Germinal Center Dark Zone harbors ATR-dependent determinants of T-cell exclusion that are also identified in aggressive lymphoma.

The germinal center (GC) dark zone (DZ) and light zone (LZ) regions spatially separate expansion and diversification from selection of antigen-specific B-cells to ensure antibody affinity maturation and B cell memory. The DZ and LZ differ significantly in their immune composition despite the lack of a physical barrier, yet the determinants of this polarization are poorly understood. This study provides novel insights into signals controlling asymmetric T-cell distribution between DZ and LZ regions. We identify spatially-resolved DNA damage response and chromatin compaction molecular features that underlie DZ T-cell exclusion. The DZ spatial transcriptional signature linked to T-cell immune evasion clustered aggressive Diffuse Large B-cell Lymphomas (DLBCL) for differential T cell infiltration. We reveal the dependence of the DZ transcriptional core signature on the ATR kinase and dissect its role in restraining inflammatory responses contributing to establishing an immune-repulsive imprint in DLBCL. These insights may guide ATR-focused treatment strategies bolstering immunotherapy in tumors marked by DZ transcriptional and chromatin-associated features.

Internationally standardized respiratory viral load testing with limited resources: A derivative-of-care calibration strategy for SARS-CoV-2.

Introduction: SARS-CoV-2 has demonstrated that, in targeted circumstances, viral quantification within respiratory specimens can valuably inform patient management, as well as research. Nevertheless, the pandemic has illustrated concomitant challenges for obtaining high-quality (and broadly comparable) respiratory viral loads. This includes a critical need for standardization and calibration, even though the necessary resources may not always be available for emergent pathogens and non-bloodstream specimens. Methods: To these ends, we describe a novel strategy for implementing quantitative SARS-CoV-2 testing with International Unit-based calibration. Earlier in the course of the pandemic-when analytic resources were far more limited-select residual SARS-CoV-2 positive specimens from routine care in our diagnostic laboratory were pooled to formulate a clinically realistic secondary standard of high volume and analyte concentration, which was cross-calibrated to the primary SARS-CoV-2 standard of the World Health Organization. Results: The resultant calibrators were integrated into the original CDC RT-qPCR assay for SARS-CoV-2, whose (now broadened) performance characteristics were defined to generate a test appropriate for both clinical and research use. This test allowed for the quantification of virus in respiratory specimens down to a validated lower limit of quantification of 103.4 IU/ml. Conclusions: By self-formulating calibrators from this derivative-of-care secondary standard, we successfully validated respiratory viral loads without the commercial availability (at that time) of quantitative assays or calibrators. As the SARS-CoV-2 pandemic continues to decline-and even beyond this pathogen-this strategy may be applicable for laboratories seeking to implement viral load testing for nontraditional specimen types despite limited resources.

Concurrent transmission of multiple carbapenemases in a long-term acute-care hospital.

OBJECTIVE: We investigated concurrent outbreaks of Pseudomonas aeruginosa carrying blaVIM (VIM-CRPA) and Enterobacterales carrying blaKPC (KPC-CRE) at a long-term acute-care hospital (LTACH A). METHODS: We defined an incident case as the first detection of blaKPC or blaVIM from a patient's clinical cultures or colonization screening test. We reviewed medical records and performed infection control assessments, colonization screening, environmental sampling, and molecular characterization of carbapenemase-producing organisms from clinical and environmental sources by pulsed-field gel electrophoresis (PFGE) and whole-genome sequencing. RESULTS: From July 2017 to December 2018, 76 incident cases were identified from 69 case patients: 51 had blaKPC, 11 had blaVIM, and 7 had blaVIM and blaKPC. Also, blaKPC were identified from 7 Enterobacterales, and all blaVIM were P. aeruginosa. We observed gaps in hand hygiene, and we recovered KPC-CRE and VIM-CRPA from drains and toilets. We identified 4 KPC alleles and 2 VIM alleles; 2 KPC alleles were located on plasmids that were identified across multiple Enterobacterales and in both clinical and environmental isolates. CONCLUSIONS: Our response to a single patient colonized with VIM-CRPA and KPC-CRE identified concurrent CPO outbreaks at LTACH A. Epidemiologic and genomic investigations indicated that the observed diversity was due to a combination of multiple introductions of VIM-CRPA and KPC-CRE and to the transfer of carbapenemase genes across different bacteria species and strains. Improved infection control, including interventions that minimized potential spread from wastewater premise plumbing, stopped transmission.

Distinct Origins and Transmission Pathways of blaKPC Enterobacterales across Three U.S. States.

Carbapenem-resistant Enterobacterales (CRE) are among the most concerning antibiotic resistance threats due to high rates of multidrug resistance, transmissibility in health care settings, and high mortality rates. We evaluated the potential for regional genomic surveillance to track the spread of blaKPC-carrying CRE (KPC-CRE) by using isolate collections from health care facilities in three U.S. states. Clinical isolates were collected from Connecticut (2017 to 2018), Minnesota (2012 to 2018), and Tennessee (2016 to 2017) through the U.S. Centers for Disease Control and Prevention's Multi-site Gram-negative Surveillance Initiative (MuGSI) and additional surveillance. KPC-CRE isolates were whole-genome sequenced, yielding 255 isolates from 214 patients across 96 facilities. Case report data on patient comorbidities, facility exposures, and interfacility patient transfer were extracted. We observed that in Connecticut, most KPC-CRE isolates showed evidence of importation from outside the state, with limited local transmission. In Minnesota, cases were mainly from sporadic importation and transmission of blaKPC-carrying Klebsiella pneumoniae ST258, and clonal expansion of blaKPC-carrying Enterobacter hormaechei ST171, primarily at a single focal facility and its satellite facilities. In Tennessee, we observed transmission of diverse strains of blaKPC-carrying Enterobacter and Klesbiella, with evidence that most derived from the local acquisition of blaKPC plasmids circulating in an interconnected regional health care network. Thus, the underlying processes driving KPC-CRE burden can differ substantially across regions and can be discerned through regional genomic surveillance. This study provides proof of concept that integrating genomic data with information on interfacility patient transfers can provide insights into locations and drivers of regional KPC-CRE burden that can enable targeted interventions.

Containment of a Verona Integron-Encoded Metallo-Beta-Lactamase-Producing Pseudomonas aeruginosa Outbreak Associated With an Acute Care Hospital Sink-Tennessee, 2018-2020.

Background: Contaminated healthcare facility wastewater plumbing is recognized as a source of carbapenemase-producing organism transmission. In August 2019, the Tennessee Department of Health (TDH) identified a patient colonized with Verona integron-encoded metallo-beta-lactamase-producing carbapenem-resistant Pseudomonas aeruginosa (VIM-CRPA). A record review revealed that 33% (4 of 12) of all reported patients in Tennessee with VIM had history of prior admission to acute care hospital (ACH) A intensive care unit (ICU) Room X, prompting further investigation. Methods: A case was defined as polymerase chain reaction detection of blaVIM in a patient with prior admission to ACH A from November 2017 to November 2020. The TDH performed point prevalence surveys, discharge screening, onsite observations, and environmental testing at ACH A. The VIM-CRPA isolates underwent whole-genome sequencing (WGS). Results: In a screening of 44% (n = 11) of 25 patients admitted to Room X between January and June 2020, we identified 36% (n = 4) colonized with VIM-CRPA, resulting in 8 cases associated with Room X from March 2018 to June 2020. No additional cases were identified in 2 point-prevalence surveys of the ACH A ICU. Samples from the bathroom and handwashing sink drains in Room X grew VIM-CRPA; all available case and environmental isolates were found to be ST253 harboring blaVIM-1 and to be closely related by WGS. Transmission ended after implementation of intensive water management and infection control interventions. Conclusions: A single ICU room's contaminated drains were associated with 8 VIM-CRPA cases over a 2-year period. This outbreak highlights the need to include wastewater plumbing in hospital water management plans to mitigate the risk of transmission of antibiotic-resistant organisms to patients.

Targeting dual oncogenic machineries driven by TAL1 and PI3K-AKT pathways in T-cell acute lymphoblastic leukemia.

T-cell acute lymphoblastic leukemia (T-ALL) is a malignancy of thymic T-cell precursors. Overexpression of oncogenic transcription factor TAL1 is observed in 40-60% of human T-ALL cases, frequently together with activation of the NOTCH1 and PI3K-AKT pathways. In this study, we performed chemical screening to identify small molecules that can inhibit the enhancer activity driven by TAL1 using the GIMAP enhancer reporter system. Among approximately 3,000 compounds, PIK- 75, a known inhibitor of PI3K and CDK, was found to strongly inhibit the enhancer activity. Mechanistic analysis demonstrated that PIK-75 blocks transcriptional activity, which primarily affects TAL1 target genes as well as AKT activity. TAL1-positive, AKT-activated T-ALL cells were very sensitive to PIK-75, as evidenced by growth inhibition and apoptosis induction, while T-ALL cells that exhibited activation of the JAK-STAT pathway were insensitive to this drug. Together, our study demonstrates a strategy targeting two types of core machineries mediated by oncogenic transcription factors and signaling pathways in T-ALL.

Receptor-ligand non-equilibrium kinetics (RLNEK) 1.0: An integrated Trackmate laminar flow chamber analysis.

Although parallel plate flow chamber assays are widely performed, extraction of kinetic parameters is limited to specialized labs with mathematical expertise and customized video-microscopy tracking tools. The recent development of Trackmate has increased researcher accessibility to tracking particles in video-microscopy experiments; however, there is a lack of tools that analyze this tracking information. We report a software tool, compatible with Trackmate, that extracts Receptor Ligand Non-Equilibrium Kinetic (RLNEK) parameters from video-microscopy data. This software should be of particular interest to the community of researchers and scientists interrogating the target-specific binding and release of immune cells.

A Robust Protocol for CRISPR-Cas9 Gene Editing in Human Suspension Cell Lines.

The implementation of clustered regularly interspaced short palindromic repeats (CRISPR)-Cas9 systems in mammalian cells has sparked an exciting new era in targeted gene editing. CRISPR-Cas9 technologies allow gene function to be interrogated by gene deletions, mutations, and truncations, and by epitope tagging and promoter activity modulation. Many robust protocols have been published to date on CRISPR-Cas9 techniques, however, most of these focus on adherent cell lines. Suspension cell lines, typically of hematolymphoid origin, such as Jurkat, Daudi, and TOLEDO, pose unique challenges to the setup of CRISPR experiments. Here, using B cell lymphoma cells as a primary model, we describe a comprehensive protocol for targeted gene manipulations using the CRISPR-Cas9 system in suspension cells. We also highlight necessary optimization steps to make this approach universal to other suspension cell lines. We first describe a detailed protocol for transient expression of the Cas9 nuclease and guide RNAs. We then suggest workflows for obtaining single-cell clones and for screening for successful homozygous knockout (KO) clones in suspension lines. This protocol aims to serve as a comprehensive resource to facilitate gene editing experiments for users starting CRISPR-Cas9 gene editing protocols on suspension cell lines or those looking to optimize their current workflows. © 2021 Wiley Periodicals LLC. Basic Protocol 1: Transient CRISPR Cas9-gRNA delivery for gene knockout by NeonTM electroporation Support Protocol 1: Designing and preparing gene-specific gRNA Support Protocol 2: Preparation of conditioned medium and culture vessels for single-cell FACS Alternate Protocol 1: Transient CRISPR Cas9-gRNA delivery for gene knockout by Nepagene electroporator Basic Protocol 2: FACS and single-cell clone generation Alternate Protocol 2: Manual cell dilution to obtain single-cell clones Basic Protocol 3: Confirming indels status in single-cell clones by PCR on genomic DNA and Sanger sequencing.

Carbapenemase production among less-common Enterobacterales genera: 10 US sites, 2018.

BACKGROUND: Historically, United States' carbapenem-resistant Enterobacterales (CRE) surveillance and mechanism testing focused on three genera: Escherichia, Klebsiella, and Enterobacter (EsKE); however, other genera can harbour mobile carbapenemases associated with CRE spread. OBJECTIVES: From January through May 2018, we conducted a 10 state evaluation to assess the contribution of less common genera (LCG) to carbapenemase-producing (CP) CRE. METHODS: State public health laboratories (SPHLs) requested participating clinical laboratories submit all Enterobacterales from all specimen sources during the surveillance period that were resistant to any carbapenem (Morganellaceae required resistance to doripenem, ertapenem, or meropenem) or were CP based on phenotypic or genotypic testing at the clinical laboratory. SPHLs performed species identification, phenotypic carbapenemase production testing, and molecular testing for carbapenemases to identify CP-CRE. Isolates were categorized as CP if they demonstrated phenotypic carbapenemase production and ≥1 carbapenemase gene (bla KPC, bla NDM, bla VIM, bla IMP, or bla OXA-48-like) was detected. RESULTS: SPHLs tested 868 CRE isolates, 127 (14.6%) were from eight LCG. Overall, 195 (26.3%) EsKE isolates were CP-CRE, compared with 24 (18.9%) LCG isolates. LCG accounted for 24 (11.0%) of 219 CP-CRE identified. Citrobacter spp. was the most common CP-LCG; the proportion of Citrobacter that were CP (11/42, 26.2%) was similar to the proportion of EsKE that were CP (195/741, 26.3%). Five of 24 (20.8%) CP-LCG had a carbapenemase gene other than bla KPC. CONCLUSIONS: Participating sites would have missed approximately 1 in 10 CP-CRE if isolate submission had been limited to EsKE genera. Expanding mechanism testing to additional genera could improve detection and prevention efforts.

Web-Based Interactive Tool to Identify Facilities at Risk of Receiving Patients with Multidrug-Resistant Organisms.

To identify facilities at risk of receiving patients colonized or infected with multidrug-resistant organisms (MDROs), we developed an interactive web-based interface for visualization of patient-sharing networks among healthcare facilities in Tennessee, USA. Using hospital discharge data and the Centers for Medicare and Medicaid Services' claims and Minimum Data Set, we constructed networks among hospitals and skilled nursing facilities. Networks included direct and indirect transfers, which accounted for <365 days in the community outside of facility admissions. Authorized users can visualize a facility of interest and tailor visualizations by year, network dataset, length of time in the community, and minimum number of transfers. The interface visualizes the facility of interest with its connected facilities that receive or send patients, the number of interfacility transfers, and facilities at risk of receiving transfers from the facility of interest. This tool will help other health departments enhance their MDRO outbreak responses.

Dietary DHA amplifies LXA4 circuits in tissues and lymph node PMN and is protective in immune-driven dry eye disease.

Recently identified regulatory PMN control immune-driven dry eye disease (DED) in females by producing the arachidonic acid (ω-6)-derived specialized pro-resolving mediator (SPM), LXA4, in lymph nodes. Dietary ω-3 docosahexaenoic acid (DHA) is protective in DED but mechanisms of action remain elusive. DHA is converted to ω-3 SPMs by PMN via the same lipoxygenases (LOX) that generate LXA4. We investigated if dietary DHA amplifies SPM formation and affects T effector cell function and/or regulatory PMN in DED. DED was induced in mice on a DHA-enriched or ω-3-deficient diet. DHA deficiency amplified DED with marked sex-specific differences. Dietary DHA protection against dry eye disease correlated with increased PMN levels in lymph nodes, ocular tissues, and unexpectedly, selective amplification of LXA4 tissue levels. Dietary DHA increased 12/15-LOX and decreased 5-LOX expression in lymph nodes and isolated lymph node PMN, which correlated with amplified LXA4 formation. Acute DHA treatment rescued DHA-deficient females from exaggerated DED by amplifying lymph node LXA4 formation, increasing Treg and decreasing TH1 and TH17 effector cells. Our results identify DHA regulation of LXA4 producing PMN in ocular tissues and lymph nodes in health and immune disease as novel mechanism and determinant for T-cell responses to routine ocular injury or stress signals.

Tree water dynamics in a drying and warming world.

Disentangling the relative impacts of precipitation reduction and vapour pressure deficit (VPD) on plant water dynamics and determining whether acclimation may influence these patterns in the future is an important challenge. Here, we report sap flux density (FD ), stomatal conductance (Gs ), hydraulic conductivity (KL ) and xylem anatomy in piñon pine (Pinus edulis) and juniper (Juniperus monosperma) trees subjected to five years of precipitation reduction, atmospheric warming (elevated VPD) and their combined effects. No acclimation occurred under precipitation reduction: lower Gs and FD were found for both species compared to ambient conditions. Warming reduced the sensibility of stomata to VPD for both species but resulted in the maintenance of Gs and FD to ambient levels only for piñon. For juniper, reduced soil moisture under warming negated benefits of stomatal adjustments and resulted in reduced FD , Gs and KL . Although reduced stomatal sensitivity to VPD also occurred under combined stresses, reductions in Gs , FD and KL took place to similar levels as under single stresses for both species. Our results show that stomatal conductance adjustments to high VPD could minimize but not entirely prevent additive effects of warming and drying on water use and carbon acquisition of trees in semi-arid regions.

Assessing the thermal dissipation sap flux density method for monitoring cold season water transport in seasonally snow-covered forests.

Productivity of conifers in seasonally snow-covered forests is high before and during snowmelt when environmental conditions are optimal for photosynthesis. Climate change is altering the timing of spring in many locations, and changes in the date of transition from winter dormancy can have large impacts on annual productivity. Sap flow methods provide a promising approach to monitor tree activity during the cold season and the winter-spring and fall-winter transitions. Although sap flow techniques have been widely used, cold season results are generally not reported. Here we examine the feasibility of using the Granier thermal dissipation (TD) sap flux density method to monitor transpiration and dormancy of evergreen conifers during the cold season. We conducted a laboratory experiment which demonstrated that the TD method reliably detects xylem water transport (when it occurs) both at near freezing temperature and at low flow rate, and that the sensors can withstand repeated freeze-thaw events. However, the dependence between sensor output and water transport rate in these experiments differed from the established TD relation. In field experiments, sensors installed in two Abies forests lasted through two winters and a summer with low failure. The baseline (no-flow) sensor output varied considerably with temperature during the cold season, and a new baseline algorithm was developed to accommodate this variation. The Abies forests differed in elevation (2070 and 2620 m), and there was a clear difference in timing of initiation and cessation of transpiration between them. We conclude that the TD method can be reliably used to examine water transport during cold periods with associated low flow conditions.

Carbon isotopic composition of forest soil respiration in the decade following bark beetle and stem girdling disturbances in the Rocky Mountains.

Bark beetle outbreaks are widespread in western North American forests, reducing primary productivity and transpiration, leading to forest mortality across large areas and altering ecosystem carbon cycling. Here the carbon isotope composition (δ(13) C) of soil respiration (δJ ) was monitored in the decade after disturbance for forests affected naturally by mountain pine beetle infestation and artificially by stem girdling. The seasonal mean δJ changed along both chronosequences. We found (a) enrichment of δJ relative to controls (<1 ‰) in near-surface soils in the first 2 years after disturbance; (b) depletion (1‰ or no change) during years 3-7; and (c) a second period of enrichment (1-2‰) in years 8-10. Results were consistent with isotopic patterns associated with the gradual death and decomposition of rhizosphere organisms, fine roots, conifer needles and woody roots and debris over the course of a decade after mortality. Finally, δJ was progressively more (13) C-depleted deeper in the soil than near the surface, while the bulk soil followed the well-established pattern of (13) C-enrichment at depth. Overall, differences in δJ between mortality classes (<1‰) and soil depths (<3‰) were smaller than variability within a class or depth over a season (up to 6‰).

Caries experience among Chinese-American children in Manhattan Chinatown.

There is little research on the oral health status of Chinese-American (CA) children in the U.S. and Asian/Pacific Islanders in general. The purpose of this study was to characterize the dental caries experience of a CA child population in Manhattan Chinatown, New York City. A five-year chart review of 545 initial dental exams of patients aged 2 to 11 was conducted at a community clinic serving an immigrant CA population. DMFT/dft were compared to National Health and Nutrition Examination Survey (NHANES) and analyzed for associations among birthplace, language and untreated tooth decay at recall. Subject mean dft was higher compared to NHANES data both in aggregate and ethnic/race subgroups. Subjects had lower DMFT ccmpared to the national data. Significant difference was found between U.S. and non-U.S.-born mean dft. Asian Pacific Islander Americans include a fast-growing immigrant pediatric population at high risk for tooth decay.

Cyanotic breath-holding spells in children respond to adenotonsillectomy for sleep-disordered breathing.

Children with breath-holding (BH) spells may demonstrate sleep-disordered breathing (SDB) during polysomnography. We studied five young children with cyanotic spells retrospectively and found both SDB and a response to adenotonsillectomy. We therefore proceeded with a prospective investigation of treatment for SDB in children with comorbid cyanotic spells. Nineteen children with cyanotic BH spells were identified and enrolled in the prospective study. Parents chose either treatment or observation. Fourteen children underwent complete SDB evaluation and treatment trials while five selected observation only (control group). Sleep and sleep-surgery specialist evaluation and polysomnography revealed the presence of a narrow upper-airway and an abnormal respiratory disturbance index in all 14 children. Nasal CPAP was not successful, but adenotonsillectomy performed near 14 months of age eliminated SDB. BH spells were eliminated 1 month after surgery, while they persisted to the end of the study (24 months of age) in the control group. In conclusion, the presence of cyanotic BH should prompt investigation and polysomnography for possible SDB. Independent treatment of SDB may hasten resolution of BH spells in these cases.

Focal akinetic seizures as the only clinical manifestation of partial epilepsy.

Episodic hemipareis is usually thought to have a vascular etiology. Ictal paresis during seizures usually occurs with other clinical signs. The exact mechanism by which weakness occurs during seizures is difficult to determine as positive and negative motor phenomenona occur in rapid succession. This case describes a girl with episodic ictal hemiparesis since infancy as the only clinical seizure manifestation with VEEG suggesting mesial frontal ictal onset.

Adenotonsillectomy and obstructive sleep apnea in children: a prospective survey.

OBJECTIVE: Prospective survey of children up to 14 years of age with OSA submitted to adenotonsillectomy. METHODS: Clinical evaluation, with questionnaires and clinical scales evaluating facial structures including tonsils and Mallampati scales and otolaryngologic evaluation; nocturnal polysomnography and repeat evaluation three to five months postsurgery. RESULTS: Of 207 successively seen children, 199 had follow-up polysomnography, and 94 had still abnormal sleep recording. Multivariate analysis indicates that Mallampati scale score 3 and 4, retro-position of mandible, enlargement of nasal inferior turbinates at +3 (subjective scale 1 to 3), and deviated septum were significantly associated with persistence of abnormal polysomnography (with high 95% CI for Mallampati scale and deviated septum). CONCLUSION: Mallampati scale scores are resultant of several facial factors involving maxilla, mandible, and oral versus oral breathing but add information on risk of partial response to adenotonsillectomy. SIGNIFICANCE: Adenotonsillectomy may not resolve obstructive sleep apnea in children.

Sleepwalking, a disorder of NREM sleep instability.

BACKGROUND AND PURPOSE: Thirty-two chronic sleepwalkers who were part of a larger, previously reported sleepwalking group all achieved control of sleepwalking after undergoing treatment for an associated sleep disorder. In the current study, all records were blindly scored to perform a cyclic alternating pattern (CAP) analysis. PATIENTS AND METHODS: Thirty-two young adult chronic sleepwalkers had polysomnography (PSG) on initial nights without sleepwalking events, as did age-matched normal controls and patients with mild sleep-disordered breathing (SDB). More than 90% of these patients with mild SDB had upper airway resistance syndrome (UARS). Ten randomly selected PSGs for sleepwalkers and matched controls also had quantitative electroencephalographic (EEG) analysis using Fast Fourier Transformation (FFT) with determination of delta power for each non-rapid eye movement (NREM)-REM sleep cycle. RESULTS: Compared to normal controls, an investigation of CAP in sleepwalkers demonstrated the presence of an abnormal CAP rate with a decrease in phase A1 and an increase in phases A2 and A3 on non-sleepwalking nights. The results of CAP analysis in sleepwalkers were similar to those obtained in age-matched UARS patients. Furthermore, the analysis of the first four NREM-REM sleep cycles reconfirmed the presence of an important decrease in delta power in sleep cycles 1 and 2 during a non-sleepwalking night in sleepwalkers compared to normal controls. CONCLUSIONS: The presence of both 'hypersynchronous slow delta' and 'burst of delta waves' have been reported in sleepwalkers, but their significance is controversial. These EEG patterns are similar to phase A1 (and possibly A2) of the CAP. Proper analysis of the sleep EEG of sleepwalkers should integrate CAP analysis. Sleepwalkers on a non-sleepwalking night present instability of NREM sleep, as demonstrated by this analysis. This instability is similar to the one noted in UARS patients. Subtle sleep disorders associated with chronic sleepwalking constitute the unstable NREM sleep background on which sleepwalking events occur. A subtle associated sleep disorder should be systematically searched for and treated in the presence of sleepwalking with abnormal CAP.