Site-specific modeling tools for predicting the impact of corrupting mainbeam targets on STAP

Biosurfactants, are surface active molecules that can be produced by renewable, industrially scalable biologic processes. DAMP4, a designer biosurfactant, enables the modification of interfaces via genetic or chemical fusion to functional moieties. However, bioconjugation of addressable amines introduces heterogeneity that limits the precision of functionalization as well as the resolution of interfacial characterization. Here we designed DAMP4 variants with cysteine point mutations to allow for site-specific bioconjugation. The DAMP4 variants were shown to retain the structural stability and interfacial activity characteristic of the parent molecule, while permitting efficient and specific conjugation of polyethylene glycol (PEG). PEGylation results in a considerable reduction on the interfacial activity of both single and double mutants. Comparison of conjugates with one or two conjugation sites shows that both the number of conjugates as well as the mass of conjugated material impacts the interfacial activity of DAMP4. As a result, the ability of DAMP4 variants with multiple PEG conjugates to impart colloidal stability on peptide-stabilized emulsions is reduced. We suggest that this is due to constraints on the structure of amphiphilic helices at the interface. Specific and efficient bioconjugation permits the exploration and investigation of the interfacial properties of designer protein biosurfactants with molecular precision. Our findings should therefore inform the design and modification of biosurfactants for their increasing use in industrial processes, and nutritional and pharmaceutical formulations.

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Site-specific N-glycosylation analysis of animal cell culture-derived Zika virus proteins

Scientific Reports ◽

10.1038/s41598-021-84682-z ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Alexander Pralow ◽

Alexander Nikolay ◽

Arnaud Leon ◽

Yvonne Genzel ◽

Erdmann Rapp ◽

...

Keyword(s):

Zika Virus ◽

Animal Cell ◽

Gradient Centrifugation ◽

Viral Envelope ◽

Protein Glycosylation ◽

High Yield ◽

Structural Protein ◽

Site Specific ◽

E Protein ◽

The Impact

AbstractHere, we present for the first time, a site-specific N-glycosylation analysis of proteins from a Brazilian Zika virus (ZIKV) strain. The virus was propagated with high yield in an embryo-derived stem cell line (EB66, Valneva SE), and concentrated by g-force step-gradient centrifugation. Subsequently, the sample was proteolytically digested with different enzymes, measured via a LC–MS/MS-based workflow, and analyzed in a semi-automated way using the in-house developed glyXtoolMS software. The viral non-structural protein 1 (NS1) was glycosylated exclusively with high-mannose structures on both potential N-glycosylation sites. In case of the viral envelope (E) protein, no specific N-glycans could be identified with this method. Nevertheless, N-glycosylation could be proved by enzymatic de-N-glycosylation with PNGase F, resulting in a strong MS-signal of the former glycopeptide with deamidated asparagine at the potential N-glycosylation site N444. This confirmed that this site of the ZIKV E protein is highly N-glycosylated but with very high micro-heterogeneity. Our study clearly demonstrates the progress made towards site-specific N-glycosylation analysis of viral proteins, i.e. for Brazilian ZIKV. It allows to better characterize viral isolates, and to monitor glycosylation of major antigens. The method established can be applied for detailed studies regarding the impact of protein glycosylation on antigenicity and human pathogenicity of many viruses including influenza virus, HIV and corona virus.

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The influence of riparian woodland on the spatial and temporal variability of stream water temperatures in an upland salmon stream

Hydrology and Earth System Sciences ◽

10.5194/hess-8-449-2004 ◽

2004 ◽

Vol 8 (3) ◽

pp. 449-459 ◽

Cited By ~ 62

Author(s):

I. A. Malcolm ◽

D. M. Hannah ◽

M. J. Donaghy ◽

C. Soulsby ◽

A. F. Youngson

Keyword(s):

Thermal Regime ◽

Temporal Variability ◽

Heat Budget ◽

Riparian Forest ◽

Stream Water ◽

Spatial And Temporal Variability ◽

Substantial Impact ◽

Site Specific ◽

The Impact ◽

Riparian Woodland

Abstract. The spatio-temporal variability of stream water temperatures was investigated at six locations on the Girnock Burn (30km2 catchment), Cairngorms, Scotland over three hydrological years between 1998 and 2002. The key site-specific factors affecting the hydrology and climatology of the sampling points were investigated as a basis for physical process inference. Particular emphasis was placed on assessing the effects of riparian forest in the lower catchment versus the heather moorland riparian zones that are spatially dominant in the upper catchment. The findings were related to river heat budget studies that provided process detail. Gross changes in stream temperature were affected by the annual cycle of incoming solar radiation and seasonal changes in hydrological and climatological conditions. Inter-annual variation in these controlling variables resulted in inter-annual variability in thermal regime. However, more subtle inter-site differences reflected the impact of site-specific characteristics on various components of the river energy budget. Inter-site variability was most apparent at shorter time scales, during the summer months and for higher stream temperatures. Riparian woodland in the lower catchment had a substantial impact on thermal regime, reducing diel variability (over a period of 24 hours) and temperature extremes. Observed inter-site differences are likely to have a substantial effect on freshwater ecology in general and salmonid fish in particular. Keywords: temperature, thermal regime, forest, salmon, hydrology, Girnock Burn, Cairngorm

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Assembly: Performing the materiality of Muslim prayer spaces

Scene ◽

10.1386/scene_00014_1 ◽

2018 ◽

Vol 6 (2) ◽

pp. 133-151 ◽

Cited By ~ 1

Author(s):

Julie Marsh

Keyword(s):

Social Boundaries ◽

Research Project ◽

Site Specific ◽

Specific Research ◽

A Site ◽

The Impact

This article reflects on the significance and impact of Assembly, a site-specific research project made and exhibited in Birmingham Central Mosque, Brick Lane Mosque and Old Kent Road Mosque from 2016 to 2020. Assembly provided an opportunity for Muslims and non-Muslims to experience Jumu’ah prayer first-hand via the site performances, which temporarily dissolved the religious/social boundaries of each mosque. Each performance highlighted the differences and relations between each site, furthering ideas of performativity in Muslim prayer spaces. This article summarizes the impact reported by each mosque community as well as reflecting upon the relationships built within the wider community.

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WATER VAPOUR WEIGHTED MEAN TEMPERATURE MODEL FOR GPS-DERIVED INTEGRATED WATER VAPOUR IN PENINSULAR MALAYSIA

ISPRS - International Archives of the Photogrammetry, Remote Sensing and Spatial Information Sciences ◽

10.5194/isprs-archives-xlii-4-w5-127-2017 ◽

2017 ◽

Vol XLII-4/W5 ◽

pp. 127-135 ◽

Cited By ~ 1

Author(s):

T. A. Musa ◽

M. H. Mazlan ◽

Y. D. Opaluwa ◽

I. A. Musliman ◽

Z. M. Radzi

Keyword(s):

Water Vapour ◽

Diurnal Cycle ◽

Specific Model ◽

Regional Model ◽

Peninsular Malaysia ◽

Site Specific ◽

Weighted Mean Temperature ◽

Integrated Water Vapour ◽

Relationship Of ◽

The Impact

This paper presents the development of TM model by using the radiosonde stations from Peninsular Malaysia. Two types of TM model were developed; site-specific and regional models. The result revealed that the estimation from site-specific model has small improvement compared to the regional model, indicating that the regional model is adequately to use in estimation of GPS-derived IWV over Peninsular Malaysia. Meanwhile, this study found that the diurnal cycle of TS has influenced the TM&ndash;TS relationship. The separation between daytime and nighttime observation can improve the relationship of TM&ndash;TS. However, the impact of diurnal cycle to IWV estimation is less than 1&thinsp;%. The TM model from Global and Tropic also been evaluated. The Tropic TM model is superior to be utilized as compared to the Global TM model.

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Bayesian Poisson hierarchical models for crash data analysis: Investigating the impact of model choice on site-specific predictions

Accident Analysis & Prevention ◽

10.1016/j.aap.2018.04.016 ◽

2018 ◽

Vol 117 ◽

pp. 181-195 ◽

Cited By ~ 9

Author(s):

S. Hadi Khazraee ◽

Valen Johnson ◽

Dominique Lord

Keyword(s):

Data Analysis ◽

Hierarchical Models ◽

Model Choice ◽

Site Specific ◽

Crash Data ◽

The Impact ◽

Crash Data Analysis

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On Developing Hybrid Modeling Methods using Metamodeling Platforms

International Journal of Information System Modeling and Design ◽

10.4018/ijismd.2015010103 ◽

2015 ◽

Vol 6 (1) ◽

pp. 47-66

Author(s):

Srdjan Zivkovic ◽

Krzystof Miksa ◽

Harald Kühn

Keyword(s):

Complex Systems ◽

Hybrid Modeling ◽

Modeling Languages ◽

Modeling Tools ◽

Analysis And Design ◽

Domain Specific ◽

Modeling Methods ◽

Model Based ◽

Domain Specific Modeling ◽

Specific Modeling

It has been acknowledged that model-based approaches and domain-specific modeling (DSM) languages, methods and tools are beneficial for the engineering of increasingly complex systems and software. Instead of general-purpose one-size-fits-all modeling languages, DSM methods facilitate model-based analysis and design of complex systems by providing modeling concepts tailored to the specific problem domain. Furthermore, hybrid DSM methods combine single DSM methods into integrated modeling methods, to allow for multi-perspective modeling. Metamodeling platforms provide flexible means for design and implementation of such hybrid modeling methods and appropriate domain-specific modeling tools. In this paper, we report on the conceptualization of a hybrid DSM method in the domain of network physical devices management, and its implementation based on the ADOxx metamodeling platform. The method introduces a hybrid modeling approach. A dedicated DSM language (DSML) is used to model the structure of physical devices and their configurations, whereas the formal language for knowledge representation OWL2 is used to specify configuration-related constraints. The outcome of the work is a hybrid, semantic technology-enabled DSM tool that allows for efficient and consistency-preserving model-based configuration of network equipment.

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Computational Modeling of the Human Microbiome

Microorganisms ◽

10.3390/microorganisms8020197 ◽

2020 ◽

Vol 8 (2) ◽

pp. 197

Author(s):

Shomeek Chowdhury ◽

Stephen S. Fong

Keyword(s):

Computational Modeling ◽

Human Health ◽

Large Scale ◽

Human Microbiome ◽

Human Microbiome Project ◽

Microbial Composition ◽

Site Specific ◽

Microbiome Research ◽

High Level ◽

The Impact

The impact of microorganisms on human health has long been acknowledged and studied, but recent advances in research methodologies have enabled a new systems-level perspective on the collections of microorganisms associated with humans, the human microbiome. Large-scale collaborative efforts such as the NIH Human Microbiome Project have sought to kick-start research on the human microbiome by providing foundational information on microbial composition based upon specific sites across the human body. Here, we focus on the four main anatomical sites of the human microbiome: gut, oral, skin, and vaginal, and provide information on site-specific background, experimental data, and computational modeling. Each of the site-specific microbiomes has unique organisms and phenomena associated with them; there are also high-level commonalities. By providing an overview of different human microbiome sites, we hope to provide a perspective where detailed, site-specific research is needed to understand causal phenomena that impact human health, but there is equally a need for more generalized methodology improvements that would benefit all human microbiome research.

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A Bayesian Mutation–Selection Framework for Detecting Site-Specific Adaptive Evolution in Protein-Coding Genes

Molecular Biology and Evolution ◽

10.1093/molbev/msaa265 ◽

2020 ◽

Author(s):

Nicolas Rodrigue ◽

Thibault Latrille ◽

Nicolas Lartillot

Keyword(s):

Adaptive Evolution ◽

Real Data ◽

Data Sets ◽

Protein Coding ◽

Site Specific ◽

Protein Coding Genes ◽

Codon Substitution ◽

Selection Framework ◽

Dna Alignment ◽

The Impact

Abstract In recent years, codon substitution models based on the mutation–selection principle have been extended for the purpose of detecting signatures of adaptive evolution in protein-coding genes. However, the approaches used to date have either focused on detecting global signals of adaptive regimes—across the entire gene—or on contexts where experimentally derived, site-specific amino acid fitness profiles are available. Here, we present a Bayesian site-heterogeneous mutation–selection framework for site-specific detection of adaptive substitution regimes given a protein-coding DNA alignment. We offer implementations, briefly present simulation results, and apply the approach on a few real data sets. Our analyses suggest that the new approach shows greater sensitivity than traditional methods. However, more study is required to assess the impact of potential model violations on the method, and gain a greater empirical sense its behavior on a broader range of real data sets. We propose an outline of such a research program.

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A new model suite to determine the influence of cosmic rays on (exo)planetary atmospheric biosignatures

Astronomy and Astrophysics ◽

10.1051/0004-6361/201935888 ◽

2019 ◽

Vol 631 ◽

pp. A101 ◽

Cited By ~ 7

Author(s):

Konstantin Herbst ◽

John Lee Grenfell ◽

Miriam Sinnhuber ◽

Heike Rauer ◽

Bernd Heber ◽

...

Keyword(s):

Cosmic Rays ◽

Energetic Particle ◽

Particle Interaction ◽

Spectral Feature ◽

Ozone Production ◽

Atmospheric Radiation ◽

Solar Energetic Particle Event ◽

Ion Chemistry ◽

Modeling Tools ◽

The Impact

Context. The first opportunity to detect indications for life outside of the Solar System may be provided already within the next decade with upcoming missions such as the James Webb Space Telescope (JWST), the European Extremely Large Telescope (E-ELT) and the Atmospheric Remote-sensing Infrared Exoplanet Large-survey (ARIEL) mission, searching for atmospheric biosignatures on planets in the habitable zone of cool K- and M-stars. Nevertheless, their harsh stellar radiation and particle environment could lead to photochemical loss of atmospheric biosignatures. Aims. We aim to study the influence of cosmic rays on exoplanetary atmospheric biosignatures and the radiation environment considering feedbacks between energetic particle precipitation, climate, atmospheric ionization, neutral and ion chemistry, and secondary particle generation. Methods. We describe newly combined state-of-the-art modeling tools to study the impact of the radiation and particle environment, in particular of cosmic rays, on atmospheric particle interaction, atmospheric chemistry, and the climate-chemistry coupling in a self-consistent model suite. To this end, models like the Atmospheric Radiation Interaction Simulator (AtRIS), the Exoplanetary Terrestrial Ion Chemistry model (ExoTIC), and the updated coupled climate-chemistry model are combined. Results. In addition to comparing our results to Earth-bound measurements, we investigate the ozone production and -loss cycles as well as the atmospheric radiation dose profiles during quiescent solar periods and during the strong solar energetic particle event of February 23, 1956. Further, the scenario-dependent terrestrial transit spectra, as seen by the NIR-Spec infrared spectrometer onboard the JWST, are modeled. Amongst others, we find that the comparatively weak solar event drastically increases the spectral signal of HNO3, while significantly suppressing the spectral feature of ozone. Because of the slow recovery after such events, the latter indicates that ozone might not be a good biomarker for planets orbiting stars with high flaring rates.

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