bluuebunny/crossref_metadata_2025_split huggingface dataset:
Resource allocation accounts for the large variability of rate-yield phenotypes across bacterial strains
Authors: Baldazzi Valentina , Ropers Delphine , Gouzé Jean-Luc , Gedeon Tomas , de Jong Hidde 
Published: April 2022

AbstractDifferent strains of a microorganism growing in the same environment display a wide variety of growth rates and growth yields. We developed a coarse-grained model to test the hypothesis that different resource allocation strategies, corresponding to different compositions of the proteome, can account for the observed rate-yield variability. The model predictions were verified by means of a database of hundreds of published rate-yield and uptake-secretion phenotypes ofEscherichia colistrains grown in standard laboratory conditions. We found a very good quantitative agreement between the range of predicted and observed growth rates, growth yields, and glucose uptake and acetate secretion rates. These results support the hypothesis that resource allocation is a major explanatory factor of the observed variability of growth rates and growth yields across different bacterial strains. An interesting prediction of our model, supported by the experimental data, is that high growth rates are not necessarily accompanied by low growth yields. The resource allocation strategies enabling high-rate, high-yield growth ofE. colilead to a higher saturation of enzymes and ribosomes, and thus to a more efficient utilization of proteomic resources. Our model thus contributes to a fundamental understanding of the quantitative relationship between rate and yield inE. coliand other microorganisms. It may also be useful for the rapid screening of strains in metabolic engineering and synthetic biology.
Light ‘em up: efficient screening of gold grids in cryo-EM
Authors: Hagen Wim J.H. 
Published: April 2022

AbstractTransmission electron cryo-microscopy (cryo-EM) allows for obtaining 3D structural information by imaging macromolecules embedded in thin layers of amorphous ice. To obtain high-resolution structural information, samples need to be thin to minimize inelastic scattering which blurs images. During data collection sessions, time spent on finding areas on the cryo-EM grid with optimal ice thickness should be minimized as imaging time on high-end Transmission Electron Microscope TEM systems is costly. Recently, grids covered with thin gold films have become popular due to their stability and reduced beam-induced motion of the sample. Gold foil grids have substantially different densities between the gold foil and ice, effectively resulting in the loss of dynamic range between thin and thick regions of ice, making it challenging to find areas with suitable ice thickness efficiently during grid screening and thus increase expensive imaging time. Here, an energy filter-based plasmon imaging is presented as a fast and easy method for grid screening of the gold grids.
Targeting Neutrophils Extracellular Traps (NETs) reduces multiple organ injury in a COVID-19 mouse model
Authors: Veras Flavio P. , Gomes Giovanni F. , Silva Bruna M. S. , Almeida Cicero J. L. R. , Silva Camila Meirelles S. , Schneider Ayda H. , Corneo Emily S. , Bonilha Caio S. , Batah Sabrina S. , Martins Ronaldo , Arruda Eurico , Fabro Alexandre T. , Alves-Filho José C. , Cunha Thiago M. , Cunha Fernando Q. 
Published: April 2022

ABSTRACTCOVID-19 is characterized by severe acute lung injury, which is associated with neutrophils infiltration and release of neutrophil extracellular traps (NETs). COVID-19 treatment options are scarce. Previous work has shown an increase in NETs release in the lung and plasma of COVID-19 patients suggesting that drugs that prevent NETs formation or release could be potential therapeutic approaches for COVID-19 treatment. Here, we report the efficacy of NET-degrading DNase I treatment in a murine model of COVID-19. DNase I decreased detectable levels of NETs, improved clinical disease, and reduced lung, heart, and kidney injuries in SARS-CoV-2-infected K18-hACE2 mice. Furthermore, our findings indicate a potential deleterious role for NETs lung tissue in vivo and lung epithelial (A549) cells in vitro, which might explain part of the pathophysiology of severe COVID-19. This deleterious effect was diminished by the treatment with DNase I. Together, our results support the role of NETs in COVID-19 immunopathology and highlight NETs disruption pharmacological approaches as a potential strategy to ameliorate COVID-19 clinical outcomes.
Selection of software and database for metagenomics sequence analysis impacts the outcome of microbial profiling and pathogen detection
Authors: Xu Ruijie , Rajeev Sreekumari , Salvador Liliana C. M. 
Published: April 2022

AbstractAimShotgun metagenomic sequencing analysis is widely used for microbial profiling of biological specimens and pathogen detection. However, very little is known about the technical biases caused by the choice of analysis software and databases. In this study, we evaluated shotgun metagenomics taxonomical profiling software to characterize the microbial compositions of biological samples collected from wild rodents.Method and ResultsUsing nine of the most widely used metagenomics software and four different databases, we analyzed shotgun metagenomic sequence data from three sets of wild rodent tissue samples. We demonstrated the discrepancies in results when different databases and software were used, which cause significant variation in microbial community characterizations. Our analysis also showed that these software differed in their ability to detect the presence of Leptospira, a major zoonotic pathogen of one health importance.ConclusionsSignificant differences in compositional profiles for the same dataset while using different databases and software combinations can result in confounding biological conclusions in microbial profiling.Significance and Impact of StudyThis study cautions that the selection of software and databases to analyze metagenomics data can influence the outcome and biological interpretation.
Reversible and gain modulation of neuronal responses and sensorimotor behavior by mid-infrared stimulation
Authors: Xiao Tong , Wu Kaijie , Ding Yali , Yang Xiao , Chang Chao , Yang Yan 
Published: April 2022

AbstractNeuromodulation serves as a cornerstone for brain sciences and clinical applications. Mid-infrared stimulation (MIRS) has been recently reported to cause non-thermal modulation of brain functions. However little knowledge of mechanisms hampers its application. Here we bridge across ion channels, neuronal signals, and behavioral performances associated with sensorimotor transformation to provide evidence of how the alternation of neuronal activity by MIRS guides the change of behavioral performance in awake-behaving pigeons. We compared effects on visually-guided eye movements by applying MIRS and electrical stimulation (ES) in the pretectal nucleus lentiformis mesencephali (nLM). Distinct from ES, we found a specific gain modulation of MIRS to alter behavior in a manner of the strength of visual inputs. Our simultaneous extracellular recordings showed that MIRS can excite and inhibit the neuronal activity in the same pretectal neuron based on its ongoing sensory responsiveness levels in awake-behaving animals. We further applied computational simulations and found that MIRS can modulate the carbonyl group (-C=O) enriched on the potassium channel to resonate, and could affect action potential generation, alter neuronal responses to sensory inputs and then guide behavior. Our findings suggest that MIRS could be a promising approach for brain researches and neurological diseases, with gene free manipulation.
ATP6AP2-to-MMP14, a key pathway for osteoblast to osteocyte transition
Authors: Xiong Lei , Guo Hao-Han , Pan Jin-Xiu , Ren Xiao , Lee Daehoon , Mei Lin , Xiong Wen-Cheng 
Published: April 2022

AbstractOsteocytes, derived from osteoblast (OB)-lineage, occupy lacunae within bone matrix and exhibit unique morphology with dendrite-like projections to form an inter-connected network. Such a network is essential for osteocytes to monitor and orchestrate bone homeostasis. Thus, it is of considerable interest to investigate how osteocytes are formed and how they built the network. Here we provide evidence for ATP6AP2, an accessory subunit of V-ATPase, in OB-lineage cells to be critical for OB-to-osteocyte transition, and osteocyte distribution, maturation, and morphogenesis. Mice (ATP6AP2Ocn-Cre) that selectively deplete ATP6AP2 in OB-lineage cells results in altered osteocyte distribution and morphology, impaired osteocyte maturation and dendrite-like processes, increased osteocyte cell death and cortical woven bone formation. Further mechanistic studies identify MMP14 (matrix metalloproteinase-14) as a critical downstream of ATP6AP2 for osteocyte differentiation. ATP6AP2 interacts with MMP14 and promotes MMP14 surface distribution largely in immature- or osteoid-osteocytes, where this pathway regulates bone matrix remodeling and osteocyte differentiation. Expression of MMP14 into ATP6AP2 knock out OB-lineage cells in the mouse cortical bone could diminish the deficits in osteocyte maturation, dendrite-like process formation, and survival. These results thus demonstrate an un-recognized function of ATP6AP2 in promoting OB-to-osteocyte transition and uncover a pathway from ATP6AP2-to-MMP14 in osteocyte differentiation.
Wastewater microorganisms impact microbial diversity and important ecological functions of stream periphyton
Authors: Carles Louis , Wullschleger Simon , Joss Adriano , Eggen Rik I.L. , Schirmer Kristin , Schuwirth Nele , Stamm Christian , Tlili Ahmed 
Published: April 2022

AbstractWastewater treatment plant effluents can impact microbial communities in receiving streams. However, little is known about the role of microorganisms in wastewater as opposed to other wastewater constituents, such as nutrients and micropollutants. We aimed therefore at determining the impact of wastewater microorganisms on the microbial diversity and function of periphyton, key microbial communities in streams. Periphyton was grown in flow-through channels that were continuously alimented with a mixture of stream water and unfiltered or ultra-filtered wastewater. Impacts were assessed on periphyton biomass, activities and tolerance to micropollutants, as well as on microbial diversity. Our results showed that wastewater microorganisms colonized periphyton and modified its community composition, resulting for instance in an increased abundance of Chloroflexi and a decreased abundance of diatoms and green algae. This led to shifts towards heterotrophy, as suggested by the changes in nutrient stoichiometry and the increased mineralization potential of carbon substrates. An increased tolerance towards micropollutants was only found for periphyton exposed to unfiltered wastewater but not to ultra-filtered wastewater, suggesting that wastewater microorganisms were responsible for this increased tolerance. Overall, our results highlight the need to consider the role of wastewater microorganisms when studying potential impacts of wastewater on the receiving water body.Environmental implicationThe present study investigates the impact of wastewater microorganisms on periphyton, i.e. communities forming the microbial skin of streambeds. We were able to disentangle specific effects of wastewater microorganisms in the context of the complex wastewater matrix. Indeed, wastewater microorganisms induced strong changes in periphyton community composition and function, suggesting the need to consider wastewater microbial communities as a stressor per se, similarly to, e.g., nutrients and micropollutants. Moreover, since periphyton is at the basis of the food web in streams, these changes may have consequences for higher trophic levels.
Differential genetic variation underlying Ammonium and Nitrate responses in Arabidopsis thaliana
Authors: Katz Ella , Knapp Anna , Lensink Mariele , Stefani Jordan , Li Jia-Jie , Shane Emily , Tuermer-Lee Kaelyn , Bloom Arnold J. , Kliebenstein Daniel J. 
Published: April 2022

AbstractNitrogen is an essential element required for plant growth and productivity. Understanding the mechanisms and natural genetic variation underlying nitrogen use in plants will facilitate engineering plant nitrogen use to maximize crop productivity while minimizing environmental costs. To understand the scope of natural variation that may influence nitrogen use, we grew 1135 Arabidopsis thaliana natural genotypes on two nitrogen sources, nitrate and ammonium, and measured both developmental and defense metabolite traits. By using different environments and focused on multiple traits, we identified a wide array of different nitrogen responses. These responses are associated with a large number of genes, most of them not previously associated with nitrogen responses. Only a small portion of these genes appear to be shared between environments or traits while most of the detected genes are predominantly specific to a developmental or defense trait under a specific nitrogen source. Finally, by using a large population we were able to identify unique nitrogen responses, like preferring ammonium or nitrate, that appear to be generated by combinations of loci rather than a few large effect loci. This suggests that it may be possible to obtain novel phenotypes in complex nitrogen responses by manipulating sets of genes with small effects rather than solely focusing on large effect single gene manipulations.One Sentence SummaryUsing a large collection of natural genotypes, and studying both developmental and metabolic responses, we found a large number of genes that are involved in the plants nitrogen response.
Chromoanagenesis in the asy1 meiotic mutant of Arabidopsis
Authors: Guo Weier , Comai Luca , Henry Isabelle M. 
Published: April 2022

AbstractChromoanagenesis is a catastrophic event that involves localized chromosomal shattering and reorganization. In this study, we report a case of chromoanagenesis resulting from defective meiosis in the MEIOTIC ASYNAPTIC MUTANT 1 (asy1) background in Arabidopsis thaliana. We provide a detailed characterization of the genomic structure of this individual with a severely shattered segment of chromosome 1. We reveal more than 300 candidate novel DNA junctions in the affected region, confirming that asy1-related defective meiosis is a potential trigger for chromoanagenesis. This is the first example of chromoanagenesis associated with female meiosis and indicates the potential for genome evolution during oogenesis.
A human embryonic limb cell atlas resolved in space and time
Authors: Zhang Bao , He Peng , Lawrence John E , Wang Shuaiyu , Tuck Elizabeth , Williams Brian A , Roberts Kenny , Kleshchevnikov Vitalii , Mamanova Lira , Bolt Liam , Polanski Krzysztof , Elmentaite Rasa , Fasouli Eirini S , Prete Martin , He Xiaoling , Yayon Nadav , Fu Yixi , Yang Hao , Liang Chen , Zhang Hui , Blain Raphael , Chedotal Alain , FitzPatrick David R. , Firth Helen , Dean Andrew , Marioni John C , Barker Roger A , Storer Mekayla A , Wold Barbara J , Zhang Hongbo , Teichmann Sarah A 
Published: April 2022

AbstractHuman limbs emerge during the fourth post-conception week as mesenchymal buds which develop into fully-formed limbs over the subsequent months. Limb development is orchestrated by numerous temporally and spatially restricted gene expression programmes, making congenital alterations in phenotype common. Decades of work with model organisms has outlined the fundamental processes underlying vertebrate limb development, but an in-depth characterisation of this process in humans has yet to be performed. Here we detail the development of the human embryonic limb across space and time, using both single-cell and spatial transcriptomics. We demonstrate extensive diversification of cells, progressing from a restricted number of multipotent progenitors to myriad mature cell states, and identify several novel cell populations, including neural fibroblasts and multiple distinct mesenchymal states. We uncover two waves of human muscle development, each characterised by different cell states regulated by separate gene expression programmes. We identify musculin (MSC) as a key transcriptional repressor maintaining muscle stem cell identity and validate this by performing MSC knock down in human embryonic myoblasts, which results in significant upregulation of late myogenic genes. Through integration of multiple anatomically continuous spatial transcriptomic samples, we spatially map single-cell clusters across a sagittal section of a whole fetal hindlimb. We reveal a clear anatomical segregation between genes linked to brachydactyly and polysyndactyly, and uncover transcriptionally and spatially distinct populations of mesenchyme in the autopod. Finally, we perform scRNA-seq on murine embryonic limbs to facilitate cross-species developmental comparison at single-cell resolution, finding substantial homology between the two species.
Snip1 and PRC2 coordinate intrinsic apoptosis, cell division, and neurogenesis in the developing brain
Authors: Matsui Yurika , Djekidel Mohamed Nadhir , Lindsay Katherine , Samir Parimal , Connolly Nina , Chen Hongfeng , Fan Yiping , Xu Beisi , Peng Jamy C. 
Published: April 2022

ABSTRACTBrain development requires the intricate balance between division, death, and differentiation of neural progenitor cells (NPCs). Here, we report the discovery of Snip1 as a key regulator of these NPC phases. The conditional deletion of Snip1 in the mouse embryonic brain causes dysplasia with robust induction of caspase 9-dependent apoptosis. In NPCs, Snip1 suppresses the genetic programs of apoptosis and developmental signaling pathways and promotes the genetic programs of cell cycle, neurogenesis, and cortical development. Mechanistically, Snip1 binds to the Polycomb complex PRC2, co-occupies gene targets with PRC2, and regulates H3K27 marks. Deletion of PRC2 is sufficient to reduce apoptosis and brain dysplasia and partially restore genetic programs and tissue development in the Snip1-depleted brain. Our findings suggest that Snip1 exerts loci-dependent regulation of PRC2 and H3K27me3 to toggle between cell fates in the developing brain.
The antibiotic phazolicin displays a dual mode of uptake in Gram-negative bacteria
Authors: Travin Dmitrii Y. , Vigouroux Armelle , Inaba-Inoue Satomi , Qu Feng , Jouan Romain , Lachat Joy , Sutormin Dmitry , Dubiley Svetlana , Beis Konstantinos , Moréra Solange , Severinov Konstantin , Mergaert Peter 
Published: April 2022

ABSTRACTPhazolicin (PHZ) is a peptide antibiotic exhibiting narrow-spectrum activity against rhizobia closely related to its producer Rhizobium sp. Pop5. Using genetic and biochemical techniques, we here identified BacA and YejABEF as two importers of PHZ in a sensitive model strain Sinorhizobium meliloti Sm1021. BacA and YejABEF are members of SLiPT and ABC transporter families of non-specific peptide importers, respectively. The uptake of PHZ by two distinct families of transporters dramatically decreases the naturally occurring rate of resistance. Moreover, since both BacA and YejABEF are essential for the development of functional symbiosis of rhizobia with leguminous plants, the acquisition of PHZ resistance via the inactivation of transporters is further disfavoured since single bacA or yejABEF mutants are unable to propagate in root nodules. Crystal structures of the periplasmic subunit YejA from S. meliloti and Escherichia coli revealed fortuitous bound peptides, suggesting a non-specific peptide-binding mechanism that facilitates the uptake of PHZ and other antimicrobial peptides.SIGNIFICANCEMany bacteria produce antimicrobial peptides to eliminate competitors and create an exclusive niche. These peptides kill bacteria by either membrane disruption or inhibiting essential intracellular processes. The Achilles heel of the latter type of antimicrobials is their dependence on transporters to enter the susceptible bacteria since mutations in such transporters result in resistance. We describe here how the ribosome-targeting peptide phazolicin, produced by Rhizobium sp. Pop5, uses two different transporters, BacA and YejABEF, to get into the cells of the symbiotic bacterium Sinorhizobium meliloti. This dramatically reduces the probability of resistance acquisition. Both transporters need to be inactivated for phazolicin resistance acquisition. Since these transporters are also crucial in S. meliloti for its symbiotic association with host plants, their inactivation in biological settings is highly unlikely. This makes PHZ an attractive lead for the development of a biocontrol agent with potential for use in agriculture.
Islamic Perspective on Nursing and the Philosophy of Science
Authors: Isworo Atyanti 
Published: April 2022

AbstractAlthough nursing theory developed in the modern Western scientific tradition has universal aspects, it is important to consider the different philosophies, beliefs and cultures of each different society to enrich the perspective and practice of nursing that is more sensitive to the patient’s background. As supported by the Transcultural Nursing Theory, in treating patients a nurse needs to pay attention to and respect the cultural preferences and beliefs of the patient. In this context, this article wants to contribute by describing the Islamic perspective on nursing in the context of nursing philosophy. Methods: This literature review uses articles published from 2018-2022 with source from databased ScienceDirect, Scopus, Sage Journals, EBSCO-Host, Springer Link, and ProQuest. The keywords used are Islamic, perspective, nursing, caring. Article selection follows “PRISMA” flow. Results: This systematic review have a total of 8 articles meet the criteria for analysis. This article has relevance both in Muslim-majority countries such as Indonesia, Malaysia and Middle Eastern countries, as well as countries where Muslims are a minority. We found 8 articles presents a number of opinions or research results that examine nursing issues and those related to it from an Islamic perspective. From a number of opinions and research findings studied, it can be concluded that although it can be said to offer universal core values, the Islamic perspective has fundamental differences with Western nursing philosophy or theory, especially in terms of the source of knowledge, the basic view of humans, and the importance of spirituality in nursing.