Author Correction: El Niño-Southern Oscillation complexity.

In this Review, the middle initial of author Kim M. Cobb was omitted. The original Review has been corrected online.

El Niño-Southern Oscillation complexity.

El Niño events are characterized by surface warming of the tropical Pacific Ocean and weakening of equatorial trade winds that occur every few years. Such conditions are accompanied by changes in atmospheric and oceanic circulation, affecting global climate, marine and terrestrial ecosystems, fisheries and human activities. The alternation of warm El Niño and cold La Niña conditions, referred to as the El Niño-Southern Oscillation (ENSO), represents the strongest year-to-year fluctuation of the global climate system. Here we provide a synopsis of our current understanding of the spatio-temporal complexity of this important climate mode and its influence on the Earth system.

Robust twenty-first-century projections of El Niño and related precipitation variability.

The El Niño-Southern Oscillation (ENSO) drives substantial variability in rainfall, severe weather, agricultural production, ecosystems and disease in many parts of the world. Given that further human-forced changes in the Earth's climate system seem inevitable, the possibility exists that the character of ENSO and its impacts might change over the coming century. Although this issue has been investigated many times during the past 20 years, there is very little consensus on future changes in ENSO, apart from an expectation that ENSO will continue to be a dominant source of year-to-year variability. Here we show that there are in fact robust projected changes in the spatial patterns of year-to-year ENSO-driven variability in both surface temperature and precipitation. These changes are evident in the two most recent generations of climate models, using four different scenarios for CO2 and other radiatively active gases. By the mid- to late twenty-first century, the projections include an intensification of both El-Niño-driven drying in the western Pacific Ocean and rainfall increases in the central and eastern equatorial Pacific. Experiments with an Atmospheric General Circulation Model reveal that robust projected changes in precipitation anomalies during El Niño years are primarily determined by a nonlinear response to surface global warming. Uncertain projected changes in the amplitude of ENSO-driven surface temperature variability have only a secondary role. Projected changes in key characteristics of ENSO are consequently much clearer than previously realized.

More extreme swings of the South Pacific convergence zone due to greenhouse warming.

The South Pacific convergence zone (SPCZ) is the Southern Hemisphere's most expansive and persistent rain band, extending from the equatorial western Pacific Ocean southeastward towards French Polynesia. Owing to its strong rainfall gradient, a small displacement in the position of the SPCZ causes drastic changes to hydroclimatic conditions and the frequency of extreme weather events--such as droughts, floods and tropical cyclones--experienced by vulnerable island countries in the region. The SPCZ position varies from its climatological mean location with the El Niño/Southern Oscillation (ENSO), moving a few degrees northward during moderate El Niño events and southward during La Niña events. During strong El Niño events, however, the SPCZ undergoes an extreme swing--by up to ten degrees of latitude toward the Equator--and collapses to a more zonally oriented structure with commensurately severe weather impacts. Understanding changes in the characteristics of the SPCZ in a changing climate is therefore of broad scientific and socioeconomic interest. Here we present climate modelling evidence for a near doubling in the occurrences of zonal SPCZ events between the periods 1891-1990 and 1991-2090 in response to greenhouse warming, even in the absence of a consensus on how ENSO will change. We estimate the increase in zonal SPCZ events from an aggregation of the climate models in the Coupled Model Intercomparison Project phases 3 and 5 (CMIP3 and CMIP5) multi-model database that are able to simulate such events. The change is caused by a projected enhanced equatorial warming in the Pacific and may lead to more frequent occurrences of extreme events across the Pacific island nations most affected by zonal SPCZ events.

Australia's Tinderbox Drought: An extreme natural event likely worsened by human-caused climate change.

We examine the characteristics and causes of southeast Australia's Tinderbox Drought (2017 to 2019) that preceded the Black Summer fire disaster. The Tinderbox Drought was characterized by cool season rainfall deficits of around -50% in three consecutive years, which was exceptionally unlikely in the context of natural variability alone. The precipitation deficits were initiated and sustained by an anomalous atmospheric circulation that diverted oceanic moisture away from the region, despite traditional indicators of drought risk in southeast Australia generally being in neutral states. Moisture deficits were intensified by unusually high temperatures, high vapor pressure deficits, and sustained reductions in terrestrial water availability. Anthropogenic forcing intensified the rainfall deficits of the Tinderbox Drought by around 18% with an interquartile range of 34.9 to -13.3% highlighting the considerable uncertainty in attributing droughts of this kind to human activity. Skillful predictability of this drought was possible by incorporating multiple remote and local predictors through machine learning, providing prospects for improving forecasting of droughts.

The role of internal variability and external forcing on southwestern Australian rainfall: prospects for very wet or dry years.

The cool-season (May to October) rainfall decline in southwestern Australia deepened during 2001-2020 to become 20.5% less than the 1901-1960 reference period average, with a complete absence of very wet years (i.e., rainfall > 90th percentile). CMIP5 and CMIP6 climate model simulations suggest that approximately 43% of the observed multi-decadal decline was externally-forced. However, the observed 20-year rainfall anomaly in 2001-2020 is outside the range of both preindustrial control and historical simulations of almost all climate models used in this study. This, and the fact that the models generally appear to simulate realistic levels of decadal variability, suggests that 43% might be an underestimate. A large ensemble from one model exhibits drying similar to the observations in 10% of simulations and suggests that the external forcing contribution is indeed larger (66%). The majority of models project further drying over the twenty-first century, even under strong cuts to greenhouse gas emissions. Under the two warmest scenarios, over 70% of the late twenty-first century years are projected to be drier than the driest year simulated during the 1901-1960 period. Our results suggest that few, if any, very wet years will occur during 2023-2100, even if strong cuts to global emissions are made.

Vapour pressure deficit determines critical thresholds for global coffee production under climate change.

Our understanding of the impact of climate change on global coffee production is largely based on studies focusing on temperature and precipitation, but other climate indicators could trigger critical threshold changes in productivity. Here, using generalized additive models and threshold regression, we investigate temperature, precipitation, soil moisture and vapour pressure deficit (VPD) effects on global Arabica coffee productivity. We show that VPD during fruit development is a key indicator of global coffee productivity, with yield declining rapidly above 0.82 kPa. The risk of exceeding this threshold rises sharply for most countries we assess, if global warming exceeds 2 °C. At 2.9 °C, countries making up 90% of global supply are more likely than not to exceed the VPD threshold. The inclusion of VPD and the identification of thresholds appear critical for understanding climate change impacts on coffee and for the design of adaptation strategies.

More accurate quantification of model-to-model agreement in externally forced climatic responses over the coming century.

Separating how model-to-model differences in the forced response (UMD) and internal variability (UIV) contribute to the uncertainty in climate projections is important, but challenging. Reducing UMD increases confidence in projections, while UIV characterises the range of possible futures that might occur purely by chance. Separating these uncertainties is limited in traditional multi-model ensembles because most models have only a small number of realisations; furthermore, some models are not independent. Here, we use six largely independent single model initial-condition large ensembles to separate the contributions of UMD and UIV in projecting 21st-century changes of temperature, precipitation, and their temporal variability under strong forcing (RCP8.5). We provide a method that produces similar results using traditional multi-model archives. While UMD is larger than UIV for both temperature and precipitation changes, UIV is larger than UMD for the changes in temporal variability of both temperature and precipitation, between 20° and 80° latitude in both hemispheres. Over large regions and for all variables considered here except temporal temperature variability, models agree on the sign of the forced response whereas they disagree widely on the magnitude. Our separation method can readily be extended to other climate variables.

Decadal climate variability in the tropical Pacific: Characteristics, causes, predictability, and prospects.

Climate variability in the tropical Pacific affects global climate on a wide range of time scales. On interannual time scales, the tropical Pacific is home to the El Niño­Southern Oscillation (ENSO). Decadal variations and changes in the tropical Pacific, referred to here collectively as tropical Pacific decadal variability (TPDV), also profoundly affect the climate system. Here, we use TPDV to refer to any form of decadal climate variability or change that occurs in the atmosphere, the ocean, and over land within the tropical Pacific. "Decadal," which we use in a broad sense to encompass multiyear through multidecadal time scales, includes variability about the mean state on decadal time scales, externally forced mean-state changes that unfold on decadal time scales, and decadal variations in the behavior of higher-frequency modes like ENSO.

Rational design of a multiepitope vaccine encoding T-lymphocyte epitopes for treatment of chronic hepatitis B virus infections.

Protein sequences from multiple hepatitis B virus (HBV) isolates were analyzed for the presence of amino acid motifs characteristic of cytotoxic T-lymphocyte (CTL) and helper T-lymphocyte (HTL) epitopes with the goal of identifying conserved epitopes suitable for use in a therapeutic vaccine. Specifically, sequences bearing HLA-A1, -A2, -A3, -A24, -B7, and -DR supertype binding motifs were identified, synthesized as peptides, and tested for binding to soluble HLA. The immunogenicity of peptides that bound with moderate to high affinity subsequently was assessed using HLA transgenic mice (CTL) and HLA cross-reacting H-2(bxd) (BALB/c x C57BL/6J) mice (HTL). Through this process, 30 CTL and 16 HTL epitopes were selected as a set that would be the most useful for vaccine design, based on epitope conservation among HBV sequences and HLA-based predicted population coverage in diverse ethnic groups. A plasmid DNA-based vaccine encoding the epitopes as a single gene product, with each epitope separated by spacer residues to enhance appropriate epitope processing, was designed. Immunogenicity testing in mice demonstrated the induction of multiple CTL and HTL responses. Furthermore, as a complementary approach, mass spectrometry allowed the identification of correctly processed and major histocompatibility complex-presented epitopes from human cells transfected with the DNA plasmid. A heterologous prime-boost immunization with the plasmid DNA and a recombinant MVA gave further enhancement of the immune responses. Thus, a multiepitope therapeutic vaccine candidate capable of stimulating those cellular immune responses thought to be essential for controlling and clearing HBV infection was successfully designed and evaluated in vitro and in HLA transgenic mice.

Generation and identification of variants with improved purification yield of Bowman-Birk protease inhibitors carrying protein binding loops.

Replacing the chymotrypsin inhibitory loop of soybean Bowman-Birk inhibitor (sBBI) with a VEGF binding peptide (BBI-AV) significantly reduces the overall purification yield when BBI-AV is produced as a fusion protein in a Bacillussubtilis expression system. The low purification yield is primarily due to a higher fraction of molecules with incorrect disulfide bond configurations after production and also after disulfide bond shuffling induced by 2-mercaptoethanol. To improve production yields, site-saturation libraries were generated at 39 out of the 66 amino acid residues of BBI-AV. Initial screens were designed to select for variants with higher trypsin inhibitory activities than the parent after treatment with a reducing agent. Secondary screens were developed to select for variants with the highest purification yields, and to also eliminate any false positives. From the screens, it was found that positively charged substitutions in the exposed hydrophobic patch region (sites 27, 29, 40, 50 & 52) are especially productive. In fact, one substitution, F50R, improves the purification yield to nearly the same level as wild-type sBBI. Productive amino acid substitutions were combined to select for the variant with the best overall yield after purification. Several variants were obtained with higher purification yields than even sBBI. The octuple variants, A13I-S25R-M27A-L29P-S31A-A40H-F50K-V52T and A13I-S25K-M27A-L29R-S31E-A40K-F50Q-V52Q, are particularly productive having greater than a five fold increase in final purification yield over the parent.

The role of the South Pacific in modulating Tropical Pacific variability.

Tropical Pacific variability (TPV) heavily influences global climate, but much is still unknown about its drivers. We examine the impact of South Pacific variability on the modes of TPV: the El Niño-Southern Oscillation (ENSO) and the Interdecadal Pacific Oscillation (IPO). We conduct idealised coupled experiments in which we suppress temperature and salinity variability at all oceanic levels in the South Pacific. This reduces decadal variability in the equatorial Pacific by ~30% and distorts the spatial pattern of the IPO. There is little change to overall interannual variability, however there is a decrease in the magnitude of the largest 5% of both El Niño and La Niña sea-surface temperature (SST) anomalies. Possible reasons for this include: (i) reduced decadal variability means that interannual SST variability is superposed onto a 'flatter' background signal, (ii) suppressing South Pacific variability leads to the alteration of coupled processes linking the South and equatorial Pacific. A small but significant mean state change arising from the imposed suppression may also contribute to the weakened extreme ENSO SST anomalies. The magnitude of both extreme El Niño and La Niña SST anomalies are reduced, and the associated spatial patterns of change of upper ocean heat content and wind stress anomalies are markedly different for both types of events.

Humans have already increased the risk of major disruptions to Pacific rainfall.

Intermittent disruptions to rainfall patterns and intensity over the Pacific Ocean lasting up to ∼ 1 year have major impacts on severe weather, agricultural production, ecosystems, and disease within the Pacific, and in many countries beyond. The frequency with which major disruptions to Pacific rainfall occur has been projected to increase over the 21st century, in response to global warming caused by large 21st century greenhouse gas emissions. Here we use the latest generation of climate models to show that humans may have contributed to the major disruption that occurred in the real world during the late 20th century. We demonstrate that although marked and sustained reductions in 21st century anthropogenic greenhouse gas emissions can greatly moderate the likelihood of major disruption, elevated risk of occurrence appears locked in now, and for at least the remainder of the 21st century.

Human population-based identification of CD4(+) T-cell peptide epitope determinants.

A human cell-based method to identify functional CD4(+) T-cell epitopes in any protein has been developed. Proteins are tested as synthetic 15-mer peptides offset by three amino acids. Percent responses within a large donor population are tabulated for each peptide in the set. Peptide epitope regions are designated by difference in response frequency from the overall background response rate for the compiled dataset. Epitope peptide responses are reproducible, with a median coefficient of variance of 21% when tested on multiple random-donor sets. The overall average response rate within the dataset increases with increasing putative human population antigenic exposure to a given protein. The background rate was high for HPV16 E6, and was low for human-derived cytokine proteins. The assay identified recall epitope regions within the donor population for the protein staphylokinase. For an industrial protease with minimal presumed population exposure, immunodominant epitope peptides were identified that were found to bind promiscuously to many HLA class II molecules in vitro. The peptide epitope regions identified in presumably unexposed donors represent a subset of the total recall epitopes. Finally, as a negative control, the assay found no peptide epitope regions in human beta2-microglobulin. This method identifies functional CD4(+) T-cell epitopes in any protein without pre-selection for HLA class II, suggests whether a donor population is pre-exposed to a protein of interest, and does not require sensitized donors for in vitro testing.

A human dendritic cell-based method to identify CD4+ T-cell epitopes in potential protein allergens.

We developed an assay to determine the location of immunodominant CD4(+) T-cell epitopes in any protein. The method uses CD4(+) T cells from community donors in conjunction with dendritic cells derived in vitro. Synthetic peptides constructed to describe the sequence of the protein of interest are cocultured with dendritic cells and CD4(+) T cells, and T-cell proliferation is measured. Data are compiled over a large replicate of human donors to pinpoint immunodominant, usually promiscuous epitope regions. We have applied this technique to a known food allergen, the Brazil nut 2S storage globulin protein, and to two potential food allergens, the Cry1Ab and Cry3Aa proteins. We show epitope data for these three proteins. This assay can be used as a tool to guide the selection and qualification of future potential food transgenes.

A Bacillus subtilis fusion protein system to produce soybean Bowman-Birk protease inhibitor.

A fusion protein based expression system was developed in the Gram-positive bacterium Bacillus subtilis to produce the soybean Bowman-Birk protease inhibitor (sBBI). The N-terminus of the mature sBBI was fused to the C-terminus of the 1st cellulose binding domain linker (CBD linker) of the BCE103 cellulase (from an alkalophilic Bacillus sp.). The strong aprE promoter was used to drive the transcription of the fusion gene and the AprE signal sequence was fused to the mature BCE103 cellulase for efficient secretion of the fusion protein into the culture medium. It was necessary to use a B. subtilis strain deficient in nine protease genes in order to reduce the proteolytic degradation of the fusion protein during growth. The fusion protein was produced in shake flasks at concentrations >1g/L. After growth, the sBBI was activated by treatment with 2-mercaptoethanol to allow the disulfide bonds to form correctly. An economical and scalable purification process was developed to purify sBBI based on acid precipitation of the fusion protein followed by acid/heat cleavage of the fusion protein at labile Asp-Pro bonds in the CBD linker. If necessary, non-native amino acids at the N- and C-termini were trimmed off using glutamyl endopeptidase I. After purification, an average of 72 mg of active sBBI were obtained from 1L of culture broth representing an overall yield of 21% based on the amount of sBBI activated before purification.

Cloning and relational analysis of 15 novel fungal endoglucanases from family 12 glycosyl hydrolase.

Cellulases belong to the large family of glycosyl hydrolases (GHs) and are produced by a variety of bacteria and fungi. These extracellular enzymes act as endoglucanases (EGs), cellobiohydrolases or beta-glucosidases. In this paper, we describe molecular screening for EGs from the GH family 12. Using three homologous sequence boxes deduced from five previously known members of the family, we analysed 22 cellulase-producing fungal strains obtained from a diverse area of the fungal kingdom. Polymerase chain reactions using degenerate primers designed to the homologous protein boxes were used to identify the family 12 homologues. Several fungi showed the presence of multiple versions of the gene, while amino acid sequence analysis showed diversity in 15 novel members of the family, ranging from 26% to 96% similarity. Our sequence analysis shows that the phylogenetic tree of family 12 EGs can be divided into four subfamilies: 12-1 (fungal group I), 12-2 (fungal group II), 12-3 ( Streptomyces group in which Rhodothermus marinus fits) and 12-4 ( Thermophiles group). Erwinia carotovora may form a new subgroup.