bluuebunny/crossref_metadata_2025_split huggingface dataset:
Plant-insect chemical communication in ecological communities: an information theory perspective
Authors: Zu Pengjuan , García-García Reinaldo , Schuman Meredith , Saavedra Serguei , Melián Carlos J. 
Published: October 2021

AbstractCross-species communication, where signals are sent by one species and perceived by others, is one of the most intriguing types of communication that functionally links different species to form complex ecological networks. Yet, global changes and human activities can affect communication by increasing the fluctuations of species composition and phenology, altering signal profiles and intensity, and introducing noises. So far, most studies on cross-species communication have focused on a few specific species isolated from ecological communities. Scaling up investigations of cross-species communication to the community level is currently hampered by a lack of conceptual and practical methodologies. Here, we propose an interdisciplinary framework based on information theory to investigate mechanisms shaping cross-species communication at the community level. We use plants and insects, the cornerstones of most ecosystems, as a showcase; and focus on chemical communication as the key communication channel. We first introduce some basic concepts of information theory, then we illustrate information patterns in plant-insect chemical communication, followed by a further exploration of how to integrate information theory into ecological and evolutionary processes to form testable mechanistic hypotheses. We conclude by highlighting the importance of community-level information as a vehicle to better understand the maintenance of ecological systems, especially when facing rapid global changes.
Enteric nervous system modulation of luminal pH modifies the microbial environment to promote intestinal health
Authors: Hamilton M. Kristina , Wall Elena S. , Guillemin Karen , Eisen Judith S. 
Published: October 2021

AbstractThe enteric nervous system (ENS) controls many aspects of intestinal homeostasis, including parameters that shape the habitat of microbial residents. Previously we showed that zebrafish lacking an ENS, due to deficiency of the sox10 gene, develop intestinal inflammation and bacterial dysbiosis, with an expansion of proinflammatory Vibrio strains. To understand the primary defects resulting in dysbiosis in sox10 mutants, we investigated how the ENS shapes the intestinal environment in the absence of microbiota and associated inflammatory responses. We found that intestinal transit, intestinal permeability, and luminal pH regulation are all aberrant in sox10 mutants, independent of microbially induced inflammation. Treatment with the proton pump inhibitor, omeprazole, corrected the more acidic luminal pH of sox10 mutants to wild type levels. Omeprazole treatment also prevented overabundance of Vibrio and ameliorated inflammation in sox10 mutant intestines. Treatment with the carbonic anhydrase inhibitor, acetazolamide, caused wild type luminal pH to become more acidic, and increased both Vibrio abundance and intestinal inflammation. We conclude that a primary function of the ENS is to regulate luminal pH, which plays a critical role in shaping the resident microbial community and regulating intestinal inflammation.Author SummaryThe intestinal microbiota is an important determinant of health and disease and is shaped by the environment of the gut lumen. The nervous system of the intestine, the enteric nervous system (ENS), helps maintain many aspects of intestinal health including a healthy microbiota. We used zebrafish with a genetic mutation that impedes ENS formation to investigate how the ENS prevents pathogenic shifts in the microbiota. We found that mutants lacking an ENS have a lower luminal pH, higher load of pathogenic bacteria, and intestinal inflammation. We showed that correcting the low pH, using the commonly prescribed pharmacological agent omeprazole, restored the microbiota and prevented intestinal inflammation. Conversely, we found that lowering the luminal pH of wild type animals, using the drug acetazolamide, caused expansion of pathogenic bacteria and increased intestinal inflammation. From these experiments, we conclude that a primary function of the ENS is to maintain normal luminal pH, thereby constraining intestinal microbiota community composition and promoting intestinal health.
Transition of Vibrio cholerae through a natural host induces resistance to environmental changes
Authors: Depelteau Jamie S. , Limpens Ronald , Nag Dhrubajyoti , Koch Bjørn E. V. , Withey Jeffrey H. , Meijer Annemarie H. , Briegel Ariane 
Published: October 2021

SummaryThe pandemic-related strains of Vibrio cholerae are known to cause diarrheal disease in animal hosts. These bacteria must overcome rapid changes in their environment, such as the transition from fresh water to the gastrointestinal system of their host. To study the morphological adjustments during environmental transitions, we used zebrafish as a natural host. Using a combination of fluorescent light microscopy, cryogenic electron tomography and serial block face scanning electron microscopy, we studied the structural changes that occur during the infection cycle. We show that the transition from an artificial nutrient-rich environment to a nutrient-poor environment has a dramatic impact on the cell shape, most notably membrane dehiscence. In contrast, excreted bacteria from the host retain a uniform distance between the membranes as well as their vibrioid shape. Inside the intestine, V. cholerae cells predominantly colonized the anterior to mid-gut, forming micro-colonies associated with the microvilli as well as within the lumen. The cells retained their vibrioid shape but changed their cell-length depending on their localization. Our results demonstrate dynamic changes in morphological characteristics of V. cholerae during the transition between the different environments, and we propose that these structural changes are critical for the pathogen’s ability to colonize host tissues.
Ad26.COV2.S Prevents SARS-CoV-2 Induced Pathways of Inflammation and Thrombosis in Hamsters
Authors: Aid Malika , Vidal Samuel J. , Piedra-Mora Cesar , Ducat Sarah , Chan Chi N. , Bondoc Stephen , Colarusso Alessandro , Starke Carly E. , Nekorchuk Michael , Busman-Sahay Kathleen , Estes Jacob D. , Martinot Amanda J. , Barouch Dan H. 
Published: October 2021

AbstractSyrian golden hamsters exhibit features of severe disease after SARS-CoV-2 challenge and are therefore useful models of COVID-19 pathogenesis and prevention with vaccines. Recent studies have shown that SARS-CoV-2 infection stimulates type I interferon, myeloid, and inflammatory signatures similar to human disease, and that weight loss can be prevented with vaccines. However, the impact of vaccination on transcriptional programs associated with COVID-19 pathogenesis and protective adaptive immune responses is unknown. Here we show that SARS-CoV-2 challenge in hamsters stimulates antiviral, myeloid, and inflammatory programs as well as signatures of complement and thrombosis associated with human COVID-19. Notably, single dose immunization with Ad26.COV2.S, an adenovirus serotype 26 vector (Ad26)-based vaccine expressing a stabilized SARS-CoV-2 spike protein, prevents the upregulation of these pathways such that the gene expression profiles of vaccinated hamsters are comparable to uninfected animals. Finally, we show that Ad26.COV2.S vaccination induces T and B cell signatures that correlate with binding and neutralizing antibody responses. These data provide further insights into the mechanisms of Ad26.COV2.S based protection against severe COVID-19 in hamsters.Author SummaryIn this study, we show that vaccination with Ad26.COV2.S protected SARS-CoV-2 challenged hamsters from developing severe COVID-19 disease by attenuating excessive proinflammatory responses, such as IL-6 and IL-1, macrophages and neutrophils signaling. Ad26 vaccination also prevented the upregulation of pathways associated with thrombosis such coagulation and clotting cascades associated with infection, and the transcriptomic profiles of vaccinated animals were largely comparable to control uninfected hamsters. In contrast, SARS-CoV-2 challenged unvaccinated hamsters showed significant increase of these proinflammatory and prothrombotic pathways and significant weight loss compared to vaccinated hamsters.
Female fruit flies cannot protect stored sperm from high temperature damage
Authors: Walsh Benjamin S. , Parratt Steven R. , Snook Rhonda R. , Bretman Amanda , Atkinson David , Price Tom A. R. 
Published: October 2021

AbstractRecently, it has been demonstrated that heat-induced male sterility is likely to shape population persistence as climate change progresses. However, an under-explored possibility is that females may be able to successfully store and preserve sperm at temperatures that sterilise males, which could ameliorate the impact of male infertility on populations. Here, we test whether females from two fruit fly species can protect stored sperm from a high temperature stress. We find that sperm carried by female Drosophila virilis are almost completely sterilised by high temperatures, whereas sperm carried by female Zaprionus indianus show only slightly reduced fertility. Heat-shocked D. virilis females can recover fertility when allowed to remate, suggesting that the delivered heat-shock is destroying stored sperm and not directly damaging females in this species. The temperatures required to reduce fertility of mated females are substantially lower than the temperatures required to destroy mature sperm in males, suggesting that females are worse than males at protecting mature sperm. This suggests that female sperm storage is unlikely to ameliorate the impacts of high temperature fertility losses in males, and instead exacerbates fertility costs of high temperatures, representing an important determinant of population persistence during climate change.
Efficient single copy integration via homology-directed repair (scHDR) by 5’modification of large DNA donor fragments in mice
Authors: Medert Rebekka , Thumberger Thomas , Tavhelidse Tinatini , Hub Tobias , Kellner Tanja , Oguchi Yoko , Dlugosz Sascha , Zimmermann Frank , Wittbrodt Joachim , Freichel Marc 
Published: October 2021

ABSTRACTCRISPR/Cas approaches have largely replaced conventional gene targeting strategies. However, homology-directed repair (HDR) in the mouse genome is not very efficient, and precisely inserting longer sequences using HDR remains challenging, given that donor constructs preferentially integrate as concatemers. Here, we show that injecting 5’biotinylated donor DNA in mouse embryos at the two-cell stage leads to efficient single-copy HDR (scHDR) alleles. Our dedicated genotyping strategy showed that these alleles occurred with a frequency of 19%, 20%, and 26%, respectively, in three independent gene loci, indicating that scHDR is dramatically boosted by 5’biotinylation. Thus, we suggest that a combination of a 5’biotinylated donor and diligent analysis of concatemer integration are prerequisites for efficiently and reliably generating conditional alleles or other large fragment knock-ins into the mouse genome.
Standardised method for cardiomyocyte isolation and purification from individual murine neonatal, infant, and adult hearts
Authors: Nicks Amy M , Holman Sara R , Chan Andrea Y , Tsang Michael , Young Paul E , Humphreys David T , Naqvi Nawazish , Husain Ahsan , Li Ming , Smith Nicola J , Iismaa Siiri E , Graham Robert M 
Published: October 2021

AbstractPrimary cardiomyocytes are invaluable for understanding postnatal heart development. However, a universal method to obtain freshly purified cardiomyocytes without using different agedependent isolation procedures and cell culture, is lacking. Here, we report the development of a standardised method that allows rapid isolation and purification of high-quality cardiomyocytes from individual neonatal through to adult C57BL/6J murine hearts. Langendorff retrograde perfusion, which is currently limited to adult hearts, was adapted for use in neonatal and infant hearts by developing an easier in situ aortic cannulation technique. Tissue digestion conditions were optimised to achieve efficient digestion of hearts of all ages in a comparable timeframe (<14 min). This resulted in a high yield (1.56-2.2×106 cells/heart) and viability (~70-100%) of cardiomyocytes post-isolation. An immunomagnetic cell separation step was then applied to yield highly purified cardiomyocytes (~95%) as confirmed by immunocytochemistry, flow cytometry, and qRT-PCR. For cell-type specific studies, cardiomyocyte DNA, RNA, and protein could be extracted in sufficient yields to conduct molecular experiments. We generated transcriptomic datasets for neonatal cardiomyocytes from individual hearts, for the first time, which revealed nine sex-specific genes (FDR<0.05) encoded on the sex chromosomes. Finally, we also developed an in situ fixation protocol that preserved the native cytoarchitecture of cardiomyocytes (~94% rodshaped post-isolation), and used it to evaluate cell morphology during cardiomyocyte maturation, as well as capture spindle-shaped neonatal cells undergoing cytokinesis. Together, these procedures allow molecular and morphological profiling of high-quality cardiomyocytes from individual hearts of any postnatal age.
Structural insights into the BRAF monomer-to-dimer transition mediated by RAS binding
Authors: Martinez Fiesco Juliana A. , Durrant David E. , Morrison Deborah K. , Zhang Ping 
Published: October 2021

AbstractRAF kinases are essential effectors of RAS, but how RAS binding initiates the conformational changes needed for autoinhibited RAF monomers to form active dimers has remained unclear. Here, we present cryo-electron microscopy structures of full-length BRAF complexes derived from mammalian cells: autoinhibited, monomeric BRAF:14-3-32:MEK and BRAF:14-3-32 complexes, and an inhibitor-bound, dimeric BRAF2:14-3-32 complex, at 3.7, 4.1, and 3.9 Å resolution, respectively. In both autoinhibited, monomeric structures, the RAS binding domain (RBD) of BRAF is resolved, revealing that the RBD forms an extensive contact interface with the 14-3-3 protomer bound to the BRAF C-terminalsite and that key basic residues required for RBD-RAS binding are exposed. Moreover, through structure-guided mutational studies, our findings indicate that RAS-RAF binding is a dynamic process and that RBD residues at the center of the RBD:14-3-3 interface have a dual function, first contributing to RAF autoinhibition and then to the full spectrum of RAS-RBD interactions.
The parallel-stranded d(CGA) duplex is a highly predictable structural motif with two conformationally distinct strands
Authors: Luteran Emily M. , Paukstelis Paul J. 
Published: October 2021

ABSTRACTDNA can adopt non-canonical structures that have important biological functions while also providing structural diversity for nanotechnology applications. Here, we describe the crystal structures of two oligonucleotides composed of d(CGA) triplet repeats in the parallel-stranded duplex form. The structure determination of four unique d(CGA)-based parallel-stranded duplexes across two crystal structures has allowed us to characterize and establish structural parameters of d(CGA) triplets in the parallel-stranded duplex form. Our results show that d(CGA) units are highly uniform, but that each strand in the duplex is structurally unique and has a distinct role in accommodating structural asymmetries induced by the C-CH+ base pair.
In situ Nuclear Matrix preparation in Drosophila melanogaster and its use in studying the components of nuclear architecture
Authors: Pathak Rashmi U , Sureka Rahul , Bihani Ashish , Varma Parul , Mishra Rakesh K 
Published: October 2021

AbstractThe study of Nuclear Matrix (NuMat) over the last 40 years has been limited to either isolated nuclei from tissues or cells grown in culture. Here, we provide a protocol for NuMat preparation in intact Drosophila melanogaster embryos and its use in dissecting the components of nuclear architecture. The protocol does not require isolation of nuclei and therefore maintains the three-dimensional milieu of an intact embryo, which is biologically more relevant compared to cells in culture. One of the advantages of this protocol is that only a small number of embryos are required. The protocol can be extended to larval tissues like salivary glands and imaginal discs with little modification. Taken together, it becomes possible to carry out such studies in parallel to genetic experiments using mutant and transgenic flies. This protocol, therefore, opens the powerful field of fly genetics to cell biology in the study of nuclear architecture.SummaryNuclear Matrix is a biochemically defined entity and a basic component of the nuclear architecture. Here we present a protocol to isolate and visualize Nuclear Matrix in situ in the intact embryos and tissues of Drosophila melanogaster and its potential applications.
Simulations of flow over a bio-inspired undulated cylinder with dynamically morphing topography
Authors: Yuasa Mikihisa , Lyons Kathleen , Franck Jennifer A. 
Published: October 2021

AbstractInspired by the geometric properties of seal whiskers, the addition of spanwise undulations on a cylinder have been shown to lower the mean and oscillatory forces and modify the frequency of flow-induced vibration when compared to smooth cylinders. Previously, computational fluid dynamics (CFD) has been used to characterize the hydrodynamic response with respect to specific geometric features. However simulations are time intensive due to complex three-dimensional meshing and computation time, limiting the number of geometric perturbations explored. A method is proposed in which the specific geometric features of this complex topography can be modified during a simulation thereby decreasing the time per geometric modification and removing the need for manual meshing of the complex structure. The surface of the seal whisker inspired geometry is parameterized into seven defining parameters, each of which is directly controlled in order to morph the surface into any realization within the defined parameter space. Once validated, the algorithm is used to explore the undulation amplitudes in the chord and thickness directions, by varying each independently from 0 to 0.3 thicknesses in increments of 0.05 at a Reynolds number of 500. The force and frequency response are examined for this matrix of geometric parameters, yielding detailed force trends not previously investigated. The impact of the bio-inspired morphing algorithm will allow for further optimization and development of force-mitigating underwater devices and other engineering applications in need of vibration suppression, frequency tuning, or force reduction.
Evaluating live microbiota biobanking using an ex vivo microbiome assay and metaproteomics
Authors: Zhang Xu , Walker Krystal , Mayne Janice , Li Leyuan , Ning Zhibin , Stintzi Alain , Figeys Daniel 
Published: October 2021

AbstractBiobanking of live microbiota is becoming indispensable for mechanistic and clinical investigations of drug-microbiome interactions and fecal microbiota transplantation. However, there is a lack of methods to rapidly and systematically evaluate whether the biobanked microbiota maintains their cultivability and functional activity. In this study, we use a rapid ex vivo microbiome assay and metaproteomics to evaluate the cultivability and the functional responses of biobanked microbiota to treatment with a prebiotic (fructo-oligosaccharide, FOS). Our results indicate that the microbiota cultivability and their functional responses to FOS treatment were well maintained by freezing in a deoxygenated glycerol buffer at -80°C for 12 months. We also demonstrate that the fecal microbiota is functionally stable for 48 hours on ice in a deoxygenated glycerol buffer, allowing off-site fecal sample collection and shipping to laboratory for live microbiota biobanking. This study provides a method for rapid evaluation of the cultivability of biobanked live microbiota. Our results show minimal detrimental influences of long-term freezing in deoxygenated glycerol buffer on the cultivability of fecal microbiota.
Fast enzymatic HCO3- dehydration supports photosynthetic water oxidation in Photosystem II from pea
Authors: Shitov Alexandr V. , Terentyev Vasily V. , Govindjee Govindjee 
Published: October 2021

AbstractCarbonic anhydrase (CA) activity, associated with Photosystem II (PSII) from Pisum sativum, has been shown to enhance water oxidation. But, the nature of the CA activity, its origin and role in photochemistry has been under debate, since the rates of CA reactions, measured earlier, were less than the rates of photochemical reactions. Here, we demonstrate high CA activity in PSII from Pisum sativum, measured by HCO3- dehydration at pH 6.5 (i.e. under optimal condition for PSII photochemistry), with kinetic parameters Km of 2.7 mM; Vmax of 2.74·10-2 mM·sec-1; kcat of 1.16·103 sec-1 and kcat/Km of 4.1·105 M-1 sec-1, showing the enzymatic nature of this activity, which kcat exceeds by ∼13 times the rate of PSII, as measured by O2 evolution. The similar dependence of HCO3- dehydration, of the maximal quantum yield of photochemical reactions and of O2 evolution on the ratio of chlorophyll/photochemical reaction center II demonstrate the interconnection of these processes on the electron donor side of PSII. Since the removal of protons is critical for fast water oxidation, and since HCO3- dehydration consumes a proton, we suggest that CA activity, catalyzing very fast removal of protons, supports efficient water oxidation in PSII and, thus, photosynthesis in general.
AtCGL160 recruits chloroplast coupling factor 1
Authors: Reiter Bennet , Rosenhammer Lea , Marino Giada , Geimer Stefan , Leister Dario , Rühle Thilo 
Published: October 2021

AbstractATP synthases couple the generation of chemical energy to a transmembrane electro-chemical potential. Like ATP synthases in bacteria and mitochondria, chloroplast ATP synthases consist of a membrane-spanning (CFO) and a soluble coupling factor (CF1). Accessory factors facilitate subunit production and orchestrate the assembly of the functional CF1-CFO complex. It was previously shown that the accessory factor CGL160 promotes the formation of plant CFO and performs a similar function in the assembly of its c-ring to that of the distantly related bacterial Atp1/UncI protein. In this study, we show that the N-terminal portion of CGL160 (AtCGL160N), which is specific to the green lineage, is required for late steps in CF1-CFO assembly in Arabidopsis thaliana. In plants that lacked this stroma-exposed domain, photosynthesis was impaired, and amounts of CF1-CFO were reduced to about 65% of the wild-type level. Loss of AtCGL160N did not perturb c-ring formation, but led to a 10-fold increase in the numbers of CF1 sub-complexes in the stroma relative to the wild type and the CF1 assembly mutant atcgld11-1. Co-immunoprecipitation and protein crosslinking assays revealed an association of AtCGL160 with CF1 subunits. Yeast two-hybrid assays localized the interaction to a stretch of AtCGL160N that binds to the thylakoid-proximal domain of CF1-β that includes the conserved DELSEED motif. We therefore propose that AtCGL160 has acquired an additional function in the recruitment of soluble CF1 to a membrane-integral CFO sub-complex, which is critical for the modulation of CF1-CFO activity and photosynthesis in chloroplasts.