ChIP-Seq and In Vivo Transcriptome Analyses of the Aspergillus fumigatus SREBP SrbA Reveals a New Regulator of the Fungal Hypoxia Response and Virulence

The Aspergillus fumigatus sterol regulatory element binding protein (SREBP) SrbA belongs to the basic Helix-Loop-Helix (bHLH) family of transcription factors and is crucial for antifungal drug resistance and virulence. The latter phenotype is especially striking, as loss of SrbA results in complete loss of virulence in murine models of invasive pulmonary aspergillosis (IPA). How fungal SREBPs mediate fungal virulence is unknown, though it has been suggested that lack of growth in hypoxic conditions accounts for the attenuated virulence. To further understand the role of SrbA in fungal infection site pathobiology, chromatin immunoprecipitation followed by massively parallel DNA sequencing (ChIP-seq) was used to identify genes under direct SrbA transcriptional regulation in hypoxia. These results confirmed the direct regulation of ergosterol biosynthesis and iron uptake by SrbA in hypoxia and revealed new roles for SrbA in nitrate assimilation and heme biosynthesis. Moreover, functional characterization of an SrbA target gene with sequence similarity to SrbA identified a new transcriptional regulator of the fungal hypoxia response and virulence, SrbB. SrbB co-regulates genes involved in heme biosynthesis and demethylation of C4-sterols with SrbA in hypoxic conditions. However, SrbB also has regulatory functions independent of SrbA including regulation of carbohydrate metabolism. Loss of SrbB markedly attenuates A. fumigatus virulence, and loss of both SREBPs further reduces in vivo fungal growth. These data suggest that both A. fumigatus SREBPs are critical for hypoxia adaptation and virulence and reveal new insights into SREBPs\u27 complex role in infection site adaptation and fungal virulence

Review: far-infrared instrumentation and technological development for the next decade

Far-infrared astronomy has advanced rapidly since its inception in the late 1950s, driven by a maturing technology base and an expanding community of researchers. This advancement has shown that observations at far-infrared wavelengths are important in nearly all areas of astrophysics, from the search for habitable planets and the origin of life to the earliest stages of galaxy assembly in the first few hundred million years of cosmic history. The combination of a still-developing portfolio of technologies, particularly in the field of detectors, and a widening ensemble of platforms within which these technologies can be deployed, means that far-infrared astronomy holds the potential for paradigm-shifting advances over the next decade. We examine the current and future far-infrared observing platforms, including ground-based, suborbital, and space-based facilities, and discuss the technology development pathways that will enable and enhance these platforms to best address the challenges facing far-infrared astronomy in the 21st century

Enzymatic conformational fluctuations along the reaction coordinate of cytidine deaminase

Analysis of the crystal structures for cytidine deaminase complexed with substrate analog 3-deazacytidine, transition-state analog zebularine 3,4-hydrate, and product uridine establishes significant changes in the magnitude of atomic-scale fluctuations along the (approximate) reaction coordinate of this enzyme. Differences in fluctuations between the substrate analog complex, transition-state analog complex, and product complex are monitored via changes in corresponding crystallographic temperature factors. Previously, we reported that active-site conformational disorder is substantially reduced in the transition-state complex relative to the two ground-state complexes. Here, this result is statistically corroborated by crystallographic data for fluorinated zebularine 3,4-hydrate, a second transition-state analog, and by multiple regression analysis. Multiple regression explains 70% of the total temperature factor variation through a predictive model for the average B-value of an amino acid as a function of the catalytic state of the enzyme (substrate, transition state, product) and five other physical and structural descriptors. Furthermore, correlations of atomic fluctuation magnitudes throughout the body of each complex are quantified through an auto-correlation function. The transition-state analog complex shows the greatest correlations between temperature factor magnitudes for spatially separated atoms, underscoring the strong ability of this reaction-coordinate species to "organize" enzymatic fluctuations. The catalytic significance for decreased atomic-scale motions in the transition state is discussed. A thermodynamic argument indicates that the significant decreases in local enzymatic conformational entropy at the transition state result in enhanced energetic stabilization there

Systematic Review of the Prevalence of Long COVID

BACKGROUND: Long COVID occurs in those infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) whose symptoms persist or develop beyond the acute phase. We conducted a systematic review to determine the prevalence of persistent symptoms, functional disability, or pathological changes in adults or children at least 12 weeks postinfection. METHODS: We searched key registers and databases from January 1, 2020 to November 2, 2021, limited to publications in English and studies with at least 100 participants. Studies in which all participants were critically ill were excluded. Long COVID was extracted as prevalence of at least 1 symptom or pathology, or prevalence of the most common symptom or pathology, at 12 weeks or later. Heterogeneity was quantified in absolute terms and as a proportion of total variation and explored across predefined subgroups (PROSPERO ID CRD42020218351). RESULTS: One hundred twenty studies in 130 publications were included. Length of follow-up varied between 12 weeks and 12 months. Few studies had low risk of bias. All complete and subgroup analyses except 1 had I2 ≥90%, with prevalence of persistent symptoms range of 0%-93% (pooled estimate [PE], 42.1%; 95% prediction interval [PI], 6.8% to 87.9%). Studies using routine healthcare records tended to report lower prevalence (PE, 13.6%; PI, 1.2% to 68%) of persistent symptoms/pathology than self-report (PE, 43.9%; PI, 8.2% to 87.2%). However, studies systematically investigating pathology in all participants at follow up tended to report the highest estimates of all 3 (PE, 51.7%; PI, 12.3% to 89.1%). Studies of hospitalized cases had generally higher estimates than community-based studies. CONCLUSIONS: The way in which Long COVID is defined and measured affects prevalence estimation. Given the widespread nature of SARS-CoV-2 infection globally, the burden of chronic illness is likely to be substantial even using the most conservative estimates

Longitudinal Results With Intratympanic Dexamethasone in the Treatment of Ménière’s Disease

To assess patient satisfaction with vertigo control using intratympanic (IT) dexamethasone (12 mg/mL) for medically refractory unilateral Meniere's disease. STUDY DESIGN: Retrospective study. SETTING: Tertiary referral neurotology clinic. PATIENTS: One hundred twenty-nine subjects diagnosed with unilateral Meniere's disease still having vertigo despite medical therapy. INTERVENTION: IT dexamethasone injections as needed to control vertigo attacks. MAIN OUTCOME MEASURE: A Kaplan-Meier time-to-event method was used to determine the rate of "survival," meaning sufficient satisfaction with vertigo control that the subject did not wish to have subsequent ablative treatment. "Failure" was defined as poor control and the choice to proceed to ablative treatment. RESULTS: Acceptable vertigo control ("survival") was achieved in 117 (91%) of 129 subjects. Vertigo control required only one dexamethasone injection in 48 (37%), 2 injections in 26 (20%), 3 injections in 18 (14%), and 4 injections in 10 (8%). More than 4 injections were needed in 15 subjects (21%). Of 12 failures (9%), 9 occurred within 6 months of the first IT dexamethasone injection. Follow-up data for 2 years were available for 96 subjects. Of these, 87 (91%) had vertigo control with IT dexamethasone, of whom 61 (70)% required no further injections after 2 years, 23 (26%) continued to receive IT dexamethasone injections, and 3 (3%) chose IT gentamicin treatment. CONCLUSION: IT dexamethasone injection therapy on an as-needed outpatient basis can provide vertigo control that is satisfactory in patients with Meniere's disease. The Kaplan-Meier method addresses the need for an outcome measure suited to repeated treatments and variable lengths of follow-up. However, due to the retrospective nature of this study, the presence of bias caused by loss of subjects from follow-up cannot be ruled out

Directly Measured Denitrification Reveals Oyster Aquaculture and Restored Oyster Reefs Remove Nitrogen at Comparable High Rates

Coastal systems are increasingly impacted by over-enrichment of nutrients, which has cascading effects for ecosystem functioning. Oyster restoration and aquaculture are both hypothesized to mitigate excessive nitrogen (N) loads via benthic denitrification. The degree to which these management activities perform similar functions for removing N, however, has not been extensively examined in New England, a place where nutrient runoff is high and increasing oyster (Crassostrea virginica) restoration and aquaculture activity is taking place. Here, we use a novel in situ methodology to directly measure net N2 and O2 fluxes across the sediment-water interface in a shallow (~1 m) coastal pond in southern Rhode Island. We collected data seasonally during 2013 and 2014 at restored oyster reefs, oyster aquaculture, oyster cultch (shell), and bare sediment. Restored oyster reefs and aquaculture had the highest mean (±SE) denitrification rates, 581.9 (±164.2) and 346 (±168.6) μmol N2−N m−2 h−1, respectively, and are among the highest recorded for oyster-dominated environments. Denitrification rates at sites with oyster cultch were 60.9 (±44.3) μmol N2−N m−2 h−1, which is substantially less than the sites with active oysters but still more than 50% higher than denitrification rates measured in bare sediment (24.4 ± 10.1 μmol N2–N m−2 h−1). The increase in denitrification rates at treatments, however, varied by season and the greatest rates for restored reefs were in the fall. Overall, the greatest aggregate denitrification rates occurred in the fall. Sediment oxygen demand (SOD) followed similar patterns but with greater overall rates in the summer, and displayed a strong linear relationship with denitrification (R2 = 0.93). Our results demonstrate that habitats associated with live oysters have higher net denitrification rates and that oyster reef restoration and oyster aquaculture may provide similar benefits to the ecosystem in terms of N removal. However, gas fluxes may also be affected where three-dimensional structure is introduced via oyster shell cultch and this appears to be seasonally-dependent. These data will be important for managers as they incorporate oysters into nutrient reduction strategies and consider system-level trade-offs in services provided by oyster reef restoration and aquaculture activities

Directly Measured Denitrification Reveals Oyster Aquaculture and Restored Oyster Reefs Remove Nitrogen at Comparable High Rates

Coastal systems are increasingly impacted by over-enrichment of nutrients, which has cascading effects for ecosystem functioning. Oyster restoration and aquaculture are both hypothesized to mitigate excessive nitrogen (N) loads via benthic denitrification. The degree to which these management activities perform similar functions for removing N, however, has not been extensively examined in New England, a place where nutrient runoff is high and increasing oyster (Crassostrea virginica) restoration and aquaculture activity is taking place. Here, we use a novel in situ methodology to directly measure net N2 and O2 fluxes across the sediment-water interface in a shallow (~1 m) coastal pond in southern Rhode Island. We collected data seasonally during 2013 and 2014 at restored oyster reefs, oyster aquaculture, oyster cultch (shell), and bare sediment. Restored oyster reefs and aquaculture had the highest mean (±SE) denitrification rates, 581.9 (±164.2) and 346 (±168.6) μmol N2−N m−2 h−1, respectively, and are among the highest recorded for oyster-dominated environments. Denitrification rates at sites with oyster cultch were 60.9 (±44.3) μmol N2−N m−2 h−1, which is substantially less than the sites with active oysters but still more than 50% higher than denitrification rates measured in bare sediment (24.4 ± 10.1 μmol N2–N m−2 h−1). The increase in denitrification rates at treatments, however, varied by season and the greatest rates for restored reefs were in the fall. Overall, the greatest aggregate denitrification rates occurred in the fall. Sediment oxygen demand (SOD) followed similar patterns but with greater overall rates in the summer, and displayed a strong linear relationship with denitrification (R2 = 0.93). Our results demonstrate that habitats associated with live oysters have higher net denitrification rates and that oyster reef restoration and oyster aquaculture may provide similar benefits to the ecosystem in terms of N removal. However, gas fluxes may also be affected where three-dimensional structure is introduced via oyster shell cultch and this appears to be seasonally-dependent. These data will be important for managers as they incorporate oysters into nutrient reduction strategies and consider system-level trade-offs in services provided by oyster reef restoration and aquaculture activities

Treg depletion potentiates checkpoint inhibition in claudin-low breast cancer

Claudin-low breast cancer is an aggressive subtype that confers poor prognosis and is found largely within the clinical triple-negative group of breast cancer patients. Here, we have shown that intrinsic and immune cell gene signatures distinguish the claudin-low subtype clinically as well as in mouse models of other breast cancer subtypes. Despite adaptive immune cell infiltration in claudin-low tumors, treatment with immune checkpoint inhibitory antibodies against cytotoxic T lymphocyte–associated protein 4 (CTLA-4) and programmed death receptor 1 (PD-1) were ineffective in controlling tumor growth. CD4+FoxP3+ Tregs represented a large proportion of the tumor-infiltrating lymphocytes (TILs) in claudin-low tumors, and Tregs isolated from tumor-bearing mice were able to suppress effector T cell responses. Tregs in the tumor microenvironment highly expressed PD-1 and were recruited partly through tumor generation of the chemokine CXCL12. Antitumor efficacy required stringent Treg depletion combined with checkpoint inhibition; delays in tumor growth were not observed using therapies that modestly diminished the number of Tregs in the tumor microenvironment. This study provides evidence that the recruitment of Tregs to the tumor microenvironment inhibits an effective antitumor immune response and highlights early Treg recruitment as a possible mechanism for the lack of response to immune checkpoint blockade antibodies in specific subtypes of cancer that are heavily infiltrated with adaptive immune cells

MicroRNA expression signature in human abdominal aortic aneurysms

Background: Abdominal aortic aneurysm (AAA) is a dilatation of the aorta affecting most frequently elderly men. Histologically AAAs are characterized by inflammation, vascular smooth muscle cell apoptosis, and extracellular matrix degradation. The mechanisms of AAA formation, progression, and rupture are currently poorly understood. A previous mRNA expression study revealed a large number of differentially expressed genes between AAA and non-aneurysmal control aortas. MicroRNAs (miRNAs), small non-coding RNAs that are post-transcriptional regulators of gene expression, could provide a mechanism for the differential expression of genes in AAA. Methods: To determine differences in miRNA levels between AAA (n = 5) and control (n = 5) infrarenal aortic tissues, a microarray study was carried out. Results were adjusted using Benjamini-Hochberg correction (adjusted p\u3c 0.05). Real-time quantitative RT-PCR (qRT-PCR) assays with an independent set of 36 AAA and seven control tissues were used for validation. Potential gene targets were retrieved from miRNA target prediction databases Pictar, TargetScan, and MiRTarget2. Networks from the target gene set were generated and examined using the network analysis programs, CytoScape® and Ingenuity Pathway Core Analysis®. Results: A microarray study identified eight miRNAs with significantly different expression levels between AAA and controls (adjusted p \u3c 0.05). Real-time qRT-PCR assays validated the findings for five of the eight miRNAs. A total of 222 predicted miRNA target genes known to be differentially expressed in AAA based on a prior mRNA microarray study were identified. Bioinformatic analyses revealed that several target genes are involved in apoptosis and activation of T cells. Conclusions: Our genome-wide approach revealed several differentially expressed miRNAs in human AAA tissue suggesting that miRNAs play a role in AAA pathogenesis. Keywords: Apoptosis, Microarray analysis, Vascular biology, miRNA-mRNA analysis, Network analysi

Review: far-infrared instrumentation and technological development for the next decade

Far-infrared astronomy has advanced rapidly since its inception in the late 1950s, driven by a maturing technology base and an expanding community of researchers. This advancement has shown that observations at far-infrared wavelengths are important in nearly all areas of astrophysics, from the search for habitable planets and the origin of life to the earliest stages of galaxy assembly in the first few hundred million years of cosmic history. The combination of a still-developing portfolio of technologies, particularly in the field of detectors, and a widening ensemble of platforms within which these technologies can be deployed, means that far-infrared astronomy holds the potential for paradigm-shifting advances over the next decade. We examine the current and future far-infrared observing platforms, including ground-based, suborbital, and space-based facilities, and discuss the technology development pathways that will enable and enhance these platforms to best address the challenges facing far-infrared astronomy in the 21st century