Ice nucleation properties of mineral dusts

Ice nucleation in clouds has a significant impact on the global hydrological cycle as well as on the radiative budget of the Earth. The AIDA cloud chamber was used to investigate the ice nucleation efficiency of various atmospherically relevant mineral dusts. From experiments with Arizona Test Dust (ATD) a humidity and temperature dependent ice nucleation active surface site density parameterization was developed to describe deposition nucleation at temperatures above 220 K. Based on these results, a parameterization for deposition nucleation initiated by desert dusts and clay minerals is proposed. The time dependence observed during the deposition nucleation experiments with ATD seems to be relevant only at very small cooling rates. Experiments with atmospherically relevant dust samples revealed large differences in the ice nucleation efficiencies among the different dusts. Volcanic ash emitted during the Eyjafjallajökull eruption in 2010 proved to be slightly less ice-active than mineral dust particles from desert areas. In contrast, soil dust particles rich in organic matter and fossile diatomite were very ice-active particles. For the soil dust particles, the soil organic matter is probably the reason for the enhanced ice nucleation efficiency compared to desert dusts which is, however, most likely not directly determined by viable organisms such as fungi or bacteria. Coatings with secondary organic compounds led to a significant deterioration of the ice nucleation efficiency observed for fossil diatomite in the immersion freezing and the deposition nucleation mode. Deposition mode nucleation initiated by mineral dust particles was suppressed by coatings with sulfuric acid whereas there was no effect on the immersion freezing properties. The immersion freezing properties of several substrates used as ice nuclei substitutes were investigated with a cold stage setup. Muscovite initiated heterogeneous ice nucleation at approximately 250 K but was much less ice-active than mineral dusts. Droplets placed on silicon wafers froze only close to the homogeneous freezing threshold. The freezing properties of these silicon wafers could be changed signicantly by modifying the wafer surface through adding regular structures such as trenches which suggests that the surface morphology may have an influence on the ice nucleation efficiencies of atmospheric particles

Pre-activation of ice-nucleating particles by the pore condensation and freezing mechanism

In spite of the resurgence in ice nucleation research a comparatively small number of studies deal with the phenomenon of pre-activation in heterogeneous ice nucleation. Fifty years ago, it was shown that various mineral dust and volcanic ash particles can be pre-activated to become nuclei for ice crystal formation even at temperatures as high as 270-271 K. Pre-activation was achieved under ice-subsaturated conditions without any preceding macroscopic ice growth by just temporarily cooling the particles to temperatures below 228 K. A two-step mechanism involving capillary condensation of supercooled water and subsequent homogeneous freezing was proposed to account for the particles\u27 enhanced ice nucleation ability at high temperatures. This work reinvestigates the efficiency of the proposed pre-activation mechanism in temperature-cycling experiments performed in a large cloud chamber with suspended particles. We find the efficiency to be highest for the clay mineral illite as well as for highly porous materials like zeolite and diatomaceous earth, whereas most aerosols generated from desert dust surface samples did not reveal a measurable pre-activation ability. The pre-activation efficiency is linked to particle pores in a certain size range. As estimated by model calculations, only pores with diameters between about 5 and 8 nm contribute to pre-activation under ice-subsaturated conditions. This range is set by a combination of requirements from the negative Kelvin effect for condensation and a critical size of ice embryos for ice nucleation and melting. In contrast to the early study, pre-activation is only observed for temperatures below 260 K. Above that threshold, the particles\u27 improved ice nucleation ability disappears due to the melting of ice in the pores

Complex plant-derived organic aerosol as ice-nucleating particles – more than the sums of their parts?

Quantifying the impact of complex organic particles on the formation of ice crystals in clouds remains challenging, mostly due to the vast number of different sources ranging from sea spray to agricultural areas. In particular, there are many open questions regarding the ice nucleation properties of organic particles released from terrestrial sources such as decaying plant material. In this work, we present results from laboratory studies investigating the immersion freezing properties of individual organic compounds commonly found in plant tissue and complex organic aerosol particles from vegetated environments, without specifically investigating the contribution from biological particles, which may contribute to the overall ice nucleation efficiency observed at high temperatures. To characterize the ice nucleation properties of plant-related aerosol samples for temperatures between 242 and 267 K, we used the Aerosol Interaction and Dynamics in the Atmosphere (AIDA) cloud chamber and the Ice Nucleation SpEctrometer of the Karlsruhe Institute of Technology (INSEKT), which is a droplet freezing assay. Individual plant components (polysaccharides, lignin, soy and rice protein) were mostly less ice active, or similarly ice active, compared to microcrystalline cellulose, which has been suggested by recent studies to be a proxy for quantifying the primary cloud ice formation caused by particles originating from vegetation. In contrast, samples from ambient sources with a complex organic matter composition (agricultural soils and leaf litter) were either similarly ice active or up to 2 orders of magnitude more ice active than cellulose. Of all individual organic plant components, only carnauba wax (i.e., lipids) showed a similarly high ice nucleation activity as that of the samples from vegetated environments over a temperature range between 245 and 252 K. Hence, based on our experimental results, we suggest considering cellulose as being representative for the average ice nucleation activity of plant-derived particles, whereas lignin and plant proteins tend to provide a lower limit. In contrast, complex biogenic particles may exhibit ice nucleation activities which are up to 2 orders of magnitude higher than observed for cellulose, making ambient plant-derived particles a potentially important contributor to the population of ice-nucleating particles in the troposphere, even though major uncertainties regarding their transport to cloud altitude remain

Intensifying inequality? Gendered trends in commercializing and diversifying smallholder farming systems in East Africa

While the commercialization and diversification of agricultural and livestock systems have been identified as key global strategies for climate change adaptation and mitigation, less is known as to the large-scale gendered impacts that are implicated in these transformations among smallholder crop and livestock farmers. This study explores these gender impacts across different farming systems and gender-respondent-household typologies using data from the Rural Household Multiple Indicator Survey (RHoMIS) in 2,859 households in three East African countries – Ethiopia, Kenya, and Tanzania. Female control scores over incomes or foodstuffs produced through both on and off farm activities were highest in farming systems that had more land and more livestock. However, increasing commercialization – defined herein as the increasing importance of crop and livestock sales to farm households – resulted in an overall decline in female control across all farming systems and gender-respondent-household typologies. In contrast, crop and livestock diversification were positively associated with female control across gender-respondent-household typologies. Analysis of specific crops and livestock products across farming systems and respondent typologies revealed women have far greater control over decisions related to consumption than decisions related to sales, although the gap between the two were less pronounced in lesser-valued livestock products (chickens, eggs). However, the analyses suggest that as sale of crops and livestock increase, female control over these areas could likely diminish, regardless of specific activity. The authors conclude that approaches to adapt to or mitigate climate change that rely on increasing market orientation of smallholder production will likely intensify men's control over benefits from production, whereas diversification will likely have a more positive impact on female control. Thus, climate adaptation strategies promoting increased diversification will likely have a more positive impact on women smallholders than commercialization alone. The authors recommend that when commercialization is the target intervention, it must be accompanied by a gender differentiated analysis of trade-offs and risks to mitigate the potential negative consequences shown in this study

Twist exome capture allows for lower average sequence coverage in clinical exome sequencing

Background Exome and genome sequencing are the predominant techniques in the diagnosis and research of genetic disorders. Sufficient, uniform and reproducible/consistent sequence coverage is a main determinant for the sensitivity to detect single-nucleotide (SNVs) and copy number variants (CNVs). Here we compared the ability to obtain comprehensive exome coverage for recent exome capture kits and genome sequencing techniques. Results We compared three different widely used enrichment kits (Agilent SureSelect Human All Exon V5, Agilent SureSelect Human All Exon V7 and Twist Bioscience) as well as short-read and long-read WGS. We show that the Twist exome capture significantly improves complete coverage and coverage uniformity across coding regions compared to other exome capture kits. Twist performance is comparable to that of both short- and long-read whole genome sequencing. Additionally, we show that even at a reduced average coverage of 70× there is only minimal loss in sensitivity for SNV and CNV detection. Conclusion We conclude that exome sequencing with Twist represents a significant improvement and could be performed at lower sequence coverage compared to other exome capture techniques

A Solve-RD ClinVar-based reanalysis of 1522 index cases from ERN-ITHACA reveals common pitfalls and misinterpretations in exome sequencing

Purpose Within the Solve-RD project (https://solve-rd.eu/), the European Reference Network for Intellectual disability, TeleHealth, Autism and Congenital Anomalies aimed to investigate whether a reanalysis of exomes from unsolved cases based on ClinVar annotations could establish additional diagnoses. We present the results of the “ClinVar low-hanging fruit” reanalysis, reasons for the failure of previous analyses, and lessons learned. Methods Data from the first 3576 exomes (1522 probands and 2054 relatives) collected from European Reference Network for Intellectual disability, TeleHealth, Autism and Congenital Anomalies was reanalyzed by the Solve-RD consortium by evaluating for the presence of single-nucleotide variant, and small insertions and deletions already reported as (likely) pathogenic in ClinVar. Variants were filtered according to frequency, genotype, and mode of inheritance and reinterpreted. Results We identified causal variants in 59 cases (3.9%), 50 of them also raised by other approaches and 9 leading to new diagnoses, highlighting interpretation challenges: variants in genes not known to be involved in human disease at the time of the first analysis, misleading genotypes, or variants undetected by local pipelines (variants in off-target regions, low quality filters, low allelic balance, or high frequency). Conclusion The “ClinVar low-hanging fruit” analysis represents an effective, fast, and easy approach to recover causal variants from exome sequencing data, herewith contributing to the reduction of the diagnostic deadlock

Solving patients with rare diseases through programmatic reanalysis of genome-phenome data.

Funder: EC | EC Seventh Framework Programm | FP7 Health (FP7-HEALTH - Specific Programme "Cooperation": Health); doi: https://doi.org/10.13039/100011272; Grant(s): 305444, 305444Funder: Ministerio de Economía y Competitividad (Ministry of Economy and Competitiveness); doi: https://doi.org/10.13039/501100003329Funder: Generalitat de Catalunya (Government of Catalonia); doi: https://doi.org/10.13039/501100002809Funder: EC | European Regional Development Fund (Europski Fond za Regionalni Razvoj); doi: https://doi.org/10.13039/501100008530Funder: Instituto Nacional de Bioinformática ELIXIR Implementation Studies Centro de Excelencia Severo OchoaFunder: EC | EC Seventh Framework Programm | FP7 Health (FP7-HEALTH - Specific Programme "Cooperation": Health)Reanalysis of inconclusive exome/genome sequencing data increases the diagnosis yield of patients with rare diseases. However, the cost and efforts required for reanalysis prevent its routine implementation in research and clinical environments. The Solve-RD project aims to reveal the molecular causes underlying undiagnosed rare diseases. One of the goals is to implement innovative approaches to reanalyse the exomes and genomes from thousands of well-studied undiagnosed cases. The raw genomic data is submitted to Solve-RD through the RD-Connect Genome-Phenome Analysis Platform (GPAP) together with standardised phenotypic and pedigree data. We have developed a programmatic workflow to reanalyse genome-phenome data. It uses the RD-Connect GPAP's Application Programming Interface (API) and relies on the big-data technologies upon which the system is built. We have applied the workflow to prioritise rare known pathogenic variants from 4411 undiagnosed cases. The queries returned an average of 1.45 variants per case, which first were evaluated in bulk by a panel of disease experts and afterwards specifically by the submitter of each case. A total of 120 index cases (21.2% of prioritised cases, 2.7% of all exome/genome-negative samples) have already been solved, with others being under investigation. The implementation of solutions as the one described here provide the technical framework to enable periodic case-level data re-evaluation in clinical settings, as recommended by the American College of Medical Genetics

Solve-RD: systematic pan-European data sharing and collaborative analysis to solve rare diseases.

For the first time in Europe hundreds of rare disease (RD) experts team up to actively share and jointly analyse existing patient's data. Solve-RD is a Horizon 2020-supported EU flagship project bringing together >300 clinicians, scientists, and patient representatives of 51 sites from 15 countries. Solve-RD is built upon a core group of four European Reference Networks (ERNs; ERN-ITHACA, ERN-RND, ERN-Euro NMD, ERN-GENTURIS) which annually see more than 270,000 RD patients with respective pathologies. The main ambition is to solve unsolved rare diseases for which a molecular cause is not yet known. This is achieved through an innovative clinical research environment that introduces novel ways to organise expertise and data. Two major approaches are being pursued (i) massive data re-analysis of >19,000 unsolved rare disease patients and (ii) novel combined -omics approaches. The minimum requirement to be eligible for the analysis activities is an inconclusive exome that can be shared with controlled access. The first preliminary data re-analysis has already diagnosed 255 cases form 8393 exomes/genome datasets. This unprecedented degree of collaboration focused on sharing of data and expertise shall identify many new disease genes and enable diagnosis of many so far undiagnosed patients from all over Europe

Solving unsolved rare neurological diseases-a Solve-RD viewpoint.

Funder: Durch Princess Beatrix Muscle Fund Durch Speeren voor Spieren Muscle FundFunder: University of Tübingen Medical Faculty PATE programFunder: European Reference Network for Rare Neurological Diseases | 739510Funder: European Joint Program on Rare Diseases (EJP-RD COFUND-EJP) | 44140962

A Living Assessment of Different Materials for Stratospheric Aerosol Injection—Building Bridges Between Model World and the Messiness of Reality

Abstract There are obstacles in better understanding the climate impacts associated with new materials that could be used for Stratospheric Aerosol Injections (SAI), like the lack of an integrated framework that combines climate modeling across scales, laboratory studies and small‐scale field experiments. Vattioni et al. (2023, https://doi.org/10.1029/2023gl105889) explored one aspect of using alternative, non‐sulfate materials for SAI. They investigated how uncertain the response of stratospheric ozone would be to alumina injections for SAI. In their study, they quantify chlorine activation rates in the presence of alumina, and then cascade these uncertainties into estimates of ozone depletion, concluding that alumina might have less detrimental impacts on stratospheric chemistry than sulfate, but with large uncertainties. Their results provide a useful basis upon which future research endeavors combining indoor and outdoor experiments and modeling may be structured to produce robust assessments of SAI impacts, benefits and uncertainties, together with clarifying what kind of research needs to be prioritized