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FIGURE 1. Morphological variation within the N. commune strains. A, B in Polyphasic characterization of Nostoc commune (Cyanobacteria, Nostocaceae) isolated from rice growing agro-ecosystems of Dima Hasao district of Assam, North-East India
FIGURE 1. Morphological variation within the N. commune strains. A, B. Plate view and liquid culture of N. commune AUS-JR/DB/ NT-003. C, D. Plate view and liquid culture of N. commune AUS-JR/DB/NT-004. E. A single colony of N. commune AUS-JR/DB/NT- 003. F. A single colony of N. commune AUS-JR/DB/NT-004. G. Disintegration of the sheath. H. Individual trichomes. I. Aseriate filaments (h: heterocyst). J. Seriate filaments. K. Ensheathed coccoid cells. L. Old colonies with reduced trichome. Bar length = 50µm.
Cell size, chlorophyll fluorescence and cadmium bioaccumulation between wild-type and mutant strains of Chlamydomonas reinhardtii upon exposure to cadmium
<p>Heavy metal contamination presents a constant threat to biological systems. Simultaneously, heavy metals have become one of the major contaminants in the aquatic ecosystem. In this regard, the investigation of heavy metal-tolerance genes in algae is relevant. <i>Chlamydomonas reinhardtii</i> is a unicellular green alga, and an excellent model organism used in heavy metal studies. In <i>C. reinhardtii</i>, a novel gene designated as Cia7, was hypothesized to play a role in heavy metal homeostasis due to CIA7's conserved cysteine-residue motif. This study compared two strains of <i>C. reinhardtii</i>, cc4425, the wild-type possessing the functional CIA7 protein and cc5013, the mutant strain possessing the disrupted cia7- gene. The hypothesis was that the expression of Cia7 contributes to an increased cadmium (Cd)-tolerance in <i>C. reinhardtii</i>. The Cd-tolerance would be described by physiological markers of microalgae health, and by intracellular accumulation of the metal. Methods: The objectives of this study were (1) to compare chlorophyll fluorescence and cell size in cc4425 and cc5013 exposed to Cd<sup>2+</sup>, and (2) to compare Cd<sup>2+</sup> bioaccumulation in cc4425 and cc5013 strains in different growth media. Flow cytometry, and inductively coupled plasma optical emission spectrometry (ICP-OES) analysis were performed. Results: There was no significant statistical difference in Cd<sup>2+</sup> bioaccumulation between the two strains, cc4425 and cc5013, regardless of growth media. However, a statistically significant difference in Cd<sup>2+</sup> bioaccumulation (p<0.0001) was determined between the media (with acetate and without acetate). The cia7- mutant, cc5013 was found to be more susceptible to a Cd<sup>2+</sup>-induced decrease in chlorophyll fluorescence and had a reduced cell size compared to cc4425, the wild-type strain. Conclusions: These observed differences between the strains suggest that CIA7's biological activity could play a direct or indirect role in increasing Cd tolerance in <i>C. reinhardtii</i>.</p>
CarcSeq measurement of lung cancer driver mutations predicts mouse strain- and sex-related incidence of spontaneous lung neoplasia
<p>The data contained herein are the fastq files collected for individual mouse lung DNA samples. Ten samples each of male and female, B6C3F1 and CD-1 mouse lung DNA were analyzed using the CarcSeq method for error-corrected next-generation sequencing as previously described [Harris, KL, Walia, V, Gong, B, et al. Quantification of cancer driver mutations in human breast and lung DNA using targeted, error-corrected CarcSeq. <i>Environ Mol Mutagen</i>. 2020; 61: 872– 889. <a href="https://doi.org/10.1002/em.22409">https://doi.org/10.1002/em.22409</a> and Karen L McKim, Meagan B Myers, Kelly L Harris, Binsheng Gong, Joshua Xu, Barbara L Parsons, CarcSeq Measurement of Rat Mammary Cancer Driver Mutations and Relation to Spontaneous Mammary Neoplasia, <em>Toxicological Sciences</em>, 2021;, kfab040, <a href="https://doi.org/10.1093/toxsci/kfab040">https://doi.org/10.1093/toxsci/kfab040</a>]. A readme text file provides the key to which sample numbers correspond with which mouse strain and sex. All the fastq files within a given folder were used to construct single strand consensus sequences, which were then subject to downstream analyses as reported in the associated publication.</p>
Fast grip force adaptation to friction relies on localized fingerpad strains
<p>Humans can quickly adjust their grip force to a change in friction at the object-skin interface during dexterous manipulation in a precision grip. To perform this adjustment, they rely on the feedback of the mechanoreceptive afferents innervating the fingertip skin. Because these tactile afferents encode information related to skin deformation, the nature of the feedback signaling a change in friction must somehow originate from a difference in the way the skin deforms when manipulating objects of different frictions. To better characterize the origin of the underlying sensory events, we asked human participants to perform a grip-lifting task with a manipulandum equipped with an optical imaging system. This system enabled to monitor fingertip skin strains through transparent plates of glass that had different levels of friction. We observed that, following an unexpected change in friction, participants adapted their grip force within 370ms after contact with the surface. By comparing the deformation patterns when unexpectedly switching from a high to a low friction condition, we found a significant increase in skin deformation inside the contact area arising over 100ms before the motor response, during the loading phase, suggesting that local and partial deformation patterns prior to lift-off are used in the nervous system to adjust the grip force as a function of the frictional condition.</p>
Figure 1 in Establishment of an isogenic strain of the desiccationsensitive tardigrade Isohypsibius myrops (Parachela, Eutardigrada) and its life history traits
Figure 1. Graphical experimental scheme of the desiccation assay. In total, 29 or 30 tardigrades were dropped onto the filter paper and placed in the sealed desiccation chamber. The humidity in the chamber was controlled by the presence of saturated salt solution or water, which had no contact with the animals.
Figure 3 in Establishment of an isogenic strain of the desiccationsensitive tardigrade Isohypsibius myrops (Parachela, Eutardigrada) and its life history traits
Figure 3. Sensitivity of the Im1 strain to desiccation. Survival rates after exposure to various humidity conditions for 1 or 2 days. Mean ƚ SD (N = 4; 30 tardigrades each).
Figure 4 in Establishment of an isogenic strain of the desiccationsensitive tardigrade Isohypsibius myrops (Parachela, Eutardigrada) and its life history traits
Figure 4. Life history traits of Im1 strain. A, longevity of Im1 strain. B, hatching time after oviposition.
Figure 5 in Establishment of an isogenic strain of the desiccationsensitive tardigrade Isohypsibius myrops (Parachela, Eutardigrada) and its life history traits
Figure 5. Simulation of population change started with a single newly hatched juvenile of Im1 strain. Theoretical change in the population was simulated based on mean values of life history traits, such as hatching time = 3.6 days; first oviposition = 10.3 days; interval of ovipositions = 2.5 days; lifespan = 18.8 days; number of eggs per clutch = 19; hatchability = 83%.
Figure 2 in Establishment of an isogenic strain of the desiccationsensitive tardigrade Isohypsibius myrops (Parachela, Eutardigrada) and its life history traits
Figure 2. Specimens of cultured Im1 strain. A, live differential interference contrast (DIC) image of an adult individual. The specimen was largely transparent, making it easy to inspect the internal structures. B, dorsal view of the head region. Arrowheads indicate two fatty droplets. C, exuviae containing five embryos. The eggshell has a smooth surface. D, DIC image of the pharyngeal apparatus. Three macroplacoids were visible (ma1, ma2, ma3). No microplacoids were observed. E, DIC image of flattened preparation of the pharyngeal apparatus clearly showing separation of macroplacoids (ma1, ma2, ma3). Scale bars = 100 µm (A, C) and 20 µm (B, D, E). Anterior is left in all panels.
Expression of degQ gene and its effect on lipopeptide production as well as formation of secretory proteases in Bacillus subtilis strains
<p><em>Bacillus subtilis</em> is described as a promising production strain for lipopeptides. In case of <em>B. subtilis</em> strains JABs24 and DSM10<sup>T</sup>, surfactin and plipastatin are produced. Lipopeptide formation is controlled, among others, by the DegU response regulator. The activating phospho-transfer by the DegS sensor kinase is stimulated by the pleiotropic regulator DegQ, resulting in enhanced DegU activation. In <em>B. subtilis</em> 168, a point mutation in the <em>degQ</em> promoter region leads to a reduction in gene expression. Corresponding reporter strains showed a 14-fold reduced expression. This effect on <em>degQ</em> expression and the associated impact on lipopeptide formation was examined for <em>B. subtilis</em> JABs24, a lipopeptide-producing derivative of strain 168, and <em>B. subtilis</em> wild-type strain DSM10<sup>T</sup>, which has a native <em>degQ</em> expression. Based on stimulatory effects of the DegU regulator on secretory protease formation, the impact of <em>degQ</em> expression on extracellular protease activity was additionally investigated. To follow the impact of <em>degQ</em>, a deletion mutant was constructed for DSM10<sup>T</sup>, while a natively expressed <em>degQ</em> version was integrated into strain JABs24. This allowed strain-specific quantification of the stimulatory effect of <em>degQ</em> expression on plipastatin and the negative effect on surfactin production in strains JABs24 and DSM10<sup>T</sup>. While an unaffected <em>degQ</em> expression reduced surfactin production in JABs24 about 25%, a 6-fold increase in plipastatin was observed. In contrast, <em>degQ</em> deletion in DSM10<sup>T</sup> increased surfactin titer by 3-fold but decreased plipastatin production by 5-fold. In addition, although significant differences in extracellular protease activity were detected, no decrease in plipastatin and surfactin produced during cultivation was observed.</p>
Asymmetric cross-strain protection for amphibians exposed to a fungal-metabolite prophylactic treatment
<p>Chytridiomycosis, an infectious disease of amphibians caused by the fungal pathogen <i>Batrachochytrium dendrobatidis</i> (Bd), poses an imminent conservation threat. The global spread of Bd has led to mass mortality events in many amphibian species, resulting in at least 90 species' extinctions to date. Exposure to Bd metabolites (i.e., non-infectious antigenic chemicals released by Bd) partially protects frogs during subsequent challenges with live Bd, suggesting its use as a prophylactic treatment and potential vaccine. However, we do not know whether Bd metabolite exposure protects against strains beyond the one used for treatment. To address this knowledge gap, we conducted a 3x2 experiment where we exposed adult Cuban treefrogs, <i>Osteopilus septentrionalis</i>, to one of three treatments (Bd metabolites from California-isolated strain JEL-270, Panamá-isolated strain JEL-419, or an artificial spring water control) and then challenged individuals with live Bd from either strain. We found that exposure to Bd metabolites from the California-isolated strain significantly reduced Bd loads of frogs challenged with the live Panamá-isolated strain, but no other treatments were found to confer protective effects. These findings demonstrate asymmetric cross-protection of a Bd metabolite prophylaxis and suggests that work investigating multiple, diverse strains is urgently needed.</p>
Self-Strain-Sensing: Comparison of Contact Materials
<p>These Datasets were used to compare different contacting methods for the development of Self-Strain-Sensing CFRP parts.</p>
QMC Raw Data for Superfulid Helium Adsorbed on Strained Graphene
<p>Data Summary</p> <p>Raw data of path integral Monte Carlo simulation for phase diagram analysis of atomic helium adsorbed on isotropically strained graphene.<br> For more details, please check README.md on Github repository</p> <p>lindenset.zip</p> <ul> <li>Raw data for linear density plot</li> <li> Corresponds to lindenset.ipynb</li> </ul> <p>OUTPUT_largebox.zip</p> <ul> <li>Raw data for simulations with N_ad = 144</li> <li>Corresponds to LargeBoxSim.ipynb</li> </ul> <p>OUTPUT_phase.zip</p> <ul> <li>Raw data for analysis of adsorption phases</li> <li>Corresponds to AdsorptionPhaseAnalyzer.ipynb</li> </ul> <p>OUTPUT_T1set.zip</p> <ul> <li>Raw data for analysis of PIMC phase diagram</li> <li>Corresponds to T1comm_phases.ipynb</li> </ul> <p>OUTPUT_vacuum.zip</p> <ul> <li>Raw data for analysis of vacuum phase boundary</li> <li>Corresponds to VacuumFinder.ipynb</li> </ul>
Novel Method for Reliable Identification of Siccibacter and Franconibacter Strains: from "Pseudo-Cronobacter" to New Enterobacteriaceae Genera
<p>Main spectrum projections of "pseudo-Cronobacter" strains from the article B. Svobodová, J. Vlach, P. Junková, L. Karamonová, M. Blažková & L. Fukal: Novel Method for Reliable Identification of Siccibacter and Franconibacter Strains: from “Pseudo-Cronobacter” to New Enterobacteriaceae Genera. <em>Applied and Environmental Microbiology</em> 2017,<strong> 83</strong>(13) e00234-17. DOI: 10.1128/AEM.00234-17.</p>
Simulations scripts for: Strain localization patterns and thrust propagation in 3-D discrete element method (DEM) models of accretionary wedges
<p>High-resolution three-dimensional discrete element method (DEM) simulations of sandbox-scale models of accretionary wedges performed in this study suggest thrusts follow a variety of propagation processes and orientations in the wedges depending on a number of factors including the stage of development of the wedge (precritical vs. critical), basal friction, and type of thrust (forward vs. backward-vergent). In terms of propagation processes, two clear mechanisms are identified. The first involves propagation from the decollement to the wedge top, similar to the standard model of thrust propagation seen in many kinematic models, and in the second, thrusts grow downward from an initial nucleation point just below the top surface of the wedge as well as upward from the decollement joining in the middle. In terms of orientation, forward-vergent thrusts initially form at Roscoe or Arthur orientations, and over shortening, form at Coulomb orientations. To arrive at these results, a wide array of continuum parameters and fields were extracted from the granular assembly of the DEM simulations, including stress, strain, strain rate, kinetic energy, Mohr-Coulomb parameters, and proximity to yielding using the Drucker-Prager criterion to visualize thrust nucleation and propagation. Lastly, the advantages and disadvantages of these continuum proxies for discerning failure in the granular assembly are considered, and the spatial and temporal relationship between proximity to yielding and strain localization (both pre-peak and persistent shear banding) in the granular model of an accretionary wedge is explored.</p>
Dyadic encounter unfamiliar female pairs over 2 days – 16p11.2 Del mouse strain – WT-WT - 5202_5191
<p>We evaluated the social interactions and communication between unfamiliar individuals in pairs. For these recordings of social behaviour and ultrasonic communication, we focused on pairs of individuals since we currently cannot identify the emitter of USVs when animals were interacting closely. Therefore, we recorded undisturbed dyadic interactions between two unfamiliar individuals (from two different housing cages) of the same age (14-20 weeks of age) and genotype for 47h (two days and nights). For that purpose, we coupled the Live Mouse Tracker system (plugin 931) with one CM16/CMPA microphone (Avisoft Bioacoustics, Glienecke, Germany) connected to the Avisoft Ultrasound Gate 416 (300 kHz sampling rate, 16-bit format; trigger: level of this channel; pre-trigger: 1 s; hold time: 1 s; duration > 0.005 s; trigger event: 2 % energy in 25-125 kHz with entropy < 50%; Avisoft Bioacoustics, Glienecke, Germany). LMT and Avisoft systems were synchronised based on the protocol described in (de Chaumont et al., 2021). Each upload includes the sqlite database from LMT (processed, with USV synchronised) and a zip file with all USVs sequences automatically recorded by Avisoft.</p>
Data from: Patterns of genomic and allochronic strain divergence in the fall armyworm, Spodoptera frugiperda
<p>Speciation is the process through which reproductive isolation develops between distinct populations. Because this process takes time, speciation studies often necessarily examine populations within a species that are at various stages of divergence. The fall armyworm, <em>Spodoptera frugiperda </em>(J.E.Smith), is comprised of two strains (R=Rice & C=Corn) that serve as a novel system to explore population divergence in sympatry. Here, we use ddRADSeq data to show that fall armyworm strains in the field are largely genetically distinct, but some interstrain hybridization occurs. Although we detected F1 hybrids of both R- and C-strain maternal origin, only hybrids with R-strain mtDNA were found to contribute to subsequent generations, possibly indicating a unidirectional barrier to gene flow. Although these strains have been previously defined as 'host plant-associated,' we recovered an equal proportion of R- and C-strain individuals in fields dominated by C-strain host plants. As an alternative to host associated divergence, we tested the hypothesis that differences in nightly activity patterns could account for reproductive isolation by genotyping temporally-collected moths. Our data indicates that strains exhibit a significant shift in the timing of their nightly activities in the field. This divergence in phenology creates a prezygotic reproductive barrier that likely maintains the genetic isolation between strains. Thus, we conclude that it may be ecologically inaccurate to refer to the C- and R- strain as 'host-associated' and they should more appropriately be considered 'allochronic strains.'</p>
Effects of strain rate and adiabatic heating on mechanical behavior of medium manganese Q&P steels - dataset
<p>The data set used in Effects of strain rate and adiabatic heating on mechanical behavior of medium manganese Q&P steels by Veera Langi</p>
Supporting data for Absorbing stress via molecular crumple zones: Strain engineering flexibility into the rigid UiO-66 material
<p>Supplementary data containing relevant structural information for the manuscript 'Absorbing stress via molecular crumple zones: Strain engineering flexibility into the rigid UiO-66 material'.</p> <p>Please also refer to https://github.com/SvenRogge/supporting-info for additional input scripts to reproduce these results and a detailed description of the different files.</p>
Antismash results for 321 strains
<p>Antismash results of 321 Streptomyces strains, which have publicly available genomes with maximum 300 contigs and minimum 90 % completeness.</p>
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.