bluuebunny/crossref_metadata_2025_split huggingface dataset:
Neural substrates of working memory updating
Authors: Nir-Cohen Gal , Kessler Yoav , Egner Tobias 
Published: November 2019

AbstractWorking memory (WM) needs to protect current content from interference and simultaneously be amenable to rapid updating with newly relevant information. An influential model suggests these opposing requirements are met via a basal ganglia (BG) - thalamus gating mechanism that allows for selective updating of prefrontal cortex (PFC) WM representations. A large neuroimaging literature supports the general involvement of the PFC, BG, and thalamus, as well as posterior parietal cortex (PPC), in WM. However, the specific functional contributions of these regions to key sub-processes of WM updating, namely gate-opening, content substitution, and gate closing, are still unknown, as common WM tasks conflate these processes. We therefore combined functional MRI with the reference-back task, specifically designed to tease apart these sub-processes. Participants compared externally presented face stimuli to a reference face held in WM, while alternating between updating and maintaining this reference, resulting in opening vs. closing the gate to WM. Gate opening and substitution processes were associated with strong BG, thalamic and fronto-parietal activation, but – intriguingly - the same activity profile was observed for sensory cortex supporting task stimulus processing (i.e., the fusiform face area). In contrast, gate closing was not reliably associated with any of these regions. These findings provide new support for the involvement of the BG in gate opening as suggested by the gating model, but qualify the model’s assumptions by demonstrating that gate closing does not seem to depend on the BG, and that gate opening also involves task-relevant sensory cortex.
CrkL is required for donor T cell migration to GvHD Target organs
Authors: Roy Nathan H. , Mammadli Mahinbanu , Burkhardt Janis K. , Karimi Mobin 
Published: November 2019

ABSTRACTThe success of cancer therapies based on allogeneic hematopoietic stem cell transplant relies on the ability to separate graft-versus-host disease (GvHD) from graft-versus-tumor (GVT) responses. Controlling donor T cell migration into peripheral tissues is a viable option to limit unwanted tissue damage, but a lack of specific targets limits progress on this front. Here, we show that the adaptor protein CrkL, but not the closely related family members CrkI or CrkII, is a crucial regulator of T cell migration.In vitro, CrkL-deficient T cells fail to polymerize actin in response to the integrin ligand ICAM-1, resulting in defective migration. Using a mouse model of GvHD/GVT, we found that while CrkL-deficient T cells can efficiently eliminate hematopoietic tumors they are unable to migrate into inflamed organs, such as the liver and small intestine, and thus do not cause GvHD. These results suggest a specific role for CrkL in trafficking to peripheral organs but not the lymphatic system. In line with this, we found that although CrkL-deficient T cells could clear hematopoietic tumors, they failed to clear the same tumor growing subcutaneously, highlighting the role of CrkL in controlling T cell migration into peripheral tissues. Our results define a unique role for CrkL in controlling T cell migration, and suggest that CrkL function could be therapeutically targeted to enhance the efficacy of immunotherapies involving allogeneic donor cells.
Engineering transplantable jejunal mucosal grafts using primary patient-derived organoids from children with intestinal failure
Authors: Meran Laween , Massie Isobel , Weston Anne , Gaifulina Riana , Faull Peter , Orford Michael , Kucharska Anna , Baulies Anna , Hirst Elizabeth , Konig Julia , Tedeschi Alfonso Maria , Pellegata Alessandro Filippo , Eli Susanna , Snijders Ambrosius P. , Collinson Lucy , Thapar Nikhil , Thomas Geriant , Eaton Simon , Bonfanti Paola , De Coppi Paolo , Li Vivian S.W. 
Published: November 2019

AbstractIntestinal failure (IF), following extensive anatomical or functional loss of small intestine (SI), has debilitating long-term effects on infants and children with this condition. Priority of care is to increase the child’s length of functional intestine, jejunum in particular, to improve nutritional independence. Here we report a robust protocol for reconstruction of autologous intestinal mucosal grafts using primary IF patient materials. Human jejunal intestinal organoids derived from paediatric IF patients can be expanded efficiently in vitro with region-specific markers preserved after long-term culture. Decellularized human intestinal matrix with intact ultrastructure is used as biological scaffolds. Proteomic and Raman spectroscopic analyses reveal highly analogous biochemical composition of decellularized human SI and colon matrix, implying that they can both be utilised as scaffolds for jejunal graft reconstruction. Indeed, seeding of primary human jejunal organoids to either SI or colonic scaffolds in vitro can efficiently reconstruct functional jejunal grafts with persistent disaccharidase activity as early as 4 days after seeding, which can further survive and mature after transplantation in vivo. Our findings pave the way towards regenerative medicine for IF patients.
High-Resolution Single-Cell 3D-Models of Chromatin Ensembles during Drosophila Embryogenesis
Authors: Sun Qiu , Perez-Rathke Alan , Czajkowsky Daniel M. , Shao Zhifeng , Liang Jie 
Published: November 2019

AbstractSingle-cell chromatin studies provide insights into how chromatin structure relates to functions of individual cells. However, balancing high-resolution and genome wide-coverage remains challenging. We describe a computational method for the reconstruction of large 3D-ensembles of single-cell (sc) chromatin conformations from population Hi-C that we apply to study embryogenesis inDrosophila. With minimal assumptions of physical properties and without adjustable parameters, our method generates large ensembles of chromatin conformations via deep-sampling. Our method identifies specific interactions, which constitute 5–6% of Hi-C frequencies, but surprisingly are sufficient to drive chromatin folding, giving rise to the observed Hi-C patterns. Modeled sc-chromatins quantify chromatin heterogeneity, revealing significant changes during embryogenesis. Furthermore,>50% of modeled sc-chromatin maintain topologically associating domains (TADs) in early embryos, when no population TADs are perceptible. Domain boundaries become fixated during development, with strong preference at binding-sites of insulator-complexes upon the mid-blastula transition. Overall, high-resolution 3D-ensembles of sc-chromatin conformations enable further in-depth interpretation of population Hi-C, improving understanding of the structure-function relationship of genome organization.
SPECC1L-deficient palate mesenchyme cells show speed and directionality defect
Authors: Goering Jeremy P. , Isai Dona Greta , Hall Everett G. , Wilson Nathan R. , Kosa Edina , Wenger Luke W. , Umar Zaid , Yousaf Abdul , Czirok Andras , Saadi Irfan 
Published: November 2019

AbstractClefts of the lip and/or palate (CL/P) are common anomalies that occur in 1/800 live births. Pathogenic SPECC1L variants identified in patients with rare atypical clefts and syndromic CL/P suggest the gene plays a primary role in face and palate development. We have generated Specc1l gene-trap (Specc1lcGT) and truncation (Specc1lΔC510) alleles that cause embryonic or perinatal lethality, respectively. Specc1lcGT/ΔC510 compound mutants show delayed and abnormal palatal shelf elevation at E14.5. By E15.5, the mutant shelves do elevate and fuse, however, the palatal rugae form abnormally. Palatogenesis requires extensive mesenchymal remodeling, especially during palatal shelf elevation. We posit that this remodeling involves collective movement of neural crest-derived palatal mesenchyme cells. Live time-lapse microscopy was performed to visualize in vitro wound-repair assays with wildtype and SPECC1L-deficient primary mouse embryonic palatal mesenchyme (MEPM) cells. SPECC1L-deficient MEPM cells consistently showed delayed closure in wound-repair assays. To evaluate which features of cellular movement were responsible, we performed automated particle image velocimetry (PIV) and manual cell tracking. The analyses revealed that both cell speed and directionality are disrupted in SPECC1L-deficient cells compared to controls. To determine if primary MEPM cells can move collectively, we assayed stream formation, which is a hallmark of collective movement. Indeed, MEPM cultures displayed correlated movement of neighboring cells. Importantly, correlation length was reduced in SPECC1L-deficient cultures, consistent with a role for SPECC1L in collective migration. Furthermore, we demonstrated that activation of the PI3K-AKT pathway with the 740Y-P small molecule can rescue the wound-closure delay in SPECC1L-deficient MEPM cells. Cell tracking analyses showed that this rescue was due to both increased speed and improved directionality. Altogether, our data showed a novel role for SPECC1L in guided movement through modulation of PI3K-AKT signaling.
Dynamic regulation of CD45 by tetraspanin CD53
Authors: Dunlock V. E. , Arp A. B. , Jansen E. , Charrin S. , van Deventer S. J. , Wright M. D. , Querol-Cano L. , Rubinstein E. , van Spriel A. B. 
Published: November 2019

AbstractT cells are central to the adaptive immune response, playing a role in both the direct and indirect killing of pathogens and transformed cells. The activation of T cells is the result of a complex signaling cascade, initiated at the T cell receptor (TCR), and ending with the induction of proliferation. CD45, a member of the protein tyrosine phosphatase family, is one of the most abundant membrane proteins on T cells and functions by regulating activation directly downstream of the TCR. As a result of alternative splicing, CD45 can be expressed in multiple isoforms, naive T cells express the CD45RA isoform, while activated T cells gain expression of CD45RO, which has been proposed to increase signaling. Though the importance of CD45 in TCR signaling, proliferation and cytokine production is well established, little is known about the regulation of CD45 activity. We discovered that the immune-specific tetraspanin CD53 directly affects the stability and function of CD45RO in T cells.We have identified CD53 as a T cell co-stimulatory molecule in primary human and murine cells. Furthermore, we have shown that the absence of CD53 leads to an altered CD45 isoform expression as a result of decreased CD45RO stability on the cell surface. This instability was accompanied by increased mobility as measured by FRAP.Together, this indicates that CD53 functions as a stabilizer of CD45RO, and therefore as a positive regulator of TCR signaling at the T cell surface. Our data provides novel insight into the role of tetraspanins in the regulation of immune signaling and may provide a new avenue for the regulation of T cell signaling.
Agrin promotes coordinated therapeutic processes leading to improved cardiac repair in pigs
Authors: Baehr Andrea , Umansky Kfir Baruch , Bassat Elad , Klett Katharina , Jurisch Victoria , Bozoglu Tarik , Hornaschewitz Nadja , Solyanik Olga , Kain David , Ferrero Bartolo , Cohen-Rabi Renee , Krane Markus , Cyran Clemens , Soehnlein Oliver , Laugwitz Karl Ludwig , Hinkel Rabea , Kupatt Christian , Tzahor Eldad 
Published: November 2019

AbstractIschemic heart diseases are classified among the leading cause of death and reduced life quality worldwide. Although revascularization strategies significantly reduce mortality after acute myocardial infarction (MI), a significant number of MI patients develop chronic heart failure over time. We have recently reported that a fragment of the extra cellular matrix (ECM) protein Agrin promotes cardiac regeneration following MI in adult mice. Here, we tested the therapeutic potential of Agrin in a preclinical porcine model, comprising either 3 or 28 days (d) reperfusion period. We first demonstrate that local (antegrade) delivery of recombinant human Agrin (rhAgrin) to the infarcted pig heart can target the affected regions in an efficient and clinically-relevant manner. Single dose of rhAgrin resulted in significant improvement in heart function, infarct size, fibrosis and adverse remodeling parameters 28 days post MI. Short-term MI experiment along with complementary murine MI studies revealed myocardial protection, improved angiogenesis, inflammatory suppression and cell cycle re-entry, as Agrin’s mechanisms of action. We conclude that a single dose of Agrin is capable of reducing ischemia reperfusion injury and improving cardiac function, demonstrating that Agrin could serve as a therapy for patients with acute MI and potentially heart failure.
Single Cell RNA Sequencing Reveals Heterogeneity of Human MSC Chondrogenesis: Lasso Regularized Logistic Regression to Identify Gene and Regulatory Signatures
Authors: Huynh Nguyen P.T. , Kelly Natalie H. , Katz Dakota B. , Pham Minh , Guilak Farshid 
Published: November 2019

AbstractBone marrow-derived mesenchymal stem cells (MSCs) exhibit the potential to undergo chondrogenesis in vitro, forming de novo tissues with a cartilage-like extracellular matrix that is rich in glycosaminoglycan and collagen type II. However, it is now apparent that MSCs comprise an inhomogeneous population of cells, and the fate of individual subpopulations during this differentiation process is not well understood. We analyzed the trajectory of MSC differentiation during chondrogenesis using single cell RNA sequencing (scRNA-seq). Using a machine learning technique – lasso regularized logistic regression – we showed that multiple subpopulations of cells existed at all stages during MSC chondrogenesis and were better-defined by transcription factor activity rather than gene expression. Trajectory analysis indicated that subpopulations of MSCs were not intrinsically specified or restricted, but instead remained multipotent and could differentiate into three main cell types: cartilage, hypertrophic cartilage, and bone. Lasso regularized logistic regression showed several advances in scRNA-seq analysis, namely identification of a small number of highly influential genes or transcription factors for downstream validation, and cell type classification with high accuracy. Additionally, we showed that MSC differentiation trajectory may exhibit donor to donor variation, although key influential pathways were comparable between donors. Our data provide an important resource to study gene expression and to deconstruct gene regulatory networks in MSC differentiation.
PGR5 is required for efficient Q cycle in the cytochromeb6fcomplex during cyclic electron flow
Authors: Buchert Felix , Mosebach Laura , Gäbelein Philipp , Hippler Michael 
Published: November 2019

AbstractProton Gradient Regulation 5 (PGR5) is involved in the control of photosynthetic electron transfer but its mechanistic role is not yet clear. Several models have been proposed to explain phenotypes such as a diminished steady state proton motive force (pmf) and increased photodamage of photosystem I (PSI). Playing a regulatory role in cyclic electron flow (CEF) around PSI, PGR5 contributes indirectly to PSI protection by enhancing photosynthetic control, which is a pH-dependent downregulation of electron transfer at the cytochromeb6fcomplex (b6f). Here, we re-evaluated the role of PGR5 in the green algaChlamydomonas reinhardtiiand conclude thatpgr5possesses a dysfunctionalb6f. Our data indicate that theb6flow-potential chain redox activity likely operated in two distinct modes – via the canonical Q cycle during linear electron flow and via an alternative Q cycle during CEF, attributing a ferredoxin-plastoquinone reductase activity to theb6f. The latter mode allowed efficient oxidation of the low-potential chain in the WTb6f. A switch between the two Q cycle modes was dependent of PGR5 and relied on unknown stromal electron carrier(s), which were a general requirement forb6factivity. In CEF-favouring conditions the electron transfer bottleneck inpgr5was theb6fand insufficient flexibility in the low-potential chain redox tuning might account for the mutantpmfphenotype and the secondary consequences. Models of our findings are discussed.
Reorienting Spatial Attention within Visual Working Memory
Authors: Han Sizhu , Ku Yixuan 
Published: November 2019

AbstractAttention and working memory (WM) are intertwined core cognitive processes. Through four experiments with 133 participants, we dissociated the impact of two types of covert spatial attention, endogenous vs. exogenous, on visual WM. Behavioral results consistently indicated that exogenous attentional cues were more advantageous than endogenous ones in enhancing the precision of visual WM under load-2, while they equalized under load-4. In addition, physiological and neural data explained the mechanisms. Converging evidence from eye-tracking, electroencephalography, and magnetoencephalography suggested that fast attentional processing induced by exogenous cues lead to early top-down information from the dorsal lateral prefrontal cortex (DLPFC) to sensory cortices. The differential frontal activities were further correlated with the behavioral distinctions between exogenous and endogenous cues, and transcranial magnetic stimulation over DLPFC at the same time period abolished the exogenous advantage. Taken together, traditionally considered bottom-up attentional processing induced by exogenous cues rapidly engages top-down signals from the frontal cortex, which leads to stronger behavioral benefits compared with the benefits produced by endogenous cues under the low load condition.
Cis-regulatory analysis of Onecut1 expression in fate-restricted retinal progenitor cells
Authors: Patoori Sruti , Jean-Charles Nathalie , Gopal Ariana , Sulaiman Sacha , Gopal Sneha , Wang Brian , Souferi Benjamin , Emerson Mark M. 
Published: November 2019

BackgroundThe vertebrate retina consists of six major classes of neuronal cells. During development, these cells are generated from a pool of multipotent retinal progenitor cells (RPCs) that express the gene Vsx2. Fate-restricted RPCs have recently been identified, with limited mitotic potential and cell fate possibilities compared to multipotent RPCs. One population of fate-restricted RPCs, marked by activity of the regulatory element ThrbCRM1, gives rise to both cone photoreceptors and horizontal cells. These cells do not express Vsx2, but co-express the transcription factors (TFs) Onecut1 and Otx2, which bind to ThrbCRM1. The components of the gene regulatory networks that control the transition from multipotent to fate-restricted gene expression are not known. This work aims to identify and evaluate cis-regulatory elements proximal to Onecut1 to identify the gene regulatory networks involved in RPC fate-restriction.MethodWe identified regulatory elements through ATAC-seq and conservation, followed by reporter assays to screen for activity based on temporal and spatial criteria. The regulatory elements of interest were subject to deletion and mutation analysis to identify functional sequences and evaluated by quantitative flow cytometry assays. Finally, we combined the enhancer::reporter assays with candidate TF overexpression to evaluate the relationship between the TFs, the enhancers, and early vertebrate retinal development. Statistical tests included ANOVA, Kruskal-Wallis, or unpaired t-tests.ResultsTwo regulatory elements, ECR9 and ECR65, were identified to be active in ThrbCRM1(+) restricted RPCs. Candidate bHLH binding sites were identified as critical sequences in both elements. Overexpression of candidate bHLH TFs revealed specific enhancer-bHLH interactions. Nhlh1 overexpression expanded ECR65 activity into the Vsx2(+) RPC population, and overexpression of NeuroD1/NeuroG2/NeuroD4 had a similar effect on ECR9. Furthermore, bHLHs that were able to activate ectopic ECR9 reporter were able to induce endogenous Otx2 expression.ConclusionsThis work reports a large-scale screen to identify spatiotemporally specific regulatory elements near the Onecut1 locus. These elements were used to identify distinct populations in the developing retina. In addition, fate-restricted regulatory elements responded differentially to bHLH factors, and suggest a role for retinal bHLHs upstream of the Otx2 and Onecut1 genes during the formation of restricted RPCs from multipotent RPCs.
An animal society based on kin competition, not kin cooperation
Authors: Vickruck Jessica L. , Richards Miriam H. 
Published: November 2019

AbstractAnimals respond to competition among kin for critical breeding resources in two ways: avoidance of direct fitness costs via dispersal of siblings to breed separately, and formation of kin-based societies in which subordinates offset direct fitness costs of breeding competition via altruism and increased indirect fitness. Here we provide the first evidence that kin competition can promote the evolution of societies based on non-kin cooperation. For eastern carpenter bees, nests are a critical breeding resource in perpetually short supply, leading to strong competition among females. Observations of individually marked and genotyped females demonstrate that sisters disperse from their natal nests to join social groups of nonrelatives. By forming social groups of non-kin, females increase their chances of successful reproduction, while avoiding the indirect fitness cost of competition among sisters.One Sentence SummaryWe describe the first known example of an animal society based on avoidance of kin competition rather than on promotion of kin cooperation.
Biophysical mechanism of ultrafast helical twisting contraction in the giant unicellular ciliate Spirostomum ambiguum
Authors: Xu L. X. , Bhamla M. S. 
Published: November 2019

The biophysical mechanism of cytoskeletal structures has been fundamental to understanding of cellular dynamics. Here, we present a mechanism for the ultrafast contraction exhibited by the unicellular ciliateSpirostomum ambiguum. Powered by a Ca2+binding myoneme mesh architecture, Spirostomum is able to twist its two ends in the same direction and fully contract to 75% of its body length within five milliseconds, followed by a slow elongation mechanism driven by the uncoiling of the microtubules. To elucidate the principles of this rapid contraction and slow elongation cycle, we used high-speed imaging to examine the same-direction coiling of the two ends of the cell and immunofluorescence techniques to visualize and quantify the structural changes in the myoneme mesh, microtubule arrays, and the cell membrane. Lastly, we provide support for our hypotheses using a simple physical model that captures key features of Spirostomum’s ultrafast twisting contraction.SIGNIFICANCEUltrafast movements are ubiquitous in nature, and some of the most fascinating ultrafast biophysical systems are found on the cellular level. Quantitative studies and models are key to understand the biophysics of these fast movements. In this work, we study Spirostomum’s ultrafast contraction by using high-speed imaging, labeling relevant cytoskeletal structures, and building a physical model to provide a biophysical mechanism especially of the helical same direction twisting of this extremely large single cell organism. Deeper understanding of how single cells can execute extreme shape changes hold potential for advancing basic cell biophysics and also inspire new cellular inspired actuators for engineering applications.