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ABSTRACT: This study aimed to evaluate the impact of copy number variants (CNV) on 13 reproduction and 12 disease traits in Holstein cattle. Intensity signal files containing log R ratio and B allele frequency information from 13,730 Holstein animals genotyped with a 95K SNP panel, and 8,467 Holstein animals genotyped with a 50K SNP panel were used to identify the CNVs. Subsequently, the identified CNVs were validated using whole-genome sequence data from 126 animals, resulting in 870 high-confidence copy number variant regions (CNVR) on 12,131 animals. Out of these, 54 CNVR had frequencies higher than or equal to 1% in the population and were used in the genome-wide association analysis (one CNVR at a time, including the G matrix). Results revealed that 4 CNVR were significantly associated with at least one of the traits analyzed in this study. Specifically, 2 CNVR were associated with 3 reproduction traits (i.e., calf survival, first service to conception, and nonreturn rate), and 2 CNVR were associated with 2 disease traits (i.e., metritis and retained placenta). These CNVR harbored genes implicated in immune response, cellular signaling, and neuronal development, supporting their potential involvement in these traits. Further investigations to unravel the mechanistic and functional implications of these CNVR on the mentioned traits are warranted.

Abstract Background Outcomes of dogs with acute kidney injury secondary to leptospirosis (AKI‐L) treated using renal replacement therapies (RRT) are poorly characterized. Hypothesis/Objectives Describe survival to discharge, short (≤30 days) and long‐term (≥6 months) outcomes of AKI‐L dogs receiving RRT and determine if there is a significant difference in maximum blood urea nitrogen (maxBUN), maximum creatinine (maxCr), maximum bilirubin (maxBili) and the number of body systems affected between survivors and non‐survivors. Animals Twenty‐two client‐owned dogs with AKI‐L receiving RRT. Methods Retrospective medical record review of dogs with AKI‐L that received RRT between 2018 and 2021. Results Sixteen of 22 (73%) dogs survived to discharge. Of the survivors, 13 (81%) were alive >30 days from discharge and 12 (75%) were alive at 6 months from discharge. Factors significantly higher in non‐survivors included number of body systems affected (survivors: 1 (19%), 2 (50%), 3 (25%) and 4 (6%) vs non‐survivors: 3 (33.3%), and 4 (66.7%); P = .01) and median maxBili (survivors: 1.9 mg/dL; range, 0.1‐41.6 vs non‐survivors: 21.0 mg/dL; range, 12.3‐38.9; P = .02). There was no significant difference in median maxBUN (survivors: 153.0 mg/dL; range, 67‐257 vs non‐survivors: 185.5 mg/dL; range, 102‐218; P = .44) and median maxCr (survivors: 9.8 mg/dL; range, 6.2‐15.9 vs non‐survivors: 9.8 mg/dL; range, 8.4‐13.5; P = .69) between survivors and non‐survivors. Conclusions and Clinical Importance Regardless of azotemia severity, dogs with AKI‐L receiving RRT have a good survival rate to discharge. The number of body systems affected and hyperbilirubinemia might be associated with worse outcomes.

ABSTRACT: The Resilient Dairy Genome Project (RDGP) is an international large-scale applied research project that aims to generate genomic tools to breed more resilient dairy cows. In this context, improving feed efficiency and reducing greenhouse gases from dairy is a high priority. The inclusion of traits related to feed efficiency (e.g., dry matter intake [DMI]) or greenhouse gases (e.g., methane emissions [CH4]) relies on available genotypes as well as high quality phenotypes. Currently, 7 countries (i.e., Australia, Canada, Denmark, Germany, Spain, Switzerland, and United States) contribute with genotypes and phenotypes including DMI and CH4. However, combining data are challenging due to differences in recording protocols, measurement technology, genotyping, and animal management across sources. In this study, we provide an overview of how the RDGP partners address these issues to advance international collaboration to generate genomic tools for resilient dairy. Specifically, we describe the current state of the RDGP database, data collection protocols in each country, and the strategies used for managing the shared data. As of February 2022, the database contains 1,289,593 DMI records from 12,687 cows and 17,403 CH4 records from 3,093 cows and continues to grow as countries upload new data over the coming years. No strong genomic differentiation between the populations was identified in this study, which may be beneficial for eventual across-country genomic predictions. Moreover, our results reinforce the need to account for the heterogeneity in the DMI and CH4 phenotypes in genomic analysis.

ABSTRACT: Feed efficiency has become an increasingly important research topic in recent years. As feed costs rise and the environmental impacts of agriculture become more apparent, improving the efficiency with which dairy cows convert feed to milk is increasingly important. However, feed intake is expensive to measure accurately on large populations, making the inclusion of this trait in breeding programs difficult. Understanding how the genetic parameters of feed efficiency and traits related to feed efficiency vary throughout the lactation period is valuable to gain understanding into the genetic nature of feed efficiency. This study used 121,226 dry matter intake (DMI) records, 120,500 energy-corrected milk (ECM) records, and 98,975 metabolic body weight (MBW) records, collected on 7,440 first-lactation Holstein cows from 6 countries (Canada, Denmark, Germany, Spain, Switzerland, and the United States), from January 2003 to February 2022. Genetic parameters were estimated using a multiple-trait random regression model with a fourth-order Legendre polynomial for all traits. Weekly phenotypes for DMI were re-parameterized using linear regressions of DMI on ECM and MBW, creating a measure of feed efficiency that was genetically corrected for ECM and MBW, referred to as genomic residual feed intake (gRFI). Heritability (SE) estimates varied from 0.15 (0.03) to 0.29 (0.02) for DMI, 0.24 (0.01) to 0.29 (0.03) for ECM, 0.55 (0.03) to 0.83 (0.05) for MBW, and 0.12 (0.03) to 0.22 (0.06) for gRFI. In general, heritability estimates were lower in the first stage of lactation compared with the later stages of lactation. Additive genetic correlations between weeks of lactation varied, with stronger correlations between weeks of lactation that were close together. The results of this study contribute to a better understanding of the change in genetic parameters across the first lactation, providing insight into potential selection strategies to include feed efficiency in breeding programs.

Abstract Background Pseudomembranous cystitis (PMC) in cats is a recognized disease, but concurrent mineralization is reported rarely and its outcome is poorly described. Hypothesis and Objectives Describe a population of cats with PMC and the prevalence of concurrent mineralization. Animals Twenty‐six cats with PMC. Methods Medical records were retrospectively reviewed (January 2016 to December 2021). Cats with an ultrasound diagnosis of PMC were included. Clinicopathologic results, imaging, treatment, and outcome were reviewed. Results All cats were male and 21 (80%) were diagnosed with urethral obstruction (UO). Five cats (23.8%) had positive urine culture (Staphylococcus felis, 3/5; Proteus mirabilis, 2/5) with a median urine pH of 8 (range, 6‐9). All cats had ultrasonographic changes suggestive of mineralization. On ultrasound examination, 10 cats (38.5%) had pseudomembranes with acoustic shadowing suggestive of mineralization, 15 (57.7%) had changes indicative of ulceration, and 8 (31%) had changes compatible with of a urachal anomaly. Twenty‐two cats received medical treatment, 4 underwent surgery (3 percutaneous cystolithotomy, 1 cystotomy). Twenty cats (77%) survived to discharge. Follow‐up ultrasound examination indicated resolution of PMC in 6/7 cats, 4 had persistent hyperechoic bladder lining. Five of 12 cats with follow‐up had a relapse of lower urinary tract signs. Conclusions and Clinical Importance Pseudomembranous cystitis was diagnosed mainly in male cats with UO and imaging findings suggestive of mineralization were present in all cases. Frequent negative urine culture suggests a different etiology than encrusting cystitis related to urease‐positive bacteria. Good outcomes can be achieved with medical management.

Abstract Background Traditional management of non‐steroidal anti‐inflammatory drug (NSAID) intoxication includes gastrointestinal decontamination, intravenous administration of fluids (IVF), and gastroprotection. Intravenous administration of lipid emulsion (ILE) and therapeutic plasma exchange (TPE) are popular novel therapeutic strategies. Hypothesis Compare outcomes of dogs treated with IVF, ILE, and TPE for NSAID intoxications and evaluate outcome predictors for drug subgroups. Animals Four hundred thirty‐four dogs with NSAID intoxications (2015‐2020). Methods Multicenter retrospective study of ibuprofen, carprofen, and naproxen intoxication. An ordinal outcome was defined as mild gastrointestinal, moderate kidney, or signs of severe central nervous system disease. Results Signs of neurological disease were overrepresented and acute kidney injury underrepresented in the TPE group among dogs exposed to kidney‐ or CNS‐toxic doses (P = .05), though all TPE dogs with signs of neurological disease had evidence of neurotoxicity at presentation. Dogs treated with IVF had a higher maximal creatinine concentration (median, 1.1 mg/dL; range, 0.4‐8.44 mg/dL) compared with IVF + ILE (median, 0.9 mg/dL; range, 0.4‐6.2 mg/dL; P = .01). Increased maximum time to presentation (P

Abstract Background Therapeutic plasma exchange (TPE) is gaining popularity for the management of nonsteroidal anti‐inflammatory drug (NSAID) overdose in dogs. Hypothesis/Objectives Describe a population of dogs treated with TPE for NSAID overdose. Animals Sixty‐two dogs with NSAID overdose treated with TPE. Methods Multicenter retrospective study of dogs treated with TPE for ibuprofen, carprofen, or naproxen overdose. Results The median dose of ibuprofen, carprofen or naproxen ingested was 533 mg/kg (range, 36‐4857 mg/kg), 217 mg/kg (range, 88‐625 mg/kg) and 138 mg/kg (range, 26‐3000 mg/kg), respectively. Based on previously established toxic ranges for each NSAID, 2 (3.2%), 14 (22.6%), and 46 (74.2%) dogs ingested a gastrointestinal, renal, and neurological toxic dose, respectively. The median time between ingestion and presentation was 4 hours (range, 1‐20 hours). The median number of plasma volumes processed was 1.6 (range, 0.4‐2.2). The median TPE session duration was 2 hours (range, 1‐4.5 hours). Circuit clotting developed during 8 (12.9%) sessions. Patient adverse events reported during 21 (33.8%) sessions consisted of urticaria (12.9%), asymptomatic hypocalcemia (9.6%), and hypotension (9.6%). The median duration of hospitalization was 2.25 days (range, 1‐11 days). Sixty‐one (98.4%) dogs survived to discharge, and none were rehospitalized. Thirty‐one (91.1%) of the 34 dogs with at least 1 follow‐up visit were not azotemic at the time of reevaluation. Conclusions and Clinical Importance This population of dogs managed with TPE had excellent outcomes, even in cases of high NSAID dose ingestion. When TPE is available and the time frame is appropriate, this extracorporeal modality should be considered for the management of NSAID overdose.

Upon invasion of Lewis rat macrophages, Toxoplasma rapidly induces programmed cell death (pyroptosis), which prevents Toxoplasma replication, possibly explaining the resistance of the Lewis rat to Toxoplasma Using a chemical mutagenesis screen, we identified Toxoplasma mutants that no longer induced pyroptosis. Whole-genome sequencing led to the identification of three Toxoplasma parasitophorous vacuole-localized dense granule proteins, GRA35, GRA42, and GRA43, that are individually required for induction of Lewis rat macrophage pyroptosis. Macrophage infection with Δgra35, Δgra42, and Δgra43 parasites led to greatly reduced cell death rates and enhanced parasite replication. Lewis rat macrophages infected with parasites containing a single, double, or triple deletion of these GRAs showed similar levels of cell viability, suggesting that the three GRAs function in the same pathway. Deletion of GRA42 or GRA43 resulted in GRA35 (and other GRAs) being retained inside the parasitophorous vacuole instead of being localized to the parasitophorous vacuole membrane. Despite having greatly enhanced replication in Lewis rat macrophages in vitro, Δgra35, Δgra42, and Δgra43 parasites did not establish a chronic infection in Lewis rats. Toxoplasma did not induce F344 rat macrophage pyroptosis, but F344 rats infected with Δgra35, Δgra42, and Δgra43 parasites had reduced cyst numbers. Thus, these GRAs determined parasite in vivo fitness in F344 rats. Overall, our data suggest that these three Toxoplasma dense granule proteins play a critical role in establishing a chronic infection in vivo, independently of their role in mediating macrophage pyroptosis, likely due to their importance in regulating protein localization to the parasitophorous vacuole membrane.IMPORTANCE Inflammasomes are major components of the innate immune system and are responsible for detecting various microbial and environmental danger signals. Upon invasion of Lewis rat macrophages, the parasite rapidly activates the NLRP1 inflammasome, resulting in pyroptosis and elimination of the parasite's replication niche. The work reported here revealed that Toxoplasma GRA35, GRA42, and GRA43 are required for induction of Lewis rat macrophage pyroptosis. GRA42 and GRA43 mediate the correct localization of other GRAs, including GRA35, to the parasitophorous vacuole membrane. These three GRAs were also found to be important for parasite in vivo fitness in a Toxoplasma-susceptible rat strain, independently of their role in NLRP1 inflammasome activation, suggesting that they perform other important functions. Thus, this study identified three GRAs that mediate the induction of Lewis rat macrophage pyroptosis and are required for pathogenesis of the parasite.

Abstract 210Po is a radioactive component of conventional cigarette tobacco smoke and is a recognized carcinogen. Despite the expanding market of heated tobacco products, no data are available on the activity of 210Po in the smoke of IQOS Heets cigarette. We determined the 210Po activity in the mainstream smoke of thirteen cigarette brands available on the Swiss market using a smoking machine and compared the results to the 210Po activity measured in the mainstream smoke of the IQOS system. In addition, we measured the 210Po and 210Pb loss on heating after uniform heating from 50 to 600 °C for several cigarette brands and the Heets cigarettes. 13.6 ± 4.1% of 210Po activity was found in the mainstream smoke in conventional cigarette smoking (7% for 210Pb). This dropped to 1.8 ± 0.3% in the mainstream smoke of IQOS Heets. Conversely, when the tobacco was heated uniformly at 330 °C, a loss of 210Po of more than 80% was observed for all type of cigarettes. Apparently, IQOS significantly reduced the 210Po and 210Pb activities in the mainstream smoke. However, our results show that only 15% of the Heets tobacco reaches 330 °C with IQOS. While IQOS reduces the 210Po and 210Pb activities in the mainstream smoke compared to conventional cigarettes, it only heats a marginal fraction of the tobacco present in the Heets cigarette. Because smoking is an addiction (mostly due to nicotine), IQOS could possibly deliver an unsatisfactory dose of nicotine to a Heets cigarette smoker, as most of the tobacco is left unaltered.

IntroductionDevelopment and validations of accurate mastitis diagnostics are crucial to make timely and evidence-based decisions on mastitis therapy in order to reduce its impact on productivity, animal welfare and practicing the prudent use of antimicrobials on dairy farms.MethodsThe objectives of this study were to assess the agreement between test results from reference laboratory and two point of care tests (Selma plus, Dipslide) and to estimate the test accuracies with Bayesian latent class models (BLCMs). In total of 509 single quarter milk samples from cows with mastitis were included in the study.ResultsAmong all analyzed mastitis pathogens, Streptococcus spp. was detected in up to one third of all analyzed samples and for Selma all Streptococcus samples were considered as Streptococcus uberis. The agreement (κ) when comparing two tests varied greatly depending on the bacteria, ranging from no agreement to good agreement (κ = negative to 0.86) depending on the prevalence of identified pathogens. Based on BLCMs to assess diagnostic test accuracies for the pathogen Streptococcus uberis, posterior sensitivities of 76, 71, and 64% for Selma plus, Dipslide and laboratory standard culture and specificities of 93%, 98% for Selma and Dipslide, respectively, were obtained.DiscussionThe two point of care rapid culture systems Dipslide and Selma plus plate can provide important preliminary pathogen identification for targeted mastitis therapy, especially when general information about growth and a rough classification of the bacteria into groups have an impact on treatment strategy. The two evaluated rapid culture systems, Dipslide and Selma plus plate, show good test accuracies for Streptococcus uberis at least at genus level. Therefore, using these tests may contribute to prudent use of antibiotics.

PURPOSE:Few studies have examined conventional catheter directed thrombolysis (CDT) for the treatment of submassive pulmonary embolism (PE). Moreover, angiographic resolution of thrombus burden following CDT has infrequently been characterized. This study describes a single-center experience treating submassive PE with CDT while utilizing repeat angiography to determine treatment efficacy.METHODS:A retrospective analysis of 140 consecutive patients who underwent CDT for submassive PE from December 2012 to June 2019 was performed. Angiographic resolution of thrombus burden after CDT was reported as high (>75%), moderate (51-75%), low (26-50%), or insignificant (≤25%). All angiograms were reviewed by two interventional radiologists. Secondary endpoints included reduction in pulmonary artery pressure (PAP) and clinical outcomes. Bleeding events were classified according to the Society of Interventional Radiology (SIR) adverse event criteria.RESULTS:CDT was performed in 140 patients with a mean rtPA dose of 25.3 mg and a mean treatment time of 26.0 hours. Angiographic resolution of thrombus burden was high in 70.0%, moderate in 19.3%, low in 5.7%, and insignificant in 3.6%; in 2 patients (1.4%) repeat angiography was not performed. Systolic PAP was reduced (47 vs. 35 mmHg, p < 0.001), mean PAP was reduced (25 vs 21 mmHg, p < 0.001), and 129 patients (92.1%) improved clinically. Patients with high or moderate resolution of thrombus burden had a clinical improvement rate of 95.2%, while patients with low or insignificant thrombus burden resolution had a clinical improvement rate of 76.9% (p=0.011). Ten patients (7.1%) had hemodynamic or respiratory decompensation requiring mechanical ventilation, systemic thrombolysis, cardiopulmonary resuscitation, or surgical intervention. Seven patients (5.0%) experienced moderate bleeding events and one patient (0.7%) with metastatic disease developed severe gastrointestinal bleeding that resulted in death. Thirty-day mortality was 1.4%.CONCLUSION:In patients with submassive PE undergoing CDT, angiographic resolution of thrombus burden is a safe and directly observable metric that can be used to determine procedural success. In this study, CDT with repeat angiography was associated with a 5.7% bleeding event rate and thirty-day mortality of 1.4%.

Human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CM) are a promising platform for cardiac studies in vitro, and possibly for tissue repair in humans. However, hiPSC-CM cells tend to retain morphology, metabolism, patterns of gene expression, and electrophysiology similar to that of embryonic cardiomyocytes. We grew hiPSC-CM in patterned islands of different sizes and shapes, and measured the effect of island geometry on action potential waveform and calcium dynamics using optical recordings of voltage and calcium from 970 islands of different sizes. hiPSC-CM in larger islands showed electrical and calcium dynamics indicative of greater functional maturity. We then compared transcriptional signatures of the small and large islands against a developmental time course of cardiac differentiation. Although island size had little effect on expression of most genes whose levels differed between hiPSC-CM and adult primary CM, we identified a subset of genes for which island size drove the majority (58%) of the changes associated with functional maturation. Finally, we patterned hiPSC-CM on islands with a variety of shapes to probe the relative contributions of soluble factors, electrical coupling, and direct cell-cell contacts to the functional maturation. Collectively, our data show that optical electrophysiology is a powerful tool for assaying hiPSC-CM maturation, and that island size powerfully drives activation of a subset of genes involved in cardiac maturation.

Objectives: We quantified adherence to COVID-19 preventive measures and explored associated factors, after the first and during the second Swiss epidemic waves.Methods: With an observational cohort study in a representative sample of individuals aged 15 years and more, we analysed the association between self-reported adherence to COVID-19 preventive measures (respect of simple hygiene rules; respect of social distancing rules; wearing a mask) and socio-demographic factors, the existence of a chronic disease, and the existence of a previous confirmed COVID-19 episode.Results: Highest adherence was to simple hygiene rules, followed by social distancing rules and mask wearing, with a slight decrease for simple hygiene rules and a strong increase for mask wearing between visits. Men were significantly less likely to respect simple hygiene rules and wear a mask in public. Participants aged 65 years and more (versus 25–64 years) and those with at least one chronic disease (versus none) were two times more likely to respect social distancing rules and wear a mask.Conclusion: Adherence to social distancing rules and mask wearing was rather poor, especially compared to other countries.

Abstract A 12 week‐old Nigerian dwarf (Capra aegagrus hircus) buck kid was hospitalized for management of obstructive urolithiasis. Postoperatively, he was inadvertently administered 16‐times greater than his calculated dose of a nonsteroidal anti‐inflammatory drug (NSAID; 17.5 mg/kg flunixin meglumine, IV). The goat was treated with intravenous administration of lipid emulsion (ILE) prior to membrane‐based therapeutic plasma exchange (mTPE) under general anesthesia. The increased coagulability inherent to small ruminants in comparison with dogs and cats warranted specific adjustments in the prescription of anticoagulation, blood flow, and filtration fraction to avoid circuit clotting during mTPE. Serum flunixin meglumine concentration measured before, during, and after mTPE revealed marked reduction in drug concentration. After the combined treatments, no clinical evidence of NSAID gastrointestinal or renal toxicosis was detected. This case report describes successful management of flunixin meglumine overdose in a small ruminant using combined ILE and mTPE.

Abstract A 3‐year‐old spayed female English Springer Spaniel was presented twice 4 months apart for investigation of hematuria and pollakiuria without urinary tract infection. Both ultrasound examinations identified a stable craniodorsal bladder wall thickening. The first cystoscopic biopsy samples indicated lymphoplasmacytic cystitis and the second polypoid cystitis. The dog was represented 8 months later for recurrent clinical signs despite medical management. Although the ultrasound examination showed stable disease, repeat cystoscopic biopsy identified transitional cell carcinoma (TCC), confirmed on tissue removed by partial cystectomy. No BRAF mutation was ever detected in urine or tissue samples. To our knowledge, this case represents the first report of presumptive malignant transformation of polypoid cystitis into an apical TCC in a dog. Dogs with polypoid cystitis should be followed closely and surgical management considered if rapid resolution is not achieved with medical management.

Abstract Background In patients with atopic dermatitis (AD), Staphylococcus aureus frequently colonizes lesions and is hypothesized to be linked to disease severity and progression. Treatments that reduce S. aureus colonization without significantly affecting the skin commensal microbiota are needed. Methods and findings In this study, we tested ATx201 (niclosamide), a small molecule, on its efficacy to reduce S. aureus and propensity to evolve resistance in vitro. Various cutaneous formulations were then tested in a superficial skin infection model. Finally, a Phase 2 randomized, double‐blind and placebo‐controlled trial was performed to investigate the impact of ATx201 OINTMENT 2% on S. aureus colonization and skin microbiome composition in patients with mild‐to‐severe AD (EudraCT:2016‐003501‐33). ATx201 has a narrow minimal inhibitory concentration distribution (.125–.5 μg/ml) consistent with its mode of action – targeting the proton motive force effectively stopping cell growth. In murine models, ATx201 can effectively treat superficial skin infections of methicillin‐resistant S. aureus. In a Phase 2 trial in patients with mild‐to‐severe AD (N = 36), twice‐daily treatment with ATx201 OINTMENT 2% effectively reduces S. aureus colonization in quantitative colony forming unit (CFU) analysis (primary endpoint: 94.4% active vs. 38.9% vehicle success rate, p = .0016) and increases the Shannon diversity of the skin microbiome at day 7 significantly compared to vehicle. Conclusion These results suggest that ATx201 could become a new treatment modality as a decolonizing agent.

Aortic root aneurysm is a common cause of morbidity and mortality in Loeys-Dietz and Marfan syndromes, where perturbations in transforming growth factor beta (TGFβ) signaling play a causal or contributory role, respectively. Despite the advantages of cross-species disease modeling, animal models of aortic root aneurysm are largely restricted to genetically engineered mice. Here, we report that zebrafish devoid of the genes encoding latent-transforming growth factor beta-binding protein 1 and 3 (ltbp1 and ltbp3, respectively) develop rapid and severe aneurysm of the outflow tract (OFT), the aortic root equivalent. Similar to syndromic aneurysm tissue, the distended OFTs display evidence for paradoxical hyperactivated TGFβ signaling. RNA-sequencing revealed significant overlap between the molecular signatures of disease tissue from mutant zebrafish and a mouse model of Marfan syndrome. Moreover, chemical inhibition of TGFβ signaling in wild-type animals phenocopied mutants but chemical activation did not, demonstrating that TGFβ signaling is protective against aneurysm. Human relevance is supported by recent studies implicating genetic lesions in LTBP3 and, potentially, LTBP1 as heritable causes of aortic root aneurysm. Ultimately, our data demonstrate that zebrafish can now be leveraged to interrogate thoracic aneurysmal disease and identify novel lead compounds through small-molecule suppressor screens. This article has an associated First Person interview with the first author of the paper.

The sequence space accessible to evolving proteins can be enhanced by cellular chaperones that assist biophysically defective clients in navigating complex folding landscapes. It is also possible, at least in theory, for proteostasis mechanisms that promote strict quality control to greatly constrain accessible protein sequence space. Unfortunately, most efforts to understand how proteostasis mechanisms influence evolution rely on artificial inhibition or genetic knockdown of specific chaperones. The few experiments that perturb quality control pathways also generally modulate the levels of only individual quality control factors. Here, we use chemical genetic strategies to tune proteostasis networks via natural stress response pathways that regulate the levels of entire suites of chaperones and quality control mechanisms. Specifically, we upregulate the unfolded protein response (UPR) to test the hypothesis that the host endoplasmic reticulum (ER) proteostasis network shapes the sequence space accessible to human immunodeficiency virus-1 (HIV-1) envelope (Env) protein. Elucidating factors that enhance or constrain Env sequence space is critical because Env evolves extremely rapidly, yielding HIV strains with antibody- and drug-escape mutations. We find that UPR-mediated upregulation of ER proteostasis factors, particularly those controlled by the IRE1-XBP1s UPR arm, globally reduces Env mutational tolerance. Conserved, functionally important Env regions exhibit the largest decreases in mutational tolerance upon XBP1s induction. Our data indicate that this phenomenon likely reflects strict quality control endowed by XBP1s-mediated remodeling of the ER proteostasis environment. Intriguingly, and in contrast, specific regions of Env, including regions targeted by broadly neutralizing antibodies, display enhanced mutational tolerance when XBP1s is induced, hinting at a role for host proteostasis network hijacking in potentiating antibody escape. These observations reveal a key function for proteostasis networks in decreasing instead of expanding the sequence space accessible to client proteins, while also demonstrating that the host ER proteostasis network profoundly shapes the mutational tolerance of Env in ways that could have important consequences for HIV adaptation.

Macrophages display flexible activation states that range between pro-inflammatory (classical activation) and anti-inflammatory (alternative activation). These macrophage polarization states contribute to a variety of organismal phenotypes such as tissue remodeling and susceptibility to infectious and inflammatory diseases. Several macrophage- or immune-related genes have been shown to modulate infectious and inflammatory disease pathogenesis. However, the potential role that differences in macrophage activation phenotypes play in modulating differences in susceptibility to infectious and inflammatory disease is just emerging. We integrated transcriptional profiling and linkage analyses to determine the genetic basis for the differential murine macrophage response to inflammatory stimuli and to infection with the obligate intracellular parasite Toxoplasma gondii. We show that specific transcriptional programs, defined by distinct genomic loci, modulate macrophage activation phenotypes. In addition, we show that the difference between AJ and C57BL/6J macrophages in controlling Toxoplasma growth after stimulation with interferon gamma and tumor necrosis factor alpha mapped to chromosome 3, proximal to the Guanylate binding protein (Gbp) locus that is known to modulate the murine macrophage response to Toxoplasma. Using an shRNA-knockdown strategy, we show that the transcript levels of an RNA helicase, Ddx1, regulates strain differences in the amount of nitric oxide produced by macrophage after stimulation with interferon gamma and tumor necrosis factor. Our results provide a template for discovering candidate genes that modulate macrophage-mediated complex traits.

Alternative splicing and mRNA editing are known to contribute to transcriptome diversity. Although alternative splicing is pervasive and contributes to a variety of pathologies, including cancer, the genetic context for individual differences in isoform usage is still evolving. Similarly, although mRNA editing is ubiquitous and associated with important biological processes such as intracellular viral replication and cancer development, individual variations in mRNA editing and the genetic transmissibility of mRNA editing are equivocal. Here, we have used linkage analysis to show that both mRNA editing and alternative splicing are regulated by the macrophage genetic background and environmental cues. We show that distinct loci, potentially harboring variable splice factors, regulate the splicing of multiple transcripts. Additionally, we show that individual genetic variability at the Apobec1 locus results in differential rates of C-to-U(T) editing in murine macrophages; with mouse strains expressing mostly a truncated alternative transcript isoform of Apobec1 exhibiting lower rates of editing. As a proof of concept, we have used linkage analysis to identify 36 high-confidence novel edited sites. These results provide a novel and complementary method that can be used to identify C-to-U editing sites in individuals segregating at specific loci and show that, beyond DNA sequence and structural changes, differential isoform usage and mRNA editing can contribute to intra-species genomic and phenotypic diversity.

Most isolates of Toxoplasma from Europe and North America fall into one of three genetically distinct clonal lineages, the type I, II and III lineages. However, in South America these strains are rarely isolated and instead a great variety of other strains are found. T. gondii strains differ widely in a number of phenotypes in mice, such as virulence, persistence, oral infectivity, migratory capacity, induction of cytokine expression and modulation of host gene expression. The outcome of toxoplasmosis in patients is also variable and we hypothesize that, besides host and environmental factors, the genotype of the parasite strain plays a major role. The molecular basis for these differences in pathogenesis, especially in strains other than the clonal lineages, remains largely unexplored. Macrophages play an essential role in the early immune response against T. gondii and are also the cell type preferentially infected in vivo. To determine if non-canonical Toxoplasma strains have unique interactions with the host cell, we infected murine macrophages with 29 different Toxoplasma strains, representing global diversity, and used RNA-sequencing to determine host and parasite transcriptomes. We identified large differences between strains in the expression level of known parasite effectors and large chromosomal structural variation in some strains. We also identified novel strain-specifically regulated host pathways, including the regulation of the type I interferon response by some atypical strains. IFNβ production by infected cells was associated with parasite killing, independent of interferon gamma activation, and dependent on endosomal Toll-like receptors in macrophages and the cytoplasmic receptor retinoic acid-inducible gene 1 (RIG-I) in fibroblasts.

Summary: To gain insights into the molecular mechanisms and pathways involved in the activation of γ-herpesvirus (MHV68)-specific T cell receptor transnuclear (TN) CD8+ T cells, we performed a comprehensive transcriptomic analysis. Upon viral infection, we observed differential expression of several thousand transcripts encompassing various networks and pathways in activated TN cells compared with their naive counterparts. Activated cells highly upregulated galectin-3. We therefore explored the role of galectin-3 in influencing anti-MHV68 immunity. Galectin-3 was recruited at the immunological synapse during activation of CD8+ T cells and helped constrain their activation. The localization of galectin-3 to immune synapse was evident during the activation of both naive and memory CD8+ T cells. Galectin-3 knockout mice mounted a stronger MHV68-specific CD8+ T cell response to the majority of viral epitopes and led to better viral control. Targeting intracellular galectin-3 in CD8+ T cells may therefore serve to enhance response to efficiently control infections. : Immune Response; Immunology; Transcriptomics; Virology Subject Areas: Immune Response, Immunology, Transcriptomics, Virology

Abstract Background Ribosomal RNA (rRNA) comprises at least 90% of total RNA extracted from mammalian tissue or cell line samples. Informative transcriptional profiling using massively parallel sequencing technologies requires either enrichment of mature poly-adenylated transcripts or targeted depletion of the rRNA fraction. The latter method is of particular interest because it is compatible with degraded samples such as those extracted from FFPE and also captures transcripts that are not poly-adenylated such as some non-coding RNAs. Here we provide a cross-site study that evaluates the performance of ribosomal RNA removal kits from Illumina, Takara/Clontech, Kapa Biosystems, Lexogen, New England Biolabs and Qiagen on intact and degraded RNA samples. Results We find that all of the kits are capable of performing significant ribosomal depletion, though there are differences in their ease of use. All kits were able to remove ribosomal RNA to below 20% with intact RNA and identify ~ 14,000 protein coding genes from the Universal Human Reference RNA sample at >1FPKM. Analysis of differentially detected genes between kits suggests that transcript length may be a key factor in library production efficiency. Conclusions These results provide a roadmap for labs on the strengths of each of these methods and how best to utilize them.