Structure and Metal Binding Properties of ZnuA, a Periplasmic Zinc Transporter from \u3cem\u3eEscherichia coli\u3c/em\u3e

ZnuA is the periplasmic Zn2+-binding protein associated with the high-affinity ATP-binding cassette ZnuABC transporter from Escherichia coli. Although several structures of ZnuA and its homologs have been determined, details regarding metal ion stoichiometry, affinity, and specificity as well as the mechanism of metal uptake and transfer remain unclear. The crystal structures of E. coli ZnuA (Eco-ZnuA) in the apo, Zn2+-bound, and Co2+-bound forms have been determined. ZnZnuA binds at least two metal ions. The first, observed previously in other structures, is coordinated tetrahedrally by Glu59, His60, His143, and His207. Replacement of Zn2+ with Co2+ results in almost identical coordination geometry at this site. The second metal binding site involves His224 and several yet to be identified residues from the His-rich loop that is unique to Zn2+ periplasmic metal binding receptors. Electron paramagnetic resonance and X-ray absorption spectroscopic data on CoZnuA provide additional insight into possible residues involved in this second site. The second site is also detected by metal analysis and circular dichroism (CD) titrations. Eco-ZnuA binds Zn2+ (estimated K d \u3c 20 nM), Co2+, Ni2+, Cu2+, Cu+, and Cd2+, but not Mn2+. Finally, conformational changes upon metal binding observed in the crystal structures together with fluorescence and CD data indicate that only Zn2+ substantially stabilizes ZnuA and might facilitate recognition of ZnuB and subsequent metal transfer

The 2011 Outburst of Recurrent Nova T Pyx: X-ray Observations Expose the White Dwarf Mass and Ejection Dynamics

The recurrent nova T Pyx underwent its sixth historical outburst in 2011, and became the subject of an intensive multi-wavelength observational campaign. We analyze data from the Swift and Suzaku satellites to produce a detailed X-ray light curve augmented by epochs of spectral information. X-ray observations yield mostly non-detections in the first four months of outburst, but both a super-soft and hard X-ray component rise rapidly after Day 115. The super-soft X-ray component, attributable to the photosphere of the nuclear-burning white dwarf, is relatively cool (~45 eV) and implies that the white dwarf in T Pyx is significantly below the Chandrasekhar mass (~1 M_sun). The late turn-on time of the super-soft component yields a large nova ejecta mass (>~10^-5 M_sun), consistent with estimates at other wavelengths. The hard X-ray component is well fit by a ~1 keV thermal plasma, and is attributed to shocks internal to the 2011 nova ejecta. The presence of a strong oxygen line in this thermal plasma on Day 194 requires a significantly super-solar abundance of oxygen and implies that the ejecta are polluted by white dwarf material. The X-ray light curve can be explained by a dual-phase ejection, with a significant delay between the first and second ejection phases, and the second ejection finally released two months after outburst. A delayed ejection is consistent with optical and radio observations of T Pyx, but the physical mechanism producing such a delay remains a mystery.Comment: Re-submitted to ApJ after revision

Modeling quality and prestige in applied linguistics journals: A bibliometric and synthetic analysis

The importance of academic journals in second language (L2) research is evident on at least two levels. Journals are, first of all, central to the process of disseminating scientific findings. Journals are also critical on a professional level as most L2 researchers must publish articles to advance their careers. However, not all journals are perceived as equal; some may be considered more prestigious or of higher quality and may, therefore, achieve a greater impact on the field. It is therefore necessary that we understand the identity and quality of L2 research journals, yet very little research (e.g., Egbert, 2007; VanPatten & Williams, 2002) has considered these issues to date. The current study sought to explore L2 journal identity and quality, and the relationship between these constructs. In order to do so, a database was compiled based on three different types of sources: (1) a questionnaire eliciting L2 researchers’ perceptions of the quality and prestige of 27 journals that publish L2 research (N = 327); (2) manual coding of different types of articles (e.g., empirical studies, review papers), data (quantitative, qualitative, mixed), research settings, and authorship patterns (K = 2,024) using the same 27 journals; and (3) bibliometric and submission data such as impact factors, citation counts, and acceptance rates. Descriptive statistics were applied to explore overall quality and prestige ratings as well as publication trends found in each journal. The relationships between those patterns and subjective ratings were also examined. In addition, regression models were built to determine the extent to which perceptions of journal quality and prestige could be explained as a function of journal and article features. We discuss the findings of the study in terms of on-going debates concerning publication practices, study quality, impact factors, journal selection, and the “journal culture” in applied linguistics

Multiyear La Niña Events and Multiseason Drought in the Horn of Africa

One of the primary sources of predictability for seasonal hydroclimate forecasts are sea surface temperatures (SSTs) in the tropical Pacific, including El Nin˜ o–Southern Oscillation. Multiyear La Nin˜ a events in particular may be both predictable at long lead times and favor drought in the bimodal rainfall regions of East Africa. However, SST patterns in the tropical Pacific and adjacent ocean basins often differ substantially between first- and second-year La Nin˜ as, which can change how these events affect regional climate. Here, we demonstrate that multiyear La Nin˜ a events favor drought in the Horn of Africa in three consecutive seasons [October–December (OND), March–May (MAM), OND]. But they do not tend to increase the probability of a fourth season of drought owing to the sea surface temperatures and associated atmospheric teleconnections in the MAM long rains season following second-year La Nin˜ a events. First-year La Nin˜ as tend to have both greater subsidence over the Horn of Africa, associated with warmer waters in the west Pacific that enhance the Walker circulation, and greater cross-continental moisture transport, associated with a warm tropical Atlantic, as compared to second-year La Nin˜ as. Both the increased subsidence and enhanced cross-continental moisture transport favors drought in the Horn of Africa. Our results provide a physical understanding of the sources and limitations of predictability for using multiyear La Nin˜ a forecasts to predict drought in the Horn of Africa

Application of the pMHC array to characterise tumour antigen specific T cell populations in leukaemia patients at disease diagnosis

Immunotherapy treatments for cancer are becoming increasingly successful, however to further improve our understanding of the T-cell recognition involved in effective responses and to encourage moves towards the development of personalised treatments for leukaemia immunotherapy, precise antigenic targets in individual patients have been identified. Cellular arrays using peptide-MHC (pMHC) tetramers allow the simultaneous detection of different antigen specific T-cell populations naturally circulating in patients and normal donors. We have developed the pMHC array to detect CD8+ T-cell populations in leukaemia patients that recognise epitopes within viral antigens (cytomegalovirus (CMV) and influenza (Flu)) and leukaemia antigens (including Per Arnt Sim domain 1 (PASD1), MelanA, Wilms’ Tumour (WT1) and tyrosinase). We show that the pMHC array is at least as sensitive as flow cytometry and has the potential to rapidly identify more than 40 specific T-cell populations in a small sample of T-cells (0.8–1.4 x 106). Fourteen of the twenty-six acute myeloid leukaemia (AML) patients analysed had T cells that recognised tumour antigen epitopes, and eight of these recognised PASD1 epitopes. Other tumour epitopes recognised were MelanA (n = 3), tyrosinase (n = 3) and WT1126-134 (n = 1). One of the seven acute lymphocytic leukaemia (ALL) patients analysed had T cells that recognised the MUC1950-958 epitope. In the future the pMHC array may be used provide point of care T-cell analyses, predict patient response to conventional therapy and direct personalised immunotherapy for patients

Self-similar shear-thickening behavior in CTAB/NaSal surfactant solutions

The effect of salt concentration Cs on the critical shear rate required for the onset of shear thickening and apparent relaxation time of the shear-thickened phase, has been investigated systematically for dilute CTAB/NaSal solutions. Experimental data suggest a self-similar behavior of the critical shear rate and relaxation time as functions of Cs. Specifically, the former ~ Cs^(-6) whereas the latter ~ Cs^(6) such that an effective Weissenberg number for the onset of the shear thickened phase is only weakly dependent on Cs. A procedure has been developed to collapse the apparent shear viscosity versus shear rate data obtained for various values of Cs into a single master curve. The effect of Cs on the elastic modulus and mesh size of the shear-induced gel phase for different surfactant concentrations is discussed. Experiments performed using different flow cells (Couette and cone-and-plate) show that the critical shear rate, relaxation time and the maximum viscosity attained are geometry-independent. The elastic modulus of the gel phase inferred indirectly by employing simplified hydrodynamic instability analysis of a sheared gel-fluid interface is in qualitative agreement with that predicted for an entangled phase of living polymers. A qualitative mechanism that combines the effect of Cs on average micelle length and Debye parameter with shear-induced configurational changes of rod-like micelles is proposed to rationalize the self-similarity of SIS formation.Comment: 27 pages, 17 figure

Phase 1 study of fianlimab, a human lymphocyte activation gene-3 (LAG-3) monoclonal antibody, plus cemiplimab in advanced melanoma

Background: Concurrent LAG-3 blockade may enhance efficacy of anti-program cell death-1 (PD-1) therapies such as cemiplimab. We present updated safety and clinical activity data from patients with advanced melanoma treated concurrently with cemiplimab and fianlimab (NCT03005782). Methods: Patients were included with unresectable or metastatic melanoma (excluding uveal melanoma) who were anti-PD-ligand (L) 1 treatment naive (expansion cohort [EC] 6) or anti-PD-(L)1 experienced within 3 months of screening (EC7). Patients received fianlimab 1600 mg + cemiplimab 350 mg intravenously every 3 weeks for 12 months (optional extra 12 months if clinically indicated). Tumours were measured every 6 weeks for 24 weeks, then every 9 weeks. In EC6 (n = 40) and EC7 (n = 15), respectively (data cutoff 9th February 2022), median age was 69.5 and 59.0 years, and median treatment duration was 37.1 and 9.0 weeks. Results: In EC6 and EC7, respectively, incidence of Grade ≥3 treatment-emergent adverse events (TEAEs) were 38% and 47%, incidence of serious TEAEs was 33% and 33%, and 18% and 13% of patients discontinued treatment due to a TEAE. Adrenal insufficiency rate was 13% and 7% in EC6 and EC7, respectively; no instances led to treatment discontinuation. Investigator-assessed objective response rate was63%(six complete responses; 19 partial responses) in EC6 and 13% (two partial responses) in EC7. Kaplan-Meier estimate of median progression-free survival was 14.2 (95% CI: 5.6-not estimated) months in EC6 and 1.4 (95% CI: 1.3-7.7) months in EC7. Median duration of response was not reached in EC6 or EC7. Conclusion: Fianlimab plus cemiplimab in advanced melanoma had a similar safety profile to anti-PD-1 monotherapies. Clinical activity in anti-PD-(L)1-naive patients appeared higher than previously reported for anti-PD-1monotherapy or anti-LAG-3 plus anti-PD-1. A Phase 3 trial (NCT05352672) investigating fianlimab plus cemiplimab in advanced melanoma is ongoing

Inflammatory cytokines regulate endothelial cell survival and tissue repair functions via NF-κB signaling

Inflammation contributes to the development of fibrotic and malignant diseases. We assessed the ability of inflammatory cytokines to modulate endothelial cell survival and functions related to tissue repair/remodeling. Treatment with interleukin (IL)-1β or tumor necrosis factor (TNF)-α (2 ng/mL) led to human pulmonary artery endothelial cells becoming spindle-shaped fibroblast-like cells. However, immunoblot and DNA microarray showed no change in most endothelial and mesenchymal markers. In the presence of IL-1β or TNF-α, cells were resistant to apoptosis induced by deprivation of serum and growth factor, and were more migratory. In addition, cells treated with IL-1β or TNF-α contracted collagen gels more robustly. In contrast, transforming growth factor-β1 did not induce these responses. RNA interference targeting nuclear factor (NF)-κB p65 blocked the effects of IL-1β or TNF-α on cell morphologic change, survival, migration, and collagen gel contraction. These results suggest that endothelial cells may contribute to tissue repair/remodeling via the NF-κB signaling in a milieu of airway inflammation

A Quantitative System for Studying Metastasis Using Transparent Zebrafish

Metastasis is the defining feature of advanced malignancy, yet remains challenging to study in laboratory environments. Here, we describe a high-throughput zebrafish system for comprehensive, in vivo assessment of metastatic biology. First, we generated several stable cell lines from melanomas of transgenic mitfa-BRAF[superscript V600E];p53[superscript −/−] fish. We then transplanted the melanoma cells into the transparent casper strain to enable highly quantitative measurement of the metastatic process at single-cell resolution. Using computational image analysis of the resulting metastases, we generated a metastasis score, μ, that can be applied to quantitative comparison of metastatic capacity between experimental conditions. Furthermore, image analysis also provided estimates of the frequency of metastasis-initiating cells (∼1/120,000 cells). Finally, we determined that the degree of pigmentation is a key feature defining cells with metastatic capability. The small size and rapid generation of progeny combined with superior imaging tools make zebrafish ideal for unbiased high-throughput investigations of cell-intrinsic or microenvironmental modifiers of metastasis. The approaches described here are readily applicable to other tumor types and thus serve to complement studies also employing murine and human cell culture systems.National Institutes of Health (U.S.) (Directors New Innovator Award DP2CA186572 and K08AR055368)Melanoma Research Alliance (Young Investigator Award)American Association for Cancer Research/American Society of Clinical Oncology (Young Investigator Award)Memorial Sloan-Kettering Cancer Center. Alan and Sandra Gerry Metastasis Research InitiativeHoward Hughes Medical Institut