BacArena: Individual-Based Metabolic Modeling of Heterogeneous Microbes in Complex Communities

Recent advances focusing on the metabolic interactions within and between cellular populations, have emphasized the importance of microbial communities for human health. Constraint-based modeling, with flux balance analysis in particular, has been established as a key approach for studying microbial metabolism, whereas individual-based modeling has been commonly used to study complex dynamics between interacting organisms. In this study, we combine both techniques into the R package BacArena (https://cran.r-project.org/package=BacArena), to generate novel biological insights into Pseudomonas aeruginosa biofilm formation as well as a seven species model community of the human gut. For our P. aeruginosa model, we found that cross-feeding of fermentation products cause a spatial differentiation of emerging metabolic phenotypes in the biofilm over time. In the human gut model community, we found that spatial gradients of mucus glycans are important for niche formations, which shape the overall community structure. Additionally, we could provide novel hypothesis concerning the metabolic interactions between the microbes. These results demonstrate the importance of spatial and temporal multi-scale modeling approaches such as BacArena

Midbrain–hindbrain malformations in patients with malformations of cortical development and epilepsy: A series of 220 patients

SummaryMidbrain–hindbrain malformations (MHM) may coexist with malformations of cortical development (MCD). This study represents a first attempt to investigate the spectrum of MHM in a large series of patients with MCD and epilepsy. We aimed to explore specific associations between MCD and MHM and to compare two groups of patients: MCD with MHM (wMHM) and MCD without MHM (w/oMHM) with regard to clinical and imaging features.Two hundred and twenty patients (116 women/104 men, median age 28 years, interquartile range 20–44 years at the time of assessment) with MCD and epilepsy were identified at the Departments of Neurology and Pediatrics, Innsbruck Medical University, Austria. All underwent high-resolution MRIs (1.5-T) between 01.01.2002 and 31.12.2011. Midbrain–hindbrain structures were visually assessed by three independent raters.MHM were seen in 17% (38/220) of patients. The rate of patients wMHM and w/oMHM differed significantly (p=0.004) in three categories of MCD (category I – to abnormal neuronal proliferation; category II – to abnormal neuronal migration; and category III – due to abnormal neuronal late migration/organization): MCD due to abnormal neuronal migration (31%) and organization (23%) were more commonly associated with MHM compared to those with MCD due to abnormal neuronal proliferation (9%). Extensive bilateral MCD were seen more often in patients wMHM compared to those w/oMHM (63% vs. 36%; p=0.004). In wMHM group compared to w/oMHM group there were higher rates of callosal dysgenesis (26% vs. 4%; p<0.001) and hippocampal abnormalities (52% vs. 27%; p<0.001). Patients wMHM were younger (median 25 years vs. 30 years; p=0.010) at the time of assessment and had seizure onset at an earlier age (median 5 years vs. 12 years; p=0.043) compared to those w/oMHM. Patients wMHM had higher rates of learning disability (71% vs. 38%; p<0.001), delayed developmental milestones (68% vs. 35%; p<0.001) and neurological deficits (66% vs. 47%; p=0.049) compared to those w/oMHM.The groups (wMHM and w/oMHM) did not differ in their response to antiepileptic treatment, seizure outcome, seizure types, EEG abnormalities and rate of status epilepticus. Presence of MHM in patients with MCD and epilepsy is associated with severe morphological and clinical phenotypes

Global network of computational biology communities: ISCB's regional student groups breaking barriers [version 1; peer review: Not peer reviewed]

Regional Student Groups (RSGs) of the International Society for Computational Biology Student Council (ISCB-SC) have been instrumental to connect computational biologists globally and to create more awareness about bioinformatics education. This article highlights the initiatives carried out by the RSGs both nationally and internationally to strengthen the present and future of the bioinformatics community. Moreover, we discuss the future directions the organization will take and the challenges to advance further in the ISCB-SC main mission: “Nurture the new generation of computational biologists”.Fil: Shome, Sayane. University of Iowa; Estados UnidosFil: Parra, Rodrigo Gonzalo. European Molecular Biology Laboratory; Alemania. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Fatima, Nazeefa. Uppsala Universitet; SueciaFil: Monzon, Alexander Miguel. Università di Padova; ItaliaFil: Cuypers, Bart. Universiteit Antwerp; BélgicaFil: Moosa, Yumna. University of KwaZulu Natal; SudáfricaFil: Da Rocha Coimbra, Nilson. Universidade Federal de Minas Gerais; BrasilFil: Assis, Juliana. Universidade Federal de Minas Gerais; BrasilFil: Giner Delgado, Carla. Universitat Autònoma de Barcelona; EspañaFil: Dönertaş, Handan Melike. European Molecular Biology Laboratory. European Bioinformatics Institute; Reino UnidoFil: Cuesta Astroz, Yesid. Universidad de Antioquia; Colombia. Universidad Ces. Facultad de Medicina.; ColombiaFil: Saarunya, Geetha. University of South Carolina; Estados UnidosFil: Allali, Imane. Universite Mohammed V. Rabat; Otros paises de África. University of Cape Town; SudáfricaFil: Gupta, Shruti. Jawaharlal Nehru University; IndiaFil: Srivastava, Ambuj. Indian Institute of Technology Madras; IndiaFil: Kalsan, Manisha. Jawaharlal Nehru University; IndiaFil: Valdivia, Catalina. Universidad Andrés Bello; ChileFil: Olguín Orellana, Gabriel José. Universidad de Talca; ChileFil: Papadimitriou, Sofia. Vrije Unviversiteit Brussel; Bélgica. Université Libre de Bruxelles; BélgicaFil: Parisi, Daniele. Katholikie Universiteit Leuven; BélgicaFil: Kristensen, Nikolaj Pagh. Technical University of Denmark; DinamarcaFil: Rib, Leonor. Universidad de Copenhagen; DinamarcaFil: Guebila, Marouen Ben. University of Luxembourg; LuxemburgoFil: Bauer, Eugen. University of Luxembourg; LuxemburgoFil: Zaffaroni, Gaia. University of Luxembourg; LuxemburgoFil: Bekkar, Amel. Universite de Lausanne; SuizaFil: Ashano, Efejiro. APIN Public Health Initiatives; NigeriaFil: Paladin, Lisanna. Università di Padova; ItaliaFil: Necci, Marco. Università di Padova; ItaliaFil: Moreyra, Nicolás Nahuel. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Ecología, Genética y Evolución de Buenos Aires. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Ecología, Genética y Evolución de Buenos Aires; Argentin

Capabilities of Gossamer-1 derived small spacecraft solar sails carrying MASCOT-derived nanolanders for in-situ surveying of NEAs

Any effort which intends to physically interact with specific asteroids requires understanding at least of the composition and multi-scale structure of the surface layers, sometimes also of the interior. Therefore, it is necessary first to characterize each target object sufficiently by a precursor mission to design the mission which then interacts with the object. In small solar system body (SSSB) science missions, this trend towards landing and sample-return missions is most apparent. It also has led to much interest in MASCOT-like landing modules and instrument carriers. They integrate at the instrument level to their mothership and by their size are compatible even with small interplanetary missions. The DLR-ESTEC Gossamer Roadmap NEA Science Working Groups‘ studies identified Multiple NEA Rendezvous (MNR) as one of the space science missions only feasible with solar sail propulsion. Parallel studies of Solar Polar Orbiter (SPO) and Displaced L1 (DL1) space weather early warning missions studies outlined very lightweight sailcraft and the use of separable payload modules for operations close to Earth as well as the ability to access any inclination and a wide range of heliocentric distances. These and many other studies outline the unique capability of solar sails to provide access to all SSSB, at least within the orbit of Jupiter. Since the original MNR study, significant progress has been made to explore the performance envelope of near-term solar sails for multiple NEA rendezvous. However, although it is comparatively easy for solar sails to reach and rendezvous with objects in any inclination and in the complete range of semi-major axis and eccentricity relevant to NEOs and PHOs, it remains notoriously difficult for sailcraft to interact physically with a SSSB target object as e.g. the Hayabusa missions do. The German Aerospace Center, DLR, recently brought the Gossamer solar sail deployment technology to qualification status in the Gossamer-1 project. Development of closely related technologies is continued for very large deployable membrane-based photovoltaic arrays in the GoSolAr project. We expand the philosophy of the Gossamer solar sail concept of efficient multiple sub-spacecraft integration to also include landers for one-way in-situ investigations and sample-return missions. These are equally useful for planetary defence scenarios, SSSB science and NEO utilization. We outline the technological concept used to complete such missions and the synergetic integration and operation of sail and lander. We similarly extend the philosophy of MASCOT and use its characteristic features as well as the concept of Constraints-Driven Engineering for a wider range of operations

Small Spacecraft Based Multiple Near-Earth Asteroid Rendezvous and Landing with Near-Term Solar Sails and ‘Now-Term‘ Technologies

Physical interaction with small solar system bodies (SSSB) is the next step in planetary science, planetary in-situ resource utilization (ISRU), and planetary defense (PD). It requires a broader understanding of the surface properties of the target objects, with particular interest focused on those near Earth. Knowledge of composition, multi-scale surface structure, thermal response, and interior structure is required to design, validate and operate missions addressing these three fields. The current level of understanding is occasionally simplified into the phrase, ”If you’ve seen one asteroid, you’ve seen one asteroid”, meaning that the in-situ characterization of SSSBs has yet to cross the threshold towards a robust and stable scheme of classification. This would enable generic features in spacecraft design, particularly for ISRU and science missions. Currently, it is necessary to characterize any potential target object sufficiently by a dedicated pre-cursor mission to design the mission which then interacts with the object in a complex fashion. To open up strategic approaches, much broader in-depth characterization of potential target objects would be highly desirable. In SSSB science missions, MASCOT-like nano-landers and instrument carriers which integrate at the instrument level to their mothership have met interest. By its size, MASCOT is compatible with small interplanetary missions. The DLR-ESTEC Gossamer Roadmap Science Working Groups‘ studies identified Multiple Near-Earth asteroid (NEA) Rendezvous (MNR) as one of the space science missions only feasible with solar sail propulsion. The Solar Polar Orbiter (SPO) study showed the ability to access any inclination, theDisplaced-L1 (DL1) mission operates close to Earth, where objects of interest to PD and for ISRU reside. Other studies outline the unique capability of solar sails to provide access to all SSSB, at least within the orbit of Jupiter, and significant progress has been made to explore the performance envelope of near-term solar sails for MNR. However, it is difficult for sailcraft to interact physically with a SSSB. We expand and extend the philosophy of the recently qualified DLR Gossamer solar sail deployment technology using efficient multiple sub-spacecraft integration to also include landers for one-way in-situ investigations and sample-return missions by synergetic integration and operation of sail and lander. The MASCOT design concept and its characteristic features have created an ideal counterpart for thisand has already been adapted to the needs of the AIM spacecraft, former part of the NASA-ESA AIDA mission. Designing the combined spacecraft for piggy-back launch accommodation enables low-cost massively parallel access to the NEA population

Solar Sails for Planetary Defense and High-Energy Missions

20 years after the successful ground deployment test of a (20 m)² solar sail at DLR Cologne, and in the light of the upcoming U.S. NEAscout mission, we provide an overview of the progress made since in our mission and hardware design studies as well as the hardware built in the course of our solar sail technology development. We outline the most likely and most efficient routes to develop solar sails for useful missions in science and applications, based on our developed ‘now-term’ and near-term hardware as well as the many practical and managerial lessons learned from the DLR-ESTEC GOSSAMER Roadmap. Mission types directly applicable to planetary defense include single and Multiple NEA Rendezvous ((M)NR) for precursor, monitoring and follow-up scenarios as well as sail-propelled head-on retrograde kinetic impactors (RKI) for mitigation. Other mission types such as the Displaced L1 (DL1) space weather advance warning and monitoring or Solar Polar Orbiter (SPO) types demonstrate the capability of near-term solar sails to achieve asteroid rendezvous in any kind of orbit, from Earth-coorbital to extremely inclined and even retrograde orbits. Some of these mission types such as SPO, (M)NR and RKI include separable payloads. For one-way access to the asteroid surface, nanolanders like MASCOT are an ideal match for solar sails in micro-spacecraft format, i.e. in launch configurations compatible with ESPA and ASAP secondary payload platforms. Larger landers similar to the JAXA-DLR study of a Jupiter Trojan asteroid lander for the OKEANOS mission can shuttle from the sail to the asteroids visited and enable multiple NEA sample-return missions. The high impact velocities and re-try capability achieved by the RKI mission type on a final orbit identical to the target asteroid‘s but retrograde to its motion enables small spacecraft size impactors to carry sufficient kinetic energy for deflection

Ferromagnetic MnSb2Te4: A p-type topological insulator with magnetic gap closing at high Curie temperatures of 45-50K

Resumen del trabajo presentado al APS March Meeting, celebrado de forma virtual del 13 al 19 de marzo de 2021Mn enables the formation of intrinsic magnetic topological insulatorsfor the quantum anomalous Hall effect with A1B2C4 stoichiometry, e. g., antiferromagnetic MnBi2Te4 with 25 K Néel temperature. Here, we showthat p-type MnSb2Te4, previously considered topologically trivial, is a ferromagnetic topological insulator with high Curie temperature of 45 to 50 K.It displays out-of-plane magnetic anisotropy, the nontrivial topology is robust in band structure calculations towards magnetic disorder, provides aDirac point of the topological surface state close to the Fermi level with out-of-plane spin polarization in spin-ARPES, and exhibits a magneticallyinduced band gap of 17 meV that closes at the Curie temperature as demonstrated by scanning tunneling spectroscopy. Moreover, it displays acritical exponent of magnetization β≈1, indicating the vicinity of a quantum critical point. We identify the influences of structural and magneticdisorder that render MnSb2Te4 the ideal system for tuning electric and magnetic properties of quantum anomalous Hall systems.Peer reviewe