Non-intubated bronchoscopic tracheobronchial surgeries with electroencephalogram-monitored intravenous anesthesia: feasibility and outcomes.

Background: Anesthesia remains challenging for bronchoscopic tracheobronchial surgeries (BTS) involving surgical manipulations for central airway obstruction within shared airways. To provide complete airway use through intervention with spontaneous breathing without endotracheal tubes, monitored non-intubated anesthesia has been successfully applied with electroencephalogram-derived monitored total intravenous anesthesia. This study evaluated the feasibility and the outcomes of BTS with monitored non-intubated anesthesia. The factors associated with desaturation and complications were also analyzed. Methods: Data from patients receiving non-intubated BTS performed between October 2019 and August 2022 were retrospectively collected. Intraoperative results and postoperative outcomes were analyzed. Results: Data of 92 patients were collected. Supraglottic airways devices and high-flow nasal oxygen were used in 68 and 24 patients respectively. Surgery was successfully completed in 87 patients (94.6%), whereas three patients required conversion to intubation because of substantial bleeding. In total, 11% of patients experienced desaturation [oxygen saturation (SpO2) <90%] for an average of 9 minutes. Unexpected admission to the intensive care unit (ICU) occurred in 12.2% (5/41) of patients from outpatient department and 7.8% (4/51) of hospitalization settings because of high-grade surgical bleeding. With comparable desaturation incidence, tracheal surgery had significantly longer desaturation times (14.5±6.9 min) than bronchial surgeries (5.8±2.6 min) did. Conclusions: Monitored non-intubated anesthesia with spontaneous breathing is feasible for BTS, with high success rate, few complications, and rapid recovery. High-grade bleeding remains the most unpredictable risk for intraoperative desaturation and postoperative ICU admission, especially in tracheal obstruction cases.

TransEBUS: The interpretation of endobronchial ultrasound image using hybrid transformer for differentiating malignant and benign mediastinal lesions.

The purpose of this study is to establish a deep learning automatic assistance diagnosis system for benign and malignant classification of mediastinal lesions in endobronchial ultrasound (EBUS) images. EBUS images are in the form of video and contain multiple imaging modes. Different imaging modes and different frames can reflect the different characteristics of lesions. Compared with previous studies, the proposed model can efficiently extract and integrate the spatiotemporal relationships between different modes and does not require manual selection of representative frames. In recent years, Vision Transformer has received much attention in the field of computer vision. Combined with convolutional neural networks, hybrid transformers can also perform well on small datasets. This study designed a novel deep learning architecture based on hybrid transformer called TransEBUS. By adding learnable parameters in the temporal dimension, TransEBUS was able to extract spatiotemporal features from insufficient data. In addition, we designed a two-stream module to integrate information from three different imaging modes of EBUS. Furthermore, we applied contrastive learning when training TransEBUS, enabling it to learn discriminative representation of benign and malignant mediastinal lesions. The results show that TransEBUS achieved a diagnostic accuracy of 82% and an area under the curve of 0.8812 in the test dataset, outperforming other methods. It also shows that several models can improve performance by incorporating two-stream module. Our proposed system has shown its potential to help physicians distinguishing benign and malignant mediastinal lesions, thereby ensuring the accuracy of EBUS examination.

Cryptosporidium-induced acute kidney injury in a patient with acquired immunodeficiency syndrome.

Cryptosporidium is a pathogen that can cause infectious enteritis especially in immunocompromised patients. Acute kidney injury, electrolyte imbalance, and acid-base disorders may occur as a result of high volumes of intestinal fluid loss, which has not been previously reported to be a common manifestation of cryptosporidiosis. Numerous antigen detection methods can be used to ensure early diagnosis of Cryptosporidium infection, which is crucial to prevent morbidities. We report a unique case of cryptosporidiosis in a 33-year-old male patient with acute kidney injury and profound hypokalemia, hyponatremia, hypocalcemia, hypophosphatemia, hypomagnesemia, and metabolic acidosis. Following the initiation of antiretroviral therapy to human immunodeficiency virus, the patient's symptoms improved and he recovered fully from kidney injury and electrolyte imbalance, highlighting the importance of early antiretroviral therapy.

Using cryoprobes of different sizes combined with cone-beam computed tomography-derived augmented fluoroscopy and endobronchial ultrasound to diagnose peripheral pulmonary lesions: a propensity-matched study.

BACKGROUND: Endobronchial ultrasound (EBUS) and cone-beam computed tomography-derived augmented fluoroscopy (CBCT-AF) are utilized for the diagnosis of peripheral pulmonary lesions (PPLs). Combining them with transbronchial cryobiopsy (TBC) can provide sufficient tissue for genetic analysis. However, cryoprobes of different sizes have varying degrees of flexibility, which can affect their ability to access the target bronchus and potentially impact the accuracy. The aim of this study was to compare the diagnostic efficacy of cryoprobes of varying sizes in CBCT-AF and EBUS for the diagnosis of PPLs. METHODS: Patients who underwent endobronchial ultrasound-guided transbronchial biopsy (EBUS-TBB) and TBC combined with CBCT-AF for PPLs diagnosis between January 2021 and May 2022 were included. Propensity score matching and competing-risks regression were utilized for data analysis. Primary outcome was the diagnostic accuracy of TBC. RESULTS: A total of 284 patients underwent TBC, with 172 using a 1.7-mm cryoprobe (1.7 group) and 112 using a 1.1-mm cryoprobe (1.1 group). Finally, we included 99 paired patients following propensity score matching. The diagnostic accuracy of TBC was higher in the 1.1 group (80.8% vs. 69.7%, P = 0.050), with a similar rate of complications. Subgroup analysis also revealed that the 1.1 group had better accuracy when PPLs were located in the upper lobe (85.2% vs. 66.1%, P = 0.020), when PPLs were smaller than 20 mm (78.8% vs. 48.8%, P = 0.008), and when intra-procedural CBCT was needed to be used (79.5% vs. 42.3%, P = 0.001). TBC obtained larger specimens than TBB in both groups. There is still a trend of larger sample size obtained in the 1.7 group, but there is no statistically different between our two study groups (40.8 mm2 vs. 22.0 mm2, P = 0.283). CONCLUSIONS: The combination of TBC with CBCT-AF and EBUS is effective in diagnosing PPLs, and a thin cryoprobe is preferred when the PPLs located in difficult areas.

Trends and Age-Period-Cohort Effect on Incidence of Male Breast Cancer from 1980 to 2019 in Taiwan and the USA.

Although male breast cancer (MBC) is globally rare, its incidence significantly increased from 1990 to 2017. The aim of this study was to examine variations in the trends of MBC incidence between populations in Taiwan and the USA from 1980 to 2019. The Taiwan Cancer Registry database and the Surveillance, Epidemiology, and End Results (SEER) Program of the National Cancer Institute of the USA were used. The age-standardized incidence rate was calculated using the world standard population in 2000. The long-term trends of the age, time period, and birth cohort effect on MBC incidence rates were estimated using the SEER Age-Period-Cohort Web Tool. The results revealed that the incidence of MBC in both countries increased from 2010 to 2019 (Taiwan: average annual percentage change (AAPC) = 2.59%; USA: AAPC = 0.64%). The age and period effects on the incidence rates in both countries strengthened, but the cohort effect was only identified in Taiwan (Rate ratio: 4.03). The identified cohort effect in this study bears resemblance to that noted in a previous investigation on female breast cancer in Taiwan. This suggests the possible presence of common environmental factors influencing breast cancer incidence in both genders, such as a high fat diet and xenoestrogen.

Effects of colonization-associated gene yqiC on global transcriptome, cellular respiration, and oxidative stress in Salmonella Typhimurium.

BACKGROUND: yqiC is required for colonizing the Salmonella enterica serovar Typhimurium (S. Typhimurium) in human cells; however, how yqiC regulates nontyphoidal Salmonella (NTS) genes to influence bacteria-host interactions remains unclear. METHODS: The global transcriptomes of S. Typhimurium yqiC-deleted mutant (ΔyqiC) and its wild-type strain SL1344 after 2 h of in vitro infection with Caco-2 cells were obtained through RNA sequencing to conduct comparisons and identify major yqiC-regulated genes, particularly those involved in Salmonella pathogenicity islands (SPIs), ubiquinone and menaquinone biosynthesis, electron transportation chains (ETCs), and carbohydrate/energy metabolism. A Seahorse XFp Analyzer and assays of NADH/NAD+ and H2O2 were used to compare oxygen consumption and extracellular acidification, glycolysis parameters, adenosine triphosphate (ATP) generation, NADH/NAD+ ratios, and H2O2 production between ΔyqiC and SL1344. RESULTS: After S. Typhimurium interacts with Caco-2 cells, yqiC represses gene upregulation in aspartate carbamoyl transferase, type 1 fimbriae, and iron-sulfur assembly, and it is required for expressing ilvB operon, flagellin, tdcABCD, and dmsAB. Furthermore, yqiC is required for expressing mainly SPI-1 genes and specific SPI-4, SPI-5, and SPI-6 genes; however, it diversely regulates SPI-2 and SPI-3 gene expression. yqiC significantly contributes to menD expression in menaquinone biosynthesis. A Kyoto Encyclopedia of Genes and Genomes analysis revealed the extensive association of yqiC with carbohydrate and energy metabolism. yqiC contributes to ATP generation, and the analyzer results demonstrate that yqiC is required for maintaining cellular respiration and metabolic potential under energy stress and for achieving glycolysis, glycolytic capacity, and glycolytic reserve. yqiC is also required for expressing ndh, cydA, nuoE, and sdhB but suppresses cyoC upregulation in the ETC of aerobically and anaerobically grown S. Typhimurium; priming with Caco-2 cells caused a reversed regulation of yiqC toward upregulation in these ETC complex genes. Furthermore, yqiC is required for maintaining NADH/NAD+ redox status and H2O2 production. CONCLUSIONS: Specific unreported genes that were considerably regulated by the colonization-associated gene yqiC in NTS were identified, and the key role and tentative mechanisms of yqiC in the extensive modulation of virulence factors, SPIs, ubiquinone and menaquinone biosynthesis, ETCs, glycolysis, and oxidative stress were discovered.

Effectiveness of Endobronchial Ultrasound-Guided Transbronchial Biopsy Combined With Tissue Culture for the Diagnosis of Sputum Smear-Negative Pulmonary Tuberculosis.

Background: Microorganisms of tuberculosis (TB) are frequently difficult to identify from the airway specimen; therefore, lung biopsy for further histologic and microbiologic study is required. Endobronchial ultrasound-guided transbronchial biopsy (EBUS-TBB) is used for the diagnosis of pulmonary malignancy, but is rarely in the TB population. The purpose of this study was to verify the effectiveness and safety of EBUS-TBB with histologic study and tissue culture in the diagnosis of sputum smear-negative pulmonary TB. Methods: Patients who underwent EBUS-TBB with histologic study and TB tissue culture for clinically suspected, but sputum smear-negative pulmonary TB from January 2016 to December 2018, were included. The accuracy of each diagnostic modality was calculated, respectively. Factors that might influence the positive rate of TB culture (washing fluid and tissue specimen) were also evaluated. Results: One hundred sixty-one patients who underwent EBUS-TBB for clinically suspected, but sputum smear-negative pulmonary TB, were enrolled, and 43 of them were finally diagnosed as having pulmonary TB. The sensitivity of washing fluid (a combination of smear, culture, and polymerase chain reaction for TB) and tissue specimen (a combination of pathology and tissue culture) via EBUS-TBB for TB diagnosis were 48.8 and 55.8%, respectively. The sensitivity for TB diagnosis would be elevated to 67.4% when both washing fluid and tissue specimens are used. The positive TB culture rate would not statistically increase with a combination of tissue specimens and washing fluid. Univariate analysis revealed that TB microorganisms would be more easily cultivated when lesions had an abscess or cavity on the computed tomography (CT) image (presence vs. absence; 62.5 vs. 26.3%, p = 0.022), heterogeneous echogenicity on the EBUS finding (heterogeneous vs. homogeneous; 93.3 vs. 21.4%, p = 0.001), or a necrotic pattern via histologic study (presence vs. absence; 70.6 vs. 30.8%, p = 0.013). Heterogeneous echogenicity in the EBUS finding was the independent predictor according to the results of multivariate analysis. None of our patients encountered major adverse events or received further intensive care after EBUS-TBB. Conclusion: Endobronchial ultrasound-guided transbronchial biopsy is safe and effective for use in diagnosing sputum smear-negative pulmonary TB. EBUS echoic feature is also a predictor of the positive TB culture rate in pulmonary TB. However, tissue culture via EBUS-TBB has little effect in improving the positive TB culture rate.

ICTV Virus Taxonomy Profile: Retroviridae 2021.

Viruses in the family Retroviridae are found in a wide variety of vertebrate hosts. Enveloped virions are 80-100 nm in diameter with an inner core containing the viral genome and replicative enzymes. Core morphology is often characteristic for viruses within the same genus. Replication involves reverse transcription and integration into host cell DNA, resulting in a provirus. Integration into germline cells can result in a heritable provirus known as an endogenous retrovirus. This is a summary of the International Committee on Taxonomy of Viruses (ICTV) Report on the family Retroviridae, which is available at ictv.global/report/retroviridae.

Cone-Beam Computed Tomography-Derived Augmented Fluoroscopy Improves the Diagnostic Yield of Endobronchial Ultrasound-Guided Transbronchial Biopsy for Peripheral Pulmonary Lesions.

BACKGROUND: Endobronchial ultrasound-guided transbronchial biopsy (EBUS-TBB) is used for the diagnosis of peripheral pulmonary lesions (PPLs), but the diagnostic yield is not adequate. Cone-beam computed tomography-derived augmented fluoroscopy (CBCT-AF) can be utilized to assess the location of PPLs and biopsy devices, and has the potential to improve the diagnostic accuracy of bronchoscopic techniques. The purpose of this study was to verify the contribution of CBCT-AF to EBUS-TBB. METHODS: Patients who underwent EBUS-TBB for diagnosis of PPLs were enrolled. The navigation success rate and diagnostic yield were used to evaluate the effectiveness of CBCT-AF in EBUS-TBB. RESULTS: In this study, 236 patients who underwent EBUS-TBB for PPL diagnosis were enrolled. One hundred fifteen patients were in CBCT-AF group and 121 were in non-AF group. The navigation success rate was significantly higher in the CBCT-AF group (96.5% vs. 86.8%, p = 0.006). The diagnostic yield was even better in the CBCT-AF group when the target lesion was small in size (68.8% vs. 0%, p = 0.026 for lesions ≤10 mm and 77.5% vs. 46.4%, p = 0.016 for lesions 10-20 mm, respectively). The diagnostic yield of the two study groups became similar when the procedures with a failure of navigation were excluded. The procedure-related complication rate was similar between the two study groups. CONCLUSION: CBCT-AF is safe, and effectively enhances the navigation success rate, thereby increasing the diagnostic yield of EBUS-TBB for PPLs.

Anorexia nervosa manifesting as massive ascites, hypercholesterolemia, and sequential binge eating in an 11-year-old girl: A case report.

RATIONALE: Anorexia nervosa (AN) is a serious eating disorder associated with a distorted body image. Hypercholesterolemia has been found in patients with AN but the mechanism of hyperlipidemia in AN remains little known. Ascites in patients with AN has been attributed to hypoalbuminemia and liver diseases, but massive ascites without the aforementioned etiologies has never been reported in AN. PATIENT CONCERNS: An 11-year-old girl was admitted for exclusion of organic underlying diseases due to severe body weight loss (18% within 3 weeks), poor appetite, and hypercholesterolemia (274 mg/dL). She complained of heartburn sensation, nausea, vomiting, constipation, and postprandial dull abdominal pain with fullness. DIAGNOSES: The patient's condition met with all 3 of the Diagnostic and Statistical Manual of Mental Disorders (DSM-5) criteria for diagnosing AN. On admission, her total cholesterol level was 337 mg/dL and hypocomplementemia (C3 55.5 mg/dL) was also found. Abdominal sonography and computed tomography scans showed massive ascites. However, neither proteinuria nor hypoalbuminemia was found. Upper gastroduodenal endoscopy showed chronic superficial gastritis and colonoscopy revealed negative findings. Ascites obtained by paracentesis demonstrated a transudate without bacterial infection, tuberculosis, or pancreatitis. Exploratory laparoscopy showed nonpurulent ascites. However, biopsies from the small intestine, mesentery, and liver showed chronic inflammation and fibrosis. INTERVENTIONS: The intensive nutritional therapy by increasing total energy intake stepwise with a combination of high-energy formula and her favorite foods. OUTCOMES: Her hypercholesterolemia, hypocomplementemia, and massive ascites resolved after her weight was restored. She developed binge eating with continuous weight gain after discharge. Her weight significantly increased to an obese level (body mass index [BMI] 25.9 kg/m) after loss to follow-up for 4 years until she returned to our emergency room due to suicide attempt. CONCLUSION: Diagnostic crossover between subtypes in anorexia nervosa might be a potential risk factor for illness severity and poor prognosis. AN can manifest as massive ascites with normal albumin concentrations that could possibly be due to chronic inflammation of the intestinal serosa, mesentery, and peritoneal surface of the liver.

Rapid on-site cytologic evaluation by pulmonologist improved diagnostic accuracy of endobronchial ultrasound-guided transbronchial biopsy.

BACKGROUND/PURPOSE: Rapid on-site cytologic evaluation (ROSE) has been shown to improve the diagnostic accuracy of endobronchial ultrasound-guided transbronchial biopsy (EBUS-TBB). However, ROSE by a cytopathologist or cytotechnologist is not always available during the procedure. The purposes of this study were to verify that a pulmonologist, after receiving training in cytology, could accurately assess an EBUS-TBB specimen on-site, and to evaluate the contribution of ROSE to EBUS-TBB. METHODS: A retrospective chart review of patients who underwent EBUS-TBB for diagnosis of peripheral pulmonary lesions (PPLs) from January 2014 to June 2017 was performed. PPLs without a malignant diagnosis were excluded. The ROSE result determined by a pulmonologist was compared to the formal imprint cytologic report and pathologic report. The diagnostic accuracy of EBUS-TBB was also compared between those with and without ROSE. RESULTS: Two hundred ninety-three patients who underwent 336 EBUS-TBB procedures for PPL diagnosis and were found to have proven malignancy were enrolled. Eighty-six procedures were performed with ROSE. With the formal imprint cytologic diagnosis as the standard, ROSE had 96.9% sensitivity, 68.2% specificity, 89.9% positive predictive value (PPV), 88.2% negative predictive value (NPV), and 89.5% diagnostic accuracy. With the formal pathologic result as the standard, ROSE had 88.2% sensitivity, 80% specificity, 97.1% PPV, 47.1% NPV, and 87.2% diagnostic accuracy, respectively. The diagnostic accuracy was significantly higher when ROSE was performed during EBUS-TBB (88.4% vs 68.0%, P < 0.001). CONCLUSION: A trained pulmonologist can interpret adequately cytologic smears on-site and effectively improve the accuracy of EBUS-TBB in the diagnosis of PPLs.

Differentiating malignant and benign lymph nodes using endobronchial ultrasound elastography.

BACKGROUND/PURPOSE: Endobronchial ultrasound (EBUS) elastography is a new technique that provides information on tissue compressibility during endobronchial ultrasound-guided transbronchial needle aspiration (EBUS-TBNA). The purposes of this study were to evaluate the utility of EBUS elastography in differentiating malignant and benign mediastinal lymph nodes (LNs) and to explore the factors that influence its accuracy. METHODS: A retrospective chart review of patients who underwent EBUS-TBNA from October 2016 to July 2017 was performed. EBUS with conventional B-mode features and elastographic patterns were compared with the final pathology results or clinical follow-up. We used the following EBUS elastographic patterns for classification: type 1, predominantly non-blue (green, yellow and red); type 2, part blue, part non-blue; type 3, predominantly blue. The potential impacts of the characteristics of LNs, the underlying lung diseases and obtaining fibrotic components from EBUS-TBNA specimens were evaluated relative to the accuracy of EBUS elastography. RESULTS: A total of 206 LNs from 94 patients were retrospectively evaluated. In classifying type 1 as 'benign' and type 3 as 'malignant,' the sensitivity, specificity, positive predictive value, negative predictive value and diagnostic accuracy rate were 90.6, 82.6, 71.6, 94.7 and 85.2%, respectively. The EBUS elastographic patterns had higher diagnostic yields and negative predictive values than conventional B-mode features. Logistic regression analysis revealed that central necrosis was a factor that influenced the accuracy of elastography in malignant LNs. The fibrotic component within benign LNs could cause an incorrect elastographic pattern. CONCLUSION: EBUS elastography is a valuable tool in discriminating benign and malignant mediastinal LNs.

Nomenclature for endogenous retrovirus (ERV) loci.

Retroviral integration into germline DNA can result in the formation of a vertically inherited proviral sequence called an endogenous retrovirus (ERV). Over the course of their evolution, vertebrate genomes have accumulated many thousands of ERV loci. These sequences provide useful retrospective information about ancient retroviruses, and have also played an important role in shaping the evolution of vertebrate genomes. There is an immediate need for a unified system of nomenclature for ERV loci, not only to assist genome annotation, but also to facilitate research on ERVs and their impact on genome biology and evolution. In this review, we examine how ERV nomenclatures have developed, and consider the possibilities for the implementation of a systematic approach for naming ERV loci. We propose that such a nomenclature should not only provide unique identifiers for individual loci, but also denote orthologous relationships between ERVs in different species. In addition, we propose that-where possible-mnemonic links to previous, well-established names for ERV loci and groups should be retained. We show how this approach can be applied and integrated into existing taxonomic and nomenclature schemes for retroviruses, ERVs and transposable elements.

Differentiating metastatic lymph nodes in lung cancer patients based on endobronchial ultrasonography features.

AIM: The aim of this study was to identify easy and relatively effective ultrasound criteria for metastatic mediastinal lymph node prediction. MATERIALS AND METHODS: A retrospective chart review of patients who underwent endobronchial ultrasound-guided transbronchial needle aspiration (EBUS-TBNA) from March 2014 to September 2016 was performed. We used the following EBUS sonographic features for metastatic lymph node prediction: 1) length of the short axis, 2) shape, 3) margin, 4) echogenicity, 5) central hilar structure, and 6) coagulation necrosis sign. These sonographic findings were compared with the final pathology results or clinical follow-up. RESULTS: A total of 227 lymph nodes were retrospectively evaluated in 133 lung cancer patients; 72% of the lymph nodes had been proven to be malignant metastasis. Logistic regression analysis revealed that the length of the short axis, shape, margin, and echogenicity were independent predictive factors for metastasis. We developed a sum score based on these four sonographic features. A larger sum score trended toward a greater possibility of malignancy. If all four predictive factors were preserved, the diagnostic accuracy, the value of the specificity and the positive predictive value of the sonographic feature would be higher than 90%. CONCLUSIONS: The sonographic features of EBUS are valuable tools in predicting metastatic lymph nodes in lung cancer patients.

Highly efficient cellular cloning using Ferro-core Micropallet Arrays.

Advancing knowledge of biological mechanisms has come to depend upon genetic manipulation of cells and organisms, relying upon cellular cloning methods that remain unchanged for decades, are labor and time intensive, often taking many months to come to fruition. Thus, there is a pressing need for more efficient processes. We have adapted a newly developed micropallet array platform, termed the "ferro-core micropallet array", to dramatically improve and accelerate the process of isolating clonal populations of adherent cells from heterogeneous mixtures retaining the flexibility of employing a wide range of cytometric parameters for identifying colonies and cells of interest. Using transfected (retroviral oncogene or fluorescent reporter construct) rat 208 F cells, we demonstrated the capacity to isolate and expand pure populations of genetically manipulated cells via laser release and magnetic recovery of single micropallets carrying adherent microcolonies derived from single cells. This platform can be broadly applied to biological research, across the spectrum of molecular biology to cellular biology, involving fields such as cancer, developmental, and stem cell biology. The ferro-core micropallet array platform provides significant advantages over alternative sorting and cloning methods by eliminating the necessity for repetitive purification steps and increasing throughput by dramatically shortening the time to obtain clonally expanded cell colonies.

Conformational Changes in the 5' End of the HIV-1 Genome Dependent on the Debranching Enzyme DBR1 during Early Stages of Infection.

Previous studies in our laboratory showed that the RNA debranching enzyme (DBR1) is not required for early steps in HIV cDNA formation but is necessary for synthesis of intermediate and late cDNA products. To further characterize this effect, we evaluated the topology of the 5' end of the HIV-1 RNA genome during early infection with and without inhibition of DBR1 synthesis. Cells were transfected with DBR1 short hairpin RNA (shRNA) followed 48 h later by infection with an HIV-1-derived vector containing an RNase H-deficient reverse transcriptase (RT). RNA was isolated at several times postinfection and treated with various RNA-modifying enzymes prior to rapid amplification of 5' cDNA ends (5' RACE) for HIV-1 RNA and quantitative reverse transcriptase PCR (qRT-PCR). In infected cells, DBR1 knockdown inhibited detection of free HIV-1 RNA 5' ends at all time points. The difference in detection of free HIV-1 RNA 5' ends in infected DBR1 knockdown versus control cells was eliminated by in vitro incubation of infected cell RNAs with yeast or human DBR1 enzyme prior to 5' RACE and qRT-PCR. This was dependent on the 2'-5' phosphatase activity of DBR1, since it did not occur when we used the catalytically inactive DBR1(N85A) mutant. Finally, HIV-1 RNA from infected DBR1 knockdown cells was resistant to RNase R that degrades linear RNAs but not RNAs in circular or lariat-like conformations. These results provide evidence for formation of a lariat-like structure involving the 5' end of HIV-1 RNA during an early step in infection and the involvement of DBR1 in resolving it.IMPORTANCE Our findings support a new view of the early steps in HIV genome replication. We show that the HIV genomic RNA is rapidly decapped and forms a lariat-like structure after entering a cell. The lariat-like structure is subsequently resolved by the cellular enzyme DBR1, leaving a 5' phosphate. This pathway is similar to the formation and resolution of pre-mRNA intron lariats and therefore suggests that similar mechanisms may be used by HIV. Our work therefore opens a new area of investigation in HIV replication and may ultimately uncover new targets for inhibiting HIV replication and for preventing the development of AIDS.

Complex Dynamics of Virus Spread from Low Infection Multiplicities: Implications for the Spread of Oncolytic Viruses.

While virus growth dynamics have been well-characterized in several infections, data are typically collected once the virus population becomes easily detectable. Earlier dynamics, however, remain less understood. We recently reported unusual early dynamics in an experimental system using adenovirus infection of human embryonic kidney (293) cells. Under identical experimental conditions, inoculation at low infection multiplicities resulted in either robust spread, or in limited spread that eventually stalled, with both outcomes occurring with approximately equal frequencies. The reasons underlying these observations have not been understood. Here, we present further experimental data showing that inhibition of interferon-induced antiviral states in cells results in a significant increase in the percentage of robust infections that are observed, implicating a race between virus replication and the spread of the anti-viral state as a central mechanism. Analysis of a variety of computational models, however, reveals that this alone cannot explain the simultaneous occurrence of both viral growth outcomes under identical conditions, and that additional biological mechanisms have to be invoked to explain the data. One such mechanism is the ability of the virus to overcome the antiviral state through multiple infection of cells. If this is included in the model, two outcomes of viral spread are found to be simultaneously stable, depending on initial conditions. In stochastic versions of such models, the system can go by chance to either state from identical initial conditions, with the relative frequency of the outcomes depending on the strength of the interferon-based anti-viral response, consistent with the experiments. This demonstrates considerable complexity during the early phase of the infection that can influence the ability of a virus to become successfully established. Implications for the initial dynamics of oncolytic virus spread through tumors are discussed.