Both SIV and SHIV are powerful tools for evaluating antibody-mediated prevention and treatment of HIV-1. However, owing to a lack of rhesus-derived SIV broadly neutralizing antibodies (bnAbs), ...testing of bnAbs for HIV-1 prevention or treatment has thus far been performed exclusively in the SHIV NHP model using bnAbs from HIV-1-infected individuals. Here we describe the isolation and characterization of multiple rhesus-derived SIV bnAbs capable of neutralizing most isolates of SIV. Eight antibodies belonging to two clonal families, ITS102 and ITS103, which target unique epitopes in the CD4 binding site (CD4bs) region, were found to be broadly neutralizing and together neutralized all SIV strains tested. A rare feature of these bnAbs and two additional antibody families, ITS92 and ITS101, which mediate strain-specific neutralizing activity against SIV from sooty mangabeys (SIVsm), was their ability to achieve near complete (i.e. 100%) neutralization of moderately and highly neutralization-resistant SIV. Overall, these newly identified SIV bnAbs highlight the potential for evaluating HIV-1 prophylactic and therapeutic interventions using fully simian, rhesus-derived bnAbs in the SIV NHP model, thereby circumventing issues related to rapid antibody clearance of human-derived antibodies, Fc mismatch and limited genetic diversity of SHIV compared to SIV.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
High-dimensional flow cytometry is the gold standard to study the human immune system in large cohorts. However, large sample sizes increase inter-experimental variation because of technical and ...experimental inaccuracies introduced by batch variability. Our high-throughput sample processing pipeline in combination with 28-color flow cytometry focuses on increased throughput (192 samples/experiment) and high reproducibility. We implemented quality control checkpoints to reduce technical and experimental variation. Finally, we integrated FlowSOM clustering to facilitate automated data analysis and demonstrate the reproducibility of our pipeline in a study with 3,357 samples. We reveal age-associated immune dynamics in 2,300 individuals, signified by decreasing T and B cell subsets with age. In addition, by combining genetic analyses, our approach revealed unique immune signatures associated with a single nucleotide polymorphism (SNP) that abrogates CD45 isoform splicing. In summary, we provide a versatile and reliable high-throughput, flow cytometry-based pipeline for immune discovery and exploration in large cohorts.
Display omitted
•We provide a sample handling and analysis pipeline for large flow cytometry studies•Pipeline is optimized for high throughput and data precision and minimizes errors•Quality controls quantify technical and experimental variation and data precision•Automated data pre-processing and unsupervised data analysis enable fast discovery
Flow cytometry-based immunophenotyping studies are crucial in human immunology research. However, large sample sizes cause non-biological data variation, which impacts precision. We developed a sample processing and analysis pipeline for high-dimensional flow cytometry that focuses on sample throughput and incorporates stringent instrument standardization, staining protocols, quality controls, and unsupervised data analysis. These measures mitigate batch effect and experimental errors and increase data precision. With our pipeline we measured 3,357 samples in 19 experiments and obtained minimal non-biological variation, showcasing its usability for large immunophenotyping studies.
Flow cytometry studies are often impacted by inter-assay data variation and low throughput, which compromises data precision. Liechti et al. provide a comprehensive high-throughput platform for large, high-dimensional flow cytometry immunophenotyping studies. Several quality controls ensure minimal experimental errors and high data precision. Furthermore, the automated, unsupervised data analysis pipeline enables rapid biological discovery.
The present study reveals cross-season connections of rainfall variability in the South China Sea (SCS) region between winter and summer. Rainfall anomalies over northern South China Sea in boreal ...summer tend to be preceded by the same sign rainfall anomalies over southern South China Sea in boreal winter (denoted as in-phase relation) and succeeded by opposite sign rainfall anomalies over southern South China Sea in the following winter (denoted as out-of-phase relation). Analysis shows that the in-phase relation from winter to summer occurs more often in El Niño/La Niña decaying years and the out-of-phase relation from summer to winter appears more frequently in El Niño/La Niña developing years. In the summer during the El Niño/La Niña decaying years, cold/warm and warm/cold sea surface temperature (SST) anomalies develop in tropical central North Pacific and the North Indian Ocean, respectively, forming an east–west contrast pattern. The in-phase relation is associated with the influence of anomalous heating/cooling over the equatorial central Pacific during the mature phase of El Niño/La Niña events that suppresses/enhances precipitation over southern South China Sea and the impact of the above east–west SST anomaly pattern that reduces/increases precipitation over northern South China Sea during the following summer. The impact of the east–west contrast SST anomaly pattern is confirmed by numerical experiments with specified SST anomalies. In the El Niño/La Niña developing years, regional air-sea interactions induce cold/warm SST anomalies in the equatorial western North Pacific. The out-of-phase relation is associated with a Rossby wave type response to anomalous heating/cooling over the equatorial central Pacific during summer and the combined effect of warm/cold SST anomalies in the equatorial central Pacific and cold/warm SST anomalies in the western North Pacific during the mature phase of El Niño/La Niña events.
This study re-explores the roles of tropical SST anomalies in modulating the anomalous cyclone over the Indo-western Pacific during strong La Niña decaying years via a series of numerical ...experiments. The results suggest that central to eastern equatorial Pacific cooling, western north Pacific (WNP) warming, and Indian Ocean cooling all contribute to the Indo-western Pacific cyclonic wind anomalies. The WNP SST anomalies play a role via a Rossby wave-type response. As the positive SST anomalies in the WNP decay, the local forcing effect decays as well. The Indian Ocean remote forcing seems to play an important role during boreal summer via cold Kelvin wave induced cyclonic shear and boundary layer convergence. During strong La Niña decaying years, the negative SST anomalies in the equatorial central to eastern Pacific can maintain and persist into summer. Such cooling could induce anomalous Walker circulation with ascending branch over the Maritime Continent to Philippines and descending branch over central to eastern Pacific, which links the WNP climate to the equatorial central and eastern Pacific SST anomalies. The convective heating over the WNP induced remotely by central to eastern Pacific cooling in turn forces atmospheric Rossby wave to its west, which may amplify the anomalous cyclone over the Indo-western Pacific.
Atmospheric Rivers (ARs), corridors of intensive water vapor transport, have received much attention recently due to their potentially large economic and societal impacts. However, a comprehensive ...understanding of the interannual variability of ARs over East Asia is still lacking. This study examines the frequency of AR occurrence over East Asia based on the EAR5 reanalysis. It is shown that the frequency of AR occurrence over East Asia displays obvious seasonality, with its peak in early boreal summer. ARs contribute to up to 50% of total precipitation and largely modulate the interannual variability of precipitation in East Asia during early boreal summer. The interannual variability of ARs over East Asia during early boreal summer is largely controlled by the Indo-western Pacific Ocean Capacitor (IPOC) effect, which is mainly triggered by El Niño-Southern Oscillation and sometimes by Indian Ocean dipole. During early boreal summer, a higher frequency of AR occurrence over East Asia is associated with anomalous anticyclonic circulation (AAC) over the Indo-western Pacific region. The AAC, the atmospheric signal of the IPOC mode, indicates an enhanced East Asian summer monsoon and a northwestward shift of the western North Pacific subtropical high, favoring the AR occurrence over East Asia. This study illustrates that a strong positive Indian Ocean dipole event could impact AR activity over East Asia in the following summer by triggering the IPOC effect. The IPOC-related signals 2–4 months ahead could be useful to predict the AR occurrence over East Asia during early boreal summer.
This study investigates the influence of southeast tropical Indian Ocean (SETIO) sea surface temperature (SST) warming on Indo-Pacific climate during the decaying phase of the 2015/16 El Niño by ...using observations and model experiments. The results show that the SETIO SST warming in spring 2016 enhanced local convection and forced a “C-shape” wind anomaly pattern in the lower troposphere. The “C-shape” wind anomaly pattern over the eastern tropical Indian Ocean consists of anomalous westerly flow south of the equator and anomalous easterly flow north of the equator. The anomalous easterly flow then extended eastward into the western North Pacific (WNP) and facilitates the development or the maintenance of an anomalous anticyclone over the South China Sea (SCS). Correspondingly, the eastern part of the Bay of Bengal, the SCS and the WNP suffered less rainfall. Such precipitation features and the associated “C-shape” wind anomaly pattern shifted northward about five latitudes in summer 2016. Additionally, the SETIO warming can induce local meridional circulation anomalies, which directly affect Indo-Pacific climate. Numerical model experiments further confirm that the SETIO SST warming plays an important role in modulating Indo-Pacific climate.
The south tropical Indian Ocean (TIO) warms following a strong El Niño, affecting Indo-Pacific climate in early boreal summer. While much attention has been given to the southwest TIO where the mean ...thermocline is shallow, this study focuses on the subsequent warming in the southeast TIO, where the mean sea surface temperature (SST) is high and deep convection is strong in early summer. The southeast TIO warming induces an anomalous meridional circulation with descending (ascending) motion over the northeast (southeast) TIO. It further anchors a “C-shaped” surface wind anomaly pattern with easterlies (westerlies) in the northeast (southeast) TIO, causing a persistent northeast TIO warming via wind–evaporation–SST feedback. The southeast TIO warming lags the southwest TIO warming by about one season. Ocean wave dynamics play a key role in linking the southwest and southeast TIO warming. South of the equator, the El Niño–forced oceanic Rossby waves, which contribute to the southwest TIO warming, are reflected as eastward-propagating oceanic Kelvin waves along the equator on the western boundary. The Kelvin waves subsequently depress the thermocline and develop the southeast TIO warming.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Abstract Tropical cyclones (TCs), commonly called as cyclones in the southern Indian Ocean (SIO), represent one of the most devastating disasters in the oceanfront regions of Africa. The present ...study explores the long-term tendency of annual mean TC genesis location in the SIO. A notable westward shift is detected in the SIO TC genesis longitude since 1979, which is linked to an increase in the TC genesis frequency in the southwestern SIO and a decrease in the TC genesis frequency in the northeastern SIO. The dipole trend pattern of the TC genesis frequency in the SIO is intimately linked to the weakening of westerly vertical wind shear over the western SIO and the strengthening of easterly vertical wind shear over the eastern SIO, resulting from a reduced meridional temperature gradient. The weakened meridional temperature gradient is attributed to the enhanced warming of the subtropical troposphere that is a response of atmospheric temperature to global warming. Our study implies a potential increase in the risks faced by coastal and island countries in eastern Africa.
This study examines the climate response to a sea surface temperature (SST) warming imposed over the southwest tropical Indian Ocean (TIO) in a coupled ocean–atmosphere model. The results indicate ...that the southwest TIO SST warming can remotely modulate the atmospheric circulation over the western North Pacific Ocean (WNP) via interbasin air–sea interaction during early boreal summer. The southwest TIO SST warming induces a "C shaped" wind response with northeasterly and northwesterly anomalies over the north and south TIO, respectively. The northeasterly wind anomalies contribute to the north TIO SST warming via a positive wind–evaporation–SST (WES) feedback after the Asian summer monsoon onset. In June, the easterly wind response extends into the WNP, inducing an SST cooling by WES feedback on the background trade winds. Both the north TIO SST warming and the WNP SST cooling contribute to an anomalous anticyclonic circulation (AAC) over the WNP. The north TIO SST warming, WNP SST cooling, and AAC constitute an interbasin coupled mode called the Indo-western Pacific Ocean capacitor (IPOC), and the southwest TIO SST warming could be a trigger for IPOC. While the summertime southwest TIO SST warming is often associated with antecedent El Niño, the warming in 2020 seems to be related to extreme Indian Ocean dipole during the autumn of 2019. The strong southwest TIO SST warming seems to partly explain the strong summer AAC of 2020 over the WNP even without a strong antecedent El Niño.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Abstract
The variation of tropical cyclone (TC) genesis over the North Indian Ocean (NIO) and South China Sea (SCS) during the post‐monsoon season is explored during 1979–2020. A zonal see‐saw ...variation of TC genesis is detected between the Arabian Sea (AS) and Bay of Bengal (BOB) –SCS (BOBSCS for brevity). More (less) TCs over the AS tend to concur with fewer (more) TCs over the BOBSCS. Analyses of both the observations and the Coupled Model Intercomparison Project Phase 6 outputs show that tripole sea surface temperature (SST) anomalies in the tropical Indian and Pacific Oceans play a crucial role in the zonal see‐saw variation of TC genesis. Positive western Indian (WI) Ocean and tropical central and eastern Pacific (CEP) Ocean SST anomalies and negative western Pacific (WP) SST anomalies induce anomalous ascending and descending motions and high and low humidity transportation to the middle troposphere over the AS and BOBSCS, respectively. Meantime, anticyclonic vorticity anomalies appear in the BOBSCS region and negative anomalies of vertical wind shear are induced over the NIO and SCS. The combined positive contributions of upward motion, mid‐level humidity increase, and low vertical wind shear favor higher TC genesis over the AS, whereas the joint negative effects of downward motion, mid‐level water vapor decrease, and lower‐level anticyclonic vorticity anomalies result in less TC genesis over the BOBSCS. Numerical experiments show a critical role of the WI SST anomalies in the dipole pattern of vertical motion, which is crucial for the zonal dipole variation of TC genesis.
Plain Language Summary
Although the tropical cyclones (TCs) frequency number that form over the South China Sea (SCS), Bay of Bengal (BOB) and Arabian Sea (AS) are relatively small, these regions are densely populated, which means that the impacts of TCs can be significant and widespread. The study presents observational and modeling evidence for a see‐saw variation of tropical cyclogenesis between the AS and BOB‐SCS during the post‐monsoon season (September–December). Composite analyses display that the zonal see‐saw connection of tropical cyclogenesis frequency over the AS and BOB‐SCS is closely linked to the zonal tripole distribution of the sea surface temperature anomalies over the tropics of the Indian and Pacific Oceans, which exert a significant influence on the vertical–zonal overturning circulation and the environmental parameters for TC formation over the AS and BOB‐SCS. We conduct an evaluation of 19 CMIP6/AMIP (CMIP6/CMIP) simulations and reveal that 53% (26%) models are able to successfully simulate the zonal dipole pattern of TC‐related variables between AS and BOB‐SCS regions. The present findings may have the potential to enhance the seasonal prediction for tropical cyclogenesis over the SCS, AS and BOB regions.
Key Points
A zonal see‐saw variation of TC genesis is detected between the Arabian Sea (AS) and the Bay of Bengal‐South China Sea (BOBSCS)
The tripole SST anomalies over the tropical Indian and Pacific Oceans play a crucial role in the zonal see‐saw variation of TC genesis
Numerical experiments show a critical role of SST anomalies in the western Indian Ocean in the dipole pattern of vertical motion
