bluuebunny/crossref_metadata_2025 huggingface dataset:
Chromatin accessibility and microRNA expression in nephron progenitor cells during kidney development
Authors: Clugston Andrew , Bodnar Andrew , Cerqueira Débora Malta , Phua Yu Leng , Lawler Alyssa , Boggs Kristy , Pfenning Andreas , Ho Jacqueline , Kostka Dennis
Published: March 2021

Mammalian nephrons originate from a population of nephron progenitor cells (NPCs), and it is known that NPCs’ transcriptomes change throughout nephrogenesis during healthy kidney development. To characterize chromatin accessibility and microRNA (miRNA) expression throughout this process, we collected NPCs from mouse kidneys at embryonic day 14.5 (E14.5) and postnatal day zero (P0) and assayed cells for transposase-accessible chromatin and small RNA expression. We observe 46,374 genomic regions of accessible chromatin, with 2,103 showing significant changes in accessibility between E14.5 and P0. In addition, we detect 1,104 known microRNAs, with 114 showing significant changes in expression. Genome-wide, changes in DNA accessibility and microRNA expression highlight biological processes like cellular differentiation, cell migration, extracellular matrix interactions, and developmental signaling pathways such as Notch. Furthermore, our data identify novel candidate cis-regulatory elements forEya1andPax8, both genes with a role in NPC differentiation; we also associate expression-changing microRNAs, includinglet-7-5p,miR-125b-5p,miR-181a-2-3p, andmiR-9-3p,with candidate cis-regulatory elements. Overall, our data characterize NPCs during kidney development and point out new candidate regulatory elements for genes and microRNA with key roles in nephrogenesis.
Implicit and explicit learning of Bayesian priors differently impacts bias during perceptual decision-making
Authors: Thakur V. N. , Basso M. A. , Ditterich J. , Knowlton B. J.
Published: March 2021

Knowledge without awareness, or implicit knowledge, influences a variety of behaviors. It is unknown however, whether implicit knowledge of statistical structure informs visual perceptual decisions or whether explicit knowledge of statistical probabilities is required. Here, we measured visual decision-making performance using a novel task in which humans reported the orientation of two differently colored translational Glass patterns; each color associated with different orientation probabilities. The task design allowed us to assess participants’ ability to learn and use a general orientation prior as well as a color specific feature prior. Classifying decision-makers based on a questionnaire revealed that both implicit and explicit learners implemented a general orientation bias by adjusting the starting point of evidence accumulation in the drift diffusion model framework. Explicit learners additionally adjusted the drift rate offset. When subjects implemented a stimulus specific bias, they did so by adjusting primarily the drift rate offset. We conclude that humans can learn priors implicitly for perceptual decision-making and depending on awareness implement the priors using different mechanisms.
Differential impact of transdiagnostic, dimensional psychopathology on multiple scales of functional connectivity
Authors: Seok Darsol , Beer Joanne , Jaskir Marc , Smyk Nathan , Jaganjac Adna , Makhoul Walid , Cook Philip , Elliott Mark , Shinohara Russell , Sheline Yvette I.
Published: March 2021

Introduction

Dimensional psychopathology strives to associate different domains of cognitive dysfunction with brain circuitry. Connectivity patterns as measured by functional magnetic resonance imaging (fMRI) exist at multiple scales, with global networks of connectivity composed of microscale interactions between individual nodes. It remains unclear how separate dimensions of psychopathology might differentially impact these different scales of organization.

Methods

Patients experiencing anxious misery symptomology (depression, anxiety and trauma; n = 192) were assessed for symptomology and received resting-state fMRI scans. Three modeling approaches (seed-based correlation analysis [SCA], support vector regression [SVR] and Brain Basis Set Modeling [BSS]), each relying on increasingly dense representations of functional connectivity patterns, were used to associate connectivity patterns with six different dimensions of psychopathology: anxiety sensitivity, anxious arousal, rumination, anhedonia, insomnia and negative affect. Importantly, a full 50 patients were held-out in a testing dataset, leaving 142 patients as training data.

Results

Different symptom dimensions were best modeled by different scales of brain connectivity: anhedonia and anxiety sensitivity were best modeled with single connections (SCA), insomnia and anxious arousal by mesoscale patterns (SVR) and negative affect and ruminative thought by broad, cortex-spanning patterns (BBS). Dysfunction within the default mode network was implicated in all symptom dimensions that were best modeled by multivariate models.

Conclusion

These results suggest that symptom dimensions differ in the degree to which they impact different scales of brain organization. In addition to advancing our basic understanding of transdiagnostic psychopathology, this has implications for the translation of basic research paradigms to human disorders.
BNT162b2 COVID-19 mRNA vaccine elicits a rapid and synchronized antibody response in blood and milk of breastfeeding women
Authors: Friedman Michal Rosenberg , Kigel Aya , Bahar Yael , Yogev Yariv , Dror Yael , Lubetzky Ronit , Many Ariel , Wine Yariv
Published: March 2021

We describe the dynamics of the vaccine-specific antibody response in the breastmilk and serum in a prospective cohort of ten lactating women who received two doses of the Pfizer-BioNTech BNT162b2 COVID-19 mRNA vaccine. The antibody response was rapid and highly synchronized between breastmilk and serum, reaching stabilization 14 days after the second dose. The predominant serum antibody was IgG. The response in the breastmilk included both IgG and IgA with neutralizing capacity.
Inhibiting microglia proliferation after spinal cord injury improves recovery in mice and nonhuman primates
Authors: Poulen Gaëtan , Aloy Emilie , Bringuier Claire M. , Mestre-Francés Nadine , Artus Emaëlle V.F. , Cardoso Maïda , Perez Jean-Christophe , Goze-Bac Christophe , Boukhaddaoui Hassan , Lonjon Nicolas , Gerber Yannick N. , Perrin Florence E.
Published: March 2021

No curative treatment is available for any deficits induced by spinal cord injury (SCI). Following injury, microglia undergo highly diverse activation processes, including proliferation, and play a critical role on functional recovery.

In a translational objective, we investigated whether a transient pharmacological reduction of microglia proliferation after injury is beneficial for functional recovery after SCI in mice and nonhuman primates. The colony stimulating factor-1 receptor (CSF1R) regulates proliferation, differentiation, and survival of microglia, we thus used an oral administration of GW2580, a CSF1R inhibitor.

First, transient post-injury GW2580 administration in mice improves motor function recovery, promotes tissues preservation and/or reorganization (identified by coherent anti-stokes Raman scattering microscopy), and modulates glial reactivity.

Second, post-injury GW2580-treatment in nonhuman primates reduces microglia proliferation, improves functional motor function recovery, and promotes tissue protection. Notably, three months after lesion microglia reactivity returned to baseline value.

Finally, to initiate the investigation on molecular mechanisms induced by a transient post-SCI GW2580-treatment, we used microglia-specific transcriptomic analysis in mice. Notably, we detected a downregulation in the expression of inflammatory-associated genes and we identified genes that were up-regulated by SCI and further downregulated by the treatment.

Thus, a transient oral GW2580 treatment post-injury may provide a promising therapeutic strategy for SCI patients and may also be extended to other central nervous system disorders displaying microglia activation.
The dynamics of cell-free DNA from urine and blood after a full marathon
Authors: Shishikura Yasuhiro , Tokinoya Katsuyuki , Aita Yuichi , Sekine Nanami , Sugasawa Takehito , Yoshida Yasuko , Kosaki Keisei , Kumamoto Shota , Ishikura Keisuke , Kuji Tomoaki , Kawakami Yasushi , Nabekura Yoshiharu , Maeda Seiji , Takekoshi Kazuhiro
Published: March 2021

Purpose

Cell-free DNA (cfDNA) has been investigated as a minimally invasive biomarker for many diseases, particularly cancer. An increase in cfDNA has been observed during exercise. Neutrophil extracellular traps (NETs) may be the origin of cfDNA in response to acute exercise, but the mechanisms of generation of cfDNA during exercise remain unclear. In this study we investigated the dynamics of serum and urinary cfDNA levels and determined the relevance of other biomarkers to serum and urinary cfDNA levels and fragment size after a full marathon.

Methods

Samples were collected from 23 healthy male subjects. Blood and urine samples were collected before and immediately, two hours, and one day after the full marathon. The measurements included serum and urinary cfDNA, creatine kinase, myoglobin, creatinine, white blood cells, platelets, and lactoferrin from blood, and amylase, albumin, and creatinine from urine.

Results

Serum and urinary cfDNA levels increased after a full marathon. Creatine kinase, myoglobin, and creatinine in blood, and albumin and creatinine in urine also increased significantly after a full marathon. Serum cfDNA showed peak values about 180 bp after the full marathon. Values over 1000 bp were present at two hours post-marathon. Urinary cfDNA showed peak values from 35 bp to 50 bp after the full marathon. Values over 1000 bp appeared at Immediately and two hours post marathon.

Conclusion

This study revealed that both serum and urinary cfDNA levels transiently increased after a full marathon. In addition, these cfDNA fragment varied in size.
Cross-modal perceptual enhancement of unisensory targets is uni-directional and does not affect temporal expectations
Authors: Ball Felix , Nentwich Annika , Noesselt Toemme
Published: March 2021

Previous studies demonstrated that redundant target stimuli can enhance performance due to multisensory interplay and interactively facilitate performance enhancements due to temporal expectations (TE; faster and accurate reactions to temporally expected targets). Here we tested whether other types of multisensory interactions – i.e. interactions evoked by temporally flanking irrelevant stimuli – can result in similar performance patterns and boost not only unisensory target perception (multi-vs. unisensory sequences) but also unisensory temporal expectations (expected vs. unexpected). To test our hypothesis, we presented sequences of 12 stimuli (10 Hz) which either consisted of auditory (A), visual (V) or alternating auditory-visual stimuli (e.g. A-V-A-V-…) with either auditory (AV(A)) or visual (AV(V)) targets. Participants had to discriminate target frequency which was unpredictable by temporal regularities (expected vs. unexpected target positions) and by stimulation sequence (A, V, AV(A), AV(V)). Moreover, we ran two experiments in which we presented redundant multisensory targets and manipulated the speed of the stimulation sequence (10 vs. 15 Hz stimulus trains) to control whether the results of Experiment 1 depended on sequence speed. Performance for unisensory targets was affected by temporally flanking distractors, with multisensory interactions selectively improving unisensory visual target perception. Yet, only redundant multisensory targets reliably affected TEs. Together, these results indicate that cross-modal facilitation of unisensory target perception in fast stimulus streams is uni-directional, but also differs from multisensory interactions evoked by redundant targets; more specifically, it appears to be context-dependent (task, design etc.) whether unisensory stimulation (unlike redundant target stimulation) allows for the generation of temporal expectations.
Daily torpor reduces the energetic consequences of habitat selection for a widespread bat
Authors: Alston Jesse M. , Dillon Michael E. , Keinath Douglas A. , Abernethy Ian M. , Goheen Jacob R.
Published: March 2021

Homeothermy requires increased metabolic rates as temperatures decline below the thermoneutral zone, so homeotherms typically select microhabitats within or near their thermoneutral zones during periods of inactivity. However, many mammals and birds are heterotherms that relax internal controls on body temperature when maintaining a high, stable body temperature is energetically costly. Such heterotherms should be less tied to microhabitats near their thermoneutral zones, and because heterotherms spend more time in torpor and expend less energy at colder temperatures, heterotherms may even select microhabitats in which temperatures are well below their thermoneutral zones. We studied how temperature and daily torpor influence selection of diurnal roosts by a heterothermic bat (Myotis thysanodes). We (1) quantified the relationship between ambient temperature and daily duration of torpor, (2) simulated daily energy expenditure over a range of microhabitat (roost) temperatures, and (3) quantified the influence of roost temperature on roost selection. While warm roosts substantially reduced energy expenditure of simulated homeothermic bats, heterothermic bats modulated their use of torpor to maintain a constant level of energy expenditure over the course of a day. Daily torpor expanded the range of energetically economical microhabitats, such that roost selection was independent of roost temperature. Our work adds to a growing literature documenting functions of torpor beyond its historical conceptualization as a last-resort measure to save energy during extended or acute energetic stress.
Mechanism of REST/NRSF Regulation of Clustered Protocadherin α Genes
Authors: Tang Yuanxiao , Jia Zhilian , Xu Honglin , Da Lin-Tai , Wu Qiang
Published: March 2021

Repressor element-1 silencing transcription factor (REST) or neuron-restrictive silencer factor (NRSF) is a zinc-finger (ZF) containing transcriptional repressor that recognizes thousands of neuron-restrictive silencer elements (NRSEs) in mammalian genomes. How REST/NRSF regulates gene expression remains incompletely understood. Here, we investigate the binding pattern and regulation mechanism of REST/NRSF in the clustered protocadherin (PCDH) genes. We find that REST/NRSF directionally forms base-specific interactions with NRSEs via tandem ZFs in an anti-parallel manner but with striking conformational changes. In addition, REST/NRSF recruitment to theHS5-1enhancer leads to the decrease of long-range enhancer-promoter interactions and downregulation of the clusteredPCDHαgenes. Thus, REST/NRSF repressesPCDHαgene expression through directional binding to a repertoire of NRSEs within the distal enhancer and variable target genes.
Smartphone-assisted real-time estimation of chlorophyll and carotenoid contents in spinach following the inversion of red and green color features
Authors: Agarwal Avinash , Dongre Piyush Kumar , Gupta Snehasish Dutta
Published: March 2021

Purpose

Chlorophyll (Chl) content is a reliable indicator of leaf nitrogen content and plant health status. Currently available methods for image-based Chl estimation require complex mathematical derivations and high-throughput imaging set-up along with multiplex image-preprocessing steps. Further, the influence of carotenoid (CAR) content has been largely ignored in the process. The present study describes a smartphone-based leaf image analysis method for real-time estimation of Chl content and Chl/CAR ratio.

Methods

Color features were obtained from RGB (red, green, blue) images of spinach leaves using a smartphone, and inverse R and G values were calculated. Correlation analysis of color indices and photosynthetic pigment (PP) contents was performed, followed by principal component analysis (PCA). Linear mathematical modeling was performed for describing regression equations for predicting PP contents.

Results

1/R and 1/G showed strong positive linear correlation (0.93 <r2< 0.96) with Chl and CAR contents, respectively. Furthermore, 1/R+1/G and [1/R]/[1/G] presented strong positive linear correlation with Chl + CAR (r2= 0.95) and Chl/CAR (r2= 0.88), respectively. PCA confirmed the association of color indices with the respective PP features, which were subsequently estimated using the correlation models. A smartphone-based companion application was developed using the linear models for non-invasive, real-time estimation of Chl content and Chl/CAR ratio.

Conclusion

The ratios 1/R and 1/G indicate the contents of Chl and CAR via linear models. The smartphone application developed using the linear models enables real-time estimation of Chl content and Chl/CAR ratio without complicated image preprocessing steps or mathematical derivations.
αB-crystallin affects the morphology of Aβ(1-40) aggregates
Authors: Müller Henrik , Dias David M. , van der Zalm Anna , Baldwin Andrew J.
Published: March 2021

αB-crystallin (ABC) is a human small heat shock protein that is strongly linked to Alzheimer’s disease (AD).In vitro, it can inhibit the aggregation and amyloid formation of a range of proteins including Aβ(1-40), a primary component of AD amyloid plaques. Despite the strong links, the mechanism by which ABC inhibits amyloid formation has remained elusive, in part due to the notorious irreproducibility of aggregation assays involving preparations of Aβ-peptides of native sequence. Here, we present a recombinant expression protocol to produce native Aβ(1-40), devoid of any modifications or exogenous residues, with yields up to 4 mg/LE. coli. This material provides highly reproducible aggregation kinetics and, by varying the solution conditions, we obtain either highly ordered amyloid fibrils or more disordered aggregates. Addition of ABC slows the aggregation of Aβ(1-40), and interferes specifically with the formation of ordered amyloid fibrils, favouring instead the more disordered aggregates. Solution-state NMR spectroscopy reveals that the interaction of ABC with Aβ(1-40) depends on the specific aggregate morphology. These results provide mechanistic insight into how ABC inhibits the formation of amyloid fibrils.

Highlights

Protocol for production of native recombinant Aβ(1-40)

Amyloid formation under physiological conditions is highly reproducible

Both ordered fibrils and disordered aggregates can be reliably formed

αB-crystallin specifically inhibits amyloid fibril assembling, favouring disordered aggregates

eTOC blurb

Mülleret al.introduce a protocol for the highly reproducible production of amyloid from native Aβ(1-40) and determine that the human chaperone ABC specifically destabilises them in favour of disordered aggregates. NMR shows that ABC can distinguish between aggregate morphologies.

Graphical Abstract
A chloride efflux transporter OsBIRG1 regulates grain size and salt tolerance in rice
Authors: Ren Zhijie , Bai Fenglin , Xu Jingwen , Wang Li , Wang Xiaohan , Zhang Qian , Feng Changxin , Niu Qi , Zhang Liying , Li Mengou , Song Jiali , Bao Fang , Liu Liangyu , He Yikun , Ma Ligeng , Qiu Jinlong , Tian Wang , Hou Congcong , Li Legong
Published: March 2021

Grain size is determined by the number of cells and cell size of the grain. Regulation of grain size is crucial for improving crop yield. However, the genes and underlying molecular mechanisms controlling grain size remain elusive. Here we report a member of Detoxification efflux carrier (DTX)/Multidrug and Toxic Compound Extrusion (MATE) family transporter,BIGRICEGRAIN 1 (BIRG1), negatively regulates the grain size in rice.BIRG1is highly expressed in reproductive organs and roots. Inbirg1grain, the size of the outer parenchyma layer cells of spikelet hulls is noticeably larger but the cell number is not altered compared with that in the wild-type (WT) grain. When expressed inXenopusoocytes, BIRG1 exhibits chloride efflux activity. In line with the role of BIRG1 in mediating chloride efflux, thebirg1mutant shows reduced tolerance to salt stress under which the chloride level is toxic. Moreover, thebirg1grains contain higher level of chloride compared to WT grains when grown under normal paddy field. Thebirg1roots accumulate more chloride than those of WT under saline condition. Collectively, our findings suggest that BIRG1 functions as a chloride efflux transporter regulating grain size and salt tolerance via controlling chloride homeostasis in rice.
Hibernation slows epigenetic aging in yellow-bellied marmots
Authors: Pinho Gabriela M. , Martin Julien G. A. , Farrell Colin , Haghani Amin , Zoller Joseph A. , Zhang Joshua , Snir Sagi , Pellegrini Matteo , Wayne Robert K. , Blumstein Daniel T. , Horvath Steve
Published: March 2021

Species that hibernate live longer than would be expected based solely on their body size. Hibernation is characterized by long periods of metabolic suppression (torpor) interspersed by short periods of increased metabolism (arousal). The torpor-arousal cycles occur multiple times during hibernation, and it has been suggested that processes controlling the transition between torpor and arousal states cause aging suppression. Metabolic rate is also a known correlate of longevity, we thus proposed the ‘hibernation-aging hypothesis’ whereby aging is suspended during hibernation. We tested this hypothesis in a well-studied population of yellow-bellied marmots (Marmota flaviventer), which spend 7-8 months per year hibernating. We used two approaches to estimate epigenetic age: the epigenetic clock and the epigenetic pacemaker. Variation in epigenetic age of 149 samples collected throughout the life of 73 females were modeled using generalized additive mixed models (GAMM), where season (cyclic cubic spline) and chronological age (cubic spline) were fixed effects. As expected, the GAMM using epigenetic ages calculated from the epigenetic pacemaker was better able to detect nonlinear patterns in epigenetic age change over time. We observed a logarithmic curve of epigenetic age with time, where the epigenetic age increased at a higher rate until females reached sexual maturity (2-years old). With respect to circannual patterns, the epigenetic age increased during the summer and essentially stalled during the winter. Our enrichment analysis of age-related CpG sites revealed pathways related to development and cell differentiation, while the season-related CpGs enriched pathways related to central carbon metabolism, immune system, and circadian clock. Taken together, our results are consistent with the hibernation-aging hypothesis and may explain the enhanced longevity in hibernators.
Long-term clinical, virological and immunological outcomes in patients hospitalized for COVID-19: antibody response predicts long COVID
Authors: García-Abellán Javier , Padilla Sergio , Fernández-González Marta , García José A. , Agulló Vanesa , Andreo María , Ruiz Sandra , Galiana Antonio , Gutiérrez Félix , Masiá Mar
Published: March 2021

Objective

Long-term data following SARS-CoV-2 infection are limited. We aimed to characterize the medium and long-term clinical, virological, and immunological outcomes after hospitalization for COVID-19, and to identify predictors of long-COVID.

Methods

Prospective, longitudinal study conducted in COVID-19 patients confirmed by RT-PCR. Serial blood and nasopharyngeal samples (NPS) were obtained for measuring SARS-CoV-2 RNA and S-IgG/N-IgG antibodies during hospital stay, and at 1, 2 and 6 months post-discharge. Genome sequencing was performed where appropriate. Patients filled out a COVID19-symptom-questionnaire (CSQ) at 2-month and 6-month visits, and those with highest scores were characterized.

Results

Of 146 patients (60% male, median age 64 years) followed-up, 20.6% required hospital readmission and 5.5% died. At 2-months and 6-months, 9.6% and 7.8% patients, respectively, reported moderate/severe persistent symptoms. SARS-CoV-2 RT-PCR was positive in NPS in 11.8% (median Ct=38) and 3% (median Ct=36) patients at 2-months and 6-months, respectively, but no reinfections were demonstrated.

Antibody titers gradually waned, with seroreversion occurring at 6 months in 27 (27.6%) patients for N-IgG and in 6 (6%) for S-IgG. Adjusted 2-month predictors of the highest CSQ scores (OR [95%CI]) were lower peak S-IgG (0.80 [0.66-0.94]) and higher WHO-severity-score (2.57 [1.20-5.86]); 6-month predictors were lower peak S-IgG (0.89 [0.79-0.99]) and female sex (2.41 [1.20-4.82]); no association was found with prolonged viral shedding.

Conclusions

Late clinical events and persistent symptoms in the medium and long term occurred in a significant proportion of patients hospitalized for COVID-19. Gender, severity of illness and weaker antibody responses, but not viral shedding, were associated with long-COVID.

This study characterizes the long-term clinical, virological, and immunological outcomes following COVID-19 hospitalization. We found a significant proportion of late clinical events and persistent symptoms. Gender, severity of illness and weaker antibody responses, but not viral shedding, predicted long-COVID.
BCOR and BCORL1 mutations disrupt PRC1.1 repressive function in leukemia by unlinking the RING-PCGF1 enzymatic core from target genes
Authors: Schaefer Eva J. , Wang Helen C. , Meyer Clifford A. , Cejas Paloma , Gearhart Micah D. , Adelman Emmalee R. , Fares Iman , Apffel Annie , Lim Klothilda , Xie Yingtian , Gibson Christopher J. , Schenone Monica , Murdock H. Moses , Wang Eunice S. , Gondek Lukasz P. , Carroll Martin P. , Vedula Rahul S. , Winer Eric S. , Garcia Jacqueline S. , Stone Richard M. , Luskin Marlise R. , Carr Steven A. , Long Henry W. , Bardwell Vivian J. , Figueroa Maria E. , Lindsley R. Coleman
Published: March 2021

BCOR and its paralog BCORL1 encode subunits of the Polycomb repressive complex 1.1 (PRC1.1) and are recurrently mutated in myeloid malignancies. We show that leukemia-associated BCOR/BCORL1 mutations unlink the PRC1.1 RING-PCGF enzymatic core from the KDM2B-containing chromatin targeting auxiliary subcomplex, either by causing complete protein loss or expression of a C-terminally truncated protein lacking the PCGF Ub-like fold discriminator (PUFD) domain. By uncoupling PRC1.1 repressive function from target genes, BCOR/BCORL1 mutations activate aberrant cell signaling programs that confer acquired resistance to treatment. This study provides a mechanistic basis for Polycomb repressive dysfunction as a key oncogenic driver in myeloid malignancies and identifies a potential strategy for targeted therapy in BCOR-mutated cancer.
Mitotic H3K9ac is controlled by phase-specific activity of HDAC2, HDAC3 and SIRT1
Authors: Gandhi Shashi , Mitterhoff Raizy , Rapoport Rachel , Farago Marganit , Greenberg Avraham , Hodge Lauren , Eden Sharon , Benner Christopher , Goran Alon , Simon Itamar
Published: March 2021

Histone acetylation levels are reduced during mitosis. To study the mitotic regulation of H3K9ac we used an array of inhibitors targeting specific histone deacetylases. We evaluated the involvement of the targeted enzymes in regulating H3K9ac during all mitotic stages by immunofluorescence and immunoblots. We identified HDAC2, HDAC3 and SIRT1 as modulators of H3K9ac mitotic levels. HDAC2 inhibition increased H3K9ac levels in prophase, whereas HDAC3 or SIRT1 inhibition increased H3K9ac levels in metaphase. Next, we performed ChIP-seq on mitotic-arrested cells following targeted inhibition of these histone deacetylases. We found that both HDAC2 and HDAC3 have a similar impact on H3K9ac, and inhibiting either of these two HDACs substantially increases the levels of this histone acetylation in promoters, enhancers and insulators. Altogether, our results support a model in which H3K9 deacetylation is a stepwise process – at prophase HDAC2 modulates most transcription-associated H3K9ac-marked loci and at metaphase HDAC3 maintains the reduced acetylation, whereas SIRT1 potentially regulates H3K9ac by impacting HAT activity.

Summary blurb

Combination of immunofluorescence, western blot and ChIP-seq revealed the interplay between HDAC2, HDAC3 and SIRT1 in H3K9 deacetylation during mitosis of mammalian cells.
Domain dependent orchestrated regulation of bacterial growth, persistence and chemotaxis by an essential GTPase, CgtA, inVibrio cholerae
Authors: Das Sagarika , Datta Partha P.
Published: March 2021

CgtA, an evolutionarily conserved GTPase, associated with the 50S ribosome controls a broad spectrum of physiological processes in bacteria. It has three structural domains, viz., N-terminal domain (NTD), GTPase domain and C-terminal domain (CTD). CgtA regulates expression of several of genes during nutritional stress inVibrio cholerae. The mechanism of transcriptional regulation by CgtA is unknown, though the NTD concomitantly with the GTPase domain participates in the process. Here, we show that thein vivodeletion of the 57 amino acids long CTD of CgtA GTPase ofV. choleraeis dispensable for viability, contrary to the complete knockdown ofcgtAgene. Slower growth was observed incgtAknockdown strain with intermittent diauxic lags in minimal media than the CTD deleted strain. Irreversible defect in colony morphology was observed in the cells with CTD deletion. Resuscitation of persister cells occurred when nutritionally deprived completecgtAknockdown cells after growing for longer periods were transferred to nutritionally enriched media. The motility of thecgtAknockdown strain was significantly reduced than the wild type cells. Furthermore, CTD deleted cells were also found to be defective in motility, but comparatively lower thancgtAknockdown cells. Elongated and slenderV. choleraecells were observed by SEM imaging uponcgtAdepletion, whereas, upon CTD deletion cellular elongation did not occur. Based on our study here, we propose that the CTD of CgtA perceives the nutritional stress response, to which the NTD and GTPase responds.
Efficient graphene oxide coating improves cryo-EM sample preparation and data collection from tilted grids
Authors: Patel Avinash , Toso Daniel , Litvak Audrey , Nogales Eva
Published: March 2021

Recent technical developments have made single particle cryo-EM a major structural biology technique, especially in the characterization of challenging samples that resist crystallization, can only be obtained in small amounts, or suffer from compositional or conformational heterogeneity. However, a number of hurdles that often challenge sample preparation still need to be overcome in order to increase the applicability and throughput of cryo-EM. These technical hurdles include obtaining enough particles per image, with close to random orientation, and without damage from interaction with the air-water interface. While coating EM grids with graphene oxide is a promising procedure for the improvement of sample preparation, it suffers from some technical problems that limit its applicability. We have modified the established drop cast method for adhering graphene oxide onto holey patterned grids to increase graphene coverage. Our method relies on the use of a polycationic polymer to coat the surface of the grid prior to graphene oxide application, thereby preventing the repulsion of the negatively charged graphene oxide sheets from the negatively charged grid surface. With this improved preparation method, we show that graphene oxide supports can increase the number of particles in the field of view by an order of magnitude with respect to open holes, while keeping them away from the damaging air-water interface. We also show how graphene oxide coated gold foil grids can be used to collect tilted cryo-EM data in order to overcome preferred orientation issues, without experiencing the large amount of drift observed with conventional amorphous carbon supports, thus allowing data collection that can lead to high-resolution reconstructions.
A rapid CRISPR competitive assay forin vitroandin vivodiscovery of potential drug targets affecting the hematopoietic system
Authors: Shen Yunbing , Jiang Long , Iyer Vaishnavi Srinivasan , Raposo Bruno , Boddul Sanjay V. , Kasza Zsolt , Wermeling Fredrik
Published: March 2021

CRISPR/Cas9 can be used as an experimental tool to inactivate genes in cells. However, a CRISPR-targeted cell population will not show a uniform genotype of the targeted gene. Instead, a mix of genotypes is generated - from wild type to different forms of insertions and deletions. Such mixed genotypes complicate analyzing the role of the targeted gene in the studied cell population. Here, we present a rapid experimental approach to functionally analyze a CRISPR-targeted cell population that does not involve generating clonal cell lines. As a simple readout, we leverage the CRISPR-induced genetic heterogeneity and use sequencing to identify how different genotypes are enriched or depleted related to the studied cellular behavior or phenotype. The approach uses standard PCR, Sanger sequencing, and a simple sequence deconvoluting software, enabling laboratories without specific in-depth knowledge to also perform these experiments. As proof of principle, we present examples studying the role of different genes for various aspects related to hematopoietic cells (T cell developmentin vivoand activationin vitro, macrophage phagocytosis, and a leukemia-like phenotype induced by overexpressing a proto-oncogene). In conclusion, we present a rapid experimental approach to identify potential drug targets related to mature immune cells, as well as normal and malignant hematopoiesis.

Highlights

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CRISPR generates genetic heterogeneity at the targeted site.

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Genetic heterogeneity complicates identifying the role of a targeted gene.

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Heterogeneity can be quantified by Sanger sequencing with sufficient sensitivity.

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Enrichment of specific genotypes can be used to identify roles for targeted genes.

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Competitive experiments show the potential of genotype enrichment as a discovery tool.

Graphical representation
Control of Parallel Hippocampal Output Pathways by Amygdalar Long-Range Inhibition
Authors: AlSubaie Rawan , Wee Ryan W S , Ritoux Anne , Mishchanchuk Karyna , Passlack Jessica , Regester Daniel , MacAskill Andrew F
Published: March 2021

Projections from the basal amygdala (BA) to the ventral hippocampus (vH) are proposed to provide information about the rewarding or threatening nature of learned associations to support appropriate goal-directed and anxiety-like behaviour. Such behaviour occurs via the differential activity of multiple, parallel populations of pyramidal neurons in vH that project to distinct downstream targets, but the nature of BA input and how it connects with these populations is unclear. Using channelrhodopsin-2-assisted circuit mapping in mice, we show that BA input to vH consists of both excitatory and inhibitory projections. Excitatory input specifically targets BA- and nucleus accumbens-projecting vH neurons, and avoids prefrontal cortex-projecting vH neurons; while inhibitory input preferentially targets BA-projecting neurons. Through this specific connectivity, BA inhibitory projections gate place-value associations by controlling the activity of nucleus accumbens-projecting vH neurons. Our results define a parallel excitatory and inhibitory projection from BA to vH that can support goal-directed behaviour.
Is galactose a hormetic sugar? Evidence from rat hippocampal redox regulatory network
Authors: Homolak J , Babic Perhoc A , Knezovic A , Kodvanj I , Virag D , Osmanovic Barilar J , Riederer P , Salkovic-Petrisic M
Published: March 2021

Galactose is a ubiquitous simple monosaccharide with yet incompletely understood biochemical and physiological role. Most of what we currently know about galactose is based on induction from the research on inherited disorders of galactose metabolism and animal models that exploit galactose-induced oxidative stress to model aging in rodents, however, recent evidence also demonstrates unique properties of galactose to conserve cellular function during the periods of starvation, and prevent and alleviate cognitive deficits in a rat model of sporadic Alzheimer’s disease. Here, we try to understand the molecular background of both detrimental and beneficial effects of galactose by exploring the acute systemic and hippocampal biochemical changes upon oral administration of galactose solution focusing primarily on the components of the redox regulatory network (RRN). Although orogastric gavage of galactose solution (200 mg/kg) was insufficient to induce systemic RRN disbalance in the first two hours upon administration, analysis of hippocampal RRN revealed a mild pro-oxidative shift accompanied by a paradoxical increase in tissue reductive capacity, suggesting overcompensation of endogenous antioxidant systems in the response to the pro-oxidative stimulus. The more thorough analysis revealed that galactose-induced increment of reductive capacity was accompanied by inflation of the hippocampal pool of nicotinamide adenine dinucleotide phosphates indicating ROS detoxification through disinhibition of the oxidative pentose phosphate pathway flux, reduced neuronal activity, and upregulation of Leloir pathway gatekeeper enzyme galactokinase-1. Based on the observed findings, and in the context of previous work on galactose, we propose a hormetic hypothesis of galactose action suggesting that the protective effects of galactose might be inseparable from its pro-oxidative effects at the biochemical level.
The conflict between social role expectations and entrepreneurial role demands among women entrepreneurs in sub-Saharan Africa: empirical study from Ethiopia
Authors: Mulu Hundera , Duysters Geert , Naudé Wim , Dijkhuizen Josette
Published: March 2021

Purpose

The purpose of this paper is to develop items for measuring the role conflict between social role expectations (SREs) and entrepreneurial role demands (ERDs) among women entrepreneurs in sub-Saharan Africa (SSA).

Design/methodology/approach

This paper uses 20 interviews and literature from SSA to develop items, a survey of 408 to conduct factor analysis and a survey of 307 to conduct criterion validity analysis.

Findings

Statistical analysis shows that the scales used adequately captured two dimensions of SRE and ERD conflict: SRE-to-ERD conflict and ERD-to-SRE conflict. It was found that the SRE-to-ERD-conflict scale is reliable and valid with the five dimensions of entrepreneurial success and that women entrepreneur’s experience significant role conflict between SREs and ERDs.

Research limitations/implications

The implication is that standard scales measuring work and family conflict, which tend to focus solely on the work and family context, cannot adequately account for role conflict among women entrepreneurs.

Practical implications

The practical implications of these findings are discussed.

Originality/value

New scale items form measuring the conflict between SREs and ERDs were developed.
Crowd-shipping for urban food rescue logistics
Authors: Mittal Anuj , Oran Gibson Nilufer , Krejci Caroline C. , Marusak Amy Ann
Published: March 2021

Purpose

The purpose of this research is to gain a better understanding of how a crowd-shipping platform can achieve a critical mass of senders and carrier crowd members to yield network effects that are necessary for the platform to grow and thrive. Specifically, this research studies the participation decisions of both senders and carriers over time and the impacts of the resulting feedback loop on platform growth and performance.

Design/methodology/approach

An agent-based model is developed and used to study dynamic behavior and network effects within a simulated crowd-shipping platform. The model allows both carriers and senders to be represented as autonomous, heterogeneous and adaptive agents, whose decisions to participate in the platform impact the participation of other agents over time. Survey data inform the logic governing agent decisions and behaviors.

Findings

The feedback loop created by individual sender and carrier agents' participation decisions generates complex and dynamic network effects that are observable at the platform level. Experimental results demonstrate the importance of having sufficient crowd carriers available when the platform is initially launched, as well as ensuring that sender and carrier participation remains balanced as the platform grows over time.

Research limitations/implications

The model successfully demonstrates the power of agent-based modeling (ABM) in analyzing network effects in crowd-shipping systems. However, the model has not yet been fully validated with data from a real-world crowd-shipping platform. Furthermore, the model's geographic scope is limited to a single census tract. Platform behavior will likely differ across geographic regions, with varying demographics and sender/carrier density.

Practical implications

The modeling approach can be used to provide the manager of a volunteer-based crowd-shipping program for food rescue with insights on how to achieve a critical mass of participants, with an appropriate balance between the number of restaurant food donation delivery requests and the number of crowd-shippers available and willing to make those deliveries.

Social implications

This research can help a crowd-shipping platform for urban food rescue to grow and become self-sustainable, thereby serving more food-insecure people.

Originality/value

The model represents both senders and the carrier crowd as autonomous, heterogeneous and adaptive agents, such that network effects resulting from their interactions can emerge and be observed over time. The model was designed to study a volunteer crowd-shipping platform for food rescue, with participant motivations driven by personal values and social factors, rather than monetary incentives.
A framework for the relationship implications of additive manufacturing (3D printing) for industrial marketing: servitization, sustainability and customer empowerment
Authors: Chaney Damien , Gardan Julien , De Freyman Julien
Published: March 2021

Purpose

The purpose of this paper is to present the relationship implications of additive manufacturing (AM), which has the ability to produce layer-by-layer three-dimensional complex products by adding material in comparison to traditional manufacturing processes which remove material – for industrial marketing.

Design/methodology/approach

After presenting the literature on customer relationships and digital technologies in business-to-business, the study uses a “zoom-out” and “zoom-in” perspective to review the extant literature on AM and then makes study propositions for industrial marketing.

Findings

Through the adoption of AM technologies, the study suggests that firms can improve their level of servitization through customized products, offer more sustainable value propositions and empower their customers through the sale of digital files, which can be considered as levers to strengthen relationships with customers.

Research limitations/implications

This paper makes several propositions regarding the relationship implications of AM for industrial marketing that further research should test.

Practical implications

This paper highlights the relational benefits that adopting AM may represent for companies.

Originality/value

While AM which is considered as an industrial revolution has generated a wide body of research in engineering and operations and technology management sciences, its impact on industrial marketing remains understudied.
Exploring frontliners' knowledge, participation and evaluation in the implementation of a pay-for-performance program (PMAQ) in primary health care in Brazil
Authors: Saddi Fabiana da Cunha , Harris Matthew , Parreira Fernanda Ramos , Pêgo Raquel Abrantes , Coelho Germano Araujo , Lozano Renata Batista , Mundim Pedro dos Santos , Peckham Stephen
Published: March 2021

Purpose

This paper employs implementation theory and the political literature on performance measurement to understand how frontline health workers know, participate and evaluate the Brazilian National Program for Improving Access and Quality of Primary Care (PMAQ, 2nd round).

Design/methodology/approach

This paper develops an implementation theory-driven qualitative analysis. The research is developed in the city of Goiania (Brazil): a challenging organizational context in primary care (PHC). Interviews were carried out with 25 frontliners – managers, doctors, nurses and community health workers. Data were thematically and hierarchically analysed according to theoretical concepts such as policy knowledge, policy adherence, forms of accountability, alternative logics, organizational capacity and policy feedback.

Findings

Results show the need to foster organizational capacity, knowledge, participation and policy feedback at the frontline. Successful implementation would require those adaptations to counteract policy challenges/failures or the emergence of alternative logics.

Research limitations/implications

The study was conducted in only one setting, however, our sample includes different types of professionals working in units with different levels of organization capacity, located in distinct HDs, expressing well the implementation of PMAQ/P4P. Qualitative researches need to be developed for further exploring the same/other factors.

Social implications

Findings can be used to improve discussions/planning and design of P4P programs in the city and State of Goias.

Originality/value

The majority of analysis of PMAQ are of a quantitative or results-based nature. This article focuses on politically significant and unanswered questions regarding the implementation of PMAQ.
The experience of speech–language therapists and audiologists when delivering bad news: A qualitative analysis
Authors: Gold Rinat , Gold Azgad
Published: March 2021

Background

As part of their professional responsibilities, speech–language therapists and audiologists are required to deliver bad news.

Aims

The aim of this qualitative study is to describe and characterize the subjective experience of speech–language therapists and audiologists when delivering bad news to clients or their family members.

Methods & Procedures

A group of 156 speech–language therapists and audiologists replied in writing to an open question asking them to describe a clinical encounter in which they delivered bad news. The texts that were generated in response to this question served as a data base. Qualitative content analysis was used to analyse data and generate themes.

Outcomes & Results

Thematic analysis of participants’ texts revealed the challenges inherent to the delivery of bad news. Four main themes emerged from text analysis: difficulty in phrasing the news; the deliverer's emotional experience; the receiver's reaction; and being alone or in companion with another healthcare provider during the delivery of the bad news.

Conclusions & Implications

Speech–language therapists and audiologists experience difficulties similar to those experienced by other healthcare professionals when delivering bad news. Nevertheless, speech–language therapists and audiologists seem to perceive the delivery of bad news situation in a broader sense than the conventional definition given to this term in the medical arena.

What this paper adds

What is already known on the subject

The task of delivering bad news is stressful to healthcare professionals. Most of the literature on the topic pertains to physicians. Little is known regarding the delivery of bad news in speech–language therapy and audiology.

What this paper adds to existing knowledge

This study highlights the challenges that speech–language therapists and audiologists encounter when delivering bad news. Furthermore, it illuminates the implicit perceptions of these professionals regarding what is considered ‘bad news’.

What are the potential or actual clinical implications of this work?

The emotional challenges associated with the delivery of bad news underscore the importance of support and training regarding the delivery of bad news. It is especially important to prepare for a client's difficult questions, and to prefer a collaborative approach to the delivery of bad news.