Genetic loci regulate Sarbecovirus pathogenesis: A comparison across mice and humans

Coronavirus (CoV) cause considerable morbidity and mortality in humans and other mammals, as evidenced by the emergence of Severe Acute Respiratory CoV (SARS-CoV) in 2003, Middle East Respiratory CoV (MERS-CoV) in 2012, and SARS-CoV-2 in 2019. Although poorly characterized, natural genetic variation in human and other mammals modulate virus pathogenesis, as reflected by the spectrum of clinical outcomes ranging from asymptomatic infections to lethal disease. Using multiple human epidemic and zoonotic Sarbecoviruses, coupled with murine Collaborative Cross genetic reference populations, we identify several dozen quantitative trait loci that regulate SARS-like group-2B CoV pathogenesis and replication. Under a Chr4 QTL, we deleted a candidate interferon stimulated gene, Trim14 which resulted in enhanced SARS-CoV titers and clinical disease, suggesting an antiviral role during infection. Importantly, about 60 % of the murine QTL encode susceptibility genes identified as priority candidates from human genome-wide association studies (GWAS) studies after SARS-CoV-2 infection, suggesting that similar selective forces have targeted analogous genes and pathways to regulate Sarbecovirus disease across diverse mammalian hosts. These studies provide an experimental platform in rodents to investigate the molecular-genetic mechanisms by which potential cross mammalian susceptibility loci and genes regulate type-specific and cross-SARS-like group 2B CoV replication, immunity, and pathogenesis in rodent models. Our study also provides a paradigm for identifying susceptibility loci for other highly heterogeneous and virulent viruses that sporadically emerge from zoonotic reservoirs to plague human and animal populations

The performance of the jet trigger for the ATLAS detector during 2011 data taking

The performance of the jet trigger for the ATLAS detector at the LHC during the 2011 data taking period is described. During 2011 the LHC provided proton–proton collisions with a centre-of-mass energy of 7 TeV and heavy ion collisions with a 2.76 TeV per nucleon–nucleon collision energy. The ATLAS trigger is a three level system designed to reduce the rate of events from the 40 MHz nominal maximum bunch crossing rate to the approximate 400 Hz which can be written to offline storage. The ATLAS jet trigger is the primary means for the online selection of events containing jets. Events are accepted by the trigger if they contain one or more jets above some transverse energy threshold. During 2011 data taking the jet trigger was fully efficient for jets with transverse energy above 25 GeV for triggers seeded randomly at Level 1. For triggers which require a jet to be identified at each of the three trigger levels, full efficiency is reached for offline jets with transverse energy above 60 GeV. Jets reconstructed in the final trigger level and corresponding to offline jets with transverse energy greater than 60 GeV, are reconstructed with a resolution in transverse energy with respect to offline jets, of better than 4 % in the central region and better than 2.5 % in the forward direction

Analysis of urinary nucleosides as helper tumor markers in hepatocellular carcinoma diagnosis

Hepatocellular carcinoma (HCC) is a common neoplasm in Taiwan, for which early diagnosis is difficult and the prognosis is usually poor. HCC is usually diagnosed by abdominal sonography and serum alpha-fetoprotein (AFP) detection. Modified nucleosides, regarded as indicators for the whole-body turnover of RNAs, are excreted in abnormal amounts in the urine of patients with malignancies and can serve as tumor markers. We analyzed the excretion patterns of urinary nucleosides from 25 HCC patients and 20 healthy volunteers by high-performance liquid chromatography/electrospray ionization tandem mass spectrometry (HPLC/ESI-MS/MS) under optimized conditions. The HPLC/ESI-MS/MS approach with selective reaction monitoring (SRM) allowed for the sensitive determination of nucleosides in human urine samples. The mean levels of the urinary nucleosides adenosine, cytidine, and inosine were significantly higher in HCC patients than healthy volunteers (average of 1.78-, 2.26-, and 1.47-fold, respectively). However, the mean levels of urinary 1-methyladenosine, 3-methylcytidine, uridine, and 2'-deoxyguanosine were not significantly different. Combined with the determination of serum AFP levels, the higher levels of urinary adenosine, cytidine, and inosine may be additional diagnosis markers for HCC in Taiwanese patients. Copyright (C) 2009 John Wiley & Sons, Ltd

Analysis of urinary nucleosides as potential tumor markers in human colorectal cancer by high performance liquid chromatography/electrospray ionization tandem mass spectrometry

Background: Increased levels of modified nucleosides have been observed in urine from patients suffering from several cancers. In this study, we evaluated whether urinary nucleosides can serve as potential tumor markers for colorectal cancer by high performance liquid chromatography-electrospray/tandem mass spectrometry (HPLC/ESI-MS/MS). Methods: A simple and specific method based on HPLC/ESI-MS/MS was developed to determine the urinary nucleosides from patients with colorectal cancer. We studied the excretion patterns of nucleosides in urine from 26 patients with colorectal cancer and 18 healthy controls. Results: The LC/MS/MS approach with selective reaction monitoring (SRM) allowed for the sensitive determination of nucleosides in human urine samples with colorectal cancer. The mean levels of 5 urinary nucleosides (adenosine, cytidine, N(2),N(2)-dimethylguanine, 8-hydroxy-2'-deoxyguanosine and uridine) were significantly higher in the patients with colorectal cancer than in the healthy adults. Conclusions: The results indicate that urinary nucleosides determined by LC/MS/MS may be useful as biological markers for colorectal cancer. Our findings suggest that LC/MS/MS is a highly specific and sensitive method for rapidly screening a large number of nucleoside that may be useful as markers for cancer in humans. (C) 2008 Elsevier B.V. All rights reserved

Comparison of Escherichia coli and klebsiella pneumoniae liver abscesses

Background: Escherichia coli and Klebsiella pneumoniae are the most common causative pathogens of pyogenic liver abscesses. The objective of this study was to compare outcome between patients with liver abscesses due to E coli and those with liver abscesses caused by K pneumoniae, we also aimed to identify separately the predictors of mortality in the 2 groups. Methods: We conducted a retrospective study of 202 patients who presented with pyogenic liver abscesses caused by either E coli or K pneumoniae from July 2000 to June 2005. Outcome of the patients was analyzed by exact logistic regression with adjustment for baseline and clinical covariates. Significant predictors of mortality in the E coli and the K pneumoniae groups were investigated by multivariate analysis of demographic and clinical variables in each group. Results: Of the 202 patients (128 men and 74 women; age range, 19 to 89 years), pyogenic liver abscess was due to E coli infection in 55 patients and K pneumoniae in 147 patients. In contrast to patients with K pneumoniae, patients with E coli liver abscess were more likely to be older and female, have a biliary abnormality or malignancy, pleural effusion, polymicrobial infection with anaerobic or multi-drug-resistant organisms, a higher APACHE II score, and to have been treated initially with ineffective antibiotics; they were also less likely to have diabetes mellitus. The cause of K pneumoniae liver abscess was often cryptogenic. The sensitivity, specificity, positive predictive value, and likelihood ratio of the presence of biliary disorders and coexisting malignancy as a predictive parameter of E coli liver abscess were 25%, 96%, 67%, and 5.45/1, respectively. The sensitivity, specificity, positive predictive value, and likelihood ratio of the presence of diabetes mellitus with an abscess of cryptogenic origin as a predictive parameter of K pneumoniae liver abscess were 39%, 84%, 81%, and 2.36/1, respectively. There was no significant difference in mortality between patients with E coli and those with K pneumoniae infections (26% vs 4%; adjusted OR, 4.2; 95% Cl, 0.63 to 27; P = 0.105). However, for patients with liver abscess caused by E coli, the APACHE 11 score at admission (OR, 1.7; 95% Cl, 1.1 to 2.6; P = 0.02 1), malignancy (OR, 26; 95% CI, 1.8 to 3 70; P = 0.016), and right-lobe abscess (OR, 0.0029; 95% CI, 0.00010 to 0.15; P = 0.004) were significant predictors of death, whereas uremia (OR, 52; 95% CI, 3.5 to 750; P = 0.004) and multi-drug-resistant isolates (OR, 26; 95% CI, 2.3 to 290; P = 0.009) were significant predictors of death in the K pneumoniae group. Conclusions: A higher APACHE II score at admission and a higher frequency of coexisting malignancy may have contributed to the higher, although not significant, mortality rate in patients with liver abscess caused by E coli infection. Clinicians should begin with broad antibiotic coverage such as a second-generation cephalosporin and an aminoglycoside with metronidazole when treating liver abscesses with E coli as the likely pathogen due to the high frequency of multi-drug-resistant isolates among E coli isolates