bluuebunny/crossref_metadata_2025_split huggingface dataset:
Derivation of Isogenic Mesodermal and Ectomesodermal Chondrocytes from Human Induced Pluripotent Stem Cells for Articular Cartilage Regeneration
Authors: Lee Ming-Song , Stebbins Matthew J. , Jiao Hongli , Huang Hui-Ching , Walzack Brian E. , Palecek Sean P. , Shusta Eric V. , Li Wan-Ju 
Published: October 2020

AbstractGenerating phenotypic chondrocytes from human pluripotent stem cells through driving developmental lineage-specific differentiation remains to be of great interest in the field of cartilage regeneration. In this study, we derived chondrocytes from human induced pluripotent stem cells (hiPSCs) along the mesodermal or ectomesodermal lineages to prepare isogenic mesodermal cell-derived chondrocytes (MC-Chs) or neural crest cell-derived chondrocytes (NCC-Chs), respectively, and further evaluated differences in their cellular and molecular characteristics and cartilage repair capabilities. Our results showed that both lineage-derived chondrocytes expressed hyaline cartilage-associated markers and were capable of forming hyaline cartilage-like tissue ectopically and at joint defects. Moreover, NCC-Chs showed the absence of markers of hypertrophic chondrocytes and revealed a closer morphological resemblance to articular chondrocytes and a greater capability of producing glycosaminoglycans and collagen type 2 at cartilage defects compared to MC-Chs. It was found that the profile of global transcript expression of NCC-Chs more closely resembled that of native chondrocytes (NCs) than that of MC-Chs. Induced by additional growth factors identified through the analysis of transcriptome comparison to NCs, both MC-Chs and NCC-Chs showed a further increase in the phenotype of hyaline cartilage chondrocytes. Results of this study reveal differences in cellular and molecular characteristics and cartilage repair capabilities between isogenic hiPSC-derived MC-Chs and NCC-Chs and demonstrate that chondrocytes derived from hiPSCs along the ectomesodermal lineage are a potential cell source for articular cartilage regeneration.
Lipid interactions of an actinoporin pore-forming oligomer
Authors: Sepehri A. , Nepal B. , Lazaridis T. 
Published: October 2020

ABSTRACTThe actinoporins are cytolytic toxins produced by sea anemones. Upon encountering a membrane, preferably containing sphingomyelin, they oligomerize and insert their N-terminal helix into the membrane, forming a pore. Whether sphingomyelin is specifically recognized by the protein or simply induces phase coexistence in the membrane has been debated. Here, we perform multimicrosecond molecular dynamics simulations of an octamer of fragaceatoxin C, a member of the actinoporin family, in lipid bilayers containing either pure 1,2-Dioleoyl-sn-Glycero-3-Phosphocholine (DOPC) or a 1:1 mixture of DOPC and palmitoyl sphingomyelin (PSM). The complex is highly stable in both environments, with only slight fraying of the inserted helices near their N-termini. Analyzing the structural parameters of the mixed membrane in the course of the simulation we see signs of a phase transition for PSM in the inner leaflet of the bilayer. In both leaflets, cross-interactions between lipids of different type decrease over time. Surprisingly, the aromatic loop thought to be responsible for sphingomyelin recognition interacts more with DOPC than PSM by the end of the simulation. These results support the notion that the key membrane property that actinoporins recognize is lipid phase coexistence.SIGNIFICANCE STATEMENTThe mechanism of selectivity of naturally produced toxins for their target membranes is not well understood. For example, actinoporins, toxins produced by sea anemones, have been reported to selectively target sphingomyelin-containing membranes. Whether they bind this lipid preferentially or recognize the phase coexistence that sphingomyelin induces is not clear. This work examines this issue by long computer simulations of an actinoporin oligomer embedded in lipid bilayers and finds no preferential interactions of the protein with sphingomyelin. Instead, the simulations show signs of phase separation, suggesting that phase coexistence is the key property that actinoporins recognize.
Longitudinal in vivo micro-CT-based approach allows spatio-temporal characterization of fracture healing patterns and assessment of biomaterials in mouse femur defect models
Authors: Wehrle Esther , Tourolle né Betts Duncan C , Kuhn Gisela A , Floreani Erica , Nambiar Malavika H , Schroeder Bryant J , Hofmann Sandra , Müller Ralph 
Published: October 2020

AbstractThorough preclinical evaluation of functionalized biomaterials for treatment of large bone defects is essential prior to clinical application. Using in vivo micro-computed tomography (micro-CT) and mouse femoral defect models with different defect sizes, we were able to detect spatio-temporal healing patterns indicative of physiological and impaired healing in three defect sub-volumes and the adjacent cortex. The time-lapsed in vivo micro-CT-based approach was then applied to evaluate the bone regeneration potential of functionalized biomaterials using collagen and BMP-2. Both collagen and BMP-2 treatment led to distinct changes in bone turnover in the different healing phases. Despite increased periosteal bone formation, 87.5% of the defects treated with collagen scaffolds resulted in non-unions. Additional BMP-2 application significantly accelerated the healing process and increased the union rate to 100%. This study further shows potential of time-lapsed in vivo micro-CT for capturing spatio-temporal deviations preceding non-union formation and how this can be prevented by application of functionalized biomaterials.This study therefore supports the application of longitudinal in vivo micro-CT for discrimination of normal and disturbed healing patterns and for the spatio-temporal characterization of the bone regeneration capacity of functionalized biomaterials.
Fast recovery of disrupted tip links induced by mechanical displacement of hair bundles
Authors: Alonso R. G. , Tobin M. , Martin P. , Hudspeth A. J. 
Published: October 2020

AbstractHearing and balance rely on the capacity of mechanically sensitive hair bundles to transduce vibrations into electrical signals that are forwarded to the brain. Hair bundles possess tip links that interconnect the mechanosensitive stereocilia and convey force to the transduction channels. A dimer of dimers, each of these links comprises two molecules of protocadherin 15 (PCDH15) joined to two of cadherin 23 (CDH23). The “handshake” that conjoins the four molecules can be disruptedin vivoby intense stimulation andin vitroby exposure to Ca2+chelators. Using hair bundles from the rat’s cochlea and the bullfrog’s sacculus, we observed that extensive recovery of mechanoelectrical transduction, hair-bundle stiffness, and spontaneous bundle oscillation can occur within seconds after Ca2+chelation, especially if hair bundles are deflected towards their short edges. Investigating the phenomenon in a two-compartment ionic environment that mimics natural conditions, we combined iontophoretic application of a Ca2+chelator to selectively disrupt the tip links of individual frog hair bundles with displacement clamping to control hair-bundle motion and measure forces. Our observations suggest that, after the normal Ca2+concentration has been restored, mechanical stimulation facilitates the reconstitution of functional tip links.Significance StatementEach of the sensory receptors responsible for hearing or balance—a hair cell—has a mechanosensitive hair bundle. Mechanical stimuli pull upon molecular filaments—the tip links—that open ionic channels in the hair bundle. Loud sounds can damage hearing by breaking the tip links; recovery by replacement of the constituent proteins then requires several hours. We disrupted the tip linksin vitroby removing the calcium ions that stabilize them, then monitored the electrical response or stiffness of hair bundles to determine whether the links could recover. We found that tip links recovered within seconds if their ends were brought back into contact. This form of repair might occur in normal ears to restore sensitivity after damage.
Concentration Sensing in Crowded Environments
Authors: Stroberg Wylie , Schnell Santiago 
Published: October 2020

ABSTRACTSignal transduction within crowded cellular compartments is essential for the physiological function of cells and organisms. While the accuracy with which receptors can probe the concentration of ligands has been thoroughly investigated in dilute systems, the effect of macromolecular crowding on the inference of concentration remains unknown. In this work we develop a novel algorithm to simulate reversible reactions between reacting Brownian particles. This facilitates the calculation of reaction rates and correlation times for ligand-receptor systems in the presence of macromolecular crowding. Using this method, we show that it is possible for crowding to increase the accuracy of estimated ligand concentration based on receptor occupancy. In particular, we find that crowding can enhance the effective association rates between small ligands and receptors to a large enough degree to overcome the increased chance of rebinding due to caging by crowding molecules. For larger ligands, crowding decreases the accuracy of the receptor’s estimate primarily by decreasing the microscopic association and dissociation rates.SIGNIFICANCEDeveloping an understanding of how cells effectively transmit signals within or between compartments under physical constraints is an important challenge for biophysics. This work investigates the effect that macromolecular crowding can have on the accuracy of a simple ligand-receptor signaling system. We show that the accuracy of an inferred ligand concentration based on the occupancy of the receptor can be enhanced by crowding under certain circumstances. Additionally, we develop a simulation algorithm that speeds the calculation of reaction rates in crowded environments and can be readily applied to other, more complex systems.
Increased wheat protein content via introgression of a HMW glutenin selectively reshapes the grain proteome
Authors: Cao Hui , Duncan Owen , Islam Shahidul , Zhang Jingjuan , Ma Wujun , Millar A. Harvey 
Published: October 2020

ABSTRACTIntrogression of a high molecular weight glutenin subunit (HMW-GS) gene,1Ay21*, into commercial wheat cultivars increased overall grain protein content and bread-making quality by unknown mechanisms. As well as increased abundance of 1Ay HMW-GS, 115 differentially expressed proteins (DEPs) were discovered between three cultivars and corresponding introgressed near-isogenic lines (NILs). Functional category analysis showed that the DEPs were predominantly other storage proteins, and proteins involved in protein synthesis, protein folding, protein degradation, stress response and grain development. Nearly half the genes encoding the DEPs showed strong co-expression patterns during grain development. Promoters of these genes are enriched in elements associated with transcription initiation and light response, indicating a potential connection between thesecis-elements and grain protein accumulation. A model of how this HMW-GS enhances the abundance of machinery for protein synthesis and maturation during grain filling is proposed. This analysis not only provides insights into how introgression of the1Ay21*improves grain protein content, but also directs selection of protein candidates for future wheat quality breeding programmes.One sentence summaryIntrogression of the 1Ay21* HMW-GS increases wheat grain protein content and improves bread-making quality in association with a broad reshaping of the grain proteome network.
Birth timing after the long feeding migration in elephant seals
Authors: Condit Richard , Beltran Roxanne S. , Robinson Patrick W. , Crocker Daniel E. , Costa Daniel P. 
Published: October 2020

AbstractNorthern elephant seals migrate long distances from feeding grounds to raise pups during a brief period on breeding beaches. Since gestation sets a parturition date months in advance, timing of the arrival must be precise. We used satellite-tracked animals to examine this timing, establishing arrival and birth dates in 106 migrating females and estimating how far they traveled in the days just before birth. Females arrived a mean of 5.5 days prior to birth (range 1-11, sd=1.6), and females arriving later in the breeding season cut that pre-birth interval by 1.8 days relative to early arrivers. There was no correlation between female body condition, nor female age, and the pre-birth interval. The last 15 days prior to birth, animals traveled as far as 1465 km. Those furthest from the colony traveled > 100 km per day, three times faster than animals near the colony at the same time. Despite migrations covering several thousand kilometers while pregnant, female elephant seals were able to time their arrival within 6 days, swimming steadily at high speed if needed. This allows them to maintain a precise annual cycle for many years consecutively.
Decolonizing Psocopteran Systematics: Holarctic Lineages Cannot Inform Diversity and Evolution in Tropics
Authors: Sarria-Rodríguez Valentina , Gonzalez-Obando Ranulfo , Rivera-Franco Nelson , Cardenas-Henao Heiber , Román-Palacios Cristian 
Published: October 2020

AbstractDespite tropical psocids comprise ~60% of species diversity within the Psocidae (Insecta, Psocodea), previous studies on the Psocidae phylogeny have poorly sampled tropical species (<40% species in trees). Here we discuss the evolution and systematics of the Psocidae based on the most comprehensive species-level sampling of the Psocidae. We sequenced and inferred the phylogenetic position of 43 previously unsampled Neotropical species from COI, H3, WNT, 18S, 16S, and 12S. Based on our phylogenies we found that Neotropical psocids are generally not closely related to morphologically similar taxa in the Holarctic region. Consequently, the monophyletic status for the major groups within Psocidae (subfamilies and tribes) is recovered only when Holarctic groups are sampled (7–10 of 11 higher-level groups are monophyletic) but violated when Neotropical species are included in the dataset (1 of 11 higher-level groups are monophyletic). Leveraging the largest phylogeny of the Psocidae, our study pinpoints the downfalls of simply extending taxonomic knowledge from lineages of a certain area to inform diversity and evolution of lineages in other regions.HighlightsTropical psocids comprise >60% of the extant family richnessPrevious phylogenies have undersampled Tropical psocidsHolarctic and Neotropical species are classified under the same morphological groupsHolarctic and Neotropical generally correspond to evolutionarily distinct lineagesPhylogenies based on Holarctic psocids poorly inform evolution in the Neotropics
A single cell view of the transcriptome during lateral root initiation inArabidopsis thaliana
Authors: Gala Hardik P. , Lanctot Amy , Jean-Baptiste Ken , Guiziou Sarah , Chu Jonah C. , Zemke Joseph E. , George Wesley , Queitsch Christine , Cuperus Josh T. , Nemhauser Jennifer L. 
Published: October 2020

AbstractRoot architecture is a major determinant of fitness, and is under constant modification in response to favorable and unfavorable environmental stimuli. Beyond impacts on the primary root, the environment can alter the position, spacing, density and length of secondary or lateral roots. Lateral root development is among the best-studied examples of plant organogenesis, yet there are still many unanswered questions about its earliest steps. Among the challenges faced in capturing these first molecular events is the fact that this process occurs in a small number of cells with unpredictable timing. Single-cell sequencing methods afford the opportunity to isolate the specific transcriptional changes occurring in cells undergoing this fate transition. Using this approach, we successfully captured the transcriptomes of initiating lateral root primordia, and discovered many previously unreported upregulated genes associated with this process. We developed a method to selectively repress target gene transcription in the xylem pole pericycle cells where lateral roots originate, and demonstrated that expression of several of these targets was required for normal root development. We also discovered novel subpopulations of cells in the pericycle and endodermal cell files that respond to lateral root initiation, highlighting the coordination across cell files required for this fate transition.One sentence summarySingle cell RNA sequencing reveals new molecular details about lateral root initiation, including the transcriptional impacts of the primordia on bordering cells.
Sequential development of embryoblast-like memory entities in human cancer tissues: An evolutionary self-repair structure with pluripotentiality
Authors: Diaz Jairo A , Sánchez Liliana , Diaz Luis A , Murillo Mauricio F , Poveda Laura , Suescun Oscar F , Castro Laura 
Published: October 2020

AbstractHidden collective organization of cancer cells can partially or completely return to embryoid genotype-phenotype with the plasticity to transform their morphology on cell embryoblast-like memory entities by expression of dormant genes that arise from embryogenesis.After hundreds of driver mutations, cancer cells gain new abilities or attributes and recapitulate early stages of embryogenesis. Our findings document how malignant tissues reactivated ancestral storage memory and elaborate inside tumor glands spiral- pyramidal-fractal chiral crystals (Tc) as geometric attractors proteins and biomimicry the primitive cellular blastocyst embryoblast fluid-filled cavity. The resultant evolutionary embryoblast-like entity has higher survivability and spatial cephalic-caudal growth organization with pluripotentiality that carry the correct DNA instructions to repair, and regenerate. The isolation and manipulation of these order structures can guide and control the regenerative pathway mechanism in human tumors as follows: modify and reprogram the phenotype of the tumor where these entities are generated, establish a reverse primordial microscopic mold to use the swirlonic collective behavior of cellular building blocks to regenerate injured tissues, convert cancer cells to a normal phenotype through regeneration using the organizational level and scale properties of reverse genetic guidance, global control of mitotic activity and morphogenetic movements avoiding their spread and metastasis, determining a better life prognosis for patients who incubate these entities in their tumors compared to those who do not express them. An emergent self-repair order structure, biological template to develop targeted therapeutic alternatives not only in cancer but also in treatment of autoimmune, viral diseases, and in regenerative medicine and rejuvenation.
Look where you go: characterizing eye movements toward optic flow
Authors: Chow Hiu Mei , Knöll Jonas , Madsen Matthew , Spering Miriam 
Published: October 2020

AbstractWhen we move through our environment, objects in the visual scene create optic flow patterns on the retina. Even though optic flow is ubiquitous in everyday life, it is not well understood how our eyes naturally respond to it. In small groups of human and non-human primates, optic flow triggers intuitive, uninstructed eye movements to the pattern’s focus of expansion (Knöll, Pillow & Huk, 2018). Here we investigate whether such intuitive oculomotor responses to optic flow are generalizable to a larger group of human observers, and how eye movements are affected by motion signal strength and task instructions. Observers (n= 43) viewed expanding or contracting optic flow constructed by a cloud of moving dots radiating from or converging toward a focus of expansion that could randomly shift. Results show that 84% of observers tracked the focus of expansion with their eyes without being explicitly instructed to track. Intuitive tracking was tuned to motion signal strength: saccades landed closer to the focus of expansion and smooth tracking was more accurate when dot contrast, motion coherence, and translational speed were high. Under explicit tracking instruction, the eyes aligned with the focus of expansion more closely than without instruction. Our results highlight the sensitivity of intuitive eye movements as indicators of visual motion processing in dynamic contexts.
Implementing and assessing an alchemical method for calculating protein-protein binding free energy
Authors: Patel Dharmeshkumar , Patel Jagdish Suresh , Ytreberg F. Marty 
Published: October 2020

ABSTRACTProtein-protein binding is fundamental to most biological processes. It is important to be able to use computation to accurately estimate the change in protein-protein binding free energy due to mutations in order to answer biological questions that would be experimentally challenging, laborious or time consuming. Although non-rigorous free energy methods are faster, rigorous alchemical molecular dynamics-based methods are considerably more accurate and are becoming more feasible with the advancement of computer hardware and molecular simulation software. Even with sufficient computational resources, there are still major challenges to using alchemical free energy methods for protein-protein complexes, such as generating hybrid structures and topologies, maintaining a neutral net charge of the system when there is a charge-changing mutation, and setting up the simulation. In the current study, we have used thepmxpackage to generate hybrid structures and topologies, and a double-system/single-box approach to maintain the net charge of the system. To test the approach, we predicted relative binding affinities for two protein-protein complexes using a non-equilibrium alchemical method based on the Crooks fluctuation theorem and compared the results with experimental values. The method correctly identified stabilizing from destabilizing mutations for a small protein-protein complex, but was not as successful to the larger, more challenging antibody complex. In addition, the correlation between predicted and experimental relative binding affinities was high for smaller complex, and low for the other larger complex.