Murine coronavirus ubiquitin-like domain is important for papain-like protease stability and viral pathogenesis

Ubiquitin-like domains (Ubls) now are recognized as common elements adjacent to viral and cellular proteases; however, their function is unclear. Structural studies of the papain-like protease (PLP) domains of coronaviruses (CoVs) revealed an adjacent Ubl domain in severe acute respiratory syndrome CoV, Middle East respiratory syndrome CoV, and the murine CoV, mouse hepatitis virus (MHV). Here, we tested the effect of altering the Ubl adjacent to PLP2 of MHV on enzyme activity, viral replication, and pathogenesis. Using deletion and substitution approaches, we identified sites within the Ubl domain, residues 785 to 787 of nonstructural protein 3, which negatively affect protease activity, and valine residues 785 and 787, which negatively affect deubiquitinating activity. Using reverse genetics, we engineered Ubl mutant viruses and found that AM2 (V787S) and AM3 (V785S) viruses replicate efficiently at 37°C but generate smaller plaques than wild-type (WT) virus, and AM2 is defective for replication at higher temperatures. To evaluate the effect of the mutation on protease activity, we purified WT and Ubl mutant PLP2 and found that the proteases exhibit similar specific activities at 25°C. However, the thermal stability of the Ubl mutant PLP2 was significantly reduced at 30°C, thereby reducing the total enzymatic activity. To determine if the destabilizing mutation affects viral pathogenesis, we infected C57BL/6 mice with WT or AM2 virus and found that the mutant virus is highly attenuated, yet it replicates sufficiently to elicit protective immunity. These studies revealed that modulating the Ubl domain adjacent to the PLP reduces protease stability and viral pathogenesis, revealing a novel approach to coronavirus attenuation. IMPORTANCE Introducing mutations into a protein or virus can have either direct or indirect effects on function. We asked if changes in the Ubl domain, a conserved domain adjacent to the coronavirus papain-like protease, altered the viral protease activity or affected viral replication or pathogenesis. Our studies using purified wild-type and Ubl mutant proteases revealed that mutations in the viral Ubl domain destabilize and inactivate the adjacent viral protease. Furthermore, we show that a CoV encoding the mutant Ubl domain is unable to replicate at high temperature or cause lethal disease in mice. Our results identify the coronavirus Ubl domain as a novel modulator of viral protease stability and reveal manipulating the Ubl domain as a new approach for attenuating coronavirus replication and pathogenesis.

Performance of gene-expression profiling test score variability to predict future clinical events in heart transplant recipients.

BACKGROUND A single non-invasive gene expression profiling (GEP) test (AlloMap®) is often used to discriminate if a heart transplant recipient is at a low risk of acute cellular rejection at time of testing. In a randomized trial, use of the test (a GEP score from 0-40) has been shown to be non-inferior to a routine endomyocardial biopsy for surveillance after heart transplantation in selected low-risk patients with respect to clinical outcomes. Recently, it was suggested that the within-patient variability of consecutive GEP scores may be used to independently predict future clinical events; however, future studies were recommended. Here we performed an analysis of an independent patient population to determine the prognostic utility of within-patient variability of GEP scores in predicting future clinical events. METHODS We defined the GEP score variability as the standard deviation of four GEP scores collected ≥315 days post-transplantation. Of the 737 patients from the Cardiac Allograft Rejection Gene Expression Observational (CARGO) II trial, 36 were assigned to the composite event group (death, re-transplantation or graft failure ≥315 days post-transplantation and within 3 years of the final GEP test) and 55 were assigned to the control group (non-event patients). In this case-controlled study, the performance of GEP score variability to predict future events was evaluated by the area under the receiver operator characteristics curve (AUC ROC). The negative predictive values (NPV) and positive predictive values (PPV) including 95 % confidence intervals (CI) of GEP score variability were calculated. RESULTS The estimated prevalence of events was 17 %. Events occurred at a median of 391 (inter-quartile range 376) days after the final GEP test. The GEP variability AUC ROC for the prediction of a composite event was 0.72 (95 % CI 0.6-0.8). The NPV for GEP score variability of 0.6 was 97 % (95 % CI 91.4-100.0); the PPV for GEP score variability of 1.5 was 35.4 % (95 % CI 13.5-75.8). CONCLUSION In heart transplant recipients, a GEP score variability may be used to predict the probability that a composite event will occur within 3 years after the last GEP score. TRIAL REGISTRATION Clinicaltrials.gov identifier NCT00761787.

Clinical usefulness of gene-expression profile to rule out acute rejection after heart transplantation: CARGO II.

AIMS A non-invasive gene-expression profiling (GEP) test for rejection surveillance of heart transplant recipients originated in the USA. A European-based study, Cardiac Allograft Rejection Gene Expression Observational II Study (CARGO II), was conducted to further clinically validate the GEP test performance. METHODS AND RESULTS Blood samples for GEP testing (AlloMap(®), CareDx, Brisbane, CA, USA) were collected during post-transplant surveillance. The reference standard for rejection status was based on histopathology grading of tissue from endomyocardial biopsy. The area under the receiver operating characteristic curve (AUC-ROC), negative (NPVs), and positive predictive values (PPVs) for the GEP scores (range 0-39) were computed. Considering the GEP score of 34 as a cut-off (>6 months post-transplantation), 95.5% (381/399) of GEP tests were true negatives, 4.5% (18/399) were false negatives, 10.2% (6/59) were true positives, and 89.8% (53/59) were false positives. Based on 938 paired biopsies, the GEP test score AUC-ROC for distinguishing ≥3A rejection was 0.70 and 0.69 for ≥2-6 and >6 months post-transplantation, respectively. Depending on the chosen threshold score, the NPV and PPV range from 98.1 to 100% and 2.0 to 4.7%, respectively. CONCLUSION For ≥2-6 and >6 months post-transplantation, CARGO II GEP score performance (AUC-ROC = 0.70 and 0.69) is similar to the CARGO study results (AUC-ROC = 0.71 and 0.67). The low prevalence of ACR contributes to the high NPV and limited PPV of GEP testing. The choice of threshold score for practical use of GEP testing should consider overall clinical assessment of the patient's baseline risk for rejection.

New aspects of estrogen action in the endometrium: Reciprocal interplay with retinoic acid pathway and a novel estrogen-regulated gene

The uterine endometrium is a major target for the estrogen. However, the molecular basis of estrogen action in the endometrium is largely unknown. I have used two approaches to study the effects of estrogen on the endometrium. One approach involved the study of the interaction between estrogen and retinoic acid (RA) pathways in the endometrium. I have demonstrated that estrogen administration to rodents and estrogen replacement therapy (ERT) in postmenopausal women selectively induced the endometrial expression of retinaldehyde dehydrogenase II (RALDH2), a critical enzyme of RA biosynthesis. RALDH2 was expressed exclusively in the stromal cells, especially in the stroma adjacent to the luminal and glandular epithelia. The induction of RALDH2 by estrogen required estrogen receptor and occurred via a direct increase in RALDH2 transcription. Among the three RA receptors, estrogen selectively induced the expression of RARα. In parallel, estrogen also increased the utilization of all-trans retinol (the substrate for RA biosynthesis) and the expression of two RA-regulated marker genes, cellular retinoic acid binding protein II (CRABP2) and tissue transglutaminase (tTG) in the endometrium. Thus estrogen coordinately upregulated both the production and signaling of RA in both the rodent and human endometrium. This coordinate upregulation of RA system appeared to play a role in counterbalancing the stimulatory effects of estrogen on the endometrium, since the depletion of endogenous RA in mice led to an increase in estrogen-stimulated stromal proliferation and endometrial Akt phosphorylation. In addition, I have also used a systematic approach (DNA microarray) to categorize genes and pathways affected by the ERT in the endometrium of postmenopausal women and identified a novel estrogen-regulated gene EIG121. EIG121 was exclusively expressed in the glandular epithelial cells of the endometrium and induced by estrogen in vivo and in cultured cell lines. Compared with the normal endometrium, EIG121 was highly overexpressed in type 1 endometrial cancer, but profoundly suppressed in type 2 endometrial tumors. Taken together, these studies suggested that estrogen regulates the expression of many genes of both the pro-proliferative and anti-proliferative pathways and the abnormality of these pathways may increase the risks for estrogen-dependent endometrial hyperplasia and endometrial cancer. ^

Racial Differences in Homeownership: The Effect of Residential Location

The rate of homeownership among African-American households is considerably lower than white households in American urban areas. This paper examines whether racial differneces in residential location outcomes are among the factors that contribute to the large racial differences in homeownership rates in major US metropolitan areas. Based on the 1985 metropolitan sample of the American Housing Survey for Philadelphia, the paper does not find any evidence that existing racial differences in residential location in Philadelphia decrease the homeownership rate among African Americans. Rather, the empirical evidence suggests that African-American residential location outcomes are associated with lower than expected racial differences in homeownership. Therefore, after controlling for neighborhood, racial differences in homeownership are larger than originally believed, and the ability of racial differences in endowments to explain hoeownership differences is more limited.

A Confirmatory Factor Analytic Study Examining the Dimensionality of Educational Achievement Tests

It is important to check the fundamental assumption of most popular Item Response Theory models, unidimensionality. However, it is hard for educational and psychological tests to be strictly unidimensional. The tests studied in this paper are from a standardized high-stake testing program. They feature potential multidimensionality by presenting various item types and item sets. Confirmatory factor analyses with one-factor and bifactor models, and based on both linear structural equation modeling approach and nonlinear IRT approach were conducted. The competing models were compared and the implications of the bifactor model for checking essential unidimensionality were discussed.

Mechanisms of adenovirus 5 E1A -mediated tumor suppression and E1A-mediated apoptosis

The adenovirus type 5 E1A gene products have numerous functions in cells, which serve as useful tools in studying the mechanisms of either oncogenesis or tumor suppression. To understand the mechanisms of E1A-mediated tumor suppression, we introduced an Ad5 E1A gene into murine melanoma cells, and characterized E1A-mediated biological functions both in vitro and in vivo. The results of the study indicated that: (i) Ad5 E1A mediated tumor suppression in rodent tumor cells; (ii) E1A-mediated tumor suppression is associated with E1A-mediated apoptosis in vivo.^ To determine which functional region(s) of E1A is(are) required for E1A-mediated apoptosis and whether E1A-mediated apoptosis is required for E1A-mediated tumor suppression, we established stable transfectants of E1A mutants, which have deletion mutation at either the N-terminal (p300-binding) or the CR2 (pRb-binding) domain or both, and then characterized biological functions both in vitro and in vivo. The results of the study indicate that the CR2 domain of E1A is required for E1A-mediated apoptosis, while the N-terminal domain of E1A is dispensable. Interestingly, either of the two domains is able to mediate tumor suppression, since mutant E1A with a single deletion at either domain still suppressed tumor growth. Importantly, deletion mutations at both the N-terminal and the CR2 domains of E1A abrogated E1A-mediated tumor suppression, suggesting both regions are required for E1A-mediated tumor suppression. The results demonstrate that E1A-mediated apoptosis is not the only mechanism for E1A-mediated tumor suppression. Thus, the N-terminal and CR2 domains of E1A mediated two independent mechanisms of tumor suppression.^ To understand the mechanism of E1A-mediated apoptosis, we examined the temporal relationship of molecular events during the apoptotic cascades after UV radiation and serum depletion in both the E1A-expressing cells and parental cells. Kinetic analysis of JNK activity indicates that the JNK pathway is greatly increased in response to UV light in E1A transfectants, suggesting that extracellular stress stimuli have been converted into intracellular stress signals with greater magnitude in E1A transfectants than those in parental cells. Thus, E1A-mediated sensitization precedes these events. As ceramide has been proposed as second messenger and upstream activator of JNK pathway for stress-induced apoptosis, we also examined the roles of ceramide in apoptosis and the relationship with JNK pathway. The results indicate that E1A transfectants do not have increased sensitivity to ceramide. Therefore, E1A-mediated sensitization to UV radiation cannot be attributed to an increased sensitivity to ceramide. Furthermore, UV-induced JNK activation correlates with UV-induced apoptosis, while lethal dose of ceramide does not activate JNK. Thus, activation of JNK pathway is independent of the ceramide pathway. In addition, E1A transfectants also have increased activation of NF-kB in response to UV. These results suggest that E1A-mediated sensitization is an early event which associates with conversion of extracellular stress stimuli into amplified intracellular signals. The mechanism of E1A-mediated sensitization and its relationship with other pathways are discussed. ^

Proceedings of the Twenty-Fifth Annual Biochemical Engineering Symposium

The Annual Biochemical Engineering Symposium Series started in 1970 when Professors Larry E. Erickson (Kansas State University) and Peter J. Reilly (then with University of Nebraska-Lincoln) got together in Manhattan, KS along with their students for a half-day powwow and technical presentation by their students. Ever since then, it has been a forum for Biochemical Engineering students in the heartland of USA to present their research to their colleagues in the form of talks and posters. The institutions actively involved with this annual symposium include Colorado State University, Kansas State University, Iowa State University, University of Colorado, University of Kansas, University of Missouri-Columbia, and University of Oklahoma. The University of lowa and University of Nebraska-Lincoln have also participated in the conference in recent years. The host institutions for the different symposia have been: Kansas State University (1, 3, 5, 9, 12, 16, 20), Iowa State University (6, 7, 10, 13, 17, 22), University of Missouri-Columbia (8, 14, 19, 25), Colorado State University (II, 15, 21), University of Colorado (18, 24), University of Nebraska-Lincoln (2, 4), University of Oklahoma (23). The next symposium will be held at Kansas State University. Proceedings of the Symposium are edited by faculty of the host institution and include manuscripts written and submitted by the presenters (students). These often include works-in-progress and final publication usually takes place in refereed journals. ContentsPatrick C. Gilcrease and Vincent G. Murphy, Colorado State University. Use of 2,4,6-Trinitrotoluene (TNT) As A Nitrogen Source By A Pseudomonas florescens Species Under Aerobic Conditions. Marulidharan Narayanan, Lawrence C. Davis, and Larry E. Erickson, Kansas State University. Biodegradation Studies of Chlorinated Organic Pollutants in a Chamber in the Presence of Alfalfa Plants. S.K. Santharam, L.E. Erickson, and L.T. Fan, Kansas State University.Surfactant-Enhanced Remediation of a Non-Aqueous Phase Contaminant in Soil. Barry Vant-Hull, Larry Gold, and Robert H. Davis, University of Colorado.The Binding of T7 RNA Polymerase to Double-Stranded RNA. Jeffrey A. Kern and Robert H. Davis, University of Colorado.Improvement of RNA Transcription Yield Using a Fed-Batch Enzyme Reactor. G. Szakacs, M. Pecs, J. Sipocz, I. Kaszas, S.R. Deecker, J.C. Linden, R.P. Tengerdy, Colorado State University.Bioprocessing of Sweet Sorghum With In Situ Produced Enzymes. Brad Forlow and Matthias Nollert, University of Oklahoma.The Effect of Shear Stress ad P-selectin Site Density on the Rolling Velocity of White Blood Cells. Martin C. Heller and Theodore W. Randolph, University of Colorado.The Effects of Plyethylene Glycol and Dextran on the Lyophilization of Human Hemoglobin. LaToya S. Jones and Theodore W. Randolph, University of Colorado.Purification of Recombinant Hepatitis B Vaccine: Effect of Virus/Surfactant Interactions. Ching-Yuan Lee, Michael G. Sportiello, Stephen Cape, Sean Ferree, Paul Todd, Craig E. Kundrot, and Cindy Barnes, University of Colorado.Application of Osmotic Dewatering to the Crystallization of Oligonucleotides for Crystallography. Xueou Deng, L.E. Erickson, and D.Y.C. Fung, Kansas State University.Production of Protein-Rich Beverages from Cheese Whey and Soybean by rapid Hydration Hydrothermal Cooking. Pedro M. Coutinho, Michael K. Dowd, and Peter J. Reilly, Iowa State University.Automated Docking of Glucoamylase Substrates and Inhibitors. J. Johansson and R.K. Bajpai, University of Missouri.Adsorption of Albumin on Polymeric Microporous Membranes.

Elements and mineralogical compostions from different sediment cores off the southern China Sea

The mineralogy, major and trace elements, and neodymium and strontium isotopes of surface sediments in the South China Sea (SCS) are documented with the aim of investigating their applicability in provenance tracing. The results indicate that mineralogical compositions alone do not clearly identify the sources for the bulk sediments in the SCS. The Nd isotopic compositions of the SCS sediments show a clear zonal distribution. The most negative epsilon-Neodymium values were obtained for sediments from offshore South China (-13.0 to -10.7), while those from offshore Indochina are slightly more positive (-10.7 to -9.4). The Nd isotopic compositions of the sediments from offshore Borneo are even higher, with epsilon-Neodymium ranging from -8.8 to -7.0, and the sediments offshore from the southern Philippine Arc have the most positive epsilon-Neodymium values, from -3.7 to +5.3. This zonal distribution in epsilon-Neodymium is in good agreement with the Nd isotopic compositions of the sediments supplied by river systems that drain into the corresponding regions, indicating that Nd isotopic compositions are an adequate proxy for provenance tracing of SCS sediments. Sr isotopic compositions, in contrast, can only be used to identify the sediments from offshore South China and offshore from the southern Philippine Arc, as the 87Sr/86Sr ratios of sediments from other regions overlapped. Similar zonal distributions are also apparent in a La-Th-Sc discrimination diagram. Sediments fromthewestmargin of the SCS, such as those fromBeibuwan Bay, offshore fromHainan Island, offshore from Indochina, and from the Sunda Shelf plot in the same field, while those offshore from the northeastern SCS, offshore from Borneo, and offshore from the southern Philippine Arc plot in distinct fields. Thus, the La-Th-Sc discrimination diagram, coupledwith Nd isotopes, can be used to trace the provenance of SCS sediments. Using this method, we re-assessed the provenance changes of sediments at Ocean Drilling Program (ODP) Site 1148 since the late Oligocene. The results indicate that sediments deposited after 23.8 Ma (above 455 mcd: meters composite depth) were supplied mainly from the eastern South China Block, with a negligible contribution from the interior of the South China Block. Sediments deposited before 26 Ma (beneath 477 mcd) were supplied mainly from the North Palawan Continental Terrane, which may retain the geochemical characteristics of the materials covered on the late Mesozoic granitoids along the coastal South China. For that the North Palawan Continental Terrane is presently located within the southern Philippine Arc but was located close to ODP Site 1148 in the late Oligocene. The weathering products of volcanic material associated with the extension of the SCS ocean crust also contributed to these sediments. The rapid change in sediment source at 26-23.8 Ma probably resulted from a sudden cessation of sediment supply from the North Palawan Continental Terrane. Wesuggest that the North Palawan Continental Terrane drifted southwards alongwith the extension of the SCS ocean crust during that time, and when the basin was large enough, the supply of sediment from the south to ODP Site 1148 at the north slope may have ceased.

Table A1 LA-ICP-MS zircon U-Pb data of Laoniushan granitoids

The NWW-striking Qinling Orogen formed in the Triassic by collision between the North China and Yangtze Cratons. Triassic granitoid intrusions, mostly middle- to high-K, calc-alkaline in composition, are widespread in this orogen, but contemporaneous intrusions are rare in the southern margin of the North China Craton, an area commonly considered as the hinterland belt of the orogen. In this paper, we report zircon U-Pb ages, elemental geochemistry, and Sr-Nd-Hf isotope data for the Laoniushan granitoid complex that was emplaced in the southern margin of the North China Craton. Zircon U-Pb dating shows that the complex was emplaced in the late Triassic (228±1 to 215±4 Ma), indicating that it is part of the post-collisional magmatism in the Qinling Orogen. The complex consists of, from early to late, biotite monzogranite, quartz diorite, quartz monzonite, and hornblende monzonite, which have a wide compositional range, e.g., SiO2=55.9-70.6 wt%, K2O+Na2O=6.6-10.2 wt%, and Mg# of 24 to 54. Rocks of the biotite monzogranite have high Al2O3(15.5-17.4 wt%), Sr(396-1398 ppm) and Ba(1284-3993 ppm) contents and La/Yb(mostly 14-30) and Sr/Y(mostly 40-97) ratios, but low Yb(mostly 1.3-1.6 ppm) and Y(mostly14-19 ppm) contents, features typical of adakite. The quartz monzonite, hornblende monzonite and quartz diorite have a shoshonitic affinity, with K2O up to 5.58 wt% and K2O/Na2O ratios averaging 1.4. The rocks are characterized by strong LREE/HREE fractionation in chondrite-normalized REE pattern, without obvious Eu anomalies, and show enrichment in large ion lithophile elements but depletion in high field strength elements (Nb, Ta, Ti). The biotite monzogranite (228 Ma) has initial 87Sr/86Sr ratios of 0.7061 to 0.7067, eNd(t) values of -9.2 to -12.6, and ?Hf(t) values of -9.0 to -15.1; whereas the shoshonitic granitoids (mainly 217-215 Ma) have similar initial 87Sr/86Sr ratios (0.7065 to 0.7075) but more radiogenic eNd(t) (-12.4 to -17.0) and eHf(t) (-14.1 to -17.0). The Sr-Nd-Hf isotope data indicate that the rocks were likely generated by partial melting of an ancient lower continental crust with heterogeneous compositions, as partly confirmed by the widespread presence of the early Paleoproterozoic inherited zircons. Mafic microgranular enclaves (MMEs), characterized by fine-grained igneous textures and an abundance of acicular apatites, are common in the Laoniushan complex. Compared with the host rocks, they have lower SiO2 (48.6-53.7 wt.%) and higher Mg# (51-56), Cr (122-393 ppm), and Ni (24-79 ppm), but equivalent Sr-Nd isotope compositions, indicating that the MMEs likely originated from an ancient enriched lithospheric mantle. The abundance of MMEs in the granitoid intrusions suggests that magma mixing plays an important role in the generation of the Laoniushan complex. Collectively, it is suggested that the Laoniushan complex was a product of post-collisional magmatism related to lithospheric extension following slab break-off. Formation of the adakitic and shoshonitic intrusions in the Laoniushan complex indicates that the Qinling Orogen had evolved into a post-collisional setting by about 230-210 Ma.

Uranium-Thorium dating and sea surface temperatures from corals from Hainan Island, South China Sea

Three mid-Holocene sea surface temperature (SST) records spanning more than 30 years were reconstructed for the northern South China Sea using Sr/Ca ratios in Porites corals. The results indicate warmer than present climates between circa 6100 yr B.P. and circa 6500 yr B.P. with the mid-Holocene average minimum monthly winter SSTs, the average maximum monthly summer SSTs, and the average annual SSTs being about 0.5°-1.4°C, 0°-2.0°C, and 0.2°-1.5°C higher, respectively, than they were during 1970-1994. Summer SSTs decrease from circa 6500 yr B.P. to circa 6100 yr B.P. with a minimum centered at circa 6300 yr B.P. The higher average summer SSTs are consistent with a stronger summer monsoon during the mid-Holocene, and the decreasing trend indicates a secular decrease of summer monsoon strength, which reflects the change in summer insolation in the Northern Hemisphere. El Niño-Southern Oscillation (ENSO) cycles were apparent in both the mid-Holocene coral and modern instrumental records. However, the ENSO variability in the mid-Holocene SSTs was weaker than that in the modern record, and the SST record with the highest summer temperatures from circa 6460 yr B.P. to 6496 yr B.P. shows no robust ENSO cycle. This agrees with other studies that indicate that stronger summer monsoon circulation may have been associated with suppressed ENSO variability during the mid-Holocene.