Showing papers by "University of Göttingen published in 2022"

ColabFold: making protein folding accessible to all

Abstract: ColabFold offers accelerated prediction of protein structures and complexes by combining the fast homology search of MMseqs2 with AlphaFold2 or RoseTTAFold. ColabFold's 40-60-fold faster search and optimized model utilization enables prediction of close to 1,000 structures per day on a server with one graphics processing unit. Coupled with Google Colaboratory, ColabFold becomes a free and accessible platform for protein folding. ColabFold is open-source software available at https://github.com/sokrypton/ColabFold and its novel environmental databases are available at https://colabfold.mmseqs.com .

Augmented neutralisation resistance of emerging omicron subvariants BA.2.12.1, BA.4, and BA.5

Abstract: The SARS-CoV-2 omicron (B.1.1.529) variant is highly resistant against antibody-mediated neutralisation due to many mutations in the spike (S) protein.1Hoffmann M Krüger N Schulz S et al.The omicron variant is highly resistant against antibody-mediated neutralization: implications for control of the COVID-19 pandemic.Cell. 2022; 185 (e11): 447-456Summary Full Text Full Text PDF PubMed Scopus (317) Google Scholar Several omicron subvariants have been detected, with BA.2.12.1 (first detected in the USA) and BA.4 and BA.5 (first detected in South Africa) currently outcompeting the previously circulating BA.1 and BA.2 subvariants in several countries. The S proteins of BA.4 and BA.5, which are identical on the protein level, and BA.2.12.1 harbour unique mutations (appendix pp 1–2), but it is largely unknown whether they differ from BA.1 and BA.2 regarding neutralisation sensitivity. We analysed neutralisation of BA.2.12.1 and BA.4/BA.5 by monoclonal antibodies and antibodies induced on vaccination or infection, making use of S-protein-bearing reporter viruses, which represent an adequate surrogate model.2Schmidt F Weisblum Y Muecksch F et al.Measuring SARS-CoV-2 neutralizing antibody activity using pseudotyped and chimeric viruses.J Exp Med. 2020; 217e20201181 Crossref Google Scholar As a reference, we used particles bearing the S proteins of either B.1 (circulating during the early phase of the pandemic), BA.1, or BA.2. We identified that all omicron subvariants robustly evaded neutralisation by six of ten antibodies, although subvariant-specific differences were noted (appendix pp 1–2). Sotrovimab, which was reported to effectively neutralise BA.1,1Hoffmann M Krüger N Schulz S et al.The omicron variant is highly resistant against antibody-mediated neutralization: implications for control of the COVID-19 pandemic.Cell. 2022; 185 (e11): 447-456Summary Full Text Full Text PDF PubMed Scopus (317) Google Scholar, 3Cameroni E Bowden JE Rosen LE et al.Broadly neutralizing antibodies overcome SARS-CoV-2 omicron antigenic shift.Nature. 2022; 602: 664-670Crossref PubMed Scopus (356) Google Scholar showed markedly reduced neutralisation of BA.2, BA.2.12.1, and BA.4/BA.5 in comparison to neutralisation of BA.1 (appendix pp 1–2). Conversely, cilgavimab showed substantial activity against all omicron subvariants except BA.1. These results are in line with those of Cao and colleagues,4Cao Y Yisimayi A Jian F et al.BA.2.12.1, BA.4 and BA.5 escape antibodies elicited by omicron infection (version 2).bioRxiv. 2022; (published online June 14.) (preprint).https://doi.org/10.1101/2022.04.30.489997Google Scholar whereas Yamasoba and colleagues5Yamasoba D Kosugi Y Kimura I et al.Neutralisation sensitivity of SARS-CoV-2 omicron subvariants to therapeutic monoclonal antibodies.Lancet Infect Dis. 2022; 22: 942-943Summary Full Text Full Text PDF PubMed Scopus (37) Google Scholar reported a significant reduction of BA.4/BA.5 neutralisation by cilgavimab in comparison with neutralisation of BA.1. S2H97 showed similar efficacy against all subvariants but required high concentrations for efficient neutralisation. Finally, bebtelovimab (LY-CoV1404) neutralised all subvariants tested with similarly high efficacy (appendix pp 1–2), in agreement with findings reported for BA.1 and BA.2.6Iketani S Liu L Guo Y et al.Antibody evasion properties of SARS-CoV-2 omicron sublineages.Nature. 2022; 604: 553-556Crossref PubMed Scopus (211) Google Scholar We next analysed neutralisation of BA.2.12.1 and BA.4/BA.5 by plasma from ten unvaccinated people in Germany (aged 20–71 years; five male and five female) who had mild infections in March–May, 2022, when BA.1 and, subsequently, BA.2 were circulating in Germany (appendix pp 3–4). BA.1 was neutralised with 2·9-times higher efficiency (measured by the fold difference in 50% neutralisation titre values between plasma pairs) than was B.1, whereas neutralisation of BA.2 was 27·2-times more efficient than of B.1 (appendix pp 1–2), suggesting that most donors were infected with BA.2. Notably, neutralisation of BA.2.12.1 was similar to that of BA.2, whereas BA.4/BA.5 neutralisation was markedly reduced compared with BA.2 and BA.2.12.1 (ie, only 1·6-times higher than B.1; appendix pp 1–2). We further analysed neutralisation by antibodies induced by vaccination (appendix pp 3–4). We identified that BA.1 and BA.2 evaded neutralisation by antibodies that were induced on triple BNT162b2 (Pfizer-BioNTech) vaccination with similar efficiency (ie, 4·3-times reduced neutralisation for BA.1 and 4·2-times reduced neutralisation for BA.2 compared with B.1), as expected,7Arora P Zhang L Rocha C et al.Comparable neutralisation evasion of SARS-CoV-2 omicron subvariants BA.1, BA.2, and BA.3.Lancet Infect Dis. 2022; 22: 766-767Summary Full Text Full Text PDF PubMed Scopus (33) Google Scholar whereas evasion by BA.2.12.1 (ie, 6·1-times reduced neutralisation compared with B.1) and particularly BA.4/BA.5 (ie, 8·1-times reduced neutralisation compared with B.1) was more efficient (appendix pp 1–2). A similar tendency was also observed for samples taken from individuals who had been triple vaccinated with BNT162b2 with subsequent BA.1 or BA.2 breakthrough infection (appendix pp 1–4). Here, we show that bebtelovimab should represent an effective treatment for patients with COVID-19, irrespective of the infecting omicron subvariant, in keeping with bebtelovimab recognising a highly conserved epitope.8Westendorf K Žentelis S Wang L et al.LY-CoV1404 (bebtelovimab) potently neutralizes SARS-CoV-2 variants.Cell Rep. 2022; 39110812 Summary Full Text Full Text PDF PubMed Scopus (63) Google Scholar Further, our findings indicate that immune evasion of BA.2.12.1 is only moderately increased relative to BA.2, suggesting that increased human-to-human transmissibility (eg, due to increased replication in the upper respiratory tract or augmented infection of cells) might contribute to the expansion of BA.2.12.1. Finally, the robust neutralisation evasion by BA.4 and BA.5 indicates that these are immune-evasion variants, which are more adept than BA.1 or BA.2 to spread in populations that are vaccinated or recovering from omicron, or both. AK, IN, SP, and MH conduct contract research (ie, testing of vaccinee sera for neutralising activity against SARS-CoV-2) for an industrial entity, unrelated to this Correspondence. GMNB served as an adviser for Moderna, unrelated to this Correspondence. All other authors declare no competing interests. SP acknowledges funding by Bundesministerium für Bildung und Forschung (01KI2006D, 01KI20328A, 01KX2021), the Ministry for Science and Culture of Lower Saxony (14–76103–184, MWK HZI COVID-19), and the German Research Foundation (PO 716/11–1, PO 716/14–1). H-MJ received funding from BMBF (01KI2043, NaFoUniMedCovid19-COVIM: 01KX2021), Bavarian State Ministry for Science and the Arts, and Deutsche Forschungsgemeinschaft through the research training groups RTG1660 and TRR130, the Bayerische Forschungsstiftung (Project CORAd), and the Kastner Foundation. GMNB acknowledges funding by German Center for Infection Research (grant no 80018019238) and a European Regional Development Fund (Defeat Corona, ZW7–8515131). Download .pdf (2.2 MB) Help with pdf files Supplementary appendix

Principles of odor coding in vertebrates and artificial chemosensory systems.

Abstract: The biological olfactory system is the sensory system responsible for the detection of the chemical composition of the environment. Several attempts to mimic biological olfactory systems have led to various artificial olfactory systems using different technical approaches. Here we provide a parallel description of biological olfactory systems and their technical counterparts. We start with a presentation of the input to the systems, the stimuli, and treat the interface between the external world and the environment where receptor neurons or artificial chemosensors reside. We then delineate the functions of receptor neurons and chemosensors as well as their overall input-output (I/O) relationships. Up to this point, our accounts of the systems go along similar lines. The next processing steps differ considerably: whereas in biology the processing step following the receptor neurons is the "integration" and "processing" of receptor neuron outputs in the olfactory bulb, this step has various realizations in electronic noses. For a long period of time, the signal processing stages beyond the olfactory bulb, i.e., the higher olfactory centers, were little studied. Only recently has there been a marked growth of studies tackling the information processing in these centers. In electronic noses, a third stage of processing has virtually never been considered. In this review, we provide an up-to-date overview of the current knowledge of both fields and, for the first time, attempt to tie them together. We hope it will be a breeding ground for better information, communication, and data exchange between very related but so far little-connected fields.

Quantum cascade of correlated phases in trigonally warped bilayer graphene

Abstract: Divergent density of states offers the unique opportunity to explore a wide variety of correlated electron physics. In the thinnest limit, this has been predicted and verified in the ultra-flat bands of magic-angle twisted bilayer graphene, the band touching points of few-layer rhombohedral graphite, and the lightly doped rhombohedral trilayer graphene. The simpler and seemingly better understood Bernal bilayer graphene is also susceptible to orbital magnetism-driven phases at charge neutrality, such as layer antiferromagnet and quantum anomalous Hall octet. Here we report the discovery of a cascade of novel correlated phases in the vicinity of electric-field-controlled Lifshitz transitions and van Hove singularities in trigonally warped bilayer graphene. We provide compelling evidence for the observation of Stoner ferromagnets - half and quarter metals. More prominently, we identify signatures consistent with a topologically nontrivial Wigner-Hall crystal at zero magnetic field and its transition to a trivial Wigner crystal, as well as two correlated metals whose behavior deviates from standard Fermi liquids. Our results in this reproducible, tunable, simple system opens a new chapter for studying strongly correlated electrons.

Formation of moiré interlayer excitons in space and time

Abstract: Moir\'e superlattices in atomically thin van-der-Waals heterostructures hold great promise for an extended control of electronic and valleytronic lifetimes, the confinement of excitons in artificial moir\'e lattices, and the formation of novel exotic quantum phases. Such moir\'e-induced emergent phenomena are particularly strong for interlayer excitons, where the hole and the electron are localized in different layers of the heterostructure. In order to exploit the full potential of correlated moir\'e and exciton physics, a thorough understanding of the ultrafast interlayer exciton formation process and the real-space wavefunction confinement in the moir\'e potential is indispensable. However, direct experimental access to these parameters is limited since most excitonic quasiparticles are optically dark. Here we show that femtosecond photoemission momentum microscopy provides quantitative access to these key properties of the moir\'e interlayer excitons. We find that interlayer excitons are dominantly formed on the sub-50~fs timescale via interlayer tunneling at the K valleys of the Brillouin zones. In addition, we directly measure energy-momentum fingerprints of the moir\'e interlayer excitons by mapping their spectral signatures within the mini Brillouin zone that is built up by the twisted heterostructure. From these momentum-fingerprints, we gain quantitative access to the modulation of the exciton wavefunction within the moir\'e potential in real-space. Our work provides the first direct access to the interlayer moir\'e exciton formation dynamics in space and time and reveals new opportunities to study correlated moir\'e and exciton physics for the future realization of exotic quantum phases of matter.

Nitrogen Atom Transfer Catalysis by Metallonitrene C−H Insertion: Photocatalytic Amidation of Aldehydes

Abstract: C-H amination and amidation by catalytic nitrene transfer are well-established and typically proceed via electrophilic attack of nitrenoid intermediates. In contrast, the insertion of (formal) terminal nitride ligands into C-H bonds is much less developed and catalytic nitrogen atom transfer remains unknown. We here report the synthesis of a formal terminal nitride complex of palladium. Photocrystallographic, magnetic, and computational characterization support the assignment as an authentic metallonitrene (Pd-N) with a diradical nitrogen ligand that is singly bonded to PdII . Despite the subvalent nitrene character, selective C-H insertion with aldehydes follows nucleophilic selectivity. Transamidation of the benzamide product is enabled by reaction with N3 SiMe3 . Based on these results, a photocatalytic protocol for aldehyde C-H trimethylsilylamidation was developed that exhibits inverted, nucleophilic selectivity as compared to typical nitrene transfer catalysis. This first example of catalytic C-H nitrogen atom transfer offers facile access to primary amides after deprotection.

Polyyne [3]Rotaxanes: Synthesis via Dicobalt Carbonyl Complexes and Enhanced Stability

Abstract: New strategies for synthesizing polyyne polyrotaxanes are being developed as an approach to stable carbyne “insulated molecular wires”. Here we report an active metal template route to polyyne [3]rotaxanes, using dicobalt carbonyl masked alkyne equivalents. We synthesized two [3]rotaxanes, both with the same C28 polyyne dumbbell component, one with a phenanthroline-based macrocycle and one using a 2,6-pyridyl cycloparaphenylene nanohoop. The thermal stabilities of the two rotaxanes were compared with that of the naked polyyne dumbbell in decalin at 80 °C, and the nanohoop rotaxane was found to be 4.5 times more stable.

Plant-Based Diets Are Not Enough? Understanding the Consumption of Plant-Based Meat Alternatives Along Ultra-processed Foods in Different Dietary Patterns in Germany

Abstract: A low-processive plant-based diet is considered valuable for a sustainable diet profile—it is supposed to meet health as well as environmental concerns. However, there is a growing trend toward plant-based meat alternatives, most of which are to be classified as ultra-processed food (UPF). The paper aimed to understand the consumption of different ultra-processed foods to describe their relation to dietary patterns and sustainability. The objective was (1) to depict the status-quo of consumption of plant-based meat alternatives along with other UPF groups (i.e., convenience products, fast foods, snacks, ultra-processed beverages) in a German sample ( n = 814) and (2) to investigate the extent to which all examined UPFs are represented in different dietary patterns (vegetarian, flexitarian, regular meat-eaters, high meat-eaters). UPF intake and dietary groups were determined using a food frequency questionnaire (FFQ). Potential factors influencing UPF consumption, such as attitudes toward sustainability and healthy eating practices, were assessed using validated and fitted psychometric scales. Overall, the frequency of UPF consumption varies significantly along the product groups studied. Plant-based meat alternatives were the least consumed food (12.3%), followed by convenience products (57.4%), fast foods (55.9%), ultra-processed beverages (80.1%), and sweet and salty snacks (97.3%). Plant-based meat alternative consumption predominated within a vegetarian diet, while other UPFs, like convenience products, fast foods, sweet and salty snacks, and ultra-processed beverages, were mainly consumed by meat-eaters. Remarkably, flexitarian diets depict low consumption of all types of ultra-processed foods. In order to meet societal sustainability goals, diets and corresponding societal and political actions should emphasize not only plant orientation but also the increase of non- and low-processed foods.

Heterogeneity of glutamatergic synapses: cellular mechanisms and network consequences.

Abstract: Chemical synapses are commonly known as a structurally and functionally highly diverse class of cell-cell contacts specialized to mediate communication between neurons. They represent the smallest ...

Interplay Between Risk Perception, Behavior, and COVID-19 Spread

Abstract: Pharmaceutical and non-pharmaceutical interventions (NPIs) have been crucial for controlling COVID-19. They are complemented by voluntary health-protective behaviour, building a complex interplay between risk perception, behaviour, and disease spread. We studied how voluntary health-protective behaviour and vaccination willingness impact the long-term dynamics. We analysed how different levels of mandatory NPIs determine how individuals use their leeway for voluntary actions. If mandatory NPIs are too weak, COVID-19 incidence will surge, implying high morbidity and mortality before individuals react; if they are too strong, one expects a rebound wave once restrictions are lifted, challenging the transition to endemicity. Conversely, moderate mandatory NPIs give individuals time and room to adapt their level of caution, mitigating disease spread effectively. When complemented with high vaccination rates, this also offers a robust way to limit the impacts of the Omicron variant of concern. Altogether, our work highlights the importance of appropriate mandatory NPIs to maximise the impact of individual voluntary actions in pandemic control.

Urbanization, Economic Development, and Ecological Environment: Evidence from Provincial Panel Data in China

Abstract: The relationship between urbanization and the ecological environment is not conclusive in the literature. We used the provincial data from China from 1998 to 2019 to empirically study the relationship between the urbanization ratio and ecological environment which is proxied by the NDVI (normalized difference vegetation index) from the remote sensing data. The results indicate that the coefficient of the interaction between urbanization and per capita GDP is statistically significant and negative (−0.0946), while the coefficient of urbanization itself is very trivial and not statistically significant. It implies that urbanization could reduce ecological quality, particularly for the high-income regions. The higher the urbanization ratio is, the larger the negative impact is. It implies that urban expansion does reduce the ecological environment. The effect of economic development level on the NDVI can be divided into three stages: the one where the NDVI improves with the increase of GDP per capita (urbanization rate of less than 77.59%), the one where the value of the NDVI is not affected by the level of GDP per capita (urbanization rate equal to 77.59%), and the one where the NDVI decreases with the increase of GDP per capita (urbanization rate of more than 77.59%).

Airborne ultra-wideband radar sounding over the shear margins and along flow lines at the onset region of the Northeast Greenland Ice Stream

Abstract: Abstract. We present a high-resolution airborne radar data set (EGRIP-NOR-2018) for the onset region of the Northeast Greenland Ice Stream (NEGIS). The radar data were acquired in May 2018 with the Alfred Wegener Institute's multichannel ultra-wideband (UWB) radar mounted on the Polar 6 aircraft. Radar profiles cover an area of ∼24 000 km2 and extend over the well-defined shear margins of the NEGIS. The survey area is centered at the location of the drill site of the East Greenland Ice-Core Project (EastGRIP), and several radar lines intersect at this location. The survey layout was designed to (i) map the stratigraphic signature of the shear margins with radar profiles aligned perpendicular to ice flow, (ii) trace the radar stratigraphy along several flow lines, and (iii) provide spatial coverage of ice thickness and basal properties. While we are able to resolve radar reflections in the deep stratigraphy, we cannot fully resolve the steeply inclined reflections at the tightly folded shear margins in the lower part of the ice column. The NEGIS is causing the most significant discrepancies between numerically modeled and observed ice surface velocities. Given the high likelihood of future climate and ocean warming, this extensive data set of new high-resolution radar data in combination with the EastGRIP ice core will be a key contribution to understand the past and future dynamics of the NEGIS. The EGRIP-NOR-2018 radar data products can be obtained from the PANGAEA data publisher (https://doi.pangaea.de/10.1594/PANGAEA.928569; Franke et al., 2021a).

The Suitability of Hybrid Fe0/Aggregate Filtration Systems for Water Treatment

Abstract: Metallic iron (Fe0) corrosion under immersed conditions (Fe0/H2O system) has been used for water treatment for the past 170 years. Fe0 generates solid iron corrosion products (FeCPs) which are known to in situ coat the surface of aggregates, including granular activated carbon (GAC), gravel, lapillus, manganese oxide (MnO2), pyrite (FeS2), and sand. While admixing Fe0 and reactive aggregates to build hybrid systems (e.g., Fe0/FeS2, Fe0/MnO2, Fe0/sand) for water treatment, it has been largely overlooked that these materials would experience reactivity loss upon coating. This communication clarifies the relationships between aggregate addition and the sustainability of Fe0/H2O filtration systems. It is shown that any enhanced contaminant removal efficiency in Fe0/aggregate/H2O systems relative to the Fe0/H2O system is related to the avoidance/delay of particle cementation by virtue of the non-expansive nature of the aggregates. The argument that aggregate addition sustains any reductive transformation of contaminants mediated by electrons from Fe0 is disproved by the evidence that Fe0/sand systems are equally more efficient than pure Fe0 systems. This demonstration corroborates the concept that aqueous contaminant removal in iron/water systems is not a process mediated by electrons from Fe0. This communication reiterates that only hybrid Fe0/H2O filtration systems are sustainable.

Phenomenology of jet angularities at the LHC

Abstract: We compute resummed and matched predictions for jet angularities in hadronic dijet and Z+jet events with and without grooming the candidate jets using the SoftDrop technique. Our theoretical predictions also account for non-perturbative corrections from the underlying event and hadronisation through parton-to-hadron level transfer matrices extracted from dedicated Monte Carlo simulations with SHERPA. Thanks to this approach we can account for non-perturbative migration effects in both the angularities and the jet transverse momentum. We compare our predictions against recent measurements from the CMS experiment. This allows us to test the description of quark- and gluon-jet enriched phase-space regions separately. We supplement our study with SHERPA results based on the matching of NLO QCD matrix elements with the parton shower. Both theoretical predictions offer a good description of the data, within the experimental and theoretical uncertainties. The latter are however sizeable, motivating higher-accuracy calculations.