Genomic distribution of satellite DNA in Vicia faba and Latyrus sativus

The aim of this thesis was to investigate the genomic distribution of satellite DNA repeats in Vicia faba and Lathyrus sativus and the association of some satellite repeats with centromeric chromatin

“Small is beautiful” – the significance of reliable determination of low- abundant therapeutic antibody glycovariants

Glycans associated with biopharmaceutical drugs play crucial roles in drug safety and efficacy, and therefore, their reliable detection and quantification is essential. Our study introduces a multi-level quantification approach for glycosylation analysis in monoclonal antibodies, focusing on minor abundant glycovariants. Mass spectrometric data is evaluated mainly employing open-source software tools. Released glycan and glycopeptide data form the basis for integrating information across different molecular and structural levels up to intact glycoproteins. A comprehensive site-specific comparison showed that indeed, variations across structural levels were observed especially for minor abundant species. Utilizing MoFi, a tool for annotating mass peaks of intact proteins, we quantify isobaric glycosylation variants at the intact protein level. Our workflow\u27s utility is demonstrated on NISTmAb, rituximab and adalimumab, profiling their minor abundant variants for the first time across diverse structural levels. This study enhances understanding and accessibility in glycosylation analysis, emphasizing the significance of minor abundant glycovariants in therapeutic antibodies

Tissue-specific signatures in tick cell line MS profiles

Abstract Background The availability of tick in vitro cell culture systems has facilitated many aspects of tick research, including proteomics. However, certain cell lines have shown a tissue-specific response to infection. Thus, a more thorough characterization of tick cell lines is necessary. Proteomic comparative studies of various tick cell lines will contribute to more efficient application of tick cell lines as model systems for investigation of host-vector-pathogen interactions. Results Three cell lines obtained from a hard tick, Ixodes ricinus, and two from I. scapularis were investigated. A cell mass spectrometry approach (MALDI-TOF MS) was applied, as well as classical proteomic workflows. Using PCA, tick cell line MS profiles were grouped into three clusters comprising IRE/CTVM19 and ISE18, IRE11 and IRE/CTVM20, and ISE6 cell lines. Two other approaches confirmed the results of PCA: in-solution digestion followed by nanoLC-ESI-Q-TOF MS/MS and 2D electrophoresis. The comparison of MS spectra of the cell lines and I. ricinus tick organs revealed 29 shared peaks. Of these, five were specific for ovaries, three each for gut and salivary glands, and one for Malpighian tubules. For the first time, characteristic peaks in MS profiles of tick cell lines were assigned to proteins identified in acidic extracts of corresponding cell lines. Conclusions Several organ-specific MS signals were revealed in the profiles of tick cell lines

At-line quantitative profiling of monoclonal antibody products during bioprocessing using HPLC-MS.

(1) Background: The N-glycosylation profile as well as the subunit assembly of monoclonal antibodies (mAbs) are strongly dependent on manufacturing conditions and thus need to be monitored during the bioprocess. Commonly, mAbs are characterized downstream of the fermentation process applying different analytical techniques like released glycan analysis, peptide mapping, or subunit profiling. However, these procedures are time-consuming and difficult to perform in real-time. (2) Methods: We applied a simple HPLC-MS workflow with minimal sample preparation to characterize mAb product quality at the intact protein level at different time points during fermentation. After harvest, the cell culture medium was centrifuged briefly. The supernatant containing the fermentation product was diluted and immediately subjected to HPLC-MS analysis. (3) Results: Besides the product of interest (mAb), the fermentation broth contained misassembled variants, mostly light chain and light chain dimer. The mAb's glycosylation profile changed over time showing an increase in galactosylated variants with G0F/G1F being the most abundant glycoform at all time points of fermentation. Furthermore, expressed protein species were relatively and absolutely quantified. The workflow was very robust despite analyzing a highly complex matrix. Relative standard deviations for retention times were below 0.5% for both intra and inter-day comparison, whereas relative procedural standard deviations for quantification of the different protein species ranged between 7 and 13%. (4) Conclusions: This approach allows for reliable analysis of product profiles of monoclonal antibody species including misassembled subunits and glycosylation variants directly from fermentation broth using a fast and robust HPLC-MS workflow

Satellite DNA in Vicia faba is characterized by remarkable diversity in its sequence composition, association with centromeres, and replication timing

Abstract Satellite DNA, a class of repetitive sequences forming long arrays of tandemly repeated units, represents substantial portions of many plant genomes yet remains poorly characterized due to various methodological obstacles. Here we show that the genome of the field bean (Vicia faba, 2n = 12), a long-established model for cytogenetic studies in plants, contains a diverse set of satellite repeats, most of which remained concealed until their present investigation. Using next-generation sequencing combined with novel bioinformatics tools, we reconstructed consensus sequences of 23 novel satellite repeats representing 0.008–2.700% of the genome and mapped their distribution on chromosomes. We found that in addition to typical satellites with monomers hundreds of nucleotides long, V. faba contains a large number of satellite repeats with unusually long monomers (687–2033 bp), which are predominantly localized in pericentromeric regions. Using chromatin immunoprecipitation with CenH3 antibody, we revealed an extraordinary diversity of centromeric satellites, consisting of seven repeats with chromosome-specific distribution. We also found that in spite of their different nucleotide sequences, all centromeric repeats are replicated during mid-S phase, while most other satellites are replicated in the first part of late S phase, followed by a single family of FokI repeats representing the latest replicating chromatin

Co-Creating a Digital Life-Integrated Self-Assessment for Older Adults: User Experience Study

BackgroundOlder adults are at increased risk of developing health disorders and functional decline. However, owing to time constraints and considerable effort, physicians rarely conduct comprehensive assessments to detect early signs of negative trajectories. If designed properly, digital technologies could identify health risks already at a preclinical stage, thereby facilitating preventive efforts and targeted intervention. For this purpose, a Life-integrated Self-Assessment (LiSA) tablet system will be developed through a structured co-creation process. ObjectiveThis study aims to investigate older adults’ perceptions of different self-assessment domains, components affecting user experience, risks and benefits associated with LiSA, characteristics of potential LiSA users, and the LiSA concept in general. MethodsA total of 10 community-dwelling older adults aged ≥70 years were recruited. In total, 6 co-creation workshops were held and started with expert input followed by semistructured discussion rounds. Participants performed hands-on activities with a tablet, including testing of preinstalled self-assessment apps. All workshops were audio recorded and additionally documented by the researchers using flipcharts, notes, and photos. Qualitative content analysis was used to analyze the data following a deductive-inductive approach guided by the Optimized Honeycomb Model for user experience. ResultsThe group (mean age 77.8, SD 5.1 years) was heterogeneous in terms of previous technology experience and health status. The mean workshop duration was 2 hours (122.5, SD 4.43 min), and an average of 8 (SD 1.15) participants attended each workshop. A total of 11 thematic categories were identified, covering results on all research questions. Participants emphasized a strong interest in conducting a digital self-assessment of physical activity and function and sensory and cognitive functions and requested additional features such as recommendations for actions or reminders. LiSA was perceived as empowering and a motivator to engage in active health care planning as well as enabling shared and informed decision-making. Concerns and barriers included the lack of technical competence, feelings of frustration, and fear of being left alone, with negative assessment results. In essence, participants expressed a positive attitude toward using LiSA repeatedly and identified it as an option to increase the chances of maintaining independence when growing older. ConclusionsThe co-creation participants supported the LiSA approach and were interested in performing regular self-assessments on a long-term basis. In their opinion, LiSA should include relevant assessments capturing physical activity and function and sensory and cognitive functions as well as recommendations for actions. It should be customizable to individual needs. These results will form the basis for a prototype. Iterative development and validation will aim to make LiSA accessible in the public domain as a reliable tablet-based system for self-assessment

Climate and carbon cycle changes from 1850 to 2100 in MPI-ESM simulations for the Coupled Model Intercomparison Project phase 5

The new Max-Planck-Institute Earth System Model (MPI-ESM) is used in the Coupled Model Intercomparison Project phase 5 (CMIP5) in a series of climate change experiments for either idealized CO2-only forcing or forcings based on observations and the Representative Concentration Pathway (RCP) scenarios. The paper gives an overview of the model configurations, experiments related forcings, and initialization procedures and presents results for the simulated changes in climate and carbon cycle. It is found that the climate feedback depends on the global warming and possibly the forcing history. The global warming from climatological 1850 conditions to 2080–2100 ranges from 1.5°C under the RCP2.6 scenario to 4.4°C under the RCP8.5 scenario. Over this range, the patterns of temperature and precipitation change are nearly independent of the global warming. The model shows a tendency to reduce the ocean heat uptake efficiency toward a warmer climate, and hence acceleration in warming in the later years. The precipitation sensitivity can be as high as 2.5% K−1 if the CO2 concentration is constant, or as small as 1.6% K−1, if the CO2 concentration is increasing. The oceanic uptake of anthropogenic carbon increases over time in all scenarios, being smallest in the experiment forced by RCP2.6 and largest in that for RCP8.5. The land also serves as a net carbon sink in all scenarios, predominantly in boreal regions. The strong tropical carbon sources found in the RCP2.6 and RCP8.5 experiments are almost absent in the RCP4.5 experiment, which can be explained by reforestation in the RCP4.5 scenario

COVID-19 in German Competitive Sports: Protocol for a Prospective Multicenter Cohort Study (CoSmo-S)

Objective: It is unclear whether and to what extent COVID-19 infection poses health risks and a chronic impairment of performance in athletes. Identification of individual health risk is an important decision-making basis for managing the pandemic risk of infection with SARS-CoV-2 in sports and return to play (RTP). Methods: This study aims 1) to analyze the longitudinal rate of seroprevalence of SARSCoV- 2 in German athletes, 2) to assess health-related consequences in athletes infected with SARS-CoV-2, and 3) to reveal effects of the COVID-19 pandemic in general and of a cleared SARS-CoV-2 infection on exercise performance. CoSmo-S is a prospective observational multicenter study establishing two cohorts: 1) athletes diagnosed positive for COVID-19 (cohort 1) and 2) federal squad athletes who perform their annual sports medical preparticipation screening (cohort 2). Comprehensive diagnostics including physical examination, laboratory blood analyses and blood biobanking, resting and exercise electrocardiogram (ECG), echocardiography, spirometry and exercise testing added by questionnaires are conducted at baseline and follow-up. Results and Conclusion: We expect that the results obtained, will allow us to formulate recommendations regarding RTP on a more evidence-based level

COVID-19 in German Competitive Sports: Protocol for a Prospective Multicenter Cohort Study (CoSmo-S)

Objective: It is unclear whether and to what extent COVID-19 infection poses health risks and a chronic impairment of performance in athletes. Identification of individual health risk is an important decision-making basis for managing the pandemic risk of infection with SARS-CoV-2 in sports and return to play (RTP). Methods: This study aims 1) to analyze the longitudinal rate of seroprevalence of SARS-CoV-2 in German athletes, 2) to assess health-related consequences in athletes infected with SARS-CoV-2, and 3) to reveal effects of the COVID-19 pandemic in general and of a cleared SARS-CoV-2 infection on exercise performance. CoSmo-S is a prospective observational multicenter study establishing two cohorts: 1) athletes diagnosed positive for COVID-19 (cohort 1) and 2) federal squad athletes who perform their annual sports medical preparticipation screening (cohort 2). Comprehensive diagnostics including physical examination, laboratory blood analyses and blood biobanking, resting and exercise electrocardiogram (ECG), echocardiography, spirometry and exercise testing added by questionnaires are conducted at baseline and follow-up. Results and Conclusion: We expect that the results obtained, will allow us to formulate recommendations regarding RTP on a more evidence-based level