bluuebunny/crossref_metadata_2025 huggingface dataset:
Evolutionary study of the412/mdg1lineage of theTy3/gypsygroup of LTR retrotransposons in Diptera
Authors: Bertocchi Natasha Avila , Torres Fabiano Pimentel , Deprá Maríndia , da Silva Valente Vera Lúcia
Published: September 2020

LTR-retrotransposons are structurally similar to retroviruses, as they possess the enzymes reverse transcriptase, Ribonuclease H, integrase, proteinase, and thegaggene and are flanked by long terminal repeats (LTRs). The412/mdg1lineage, belonging to theTy3/Gypsygroup, consists of the TEs412, mdg1, stalker, pilgrim, andblood. The412/mdg1lineage is distinguished from the others in thegypsygroup in that it has small ORFs at the beginning of the TE and is highly similar to thepolORF among the TEs that make up the lineage. In this study, our aim was to elucidate the evolutionary history of the412/mdg1lineage in the 127 dipteran genomes available to date, and the characteristics of the sequences in each genome. We used the canonical TE412probe described inDrosophila melanogasteras the query. We found sequences homologous to the412/mdg1lineage restricted to the suborder Brachycera. These sequences are widely distributed in drosophilids but are also present in other groups of flies. We note the presence of the412/mg1lineage in tsetse flies (Glossina). Furthermore, our results showed an elaborate evolutionary history for thepolORF in the412/mdg1lineage of the LTR-Retrotransposon.
QuickFigures: a tool to quickly transform microscope images into quality figures
Authors: Mazo Gregory
Published: September 2020

Publications involving fluorescent microscopy generally contain many panels with split channels, merged images, scale bars and label text. Assembling and editing these figures with even spacing, consistent font, text position, accurate scale bars and other features can be tedious and time consuming. In order to save time and streamline the process I have created a toolset called QuickFigures.
Introduction of a precocious metamorphosis BmNPV infection in the latter half of the fifth instar silkworm larvae
Authors: Xu Pingzhen , Zhang Meirong , Wang Xueyang , Wu Yangchun
Published: September 2020

The silkworm,Bombyx mori, is a complete metamorphosis insect, the model to study insect physiology and biochemistry.Bombyx morinucleopolyhedrovirus (BmNPV) is a principal pathogen of the silkworm and its host range is restricted to silkworm larvae, requiring interaction with larvae to accomplish virus replication. Prothoracic glands (PGs) are a model for synthetic ecdysone with regulating insect growth and development. This study performed a transcriptome analysis of silkworm PGs after BmNPV infection. Transcriptome data were annotated with KEGG, GO, and shown to be of high quality by RT-qPCR. The spatial expression profiles ofBmJingandBmArylindicate that they may be specifically expressed in silkworm PGs. The RT-qPCR results of the DEGs in the PGs of BmNPV-infected larvae at 24, 48, and 72 h and at the developmental stages of days-6 and 7, comparing to day-3, reveal that the DEGs may be related to the BmNPV infection via promoting early maturation in the latter half of the silkworm fifth instar. This study is the first report on the identification of possible genes in PGs correlating with the precocious molting and metamorphosis of silkworm larvae under BmNPV infection in the latter half of the fifth instar. Our findings will help to address the interactions between BmNPV infection and host developmental response. This work provides a new perspective on BmNPV infection and host developmental response, as well as suggesting candidate genes for further research.
Ribosomal protein S7 ubiquitination during ER stress in yeast is associated with selective mRNA translation and stress outcome
Authors: Matsuki Yasuko , Matsuo Yoshitaka , Nakano Yu , Iwasaki Shintaro , Yoko Hideyuki , Udagawa Tsuyoshi , Li Sihan , Saeki Yasushi , Yoshihisa Tohru , Tanaka Keiji , Ingolia Nicholas T. , Inada Toshifumi
Published: September 2020

eIF2α phosphorylation-mediated translational regulation is crucial for global translation repression by various stresses, including the unfolded protein response (UPR). However, translational control during UPR has not been demonstrated in yeast. This study investigated ribosome ubiquitination-mediated translational controls during UPR. Tunicamycin-induced ER stress enhanced the levels of ubiquitination of the ribosomal proteins uS10, uS3 and eS7. Not4-mediated monoubiquitination of eS7A was required for resistance to tunicamycin, whereas E3 ligase Hel2-mediated ubiquitination of uS10 was not. Ribosome profiling showed that the monoubiquitination of eS7A was crucial for translational regulation, including the upregulation of the spliced form of HAC1 (HAC1i) mRNA and the downregulation of Histidine triad NucleoTide-binding 1 (HNT1) mRNA. Downregulation of the deubiquitinating enzyme complex Upb3-Bre5 increased the levels of ubiquitinated eS7A during UPR in an Ire1-independent manner. These findings suggest that the monoubiquitination of ribosomal protein eS7A plays a crucial role in translational controls during the ER stress response in yeast.
Evolutionary ecology of natural comammoxNitrospirapopulations
Authors: Palomo Alejandro , Dechesne Arnaud , Cordero Otto X. , Smets Barth F.
Published: September 2020

Microbes commonly exists in diverse and complex communities where species interact, and their genomic repertoires evolve over time. Our understanding of species interactions and evolution has increased in the last decades, but most studies of evolutionary dynamics are based on single species in isolation or in experimental systems composed of few interacting species. Here, we use the microbial ecosystem found in groundwater-fed sand filters as a model to avoid this limitation. In these open systems, diverse microbial communities experience relatively stable conditions, and the coupling between chemical and biological processes is generally well defined. Metagenomic analysis of 12 sand filters revealed systematic co-occurrence of at least five comammoxNitrospiraspecies, likely promoted by low ammonium concentrations. TheseNitrospiraspecies showed intra-population sequence diversity, although possible clonal expansion was detected in few abundant local comammox populations. They showed low homologous recombination and strong purifying selection, the latter process being especially strong in genes essential in energy metabolism. Positive selection was detected on genes related to resistance to foreign DNA and phages. We found that, compared to other habitats, groundwater-fed sand filters impose strong purifying selection and low recombination on comammoxNitrospirapopulations. These results suggest that evolutionary processes are more affected by habitat type than by species identity. Together, this study improves our understanding of species interactions and evolution in complex microbial communities, and sheds light on the environmental dependency of evolutionary processes.
Human marginal zone B cell development from early T2 progenitors
Authors: Tull Thomas J. , Pitcher Michael J. , Guesdon William , Siu Jacqueline H. , Lebrero-Fernández Cristina , Zhao Yuan , Petrov Nedyalko , Heck Susanne , Ellis Richard , Dhami Pawan , Kadolsky Ulrich D. , Kleeman Michelle , Kamra Yogesh , Fear David J. , John Susan , Jassem Wayel , Groves Richard W. , Sanderson Jeremy D. , Robson Michael D. , D’Cruz David , Bemark Mats , Spencer Jo
Published: September 2020

B cells emerge from the bone marrow as transitional (TS) B cells that differentiate through T1, T2 and T3 stages to become naïve B cells. We have identified a bifurcation of human B cell maturation from the T1 stage forming IgMhiand IgMlodevelopmental trajectories. IgMhiT2 cells have higher expression of α4β7 integrin and lower expression of IL4 receptor (IL4R) compared to the IgMlobranch and are selectively recruited into gut-associated lymphoid tissue. IgMhiT2 cells also share transcriptomic features with marginal zone B cells (MZB). Lineage progression from T1 cells to MZB via an IgMhitrajectory is identified by pseudotime analysis of scRNA-sequencing data. Reduced frequency of IgMhigut homing T2 cells is observed in severe SLE and is associated with reduction of MZB and their putative IgMhiprecursors. The collapse of the gut-associated MZB maturational axis in severe SLE affirms its existence and importance for maintaining health.
Robust Self-Regeneratable Stiff Living Materials
Authors: Manjula-Basavanna Avinash , Duraj-Thatte Anna , Joshi Neel S.
Published: September 2020

Living systems have not only the exemplary capability to fabricate materials (e.g.wood, bone) under ambient conditions but they also consist of living cells that imbue them with properties like growth and self-regeneration. Like a seed that can grow into a sturdy living wood, we wondered: can living cells alone serve as the primary building block to fabricate stiff materials? Here we report the fabrication of stiff living materials (SLMs) produced entirely from microbial cells, without the incorporation of any structural biopolymers (e.g.cellulose, chitin, collagen) or biominerals (e.g.hydroxyapatite, calcium carbonate) that are known to impart stiffness to biological materials. Remarkably, SLMs are also lightweight, strong, resistant to organic solvents and can self-regenerate. This living materials technology can serve as a powerful biomanufacturing platform to design and develop sustainable structural materials, biosensors, self-regulators, self-healing and environment-responsive smart materials.
Human inbreeding has decreased in time through the Holocene
Authors: Ceballos Francisco C. , Gürün Kanat , Altınışık N. Ezgi , Gemici Hasan Can , Karamurat Cansu , Koptekin Dilek , Vural Kıvılcım Başak , Sürer Elif , Erdal Yılmaz Selim , Götherström Anders , Özer Füsun , Atakuman Çiğdem , Somel Mehmet
Published: September 2020

The history of human inbreeding is controversial. The development of sedentary agricultural societies may have had opposite influences on inbreeding levels. On the one hand, agriculture and food surplus may have diminished inbreeding by increasing population sizes and lowering endogamy, i.e. inbreeding due to population isolation. On the other hand, increased sedentism, as well as the advent of private property may have promoted inbreeding through the emergence of consanguineous marriage customs or via ethnic and caste endogamy. The net impact is unknown, and to date, no systematic study on the temporal frequency of inbreeding in human societies has been conducted. Here we present a new approach for reliable estimation of runs of homozygosity (ROH) in genomes with ≥3x mean coverage across >1 million SNPs, and apply this to 440 ancient Eurasian genomes from the last 15,000 years. We show that the frequency of inbreeding, as measured by ROH, has decreased over time. The strongest effect is associated with the Neolithic transition, but the trend has since continued, indicating a population size effect on inbreeding prevalence. We further show that most inbreeding in our historical sample can be attributed to endogamy, although singular cases of high consanguinity can also be found in the archaeogenomic record.

Highlights

A study of 440 ancient genomes shows inbreeding decreased over time.

The decrease appears linked with population size increase due to farming.

Extreme consanguineous matings did occur among farmers, but rarely.
Integrating identification and quantification uncertainty for differential protein abundance analysis with Triqler
Authors: The Matthew , Käll Lukas
Published: September 2020

Protein quantification for shotgun proteomics is a complicated process where errors can be introduced in each of the steps. Triqler is a Python package that estimates and integrates errors of the different parts of the label-free protein quantification pipeline into a single Bayesian model. Specifically, it weighs the quantitative values by the confidence we have in the correctness of the corresponding PSM. Furthermore, it treats missing values in a way that reflects their uncertainty relative to observed values. Finally, it combines these error estimates in a single differential abundance FDR that not only reflects the errors and uncertainties in quantification but also in identification. In this tutorial, we show how to (1) generate input data for Triqler from quantification packages such as MaxQuant and Quandenser, (2) run Triqler and what the different options are, (3) interpret the results, (4) investigate the posterior distributions of a protein of interest in detail and (5) verify that the hyperparameter estimations are sensible.
Dual-view oblique plane microscopy (dOPM)
Authors: Sparks Hugh , Dent Lucas , Bakal Chris , Behrens Axel , Salbreux Guillaume , Dunsby Chris
Published: September 2020

We present a new folded dual-view oblique plane microscopy (OPM) technique termed dOPM that enables two orthogonal views of the sample to be obtained by translating a pair of tilted mirrors in refocussing space. Using a water immersion 40× 1.15 NA primary objective, deconvolved image volumes of 200 nm beads were measured to have full width at half maxima (FWHM) of 0.35±0.04 μm and 0.39±0.02 μm laterally and 0.81±0.07 μm axially. The laterally integrated z-sectioning value was 1.33±0.45 μm using light-sheet FWHM in the frames of the two views of 4.99±0.58 μm and 4.89±0.63 μm. To qualitatively demonstrate that the system can reduce shadow artefacts while providing a more isotropic resolution, a multi-cellular spheroid approximately 100 μm in diameter was imaged.
Reduced long-lasting insecticidal net efficacy and pyrethroid insecticide resistance are associated with over-expression ofCYP6P4, CYP6P3andCYP6Z1in populations ofAnopheles coluzziifrom South-East Côte d’Ivoire
Authors: Meiwald Anne , Clark Emma , Kristan Mojca , Edi Constant , Jeffries Claire L. , Pelloquin Bethanie , Irish Seth R. , Walker Thomas , Messenger Louisa A.
Published: September 2020

Background

Resistance to major public health insecticides in Côte d’Ivoire has intensified and now threatens the long-term effectiveness of malaria vector control interventions.

Methods

This study evaluated the bioefficacy of conventional and next-generation long-lasting insecticidal nets (LLINs), determined resistance profiles, and characterized molecular and metabolic mechanisms in wildAnopheles coluzziifrom South-East Côte d’Ivoire in 2019.

Results

Phenotypic resistance was intense: more than 25% of mosquitoes survived exposure to ten times the doses of pyrethroids required to kill susceptible populations. Similarly, 24-hour mortality to deltamethrin-only LLINs was very low and not significantly different to an untreated net. Sub-lethal pyrethroid exposure did not induce significant delayed vector mortality 72 hours later. In contrast, LLINs containing the synergist piperonyl butoxide (PBO), or new insecticides, clothianidin and chlorfenapyr, were highly toxic toAn. coluzzii. Pyrethroid-susceptibleAn. coluzziiwere significantly more likely to be infected with malaria, compared to those that survived insecticidal exposure. Pyrethroid resistance was associated with significant over-expression ofCYP6P4, CPY6Z1andCYP6P3.

Conclusions

Study findings raise concerns regarding the operational failure of standard LLINs and support the urgent deployment of vector control interventions incorporating PBO, chlorfenapyr or clothianidin in areas of high resistance intensity in Côte d’Ivoire.
Functional genomic screens identify human host factors for SARS-CoV-2 and common cold coronaviruses
Authors: Wang Ruofan , Simoneau Camille R. , Kulsuptrakul Jessie , Bouhaddou Mehdi , Travisano Katherine , Hayashi Jennifer M. , Carlson-Stevermer Jared , Oki Jennifer , Holden Kevin , Krogan Nevan J. , Ott Melanie , Puschnik Andreas S.
Published: September 2020

TheCoronaviridaeare a family of viruses that causes disease in humans ranging from mild respiratory infection to potentially lethal acute respiratory distress syndrome. Finding host factors that are common to multiple coronaviruses could facilitate the development of therapies to combat current and future coronavirus pandemics. Here, we conducted parallel genome-wide CRISPR screens in cells infected by SARS-CoV-2 as well as two seasonally circulating common cold coronaviruses, OC43 and 229E. This approach correctly identified the distinct viral entry factors ACE2 (for SARS-CoV-2), aminopeptidase N (for 229E) and glycosaminoglycans (for OC43). Additionally, we discovered phosphatidylinositol phosphate biosynthesis and cholesterol homeostasis as critical host pathways supporting infection by all three coronaviruses. By contrast, the lysosomal protein TMEM106B appeared unique to SARS-CoV-2 infection. Pharmacological inhibition of phosphatidylinositol phosphate biosynthesis and cholesterol homeostasis reduced replication of all three coronaviruses. These findings offer important insights for the understanding of the coronavirus life cycle as well as the potential development of host-directed therapies.
Pathway Analysis within Multiple Human Ancestries Reveals Novel Signals for Epistasis in Complex Traits
Authors: Turchin Michael C. , Darnell Gregory , Crawford Lorin , Ramachandran Sohini
Published: September 2020

Genome-wide association (GWA) studies have identified thousands of significant genetic associations in humans across a number of complex traits. However, the majority of these studies focus on linear additive relationships between genotypic and phenotypic variation. Epistasis, or non-additive genetic interactions, has been identified as a major driver of both complex trait architecture and evolution in multiple model organisms; yet, this same phenomenon is not considered to be a significant factor underlying human complex traits. There are two possible reasons for this assumption. First, most large GWA studies are conducted solely with European cohorts; therefore, our understanding of broad-sense heritability for many complex traits is limited to just one ancestry group. Second, current epistasis mapping methods commonly identify significant genetic interactions by exhaustively searching across all possible pairs of SNPs. In these frameworks, estimated epistatic effects size are often small and power can be low due to the multiple testing burden. Here, we present a case study that uses a novel region-based mapping approach to analyze sets of variants for the presence of epistatic effects across six diverse subgroups within the UK Biobank. We refer to this method as the “MArginal ePIstasis Test for Regions” or MAPIT-R. Even with limited sample sizes, we find a total of 245 pathways within the KEGG and REACTOME databases that are significantly enriched for epistatic effects in height and body mass index (BMI), with 67% of these pathways being detected within individuals of African ancestry. As a secondary analysis, we introduce a novel region-based “leave-one-out” approach to localize pathway-level epistatic signals to specific interacting genes in BMI. Overall, our results indicate that non-European ancestry populations may be better suited for the discovery of non-additive genetic variation in human complex traits — further underscoring the need for publicly available, biobank-sized datasets of diverse groups of individuals.
TAEL 2.0: An Improved Optogenetic Expression System for Zebrafish
Authors: LaBelle Jesselynn , Ramos-Martinez Adela , Shen Kyle , Motta-Mena Laura B. , Gardner Kevin H. , Materna Stefan C. , Woo Stephanie
Published: September 2020

Inducible gene expression systems are valuable tools for studying biological processes. We previously developed an optogenetic gene expression system called TAEL that is optimized for use in zebrafish. When illuminated with blue light, TAEL transcription factors dimerize and activate gene expression downstream of the TAEL-responsive C120 promoter. By using light as the inducing agent, the TAEL/C120 system overcomes limitations of traditional inducible expression systems by enabling fine spatial and temporal regulation of gene expression. Here, we describe ongoing efforts to improve the TAEL/C120 system. We made modifications to both the TAEL transcriptional activator and the C120 regulatory element, collectively referred to as TAEL 2.0. We demonstrate that TAEL 2.0 consistently induces higher levels of reporter gene expression and at a faster rate, but with comparable background and toxicity as the original TAEL system. With these improvements, we were able to create functional stable transgenic lines to express the TAEL 2.0 transcription factor either ubiquitously or with a tissue-specific promoter. We demonstrate that the ubiquitous line in particular can be used to induce expression at late embryonic and larval stages, addressing a major deficiency of the original TAEL system. This improved optogenetic expression system will be a broadly useful resource for the zebrafish community.
The impact of the fragile health system on the implementation of health policies in Yemen
Authors: Hussein Taha , Dureab Fekri , Al-Waziza Raof , Noman Hanan , Hennig Lisa , Jahn Albrecht
Published: September 2020

Background

The on-going humanitarian crisis in Yemen is one of the worst in the world, with more than14 million people in acute need. The conflict in Yemen deteriorated the country’s already fragile health system and lead to the collapse of more than half of the health facilities. Health system fragmentation is also a problem in Yemen, which is complicated by the existence of two health ministries with different strategies. The aim of this study is to evaluate the effect of health system fragmentation on the implementation of health policies in Yemen across the global agendas of Universal Health Coverage (UHC), Health Security (GHS) and Health Promotion (HP) in the context of WHO’s priorities achieving universal health coverage, addressing health emergencies and promoting healthier populations.

Methods

The study is qualitative research using key informant in-depth interviews and documents analysis.

Results

There are many health stakeholders in Yemen, including the public, private, and NGO sectors - each with different priorities and interests, which did not always align with national policies and strategies. The WHO and Ministry of Public Health and Population (MoPHP) are the main supporters to implement all policies related to the UHC, GHS and HP agendas. Interestingly, initiatives initially pursuing a health security approach to control the cholera epidemic realigned with the UHC concept and moved from an initial focus on health security, to propose a minimum health service package, a classical UHC intervention. Overall, Universal Health Coverage is the most adapted agenda, health security agendas were highly disrupted due to conflicts and health staffs were caught unprepared for emerging outbreaks. The health promotion agenda was largely ignored.

Conclusion

Restoring peace, building on synergies between the three health agendas through joint planning between the MoPHP and other health actors are highly recommended.
Hybridisation capture allows DNA damage analysis of ancient marine eukaryotes
Authors: Armbrecht L. , Hallegraeff G. , Bolch C.J.S. , Woodward C. , Cooper A.
Published: September 2020

Marine sedimentary ancient DNA (sedaDNA) is increasingly used to study past ocean ecosystems, however, studies have been severely limited by the very low amounts of DNA preserved in the subseafloor, and the lack of bioinformatic tools to authenticatesedaDNA in metagenomic data. We applied a hybridisation capture ‘baits’ technique to target marine eukaryotesedaDNA (specifically, phytoplankton, ‘Phytobaits1’; and harmful algal bloom taxa, ‘HABbaits1’), which resulted in up to 4- and 9-fold increases, respectively, in the relative abundance of eukaryotes compared to shotgun sequencing. We further used the new bioinformatic tool ‘HOPS’ to authenticate thesedaDNA component, establishing a new proxy to assesssedaDNA authenticity, the Ancient: Default (A:D) sequences ratio, here positively correlated with subseafloor depth, and generated the first-ever DNA damage profiles of a key phytoplankton, the ubiquitous coccolithophoreEmiliania huxleyi.Our study opens new options for the detailed investigation of marine eukaryotes and their evolution over geological timescales.
Homing Choices of Breast Cancer Cells Revealed by Tissue Specific Invasion and Extravasation Lab-on-a-chip Platforms
Authors: Firatligil-Yildirir Burcu , Bati-Ayaz Gizem , Tahmaz Ismail , Bilgen Muge , Pesen-Okvur Devrim , Yalcin-Ozuysal Ozden
Published: September 2020

Metastasis is one of the major obstacles for breast cancer patients. Limitations of current models demand the development of novel platforms to predict metastatic potential and homing choices of cancer cells. Here, two novel Lab-on-a-chip (LOC) platforms, invasion/chemotaxis (IC-chip) and extravasation (EX-chip), are presented for the quantitative assessment of invasion and extravasation, towards specific tissues. On IC-chip, invasive MDA-MB-231, but not non-invasive MCF-7 breast cancer cells invaded lung and liver microenvironments. Lung-specific but not bone-specific MDA-MB-231 clones efficiently invaded lung microenvironment, stressing ability of IC-chip to demonstrate differentin vivometastatic behaviors. On EX-chip, MDA-MB-231 cells extravasated more into the lung microenvironment compared to the liver and breast highlighting the potency of the platform to mimicin vivohoming choices. Overall, this study presents IC-chip and EX-chip that can determine tissue-specific invasion and extravasation potentials of cancer cells providing the groundwork for novel diagnostic tools to predict metastasis risk.
First 3D-Structural Data of Full-length Rod-Outer-Segment Guanylyl Cyclase 1 in Bovine Retina by Cross-linking/Mass Spectrometry
Authors: Rehkamp Anne , Tänzler Dirk , Tüting Christian , Kastritis Panagiotis L. , Iacobucci Claudio , Ihling Christian H. , Kipping Marc , Koch Karl-Wilhelm , Sinz Andrea
Published: September 2020

The rod-outer-segment guanylyl cyclase 1 (ROS-GC1) is a key transmembrane protein for retinal phototransduction. Mutations of ROS-GC1 correlate with different retinal diseases that often lead to blindness. No structural data are available for ROS-GC1 so far. We performed a 3D-structural analysis of native ROS-GC1 from bovine retina by cross-linking/mass spectrometry (XL-MS) and computational modeling. Absolute quantification and activity measurements of native ROS-GC1 were performed by MS-based assays directly in bovine retina samples. Our data present the first 3D-structural analysis of active, full-length ROS-GC1 in bovine retina. We propose a novel domain organization for the intracellular domain ROS-GC1. Our XL-MS data reveal that the α-helical domain connecting the kinase homology and catalytic domains can acquire different conformations. Also, the XL-MS data of native ROS-GC1 in bovine retina agree with a dimeric architecture. Our integrated approach can serve as a blueprint for conducting 3D-structural studies of membrane proteins in their native environment.
hcga: Highly Comparative Graph Analysis for network phenotyping
Authors: Peach Robert L. , Arnaudon Alexis , Schmidt Julia A. , Palasciano Henry A. , Bernier Nathan R. , Jelfs Kim , Yaliraki Sophia , Barahona Mauricio
Published: September 2020

Abstract

Networks are widely used as mathematical models of complex systems across many scientific disciplines, not only in biology and medicine but also in the social sciences, physics, computing and engineering. Decades of work have produced a vast corpus of research characterising the topological, combinatorial, statistical and spectral properties of graphs. Each graph property can be thought of as a feature that captures important (and some times overlapping) characteristics of a network. In the analysis of real-world graphs, it is crucial to integrate systematically a large number of diverse graph features in order to characterise and classify networks, as well as to aid network-based scientific discovery. In this paper, we introduce HCGA, a framework for highly comparative analysis of graph data sets that computes several thousands of graph features from any given network. HCGA also offers a suite of statistical learning and data analysis tools for automated identification and selection of important and interpretable features underpinning the characterisation of graph data sets. We show that HCGA outperforms other methodologies on supervised classification tasks on benchmark data sets whilst retaining the interpretability of network features. We also illustrate how HCGA can be used for network-based discovery through two examples where data is naturally represented as graphs: the clustering of a data set of images of neuronal morphologies, and a regression problem to predict charge transfer in organic semiconductors based on their structure. HCGA is an open platform that can be expanded to include further graph properties and statistical learning tools to allow researchers to leverage the wide breadth of graph-theoretical research to quantitatively analyse and draw insights from network data.
Mitochondrial alternative oxidase contributes to successful tardigrade anhydrobiosis
Authors: Wojciechowska Daria , Karachitos Andonis , Roszkowska Milena , Rzeźniczak Wiktor , Sobkowiak Robert , Kaczmarek Łukasz , Kosicki Jakub , Kmita Hanna
Published: September 2020

Anhydrobiosis can be described as an adaptation to lack of water. This adaptation provides some organisms including tardigrades with a set of capabilities allowing them to survive extreme conditions that even do not exist on Earth. However, the underlying cellular mechanisms are still not explained. Available data assumes important contribution of mitochondrial proteins. Since mitochondrial alternative oxidase (AOX) described as a drought response element has recently been proposed for various invertebrates including tardigrades, we have decided to check if AOX is involved in successful anhydrobiosis of tardigrades.Milnesium inceptumwas used as a model for the study. We confirmed functionality ofM. inceptumAOX and estimated its activity contribution to anhydrobiosis of different duration. We observed that AOX activity was particularly important forM. inceptumrevival after longer-term anhydrobiosis but did not affect rehydration stage. The results may contribute to explanation and then application of anhydrobiosis underlying mechanisms.
Douglas fir and Norway spruce admixtures to beech forests along in Northern Germany – Are soil nutrient conditions affected?
Authors: Foltran Estela Covre , Ammer Christian , Lamersdorf Norbert
Published: September 2020

The establishment of mixed forest stands can be seen as an option to improve soil nutrient conditions and to protect forest ecosystems from various impacts of climate change. Our study analyzed groups of pure mature European beech (Fagus sylvatica; B), Douglas fir (Pseudotsuga menziesii; D) and Norway spruce (Picea abies; S) stands as well as mixtures of beech with either Douglas fir (DB) or spruce (SB), i.e. 5 forest stands per site along Northern Germany with two regionally clearly differing sites conditions (i.e., 3 loess-influenced, loamy sites in the Solling region, southern Lower Saxony and 4 sandy lowland sites further north). In order to determine possible influences of the tree species and their mixtures on soil properties, the organic layer and the mineral topsoil were first chemically characterized for all 35 plots down to a depth of 30 cm (pH, C, N, P, CEC, exchangeable nutrient cation contents and stocks, base saturation-BS). Our results indicated, independent of sites condition, that pure S stands showed the lowest pH and BS, meanwhile B the highest BS. The impact of D varied depending on site condition. On sandy soils, pure D showed higher pH and BS than under pure S, while on loamy soils the pH under D and B was lower than under S. Regarding cations stocks under sandy soils conditions, S stands and its admixture SB depleted soil Ca and Mg stocks more than pure D and B. In contrast, under loamy soil conditions B showed depleted (lowest) soil exchangeable Ca and Mg stocks more than under S stands. Soil exchangeable K under mixed stands were among the highest compared to pure stands, independent of the site condition. Thus, mixed species stands generally decreased soil base cation depletion compared to pure conifer stands. Admixtures of Douglas-fir (DB) seem to lead to smaller changes in pH, CEC and BS than those of Norway spruce, this effect become more important at sandy soil sites. Therefore, forest management may consider mixtures of European beech and Douglas fir as a reasonable management option without apprehending negative effects on soil chemistry.
ICP-MS analysis of metal and metalloid concentrations of common microbiological growth media reveals presence of heavy metals
Authors: Ng Wenfa
Published: September 2020

Trace elements such as cobalt and manganese play important roles as cofactors of enzymes, and thus, they collectively impact on biochemistry and cellular metabolism. Hence, it is of importance to gain an understanding of the trace metal and metalloid concentrations of growth medium in order to fully account for the growth performance of the bacterium. But, this aspect of microbial cell cultivation is usually neglected. Advent of instrumented techniques for metals and metalloid analysis such as inductively coupled plasma mass spectrometry (ICP-MS) has significantly facilitated trace element analysis at the parts per billion (ppb) to parts per million (ppm) level in aqueous matrixes free of organic interference. In this work, ICP-MS was utilized as the principal tool for profiling the range of metals and metalloids in different microbiological growth medium ranging from minimal salts medium to complex chemically undefined medium. Growth media examined include: LB Lennox, LB Lennox + 2 g/L glucose, LB Lennox (buffered, 89 mM phosphate), LB Lennox (buffered, 89 mM phosphate) + 6 g/L glucose, formulated medium + 6 g/L glucose, Tryptic Soy Broth, M9 medium, and M9 + 1 g/L yeast extract medium. Results reveal detection of elevated concentrations of chromium, copper and cadmium in different versions of LB Lennox and Tryptic Soy Broth. Concentrations of the above heavy metals in the tens of ppm range meant that the growth media could only support the growth of environmental bacteria with some resistance to heavy metal toxicity. On the other hand, no heavy metals were detected in M9 minimal salts medium or a modified version with supplementation of 1 g/L yeast extract. This indicated that minimal salts media may have less of a problem with heavy metal contamination compared to chemically undefined microbiological growth media. Collectively, the results highlight the essentiality of conducting a comprehensive profiling experiment for detecting different metals and metalloids at trace levels in microbiological growth medium. Such data would in addition to offering a deeper understanding of some peculiar growth behaviour from some microorganisms, may also help identify contamination issue during manufacture that preclude use of the media in cultivating many laboratory domesticated microorganisms.

Subject areas

biochemistry, biotechnology, cell biology, microbiology, biochemical engineering,
Single-cell transcriptomics, scRNA-Seq and C1 CAGE discovered distinct phases of pluripotency during naïve-to-primed conversion in mice
Authors: Böttcher Michael , Tada Yuhki , Moody Jonathan , Kondo Masayo , Ura Hiroki , Abugessaisa Imad , Kasukawa Takeya , Hon Chung-Chau , Nagao Koji , Carninci Piero , Abe Kuniya
Published: September 2020

Background

Two types of mammalian pluripotent stem cells (PSC), i.e. naïve and primed possess distinct cellular characteristics. It is largely unknown how these differences are generated during naïve-to-primed transition process. We have established a robustin vitrotransition system using a Wnt inhibitor for the first time and analyzed dynamic changes in cellular status via single-cell RNA-sequencing and C1 CAGE analyses.

Results

Analysis of known marker genes suggested that the cell transition process progresses as expected. However, cluster analyses revealed a sudden increase in expression profile diversities three and four days after induction of the transition. These expression diversities can be reconciled by the presence of two subpopulations with distinct transcription profiles emerging at these time points. One of the subpopulations appears transiently, and surprisingly these cells showed a global downregulation of gene expression. Moreover, initiation of random X chromosome inactivation (XCI) coincides with the appearance of these transient cells. The other subpopulation can be maintained as a stem cell line and possesses expression profiles more similar to those of primed epiblast stem cells (EpiSC) than embryonic stem cells (ESC). However, there are important differences in gene expression related to epithelial-mesenchymal transition (EMT), suggesting that this subpopulation may represent a novel pluripotent state that has an intermediate cellular phenotype between ESC and EpiSC.

Conclusions

These findings should contribute to our understanding of the establishment and maintenance of distinct differentiation statuses of mammalian PSCs and provide new insights into the pluripotency spectrum in general.
Genome-wide dynamics of RNA synthesis, processing, and degradation without RNA metabolic labeling
Authors: Furlan Mattia , Galeota Eugenia , Gaudio Nunzio Del , Dassi Erik , Caselle Michele , de Pretis Stefano , Pelizzola Mattia
Published: September 2020

The quantification of the kinetic rates of RNA synthesis, processing, and degradation are largely based on the integrative analysis of total and nascent transcription, the latter being quantified through RNA metabolic labeling. We developed INSPEcT−, a computational method based on the mathematical modeling of premature and mature RNA expression that is able to quantify kinetic rates from steady-state or time course total RNA-seq data without requiring any information on nascent transcripts. Our approach outperforms available solutions, closely recapitulates the kinetic rates obtained through RNA metabolic labeling, improves the ability to detect changes in transcript half-lives, reduces the cost and complexity of the experiments, and can be adopted to study experimental conditions in which nascent transcription cannot be readily profiled. Finally, we applied INSPEcT− to the characterization of post-transcriptional regulation landscapes in dozens of physiological and disease conditions. This approach was included in the INSPEcT Bioconductor package, which can now unveil RNA dynamics from steady-state or time course data, with or without the profiling of nascent RNA.
Misorientation relationships in goethite, hematite and magnetite: a case study of iron-formation rocks from the Iron Quadrangle, Brazil
Authors: Barbosa Paola , Lagoeiro Leonardo , Mota e Nogueira Victor
Published: September 2020

The transformation behavior between iron oxides and oxyhydroxides like magnetite, hematite and goethite is still not entirely understood. Crystallographic similarities allow one to predict topotactic relationships between them. The related crystallographic aspects have been explored by means of electron backscatter diffraction (EBSD). Samples from natural aggregates of magnetite, hematite and goethite were collected from iron-formation rocks that outcrop in the southeast of Brazil, in a region known for large deposits of iron and other ores. EBSD misorientation data indicate a pronounced relationship between these iron phases. The transformation seems to be related to the oxygen framework. The original close-packed cubic arrangement of O atoms in magnetite changes to a hexagonal close-packed framework in hematite, i.e. {111} of magnetite is parallel to {0001} of hematite. The matrix in which the magnetite grains are embedded is made of aggregates of hematite and goethite. In the matrix, the coincidence observed in the magnetite grains is not observed. On the other hand, the well known twin boundary relationships already described for these mineral phases can be observed here as an orientation relationship in three-dimensional misorientation space. The spatial data of axis–angle pairs suggest that the twin boundaries serve as facilitating surfaces for phase transformation in the Fe–O–OH system. The main conclusion of this study is that the transformation occurred in the solid state with the newly transformed goethite inheriting the crystallographic orientations of the former crystals and that this phenomenon is better recognized by combining observations of misorientation relationships. In the matrix, such a relation is not observed and, for that reason, the minerals in the matrix are thought to have been formed by a different process, which might have involved dissolution and precipitation of the phase newly out of solution.
Synthesis and crystal structure of peptide dimethyl biphenyl hybrid C52H60N6O10·0.25H2O
Authors: Nguyen Xuan Tu , Le Thuy Quynh , Bui Thi Tra My , Mac Dinh Hung , Bui Thai Thanh Thu
Published: September 2020

The synthesis and crystal structure of peptide 6,6′-dimethyl biphenyl hybrid are described. The title compound was synthesized by reaction between 6,6′-dimethyl-[1,1′-biphenyl]-2,2′-dicarbonyl dichloride in CH2Cl2, amine HN–proline–phenylalanine–alanine–COOMe and Et3N at 273 K under N2 atmosphere and characterized by single-crystal X-ray diffraction. The asymmetric unit contains one peptide molecule and a quarter of a water molecule. A disorder of a methyl and methoxycarbonyl group of one alanine residue is observed with occupancy ratio 0.502 (6):0.498 (6). The structure is consolidated by intra- and intermolecular hydrogen bonds.
Re-refinement of sodium ammonium sulfate dihydrate at 170 K
Authors: Eckhardt Tamira , Wagner Christoph , Imming Peter , Seidel Rüdiger W.
Published: September 2020

The title compound, sodium ammonium sulfate dihydrate (SASD), NaNH4SO4·2H2O, a synthetic analogue of the mineral lecontite, is a well known ferroelectric. The crystal structure of the paraelectric phase has been re-refined at 170 K on the basis of single-crystal X-ray data, improving the previous study [Arzt & Glazer (1994). Acta Cryst. B50, 425–431] in terms of accuracy regarding hydrogen-atom positions and thus details of the hydrogen bonding. O—H...O and N—H...O hydrogen bonds between the principal building units [Na(OH2)4O2 octahedra, SO4 tetrahedra and ammonium cations] constitute a three-dimensional network structure.
Parental child feeding practices and growth status of Orang Asli children in Negeri Sembilan, Malaysia
Authors: Raymond Leprince Jovita , Sariman Sarina , Basir Mohammed Rahmah Begam
Published: September 2020

Purpose

The purpose of this paper is to determine the relationship between parental child feeding practices with growth status of Orang Asli (OA) children in Negeri Sembilan.

Design/methodology/approach

This is a cross-sectional study conducted amongst 190 OA children aged 4–6 years studying at Tabika KEMAS OA in Negeri Sembilan. Mothers were interviewed to obtain socio-demographic information while feeding practices were assessed using Malay version of Comprehensive Feeding Practices Questionnaire (CFPQ-M). Growth status of the children were determined using WHO ANTHRO Plus software. Three indicators of growth status assessed were weight-for-age (WAZ), height-for-age (HAZ) and body mass index (BMI)-for-age (BAZ) z-scores.

Findings

The mean score for feeding practices used by the mothers while feeding their child showed that most of the mothers practiced modelling (3.71 ± 0.82), encouraging balance and variety (3.52 ± 0.76) and environment (3.66 ± 0.66) while the practice of restriction to weight (1.85 ± 0.79) and emotional regulation (2.20 ± 0.96) were low. Most of the OA children had normal WAZ (70.0%), HAZ (71.1%) and BAZ (84.2%). Amongst the three indicators of growth status, BAZ was used to study the relationship with feeding practices. The use of feeding practices such as pressure (r = −0.34, p < 0.01), food as a reward (r = −0.23, p=<0.01), child control (r = −0.18, p = 0.01) and restriction to weight (r = 0.19, p = 0.01) were associated with BAZ.

Research limitations/implications

This study only focussed on OA children of Temuan and Semelai sub-ethnics studying at kindergarten specific for OA children, thus findings could not be generalised to the entire OA population in Malaysia.

Social implications

There is a need to address the OA population as they continue to be amongst the most disadvantaged population often affected with poor health and social outcomes.

Originality/value

In this study, a wide range of scales in that represents different feeding practices in CFPQ-M was assessed instead of focussing on limited type of feeding practices. Thus, a better understanding was observed regarding the healthy and unhealthy feeding practices. The result of this study could be useful to update the existing literature of OA research, and to plan suitable interventions with regards to feeding practices and growth status of the children, especially amongst this vulnerable community.
The influence of food trucks' service quality on customer satisfaction and its impact toward customer loyalty
Authors: Gopi Bagyalakshmi , Samat Nusrah
Published: September 2020

Purpose

Service quality has been highlighted as the vital element in fulfilling customers' needs, which contributes to the customers' evaluation on the services given. As food truck business is increasingly popular in Malaysia, it is important for the food trucks' service provider to ensure that their service quality meets the standard to satisfy the customers in order to build customer loyalty. Therefore, the aim of this study is to investigate the relationship between food trucks' service quality with customer satisfaction and its impact toward customer loyalty. The customer service was measured using service quality (SERVQUAL) attributes (tangibles, reliability, responsiveness, assurance and empathy).

Design/methodology/approach

A quantitative study was conducted to examine the influence of food trucks' service quality on customer satisfaction and its impact toward customer loyalty. A total of 100 food truck customers have been randomly selected to answer the self-administered questionnaire. Data collected were analyzed using frequency, descriptive, reliability, Pearson correlation and regression analysis.

Findings

Findings indicated that three out of five attributes of service quality have significant relationships toward customer satisfaction. They are tangibles (β = 0.225, p < 0.05), reliability (β = 0.349, p < 0.05) and assurance (β = 0.311, p < 0.05). Moreover, the customer loyalty (β = 0.643, p < 0.01) has a significant relationship with customer satisfaction.

Originality/value

Service quality can be characterized as the discrepancy between customer service standards and actual service. When expectations are higher than performance, perceived quality is less than acceptable and therefore consumer disappointment exists which eventually decreases customer loyalty toward a product or services. The study suggested that physical image of the food trucks' service like physical facilities, how the service being performed and also courtesy and knowledge of the food trucks' employees are very important to transfer confidence and trust to customers, which then will influence them to be loyal.