uBin – a manual refining tool for metagenomic bins designed for educational purposes

AbstractResolving bacterial and archaeal genomes from metagenomes has revolutionized our understanding of Earth’s biomes, yet producing high quality genomes from assembled fragments has been an ever-standing problem. While automated binning software and their combination produce prokaryotic bins in high-throughput, their manual refinement has been slow and sometimes difficult. Here, we present uBin, a GUI-based, standalone bin refiner that runs on all major operating platforms and was specifically designed for educational purposes. When applied to the public CAMI dataset, refinement of bins was able to improve 78.9% of bins by decreasing their contamination. We also applied the bin refiner as a standalone binner to public metagenomes from the International Space Station and demonstrate the recovery of near-complete genomes, whose replication indices indicate active proliferation of microbes in Earth’s lower orbit. uBin is an easy to install software for bin refinement, binning of simple metagenomes and communication of metagenomic results to other scientists and in classrooms. The software is open source and available under https://github.com/ProbstLab/uBin.

Download Full-text

Technology of high quality protein crystals’ obtaining aboard the ISS at execution of joint Japanese–Russian experiments

Space engineering and technology ◽

10.33950/spacetech-2308-7625-2020-2-5-25 ◽

2020 ◽

pp. 5-25

Author(s):

Koji INAKA ◽

Saori ICHIMIZU ◽

Izumi YOSHIZAKI ◽

Kiyohito KIHIRA ◽

Elena G. LAVRENKO ◽

...

Keyword(s):

Drug Design ◽

International Space Station ◽

Space Station ◽

Protein Crystals ◽

Diffusion Method ◽

X Ray Diffraction ◽

High Quality ◽

International Space ◽

X Ray ◽

High Quality Protein

A series of space experiments aboard the International Space Station (ISS) associated with high-quality Protein Crystal Growth (PCG) in microgravity conditions can be considered as a unique and one of the best examples of fruitful collaboration between Japanese and Russian scientists and engineers in space, which includes also other ISS International Partners. X-ray diffraction is still the most powerful tool to determine the protein three dimensional structure necessary for Structure based drug design (SBDD). The major purpose of the experiment is to grow high quality protein crystals in microgravity for X-ray diffraction on Earth. Within one and a half decade, Japan and Russia have established an efficient process over PCG in space to support latest developments over drug design and structural biology. One of the keys for success of the experiment lies in how precisely pre-launch preparations are made. Japanese party provides flight equipment for crystallization and ensures the required environment to support the experiment aboard of the ISS’s Kibo module, and also mainly takes part of the experiment ground support such as protein sample characterization, purification, crystallization screening, and solution optimization for microgravity experiment. Russian party is responsible for integration of the flight items equipped with proteins and precipitants on board Russian transportation space vehicles (Soyuz or Progress), for delivery them at the ISS, transfer to Kibo module, and returning the experiments’ results back on Earth aboard Soyuz manned capsule. Due to close cooperation of the parties and solid organizational structure, samples can be launched at the ISS every half a year if the ground preparation goes smoothly. The samples are crystallized using counter diffusion method at 20 degree C for 1–2.5 months. After samples return, the crystals are carefully taken out from the capillary, and frozen for X-ray diffraction at SPring8 facility in Japan. Extensive support of researchers from both countries is also a part of this process. The paper analyses details of the PCG experiment scheme, unique and reliable technology of its execution, and contains examples of the application. Key words: International Space Station, Protein crystals, Microgravity, International collaboration.

Download Full-text

An open-source universal strain software platform for monitoring left ventricular systolic function in astronauts on the International Space Station

Heart Lung and Circulation ◽

10.1016/j.hlc.2015.04.077 ◽

2015 ◽

Vol 24 ◽

pp. S80-S81 ◽

Cited By ~ 1

Author(s):

P. Gladding ◽

S. Anwar ◽

K. Negishi ◽

Z. Popovic ◽

J. Odabashian ◽

...

Keyword(s):

Open Source ◽

International Space Station ◽

Systolic Function ◽

Space Station ◽

Left Ventricular Systolic Function ◽

Left Ventricular ◽

Software Platform ◽

Ventricular Systolic Function ◽

International Space

Download Full-text

Pool Boiling Heat Transfer on the International Space Station: Experimental Results and Model Verification

Journal of Heat Transfer ◽

10.1115/1.4006846 ◽

2012 ◽

Vol 134 (10) ◽

Cited By ~ 20

Author(s):

Rishi Raj ◽

Jungho Kim ◽

John McQuillen

Keyword(s):

Heat Transfer ◽

International Space Station ◽

Boiling Heat Transfer ◽

Pool Boiling ◽

Space Station ◽

High Quality ◽

Low Gravity ◽

International Space ◽

Pool Boiling Heat Transfer ◽

Poor Understanding

The relatively poor understanding of gravity effects on pool boiling heat transfer can be attributed to the lack of long duration high-quality microgravity data, g-jitter associated with ground-based low gravity facilities, little data at intermediate gravity levels, and a poor understanding of the effect of important parameters even at earth gravity conditions. The results of over 200 pool boiling experiments with n-perfluorohexane as the test fluid performed aboard the International Space Station (ISS) are presented in this paper. A flat, transparent, constant temperature microheater array was used to perform experiments over a wide range of temperatures (55 °C < Tw < 107.5 °C), pressures (0.58 atm < P < 1.86 atm), subcoolings (1 °C ≤ ΔTsub ≤ 26 °C), and heater sizes (4.2 mm ≤ Lh ≤ 7.0 mm). The boiling process was visualized from the side and bottom. Based on this high quality microgravity data (a/g<10−6), the recently reported gravity scaling parameter for heat flux, which was primarily based on parabolic flight experiments, was modified to account for these new results. The updated model accurately predicts the experimental microgravity data to within ±20%. The robustness of this framework in predicting low gravity heat transfer is further demonstrated by predicting many of the trends in the pool boiling literature that cannot be explained by any single model.

Download Full-text

Significance of Changes in the Skin Fungal Microbiomes of Astronauts Staying on the International Space Station

Journal of Disaster Research ◽

10.20965/jdr.2015.p1031 ◽

2015 ◽

Vol 10 (6) ◽

pp. 1031-1034 ◽

Cited By ~ 1

Author(s):

Takashi Sugita ◽

◽

Otomi Cho

Keyword(s):

International Space Station ◽

Space Station ◽

Extended Period ◽

Skin Microbiome ◽

High Quality ◽

International Space ◽

Highly Sensitive ◽

Fungal Microbiome ◽

Closed Environment

A wide variety of microorganisms colonize the human skin and are important to maintaining human health. However, this community is highly sensitive to perturbations, and diseases can develop when the skin microbiome is disrupted by a change in host or environmental conditions. The International Space Station (ISS) is a closed environment, and astronauts on the ISS do not wash their bodies as frequently as when they are on the ground. The maintenance of a balanced skin microbiome is important to overall health, disease prevention, and a high quality of life while on the ISS. The skin fungal microbiome is dominated by Malassezia sp. These lipophilic fungi are ubiquitous across different skin types, whereas changes in the levels of M. globosa and M. restricta are correlated with the formation of seborreich dermatitis/dandruff. The Malassezia microbiome on the skin of astronauts staying on the ISS changed, and there was a reduction in skin fungal microbial diversity. These findings provide useful information about temporal changes in the hygiene of astronauts who are on the ISS for an extended period and indicate that Malassezia microbiome as microbiological markers of skin hygiene.

Download Full-text

Modeling lightning observations from space-based platforms (CloudScat.jl 1.0)

Geoscientific Model Development ◽

10.5194/gmd-13-5549-2020 ◽

2020 ◽

Vol 13 (11) ◽

pp. 5549-5566

Author(s):

Alejandro Luque ◽

Francisco José Gordillo-Vázquez ◽

Dongshuai Li ◽

Alejandro Malagón-Romero ◽

Francisco Javier Pérez-Invernón ◽

...

Keyword(s):

Open Source ◽

International Space Station ◽

Optical Radiation ◽

Multispectral Imaging ◽

Space Station ◽

Computer Code ◽

Lightning Flash ◽

International Space ◽

Imaging Array

Abstract. We describe a computer code that simulates how a satellite observes optical radiation emitted by a lightning flash after it is scattered within an intervening cloud. Our code, CloudScat.jl, is flexible, fully open source and specifically tailored to modern instruments such as the Modular Multispectral Imaging Array (MMIA) component of the Atmosphere–Space Interactions Monitor (ASIM) that operates from the International Space Station. In this article, we describe the algorithms implemented in the code and discuss several applications and examples, with an emphasis on the interpretation of MMIA data.

Download Full-text

International Space Station Open-Source Data

Patterns ◽

10.1016/j.patter.2020.100172 ◽

2020 ◽

Vol 1 (9) ◽

pp. 100172

Author(s):

Lara Elisabeth Warren

Keyword(s):

Open Source ◽

International Space Station ◽

Space Station ◽

International Space ◽

Open Source Data ◽

Source Data

Download Full-text

Modeling lightning observations from space-based platforms (CloudScat.jl 1.0)

10.5194/gmd-2020-161 ◽

2020 ◽

Author(s):

Alejandro Luque ◽

Francisco José Gordillo-Vázquez ◽

Dongshuai Li ◽

Alejandro Malagón-Romero ◽

Francisco Javier Pérez-Invernón ◽

...

Keyword(s):

Open Source ◽

International Space Station ◽

Optical Radiation ◽

Multispectral Imaging ◽

Space Station ◽

Computer Code ◽

Lightning Flash ◽

International Space ◽

Imaging Array

Abstract. We describe a computer code that simulates how a satellite observes optical radiation emitted by a lightning flash after it is scattered within an intervening cloud. Our code, CloudScat.jl, is flexible, fully open source and specifically tailored to modern instruments such as the Modular Multispectral Imaging Array (MMIA) component of the Atmosphere-Space Interactions Monitor (ASIM) that operates from the International Space Station. In this article we describe the algorithms implemented in the code and discuss several applications and examples, with an emphasis on the interpretation of MMIA data.

Download Full-text