.

Mitochondrial Fission Governed by Drp1 Regulates Exogenous Fatty Acid Usage and Storage in Hela Cells.

In the presence of high abundance of exogenous fatty acids, cells either store fatty acids in lipid droplets or oxidize them in mitochondria. In this study, we aimed to explore a novel and direct role of mitochondrial fission in lipid homeostasis in HeLa cells. We observed the association between mitochondrial morphology and lipid droplet accumulation in response to high exogenous fatty acids. We inhibited mitochondrial fission by silencing dynamin-related protein 1(DRP1) and observed the shift in fatty acid storage-usage balance. Inhibition of mitochondrial fission resulted in an increase in fatty acid content of lipid droplets and a decrease in mitochondrial fatty acid oxidation. Next, we overexpressed carnitine palmitoyltransferase-1 (CPT1), a key mitochondrial protein in fatty acid oxidation, to further examine the relationship between mitochondrial fatty acid usage and mitochondrial morphology. Mitochondrial fission plays a role in distributing exogenous fatty acids. CPT1A controlled the respiratory rate of mitochondrial fatty acid oxidation but did not cause a shift in the distribution of fatty acids between mitochondria and lipid droplets. Our data reveals a novel function for mitochondrial fission in balancing exogenous fatty acids between usage and storage, assigning a role for mitochondrial dynamics in control of intracellular fuel utilization and partitioning.

Offset of apparent hyperpolarized 13 C lactate flux by the use of adjuvant metformin in ionizing radiation therapy in vivo.

An increase in hyperpolarized (HP) [1-13 C]lactate production has been suggested as a biomarker for cancer occurrence as well as for response monitoring of cancer treatment. Recently, the use of metformin has been suggested as an anticancer or adjuvant treatment. By regulating the cytosolic NAD+ /NADH redox state, metformin stimulates lactate production and increases the HP [1-13 C]lactate conversion rate in the kidney, liver, and heart. In general, increased HP [1-13 C]lactate is regarded as a sign of cancer occurrence or tumor growth. Thus, the relationship between the tumor suppression effect of metformin and the change in metabolism monitored by HP [1-13 C]pyruvate MRS in cancer treatment needs to be investigated. The present study was performed using a brain metastasis animal model with MDA-MB-231(BR)-Luc breast cancer cells. HP [1-13 C]pyruvate MRS, T2 -weighted MRI, and bioluminescence imaging were performed in groups treated with metformin or adjuvant metformin and radiation therapy. Metformin treatment alone did not display a tumor suppression effect, and the HP [1-13 C]lactate conversion rate increased. In radiation therapy, the HP [1-13 C]lactate conversion rate decreased with tumor suppression, with a p-value of 0.028. In the adjuvant metformin and radiation treatment, the tumor suppression effect increased, with a p-value of 0.001. However, the apparent HP [1-13 C]lactate conversion rate (Kpl ) was observed to be offset by two opposite effects: a decrease on radiation therapy and an increase caused by metformin treatment. Although HP [1-13 C]pyruvate MRS could not evaluate the tumor suppression effect of adjuvant metformin and radiation therapy due to the offset phenomenon, metabolic changes following only metformin pre-treatment could be monitored. Therefore, our results indicate that the interpretation of HP [1-13 C]pyruvate MRS for response monitoring of cancer treatment should be carried out with caution when metformin is used as an adjuvant cancer therapy.

Hunger-promoting AgRP neurons trigger an astrocyte-mediated feed-forward autoactivation loop in mice.

Hypothalamic feeding circuits have been identified as having innate synaptic plasticity, mediating adaption to the changing metabolic milieu by controlling responses to feeding and obesity. However, less is known about the regulatory principles underlying the dynamic changes in agouti-related protein (AgRP) perikarya, a region crucial for gating of neural excitation and, hence, feeding. Here we show that AgRP neurons activated by food deprivation, ghrelin administration, or chemogenetics decreased their own inhibitory tone while triggering mitochondrial adaptations in neighboring astrocytes. We found that it was the inhibitory neurotransmitter GABA released by AgRP neurons that evoked this astrocytic response; this in turn resulted in increased glial ensheetment of AgRP perikarya by glial processes and increased excitability of AgRP neurons. We also identified astrocyte-derived prostaglandin E2, which directly activated - via EP2 receptors - AgRP neurons. Taken together, these observations unmasked a feed-forward, self-exciting loop in AgRP neuronal control mediated by astrocytes, a mechanism directly relevant for hunger, feeding, and overfeeding.

Drp1 is required for AgRP neuronal activity and feeding.

The hypothalamic orexigenic Agouti-related peptide (AgRP)-expressing neurons are crucial for the regulation of whole-body energy homeostasis. Here, we show that fasting-induced AgRP neuronal activation is associated with dynamin-related peptide 1 (DRP1)-mediated mitochondrial fission and mitochondrial fatty acid utilization in AgRP neurons. In line with this, mice lacking Dnm1l in adult AgRP neurons (Drp1 cKO) show decreased fasting- or ghrelin-induced AgRP neuronal activity and feeding and exhibited a significant decrease in body weight, fat mass, and feeding accompanied by a significant increase in energy expenditure. In support of the role for mitochondrial fission and fatty acids oxidation, Drp1 cKO mice showed attenuated palmitic acid-induced mitochondrial respiration. Altogether, our data revealed that mitochondrial dynamics and fatty acids oxidation in hypothalamic AgRP neurons is a critical mechanism for AgRP neuronal function and body-weight regulation.

Artificial neural network for multi-echo gradient echo-based myelin water fraction estimation.

PURPOSE: To demonstrate robust myelin water fraction (MWF) mapping using an artificial neural network (ANN) with multi-echo gradient-echo (GRE) signal. METHODS: Multi-echo gradient-echo signals simulated with a three-pool exponential model were used to generate the training data set for the ANN, which was designed to yield the MWF. We investigated the performance of our proposed ANN for various conditions using both numerical simulations and in vivo data. Simulations were conducted with various SNRs to investigate the performance of the ANN. In vivo data with high spatial resolutions were applied in the analyses, and results were compared with MWFs derived by the nonlinear least-squares algorithm using a complex three-pool exponential model. RESULTS: The network results for the simulations show high accuracies against noise compared with nonlinear least-squares MWFs: RMS-error value of 5.46 for the nonlinear least-squares MWF and 3.56 for the ANN MWF at an SNR of 150 (relative gain = 34.80%). These effects were also found in the in vivo data, with reduced SDs in the region-of-interest analyses. These effects of the ANN demonstrate the feasibility of acquiring high-resolution myelin water images. CONCLUSION: The simulation results and in vivo data suggest that the ANN facilitates more robust MWF mapping in multi-echo gradient-echo sequences compared with the conventional nonlinear least-squares method.

Blind Source Separation for Myelin Water Fraction Mapping Using Multi-Echo Gradient Echo Imaging.

In conventional gradient-echo myelin water imaging (GRE-MWI), myelin water fraction (MWF) is estimated by fitting the multi-echo gradient recalled echo (mGRE) signal to a pre-assumed numerical model (e.g., multi-component exponential curves or three component exponential curves). However, in mGRE, imaging artifacts (e.g., voxel spread function and physiological noise) and noise render the signal to deviate from the numerical model, leading to misfit of the model parameters. Here, as an alternative to the model-based GRE-MWI, a blind source separation (BSS) technique for the separation of multi-exponential mGRE signal is proposed. Among the various BSS techniques, a modified robust principal component analysis (rPCA) is presented to separate signal sources by enforcing the data-driven properties such as "low rankness" and "sparsity." Considering the signal evolution of T2∗ relaxation (i.e., non-negative exponential decay), low rankness of exponential decay was enforced by nonnegative matrix factorization (NMF) and hankelization. This method provides the separation of slow-decaying, fast-decaying exponential components and artifact components from mGRE images. After the separation, MWF map is reconstructed as the ratio of the fast-decaying component to the total decaying components. The proposed method was demonstrated in numerical simulations and in vivo scans. The method provided a robust estimation of MWF in the presence of statistical noise and imaging artifacts.

Dynamic hyperpolarized 13 C MR spectroscopic imaging using SPICE in mouse kidney at 9.4 T.

This study aims to investigate the feasibility of dynamic hyperpolarized 13 C MR spectroscopic imaging (MRSI) using the SPectroscopic Imaging by exploiting spatiospectral CorrElation (SPICE) technique and an estimation of the spatially resolved conversion constant rate (kpl ). An acquisition scheme comprising a single training dataset and several imaging datasets was proposed considering hyperpolarized 13 C circumstances. The feasibility and advantage of the scheme were investigated in two parts: (a) consistency of spectral basis over time and (b) accuracy of the estimated kpl . The simulations and in vivo experiments support accurate kpl estimation with consistent spectral bases. The proposed method was implemented in an enzyme phantom and via in vivo experiments. In the enzyme phantom experiments, spatially resolved homogeneous kpl maps were observed. In the in vivo experiments, normal diet (ND) mice and high-fat diet (HFD) mice had kpl (s-1 ) values of medullar (ND: 0.0119 ± 0.0022, HFD: 0.0195 ± 0.0005) and cortical (ND: 0.0148 ±0.0023, HFD: 0.0224 ±0.0054) regions which were higher than vascular (ND: 0.0087 ±0.0013, HFD: 0.0132 ±0.0050) regions. In particular, the kpl value in the medullar region exhibited a significant difference between the two diet groups. In summary, the feasibility of using modified SPICE for dynamic hyperpolarized 13 C MRSI was demonstrated via simulations and in vivo experiments. The consistency of spectral bases over time and the accuracy of the estimated kpl values validate the proposed acquisition scheme, which comprises only a single training dataset. The proposed method improved the spatial resolution of dynamic hyperpolarized 13 C MRSI, which could be used for kpl estimation using high signal-to-noise ratio spectral bases.

Hyperpolarized [1-13C]lactate flux increased in the hippocampal region in diabetic mice.

Increasing evidence suggests there is a relationship between cognitive impairment and metabolic dysfunction. Diabetes is a chronic disease, and metabolic factors affecting brain metabolisms, such as serum glucose, insulin, and glucagon, are altered according to disease progression. In our previous study, we applied hyperpolarized [1-13C] pyruvate magnetic resonance spectroscopy in prediabetic mice after feeding them a 60% high-fat diet (HFD) for 6 months. Ultimately, we detected significantly increased [1-13C]lactate conversion in the whole brain and an almost five-fold increased [1-13C]lactate/pyruvate ratio in the hippocampal region. In the present study, we induced diabetes in mice by injecting streptozotocin and feeding them an HFD for 6 months. Unlike in prediabetic mice, [1-13C]lactate conversion in the diabetic mice did not differ from that in the control group, but [1-13C]lactate/total 13C ratio showed an almost 1.4-fold increase in the hippocampal region. We measured the amount of the lactate and mRNA levels of glucose transporters from isolated hippocampus and cortex samples. In the hippocampus, significantly decreased GLUT1 mRNA levels and increased lactate were detected, suggesting an inconsistency between glucose and pyruvate metabolism. Pyruvate can be produced from oxaloacetate as well as glucose. We investigated ATP citrate lyase (ACLY) because it cleaves citrate into oxaloacetate and acetyl CoA. Phosphorylated ACLY (Ser455), the active form, was increased in both hippocampus and cortex samples of mice injected with streptozotocin and fed an HFD. Also, phosphorylated ACLY/total ACLY showed a positive correlation with lactate amount in the hippocampus. Our results suggest that the brain has different responses to diabetic progression, but, in the hippocampus, maintains metabolic alteration toward increasing lactate production from the prediabetic to the diabetic stage. We suggest that ACLY-mediated pyruvate be used to support lactate levels in the hippocampus in cases of limited glucose availability.

Hyperpolarized [1-13C] pyruvate MR spectroscopy detect altered glycolysis in the brain of a cognitively impaired mouse model fed high-fat diet.

Higher dietary intakes of saturated fatty acid increase the risk of developing Alzheimer's disease and dementia, and even in people without diabetes higher glucose levels may be a risk factor for dementia. The mechanisms causing neuronal dysfunction and dementia by consuming high-fat diet degrading the integrity of the blood-brain barrier (BBB) has been suggested but are not yet fully understood, and metabolic state of the brain by this type of insult is still veiled. The objective of this study was to investigate the effect of high-fat diet on the brain metabolism by a multimodal imaging method using the hyperpolarizedcarbon 13 (13C)-pyruvate magnetic resonance (MR) spectroscopy and dynamic contrast-enhanced MR imaging in conjunction with the biochemical assay and the behavior test in a mouse model fed high-fat diet (HFD). In mice were fed 60% HFD for 6 months, hyperpolarized [1-13C] pyruvate MR spectroscopy showed decreased perfusion (p < 0.01) and increased conversion from pyruvate to lactate (p < 0.001) in the brain. The hippocampus and striatum showed the highest conversion ratio. The functional integrity of the blood-brain barrier tested by dynamic contrast-enhanced MR imaging showed no difference to the control. Lactate was increased in the cortex (p < 0.01) and striatum (p < 0.05), while PDH activity was decreased in the cortex (p < 0.01) and striatum (p < 0.001) and the phosphorylated PDH was increased in the striatum (p < 0.05). Mice fed HFD showed less efficiency in learning memory compared with control (p < 0.05). To determine whether hyperpolarized 13C-pyruvate magnetic resonance (MR) spectroscopy could detect a much earier event in the brain. Mice fed HFD for 3 months did not show a detectable cognitive decline in water maze based learning memory. Hyperpolarized [1-13C] pyruvate MR spectroscopy showed increased lactate conversion (P < .001), but no difference in cerebral perfusion. These results suggest that the increased hyperpolarized [1-13C] lactate signal in the brain of HFD-fed mice represent that altered metabolic alteration toward to glycolysis and hypoperfusion by the long-term metabolic stress by HFD further promote to glycolysis. The hyperpolarized [1-13C] pyruvate MR spectroscopy can be used to monitor the brain metabolism and will provide information helpful to understand the disease process.

The 7q11.23 Protein DNAJC30 Interacts with ATP Synthase and Links Mitochondria to Brain Development.

Despite the known causality of copy-number variations (CNVs) to human neurodevelopmental disorders, the mechanisms behind each gene's contribution to the constellation of neural phenotypes remain elusive. Here, we investigated the 7q11.23 CNV, whose hemideletion causes Williams syndrome (WS), and uncovered that mitochondrial dysfunction participates in WS pathogenesis. Dysfunction is facilitated in part by the 7q11.23 protein DNAJC30, which interacts with mitochondrial ATP-synthase machinery. Removal of Dnajc30 in mice resulted in hypofunctional mitochondria, diminished morphological features of neocortical pyramidal neurons, and altered behaviors reminiscent of WS. The mitochondrial features are consistent with our observations of decreased integrity of oxidative phosphorylation supercomplexes and ATP-synthase dimers in WS. Thus, we identify DNAJC30 as an auxiliary component of ATP-synthase machinery and reveal mitochondrial maladies as underlying certain defects in brain development and function associated with WS.

High resolution hyperpolarized 13 C MRSI using SPICE at 9.4T.

PURPOSE: To test the feasibility of using the SPICE (SPectroscopic Imaging by exploiting spatiospectral CorrElation) technique, which uses the partial separability of spectroscopic data, for high resolution hyperpolarized (HP) 13 C spectroscopic imaging. METHODS: Numerical simulations were performed to investigate the impact of transient HP signals on SPICE reconstruction. Furthermore, spectroscopic imaging exams from SPICE and conventional EPSI (echo-planar spectroscopic imaging) were simulated for comparison. For in vivo experiments, HP 13 C SPICE was performed in a mouse kidney by means of the injection of HP [1-13 C] pyruvate at 9.4T. RESULTS: The variation of lactate/pyruvate from the simulated SPICE was less than 4% under various factors that affect the transient HP signal, suggesting that the impact is negligible. We found that while HP 13 C EPSI was limited to the low signal-to-noise ratio (SNR) of lactate, these limitations were mitigated through HP 13 C SPICE, facilitating the improved SNR of lactate and the distinction of tissues. Acquisition of a high resolution HP 13 C spectroscopic image was possible for the in vivo experiments. With the fine structural information, the acquired image showed higher signal of pyruvate and lactate in the renal cortices than in the medullas, which is known to be attributed to higher activity of lactate dehydrogenase. CONCLUSION: The feasibility of HP 13 C SPICE was investigated. Simulation studies were conducted and in vivo experiments were performed in the mouse kidney at 9.4T. Results confirmed that a high resolution HP 13 C spectroscopic image with adequate spectral resolution can be obtained. Magn Reson Med 80:703-710, 2018. © 2018 International Society for Magnetic Resonance in Medicine.

Reconstitution of the CstF complex unveils a regulatory role for CstF-50 in recognition of 3'-end processing signals.

Cleavage stimulation factor (CstF) is a highly conserved protein complex composed of three subunits that recognizes G/U-rich sequences downstream of the polyadenylation signal of eukaryotic mRNAs. While CstF has been identified over 25 years ago, the architecture and contribution of each subunit to RNA recognition have not been fully understood. In this study, we provide a structural basis for the recruitment of CstF-50 to CstF via interaction with CstF-77 and establish that the hexameric assembly of CstF creates a high affinity platform to target various G/U-rich sequences. We further demonstrate that CstF-77 boosts the affinity of the CstF-64 RRM to the RNA targets and CstF-50 fine tunes the ability of the complex to recognize G/U sequences of certain lengths and content.

Flow-suppressed hyperpolarized 13 C chemical shift imaging using velocity-optimized bipolar gradient in mouse liver tumors at 9.4 T.

PURPOSE: To optimize and investigate the influence of bipolar gradients for flow suppression in metabolic quantification of hyperpolarized 13 C chemical shift imaging (CSI) of mouse liver at 9.4 T. METHODS: The trade-off between the amount of flow suppression using bipolar gradients and T2* effect from static spins was simulated. A free induction decay CSI sequence with alternations between the flow-suppressed and non-flow-suppressed acquisitions for each repetition time was developed and was applied to liver tumor-bearing mice via injection of hyperpolarized [1-13 C] pyruvate. RESULTS: The in vivo results from flow suppression using the velocity-optimized bipolar gradient were comparable with the simulation results. The vascular signal was adequately suppressed and signal loss in stationary tissue was minimized. Application of the velocity-optimized bipolar gradient to tumor-bearing mice showed reduction in the vessel-derived pyruvate signal contamination, and the average lactate/pyruvate ratio increased by 0.095 (P < 0.05) in the tumor region after flow suppression. CONCLUSION: Optimization of the bipolar gradient is essential because of the short 13 C T2* and high signal in venous flow in the mouse liver. The proposed velocity-optimized bipolar gradient can suppress the vascular signal, minimizing T2*-related signal loss in stationary tissues at 9.4 T. Magn Reson Med 78:1674-1682, 2017. © 2016 International Society for Magnetic Resonance in Medicine.

Rtr1 is a dual specificity phosphatase that dephosphorylates Tyr1 and Ser5 on the RNA polymerase II CTD.

The phosphorylation state of heptapeptide repeats within the C-terminal domain (CTD) of the largest subunit of RNA polymerase II (PolII) controls the transcription cycle and is maintained by the competing action of kinases and phosphatases. Rtr1 was recently proposed to be the enzyme responsible for the transition of PolII into the elongation and termination phases of transcription by removing the phosphate marker on serine 5, but this attribution was questioned by the apparent lack of enzymatic activity. Here we demonstrate that Rtr1 is a phosphatase of new structure that is auto-inhibited by its own C-terminus. The enzymatic activity of the protein in vitro is functionally important in vivo as well: a single amino acid mutation that reduces activity leads to the same phenotype in vivo as deletion of the protein-coding gene from yeast. Surprisingly, Rtr1 dephosphorylates not only serine 5 on the CTD but also the newly described anti-termination tyrosine 1 marker, supporting the hypothesis that Rtr1 and its homologs promote the transition from transcription to termination.

Sequencing, phylogenetic analysis, and potential recombination events of infectious bronchitis viruses isolated in Korea.

The S2 glycoprotein and membrane (M) protein genes and S1 glycoprotein and nucleocapsid (N) genes of 11 Korean infectious bronchitis virus (IBV) isolates were amplified by RT-PCR, cloned, and sequenced. The resultant nucleotide sequences were compared with the published sequences for non-Korean IBV strains. Korean IBV isolates formed two independent subclusters within the phylogenetic tree based on S2 glycoprotein gene sequences. However, four and two different clusters were formed in the phylogenetic tree based on S1 glycoprotein and M gene sequences, respectively. In particular, Korean IBV K446-01 and K203-02 strains appeared to be the result of recombination between an indigenous Korean IBV strains and a vaccine strain (Massachusetts serotype) currently used in Korea. The recent IBV isolate, K026-10, formed a new subgroup that was closely related to traditional Korean IBV group in a phylogenetic tree based on the S1 and S2 genes, but it was grouped into the traditional Korean IBV cluster in a phylogenetic tree based on the M and N genes. Our data show that field IBVs in Korea are continuing to evolve and that vaccine strains might actually play a critical role in the appearance of new IBV strains via recombination in the field.