bluuebunny/crossref_metadata_2025 huggingface dataset:
Increased activity of IRE1 improves the clinical presentation of EAE
Authors: Bracchi‐Ricard Valerie , Nguyen Kayla , Ricci Daniela , Gaudette Brian , Henao‐Mejia Jorge , Brambilla Roberta , Martynyuk Tetyana , Gidalevitz Tali , Allman David , Bethea John R. , Argon Yair
Published: November 2023

Activation of the endoplasmic reticulum (ER) stress sensor inositol‐requiring enzyme‐1α (IRE1α) contributes to neuronal development and is known to induce neuronal remodeling in vitro and in vivo. On the contrary, excessive IRE1 activity is often detrimental and may contribute to neurodegeneration. To determine the consequences of increased activation of IRE1α, we used a mouse model expressing a C148S variant of IRE1α with increased and sustained activation. Surprisingly, the mutation did not affect the differentiation of highly secretory antibody‐producing cells but exhibited a beneficial effect in a mouse model of experimental autoimmune encephalomyelitis (EAE). Although mechanical allodynia was unaffected, significant improvement in motor function was found in IRE1C148S mice with EAE relative to wild type (WT) mice. Coincident with this improvement, there was reduced microgliosis in the spinal cord of IRE1C148S mice, with reduced expression of proinflammatory cytokine genes. This was accompanied by reduced axonal degeneration and enhanced 2',3'‐cyclic nucleotide 3'‐phosphodiesterase (CNPase) levels, suggesting improved myelin integrity. Interestingly, while the IRE1C148S mutation is expressed in all cells, the reduction in proinflammatory cytokines and in the microglial activation marker ionized calcium‐binding adapter molecule (IBA1), along with preservation of phagocytic gene expression, all point to microglia as the cell type contributing to the clinical improvement in IRE1C148S animals. Our data suggest that sustained increase in IRE1α activity can be beneficial in vivo, and that this protection is cell type and context dependent. Considering the overwhelming but conflicting evidence for the role of ER stress in neurological diseases, a better understanding of the function of ER stress sensors in physiological contexts is clearly needed.
Levels of Albumin and Impact on Loop Diuretic and Albumin Co-administration in Heart Failure
Authors: Lai Megan , Lam Jade C. , Radosevich John J. , Patanwala Asad E. , Vijayakrishnan Rajakrishnan
Published: November 2023

Management of heart failure (HF) requires the use of loop diuretics to relieve congestion and improve symptoms. When loop diuretics alone fail to induce adequate diuresis, albumin has been proposed to enhance loop diuretic delivery and promote redistribution of fluid for excretion by the kidneys. Despite the theoretical benefits of albumin, studies suggesting its benefit in HF are scarce and the co-administration of loop diuretics and albumin remains controversial. This retrospective, observational study evaluated patients with HF 18 years or older who received concomitant intravenous loop diuretic and albumin administration. The primary objective was to evaluate the association of serum albumin level with urine output (UOP) in hospitalized patients with HF who received concomitant albumin and loop diuretic therapy. Secondary endpoints included total weight loss after 72 hours, and ICU and hospital lengths of stay. In total, 276 patients were included for analysis. There was no association between initial serum albumin level and 72-hour UOP (coefficient −623.1, 95% confidence interval −1558.6 to 312.4; P = 0.191) or weight difference at 72 hours (coefficient −1.0, 95% confidence interval −2.4 to 0.3; P = 0.131). Lower albumin levels were associated with longer ICU (P = 0.034) and hospital (P = 0.039) lengths of stay. Concomitant thiazide diuretic use and increasing loop diuretic doses were associated with increased 72-hour UOP. The results of our study suggests that providers should avoid using baseline albumin levels as guidance for albumin dosing in HF. Given the lack of comparator groups, larger randomized controlled trials should be done to provide a definitive role for albumin to enhance diuresis in patients with HF on intravenous loop diuretics.
Anatomic Anomalies of the Nerves Treated during Headache Surgery
Authors: Peled Ziv M. , Gfrerer Lisa , Hagan Rob , Al-Kassis Salam , Savvides Georgia , Austen Gerald , Valenti Alyssa , Chinta Malini
Published: November 2023

Background:

Headache surgery is a well-established, viable option for patients with chronic head pain/migraines refractory to conventional treatment modalities. These operations involve any number of seven primary nerves. In the occipital region, the surgical targets are the greater, lesser, and third occipital nerves. In the temporal region, they are the auriculotemporal and zygomaticotemporal nerves. In the forehead, the supraorbital and supratrochlear are targeted. The typical anatomic courses of these nerves are well established and documented in clinical and cadaveric studies. However, variations of this “typical” anatomy are quite common and relatively poorly understood. Headache surgeons should be aware of these common anomalies, as they may alter treatment in several meaningful ways.

Methods:

In this article, we describe the experience of five established headache surgeons encompassing over 4000 cases with respect to the most common anomalies of the nerves typically addressed during headache surgery. Descriptions of anomalous nerve courses and suggestions for management are offered.

Results:

Anomalies of all seven nerves addressed during headache operations occur with a frequency ranging from 2% to 50%, depending on anomaly type and nerve location. Variations of the temporal and occipital nerves are most common, whereas anomalies of the frontal nerves are relatively less common. Management includes broader dissection and/or transection of accessory injured nerves combined with strategies to reduce neuroma formation such as targeted reinnervation or regenerative peripheral nerve interfaces.

Conclusions:

Understanding these myriad nerve anomalies is essential to any headache surgeon. Implications are relevant to preoperative planning, intraoperative dissection, and postoperative management.
Mediators of Visual Acuity in Descemet Membrane Endothelial Keratoplasty and Ultrathin Descemet Stripping Automated Endothelial Keratoplasty
Authors: Lin Charles C. , Chamberlain Winston D. , Kakigi Caitlin , Arnold Benjamin F. , Rose-Nussbaumer Jennifer
Published: November 2023

Purpose:

The aim of this study was to investigate mediators of visual acuity in ultrathin Descemet stripping automated endothelial keratoplasty (UT-DSAEK) compared with Descemet membrane endothelial keratoplasty (DMEK).

Methods:

This was a prespecified secondary analysis of the Descemet Endothelial Thickness Comparison Trial, a prospective, randomized controlled trial comparing UT-DSAEK with DMEK. Subjects with Fuchs endothelial dystrophy or pseudophakic bullous keratopathy presenting to 2 academic centers were enrolled and randomized to either UT-DSAEK (n = 25 eyes) or DMEK (n = 25 eyes). Higher order aberrations (HOAs) and corneal densitometry were measured with Pentacam Scheimpflug imaging at 3, 6, 12, and 24 months.

Results:

The posterior corneal surface at the 6.0-mm optical zone had significantly less total HOAs (P <0.001) in the DMEK group compared with UT-DSAEK at 24 months. Anterior and posterior corneal densitometry improved from baseline to 24 months for both UT-DSAEK and DMEK, but there was no significant difference between the 2 groups. Corneal densitometry and posterior HOAs were both associated with best-corrected visual acuity (P <0.05). DMEK had 1.3 logarithm of the minimum angle of resolution better visual acuity compared with UT-DSAEK at 24 months. Approximately 64% of this effect was mediated through posterior HOAs, whereas none was mediated through anterior HOAs or densitometry.

Conclusions:

Decreased posterior HOAs mediate better visual acuity and account for improved vision after DMEK compared with UT-DSAEK. Corneal light scatter as measured by densitometry is similar between UT-DSAEK and DMEK, indicating that the increased thickness and stromal–stromal interface in UT-DSAEK do not significantly affect visual acuity.
Robotic pancreas surgery for pancreatic cancer
Authors: Hays Sarah B. , Rojas Aram E. , Hogg Melissa E.
Published: November 2023

Since the introduction of robotic pancreas surgery in the early 2000s, there has been significant increase in the adoption of the robot to perform complex pancreatic resections. However, utilization of the robot for pancreatic cancer has lagged behind due to concern for inferior oncologic outcomes. Furthermore, research in this field has previously been limited to small, single institution observational studies. Recent and ongoing randomized controlled trials in robotic distal pancreatectomy and robotic pancreatoduodenectomy have aimed to address concerns regarding the use of robotic techniques in pancreatic cancer. Together, these studies suggest similar, if not improved, outcomes with a robotic approach, including shorter hospital stays, expedited recovery with less postoperative complications, and equivalent resection rates, when compared to the standard open approaches. Additionally, surgical training in robotic pancreas surgery is of equal importance for patient safety. This review summarizes the available literature on the efficacy and safety of robotic pancreas surgery for pancreatic cancer, with specific focus on robotic distal pancreatectomy and robotic pancreatoduodenectomy.
Preferred reporting of case series in surgery (PROCESS) 2023 guidelines
Authors: Mathew Ginimol , Sohrabi Catrin , Franchi Thomas , Nicola Maria , Kerwan Ahmed , Agha Riaz ,   PROCESS Group
Published: November 2023

Introduction:

The PROCESS guidelines were developed in 2016 in order to improve the reporting quality of surgical case series. Since its inception, it has been updated twice, in 2018 and 2020, and has been cited over 1000 times. PROCESS guidelines have enjoyed great acceptance within the surgical research community. Our aim is to update the PROCESS guidelines in order to maintain its applicability in the field of surgical research.

Methods:

A PROCESS 2023 steering group was created. By working in collaboration, members of this group came up with proposals to update the PROCESS 2020 guidelines. These proposals were presented to an expert panel of researchers, who in turn scrutinised these proposals and decided whether they should become part of PROCESS 2023 guidelines or not, through a Delphi consensus exercise.

Results:

A total of 38 people participated in the development of PROCESS 2023 guidelines. The majority of items received a score between 7 and 9 from >70% of the participants, indicating consensus with the proposed changes to those items. However, two items (3c and 6a) received a score between 7 and 9 from <70% of the participants, indicating a lack of consensus with the proposed changes to those items. Those items will remain unchanged.

Discussion:

The updated PROCESS 2023 guidelines are presented with an aim to continue improving the reporting quality of case series in surgery.
Impact of Gonadotropin-Releasing Hormone agonist and hormone replacement therapy on pregnancy outcomes in single euploid frozen-thawed embryo transfer for patients with endometrial polyps
Authors: Zhao Qing , Li Jie , Wang Wei-Lin , Liu Ying-Bo , Li Jing , Ni Tian-Xiang , Zhou Wei , Zhang Qian , Yan Jun-Hao
Published: November 2023

Objective:

While consensus on the optimal endometrial preparation protocol for frozen-thawed embryo transfer (FET) is lacking, this is particularly true for patients with infertility and a history of endometrial polyps (EPs). In this study, we aimed to investigate whether a gonadotropin-releasing hormone agonist combined with hormone replacement therapy (GnRHa-HRT) could improve pregnancy outcomes in single euploid FET for patients with a history of EPs.

Methods:

In this retrospective cohort study, 395 women who underwent their first single euploid FET cycle were divided into groups according to endometrial preparation protocols as follows: natural cycle (NC) (n=220), hormone replacement therapy (HRT) (n=122), and GnRHa-HRT groups (n=53). Subsequently, the FET cycles in the three groups were subdivided according to maternal age. All patients underwent hysteroscopic polypectomy before FET, and their EPs were confirmed by pathology.

Results:

No statistically significant differences were observed in live birth rates among the three groups (58.64% vs. 58.20% vs. 56.60%, P=0.964). Furthermore, the rates of miscarriage, ectopic pregnancy, premature live birth, and pregnancy complications were comparable among the three groups (P >0.05). After adjusting for potential confounding factors, no significant differences in pregnancy outcomes were reported between the groups (adjusted odds ratios [OR] and 95% credible intervals [CI] for live birth rate, HRT vs. NC: 1.119, 0.660–1.896, P=0.677; GnRHa-HRT vs. NC: 1.165, 0.610–2.226, P=0.643). Additionally, the pregnancy outcomes of the FET cycle were not influenced by the endometrial preparation protocols in the subgroups when stratified by maternal age (P >0.05).

Conclusion:

GnRHa-HRT did not improve the pregnancy outcomes of the single euploid FET in patients with a history of EPs.
Whale shark residency and small-scale movements around oil and gas platforms in Qatar
Authors: Bach Steffen S. , Robinson David P. , Jaidah Mohammed Y. , Pierce Simon J. , Thoppil Prasad , Rohner Christoph A.
Published: November 2023

Artificial structures in the ocean can influence the movements and residency of migratory fishes. Whale sharks seasonally aggregate near oil and gas platforms in Qatar to feed on fish spawn, creating one of the largest aggregations for the species. We used passive acoustic telemetry to examine their fine-scale movements, residency, and seasonality and investigate whether the platforms influence their habitat use in the area. Tags had a mean retention of 161 ±186 SD days and 32 of the 117 tags were recorded in multiple seasons in the acoustic array (21 stations). Most detections were recorded during the season that was established with other methods from May to September, confirming that this whale shark aggregation is seasonal. Whale sharks stayed up to 77 consecutive days in the array (mean = 16 ± 12.51 days) and had a mean residency index Rmaxof 0.31, highlighting the importance of this site to their ecology. While most detections were made at a receiver near a platform, other platforms had few detections and the distance from the centre of the aggregation was the main explanatory variable in a GLM, indicating that the platforms do not influence the whale shark’s habitat use. Instead, they moved with the current during the morning, when they feed on fish eggs at the surface which also float with the current, and swam against the current in the late afternoon and at night to be at the presumed fish spawning site again in the early morning. Our results highlight the importance of this small feeding area for whale sharks which face a high threat level in the region.
Identification of mouse CD4+T cell epitopes in SARS-CoV-2 BA.1 spike and nucleocapsid for use in peptide:MHCII tetramers
Authors: Moreno Laura Bricio , de Albuquerque Juliana Barreto , Neary Jake M. , Nguyen Thao , Hastie Kathryn M. , Landeras-Bueno Sara , Hariharan Chitra , Nathan Anusha , Getz Matthew A. , Gayton Alton C. , Khatri Ashok , Gaiha Gaurav D. , Saphire Erica Ollmann , Luster Andrew D. , Moon James J.
Published: November 2023

Understanding adaptive immunity against SARS-CoV-2 is a major requisite for the development of effective vaccines and treatments for COVID-19. CD4+T cells play an integral role in this process primarily by generating antiviral cytokines and providing help to antibody-producing B cells. To empower detailed studies of SARS-CoV-2-specific CD4+T cell responses in mouse models, we comprehensively mapped I-Ab-restricted epitopes for the spike and nucleocapsid proteins of the BA.1 variant of concern via IFNγ ELISpot assay. This was followed by the generation of corresponding peptide:MHCII tetramer reagents to directly stain epitope-specific T cells. Using this rigorous validation strategy, we identified 6 reliably immunogenic epitopes in spike and 3 in nucleocapsid, all of which are conserved in the ancestral Wuhan strain. We also validated a previously identified epitope from Wuhan that is absent in BA.1. These epitopes and tetramers will be invaluable tools for SARS-CoV-2 antigen-specific CD4+T cell studies in mice.
Inositolphosphate glycans accumulate and suppress plant defense during Arabidopsis/Botrytis interaction
Authors: Lelas Luka , Rouffet Justine , Filachet Alexis , Sechet Julien , Akary Elodie , Desprez Thierry , Vernhettes Samantha , Voxeur Aline
Published: November 2023

This study investigates the presence and significance of previously undiscovered oligosaccharides that accumulate during the interaction betweenArabidopsis thalianaandBotrytis cinerea, a pathogenic fungus. Initially focused on characterizing cell wall-derived oligosaccharides, the research uncovered inositol phosphate glycans (IPGs) originating from plant sphingolipids, specifically glycosylinositol phosphorylceramides. Advanced chromatography, mass spectrometry techniques and molecular biology were employed to identify these IPGs, determine their origins, and study their role in theA. thaliana-B. cinereainteraction. Contrary to the conventional belief that oligosaccharides trigger plant defense, this research suggests thatB. cinereareleases IPGs identical to those generated by host plant to actually downregulate plant defense mechanisms. This discovery offers insight into the dynamic strategies used byB. cinereato evade plant defenses and establish successful infections.

One-Sentence Summary

A plant pathogen releases products identical to those generated by host plant that aids in evasion of the plant defense.
Germ fate determinants protect germ precursor cell division by restricting septin and anillin levels at the division plane
Authors: Connors Caroline Q. , Mauro Michael S. , Tristian Wiles J. , Countryman Andrew D. , Martin Sophia L. , Lacroix Benjamin , Shirasu-Hiza Mimi , Dumont Julien , Kasza Karen E. , Davies Timothy R. , Canman Julie C.
Published: November 2023

Animal cell cytokinesis, or the physical division of one cell into two, is thought to be driven by constriction of an actomyosin contractile ring at the division plane. The mechanisms underlying cell type-specific differences in cytokinesis remain unknown. Germ cells are totipotent cells that pass genetic information to the next generation. Previously, usingformincyk-1(ts)mutantC. elegansembryos, we found that the P2 germ precursor cell is protected from cytokinesis failure and can divide without detectable F-actin at the division plane. Here, we identified two canonical germ fate determinants required for P2-specific cytokinetic protection: PIE-1 and POS-1. Neither has been implicated previously in cytokinesis. These germ fate determinants protect P2 cytokinesis by reducing the accumulation of septinUNC-59and anillinANI-1at the division plane, which here act as negative regulators of cytokinesis. These findings may provide insight into cytokinetic regulation in other cell types, especially in stem cells with high potency.
Targeted micro-fiber arrays for measuring and manipulating localized multi-scale neural dynamics over large, deep brain volumes during behavior
Authors: Vu Mai-Anh T. , Brown Eleanor H. , Wen Michelle J. , Noggle Christian A. , Zhang Zicheng , Monk Kevin J. , Bouabid Safa , Mroz Lydia , Graham Benjamin M. , Zhuo Yizhou , Li Yulong , Otchy Timothy M. , Tian Lin , Davison Ian G. , Boas David A. , Howe Mark W.
Published: November 2023

Neural population dynamics relevant for behavior vary over multiple spatial and temporal scales across 3-dimensional volumes. Current optical approaches lack the spatial coverage and resolution necessary to measure and manipulate naturally occurring patterns of large-scale, distributed dynamics within and across deep brain regions such as the striatum. We designed a new micro-fiber array and imaging approach capable of chronically measuring and optogenetically manipulating local dynamics across over 100 targeted locations simultaneously in head-fixed and freely moving mice. We developed a semi-automated micro-CT based strategy to precisely localize positions of each optical fiber. This highly-customizable approach enables investigation of multi-scale spatial and temporal patterns of cell-type and neurotransmitter specific signals over arbitrary 3-D volumes at a spatial resolution and coverage previously inaccessible. We applied this method to resolve rapid dopamine release dynamics across the striatum volume which revealed distinct, modality specific spatiotemporal patterns in response to salient sensory stimuli extending over millimeters of tissue. Targeted optogenetics through our fiber arrays enabled flexible control of neural signaling on multiple spatial scales, better matching endogenous signaling patterns, and spatial localization of behavioral function across large circuits.
N-Glycans on the extracellular domain of the Notch1 receptor control Jagged-1 induced Notch signalling and myogenic differentiation of S100β resident vascular stem cells
Authors: Corcoran Eoin , Olayinka Abidemi , di Luca Mariana , Gusti Yusof , Hakimjavadi Roya , O’Connor Brendan , Redmond Eileen M. , Cahill Paul A.
Published: November 2023

Notch signalling, critical for development and postnatal homeostasis of the vascular system, is highly regulated by several mechanisms including glycosylation. While the importance of O-linked glycosylation is widely accepted, the structure and function of N-glycans has yet to be defined. Here, we take advantage of lectin binding assays in combination with pharmacological, molecular, and site-directed mutagenetic approaches to study N-glycosylation of the Notch1 receptor. We find that several key oligosaccharides containing bisecting or core fucosylated structures decorate the receptor, control expression and receptor trafficking, and dictate Jagged-1 activation of Notch target genes and myogenic differentiation of multipotent S100β vascular stem cells. N-glycans at asparagine (N) 1241 and 1587 protect the receptor from accelerated degradation, while the oligosaccharide at N888 directly affects signal transduction. Conversely, N-linked glycans at N959, N1179, N1489 do not impact canonical signalling but inhibit differentiation. Our work highlights a novel functional role for N-glycans in controlling Notch1 signalling and differentiation of vascular stem cells.

Teaser

A sweet development in Notch regulation of vascular smooth muscle cell differentiation
The coexistence of localized and distributed behavioral information in neural activity
Authors: Yadav Gaurang , Daniels Bryan C.
Published: November 2023

The degree to which control of an animal’s behavior is localized within particular neurons or distributed over large populations is central to understanding mechanisms of decision-making in brains. A first step in answering this question comes from understanding the scales at which neural activity is predictive of behavior. Here, we demonstrate how information measures at the individual, pairwise, and larger group levels characterize the localization of predictive information. We demonstrate these tools using high-dimensional neural data related to nematode and macaque behavioral decisions. Intriguingly, in both examples we find that similar behavioral information coexists across scales: the same information can be extracted from small groups of individually informative neurons or larger groups of randomly chosen neurons that individually have little predictive power. Our results suggest that methods for causal inference may miss potential causal pathways if they are biased toward finding localized control mechanisms.
Comparing neural models using their perceptual discriminability predictions
Authors: Zhou Jing Yang , Chun Chanwoo , Subramanian Ajay , Simoncelli Eero P.
Published: November 2023

Internal representations are not uniquely identifiable from perceptual measurements: different representations can generate identical perceptual predictions, and similar representations may predict dissimilar percepts. Here, we generalize a previous method (“Eigendistortions” – Berardino et al., 2017) to enable comparison of models based on their metric tensors, which can be verified perceptually. Metric tensors characterize sensitivity to stimulus perturbations, reflecting both the geometric and stochastic properties of the representation, and providing an explicit prediction of perceptual discriminability. Brute force comparison of model-predicted metric tensors would require estimation of human perceptual thresholds along an infeasibly large set of stimulus directions. To circumvent this “perceptual curse of dimensionality”, we compute and measure discrimination capabilities for a small set of most-informative perturbations, reducing the measurement cost from thousands of hours (a conservative estimate) to a single trial. We show that this single measurement, made for a variety of different test stimuli, is sufficient to differentiate models, select models that better match human perception, or generate new models that combine the advantages of existing models. We demonstrate the power of this method in comparison of (1) two models for trichromatic color representation, with differing internal noise; and (2) two autoencoders trained with different regularizers.
The impact of collective load transport on the individual walking
Authors: Sghaier N. , Pasquaretta C. , Turpin N A. , Moretto P.
Published: November 2023

Collective handling is a collaborative strategy that involves two or more people in carrying out load transport. Different positions can be adopted, depending on the handle locations of the transported load, external constraints and the capacities of the carriers. The most adopted collective transport in our daily life is stretcher type transport. However, very little research has focused on the kinematic modifications caused by this type of transport. This research aims to evaluate and quantify the modifications of the locomotor pattern of stretcher transport. Our results highlighted a modification of walking parameters (step length, duration of the walking cycle, speed of execution, etc.), an increase in energy cost but above all a modification of the walking pattern with a reduction in joint range of motion. These results could be used to establish new recommendations for musculoskeletal disorders.
Protein-lipid interactions drive presynaptic assembly upstream of cell adhesion molecules
Authors: Frankel Elisa B. , Tiroumalechetty Araven , Henry Parise S. , Su Zhaoqian , Wu Yinghao , Kurshan Peri T.
Published: November 2023

Textbook models of synaptogenesis position cell adhesion molecules such as neurexin as initiators of synapse assembly. Here we discover a mechanism for presynaptic assembly that occurs prior to neurexin recruitment, while supporting a role for neurexin in synapse maintenance. We find that the cytosolic active zone scaffold SYD-1 interacts with membrane phospholipids to promote active zone protein clustering at the plasma membrane, and subsequently recruits neurexin to stabilize those clusters. Employing molecular dynamics simulations to model intrinsic interactions between SYD-1 and lipid bilayers followed byin vivotests of these predictions, we find that PIP2-interacting residues in SYD-1’s C2 and PDZ domains are redundantly necessary for proper active zone assembly. Finally, we propose that the uncharacterized yet evolutionarily conserved short γ isoform of neurexin represents a minimal neurexin sequence that can stabilize previously assembled presynaptic clusters, potentially a core function of this critical protein.
Multiple Guidance Mechanisms Control Axon Growth to Generate Precise T-shaped Bifurcation during Dorsal Funiculus Development in the Spinal Cord
Authors: Curran Bridget M , Nickerson Kelsey R , Yung Andrea R , Goodrich Lisa V , Jaworski Alexander , Tessier-Lavigne Marc , Ma Le
Published: November 2023

The dorsal funiculus in the spinal cord relays somatosensory information to the brain. It is made of T-shaped bifurcation of dorsal root ganglion (DRG) sensory axons. Our previous study has shown that Slit signaling is required for proper guidance during bifurcation, but loss of Slit does not affect all DRG axons. Here, we examined the role of the extracellular molecule Netrin-1 (Ntn1). Using wholemount staining with tissue clearing, we showed that mice lacking Ntn1 have axons escaping from the dorsal funiculus at the time of bifurcation. Genetic labeling confirmed that these misprojecting axons come from DRG neurons. Single axon analysis showed that loss of Ntn1 does not affect bifurcation but rather alters turning angles. To distinguish their guidance functions, we examined mice with triple deletion of Ntn1, Slit1, and Slit2 and found a completely disorganized dorsal funiculus. Comparing mice with different genotypes using immunolabeling and single axon tracing revealed additive guidance errors, demonstrating the independent roles of Ntn1 and Slit. Moreover, the same defects were observed in embryos lacking their cognate receptors. Thesein vivostudies thus demonstrate the presence of multi-factorial guidance mechanisms that ensure proper formation of a common branched axonal structure during spinal cord development.
Minimum changes in sleep, physical activity, and nutrition associated with clinically important reductions in all-cause mortality risk: a prospective cohort study
Authors: Stamatakis Emmanuel , Koemel Nicholas A. , Biswas Raaj K. , Ahmadi Matthew N. , Allman-Farinelli Margaret , Trost Stewart G. , Eroglu Elif I. , Cruz Borja del Pozo , Bin Yu Sun , Postnova Svetlana , Simpson Stephen , Duncan Mitch , Dumuid Dorothea , Fontana Luigi , Brown Helen , Maher Carol , Cistulli Peter A.
Published: November 2023

Background

Sleep, physical activity, and nutrition (SPAN) are crucial modifiable factors for health, yet most research has examined them independently rather than exploring their combined and incremental impact on disease risk and mortality.

Objective

To determine the collective associations of SPAN exposures and establish clinically relevant targets for reducing all-cause mortality risk.

Methods

This study included 59,078 UK Biobank participants with valid wearable tracker and nutrition data (Median age [IQR]: 64.0 [7.8] years; 45.4% male). Sleep duration (hours/day) and moderate to vigorous physical activity duration (MVPA; mins/day) were calculated using a machine learning based wearable data schema. A 10-item diet quality score (DQS) assessed the consumption of vegetables, fruits, fish, dairy, whole grains, and vegetable oils, as well as lower intakes of refined grains, processed meats, unprocessed red meats, and sugar-sweetened beverages using a food frequency questionnaire. The DQS assigned values from 0-10 for each component, totalling 100 points, with higher values indicating higher diet quality. Associations with all-cause mortality were explored using Cox proportional hazard models with combinations of SPAN exposure tertiles.

Results

During the median 8.1-year follow-up period, 2,458 deaths occurred. MVPA exhibited the strongest overall effect on mortality risk, followed by sleep (with a U- shaped relationship), and diet quality. Compared to the referent group of combined SPAN exposure (lowest tertiles for all three behaviours), the optimal SPAN combination involving moderate sleep duration (7.2-8.0 hours/day), high MVPA (42-103 mins/day), and high DQS (57.5-72.5) was associated with a hazard ratio (HR) of 0.45 (95% CI: 0.37, 0.53). Relative to the 5th percentile of sleep (5.5 hours/day), physical activity (7.3 mins/day), and nutrition (36.9 DQS), a minimum increase of 15 mins/day of sleep, 1.6 min/day MVPA, and 5 DQS points was associated with a 10% reduction in all-cause mortality risk (HR: 0.90; 95% CI: 0.88, 0.93). Additionally, compared to the referent group, an additional 75 mins/day of sleep, 12.5 min/day MVPA, and 25 DQS points was associated with a 50% reduction in all-cause mortality risk (HR: 0.50; 95%CI: 0.44, 0.58).

Conclusion

These findings underscore the importance of combined incremental lifestyle modifications in reducing the risk of all-cause mortality.
16p11.2 Microduplication is Associated with Lobule-Specific Abnormalities in Cerebellar Structure and Function
Authors: Hayes Cessily , Halverson Hunter , Keeran Krisha , Tison Krislen , Jacobo Kamilla , Karki Asriya , Herring Isaias , Tunuguntla Swetha , Pace Martha , Doan Binh , Wen Hsiang , Klomp Annette , Lauffer Marisol , Gaine Marie E. , Parker Krystal , Williams Aislinn J.
Published: November 2023

The 16p11.2 microduplication (16p11.2dp/+) is associated with several neuropsychiatric disorders including schizophrenia, autism spectrum disorder, bipolar disorder, intellectual disability, and attention deficit/hyperactivity disorder (ADHD). Cerebellar abnormalities have been increasingly implicated in these neuropsychiatric disorders, including those conferred by 16p11.2 microduplication. In 16p11.2dp/+mouse models, the cerebellum is a site of transcriptional dysregulation, and cerebellar microcephaly has been reported in humans with 16p11.2 microduplication. Despite mounting evidence indicating a role for the cerebellum in neuropsychiatric disorders associated with this CNV, cerebellar cellular structure and cerebellar-dependent behavior in mice with 16p11.2 microduplication remain uncharacterized. To address this, we histologically labeled Purkinje cells (PCs) and molecular layer interneurons (MLIs) in a mouse model of 16p11.2 microduplication. We did not find any structural differences in cerebellar lobule IV/V, nor did we observe impairments in gait or motor coordination, behaviors that are associated with lobule IV/V. In contrast, we discovered a significant increase in calbindin/parvalbumin-positive PCs mislocalized to the granule layer of cerebellar lobule VI in 16p11.2dp/+mice compared to wild-type (WT) littermates. Additionally, we found a significant decrease in parvalbumin-positive MLIs without a decrease in total DAPI-positive cell counts in lobule VI of 16p11.2dp/+mice compared to WT littermates. Cerebellar lobule VI is associated with delay eyeblink conditioning, and 16p11.2dp/+mice are impaired in cerebellum-dependent associative learning on this task. Specifically, 16p11.2dp/+mice showed deficits in both conditioned response (CR) percentage and CR onset latency relative to WT mice. These results suggest that lobule VI–specific alterations to PC localization and MLI parvalbumin expression in 16p11.2dp/+mice impair both cerebellar learning and adaptive timing of cerebellar-driven, conditioned responses. Thus, we have identified novel structural and functional alterations in the cerebellum that are associated with 16p11.2 microduplication. Importantly, individuals with schizophrenia and ADHD also show CR acquisition deficits in delay eyeblink conditioning. Together, these data suggest that the behavioral impairments in 16p11.2dp/+mice resemble impairments seen in neuropsychiatric disorders linked to 16p11.2 microduplication in humans. Further investigation of cerebellar cortex neurons in 16p11.2dp/+mice may provide insights into the pathogenesis of neuropsychiatric disorders linked to this copy number variant.
Detecting Protein-DNA Binding in Single Molecules using Antibody Guided Methylation
Authors: Thatavarty Apoorva , Sagy Naor , Erdos Michael R , Lee Isac , Simpson Jared T , Timp Winston , Collins Francis S , Bar Daniel Z
Published: November 2023

Characterization of DNA binding sites for specific proteins is of fundamental importance in molecular biology. It is commonly addressed experimentally by chromatin immunoprecipitation and sequencing (ChIP-seq) of bulk samples (103-107cells). We have developed an alternative method that uses a Chromatin Antibody-mediated Methylating Protein (ChAMP) composed of a GpC methyltransferase fused to protein G. By tethering ChAMP to a primary antibody directed against the DNA-binding protein of interest, and selectively switching on its enzymatic activityin situ, we generated distinct and identifiable methylation patterns adjacent to the protein binding sites. This method is compatible with methods of single-cell methylation-detection and single molecule methylation identification. Indeed, as every binding event generates multiple nearby methylations, we were able to confidently detect protein binding in long single molecules.

Abstract Figure

Graphical abstract

(i) ChAMP is added to fix and permeabilized cells, where it binds (ii) any antibody, and upon the addition of SAM, methylates nearby GpC sites, to be detected by sequencing (iii-iv).
Transcriptional inhibition after irradiation occurs preferentially at highly expressed genes in a manner dependent on cell cycle progression
Authors: Chen Zulong , Wang Xin , Gao Xinlei , Arslanovic Nina , Chen Kaifu , Tyler Jessica
Published: November 2023

In response to DNA double strand damage, ongoing transcription is inhibited to facilitate accurate DNA repair while transcriptional recovery occurs after DNA repair is complete. However, the mechanisms at play and identity of the transcripts being regulated in this manner are unclear. In contrast to the situation following UV damage, we found that transcriptional recovery after ionizing radiation (IR) occurs in a manner independent of the HIRA histone chaperone. Sequencing of the nascent transcripts identified a programmed transcriptional response, where certain transcripts and pathways are rapidly downregulated after IR, while other transcripts and pathways are upregulated. Specifically, most of the loss of nascent transcripts occurring after IR is due to inhibition of transcriptional initiation of the highly transcribed histone genes and the rDNA. To identify factors responsible for transcriptional inhibition after IR in an unbiased manner, we performed a whole genome gRNA library CRISPR / Cas9 screen. Many of the top hits in our screen were factors required for protein neddylation. However, at short times after inhibition of neddylation, transcriptional inhibition still occurred after IR, even though neddylation was effectively inhibited. Persistent inhibition of neddylation blocked transcriptional inhibition after IR, and it also leads to cell cycle arrest. Indeed, we uncovered that many inhibitors and conditions that lead to cell cycle arrest in G1or G2phase also prevent transcriptional inhibition after IR. As such, it appears that transcriptional inhibition after IR occurs preferentially at highly expressed genes in cycling cells.
Volume Electron Microscopy Reveals Unique Laminar Synaptic Characteristics in the Human Entorhinal Cortex
Authors: Plaza-Alonso Sergio , Cano-Astorga Nicolás , DeFelipe Javier , Alonso-Nanclares Lidia
Published: November 2023

The entorhinal cortex (EC) plays a pivotal role in memory function and spatial navigation, connecting the hippocampus with the neocortex. The EC integrates a wide range of cortical and subcortical inputs, but its synaptic organization in the human brain is largely unknown. We used volume electron microscopy to perform a 3D analysis of the microanatomical features of synapses in all layers of the medial EC (MEC) from the human brain. Using this technology, 12,974 synapses were fully 3D reconstructed at the ultrastructural level. The MEC presented a distinct set of synaptic features, differentiating this region from other human cortical areas. Furthermore, ultrastructural synaptic characteristics within the MEC was predominantly similar, although layers I and VI exhibited several synaptic characteristics that were distinct from other layers. The present study constitutes an extensive description of the synaptic characteristics of the neuropil of all layers of the EC, a crucial step to better understand the connectivity of this cortical region, in both health and disease.
Localized oxygen control in a microfluidic osteochondral interface model recapitulates bone-cartilage crosstalk during osteoarthritis
Authors: Ong Louis Jun Ye , Sun Antonia Rujia , Wang Zhongzheng , Lee Jayden , Pradasadam Indira , Toh Yi-Chin
Published: November 2023

Osteoarthritis (OA) is characterized by the dysregulation of the osteochondral interface between bone and cartilage.In vitromodels that accurately mimic this interface hold great potential for understanding OA pathophysiology and screening therapeutic agents. Presently, research efforts have focused on emulating heterogeneity in structural and mechanical attributes of the extracellular matrix (ECM) at the osteochondral interface. However, the precise simulation of differential oxygen gradients experienced by chondrocytes and osteoblasts in vivo remains a substantial obstacle for modeling osteo-chondral interactions effectively. To overcome this limitation, we show that micropatterned granular hydrogels, which are small microgel particles swelled in liquid culture media to create a shear-yielding jammed-packed solid, can be used to control the delivery of oxygen scavenging agents in a simple and scalable manner. Hypoxic granular hydrogels formulated with Oxyrase™ could maintain <1% oxygen concentration in a conventional cell culture incubator. Primary human chondrocytes maintained in the hypoxic hydrogels expressed a more anabolic phenotype similar to those cultured in a hypoxic incubator. The granular hydrogels can be readily patterned in a microfluidic device to generate a localized hypoxic environment, mimicking the differential oxygen levels at the osteochondral tissue interface (i.e. osteoblast at 20% and chondrocyte at 2% oxygen). Using this microfluidic coculture model, we paired healthy human chondrocytes with osteoblasts isolated from non-sclerotic and sclerotic subchondral bone to investigate how oxygen environment modulates osteoblast-chondrocyte crosstalk during OA. In a differential oxygen environment, the osteoblast-chondrocyte co-culture model showed sclerotic osteoblasts inducing chondrocyte collagen expression changes through increased MMP13 and ADAM15 production, unlike in a uniform normoxic oxygen environment, where the change was driven by altered collagen gene expression favoring Type I over Type II collagen. Furthermore, differential oxygen conditions enabled the identification of extensive transcriptional alterations induced by sclerotic osteoblasts, which involved inflammatory NF-κβ, TGF-β/BMP, and IGF signaling pathways, that was otherwise not detectable in a uniform normoxic co-culture. The microfluidic model with localized oxygen variations effectively mimics physiologically relevant osteoblast-chondrocyte crosstalk, providing valuable insights into OA pathophysiology.
Grasp Orientation in Ambiguous Settings is Sensitive to Prior Object Motion
Authors: Maffitt Natalie J , Cairns Emma G , Wozna Julia , Soteropoulos Demetris S , Kraskov Alexander
Published: November 2023

The wrist posture chosen to grasp an object is normally consistent, determined by the optimal, most efficient strategy learnt from previous experience. Yet in certain settings, despite object properties remaining constant and intention the same, the action chosen by an individual can vary with a lack of clear preference for one posture over another. This is referred to as motor ambiguity. Here, we investigate the influence of preceding dynamically changing visual information on participants’ choice between two possible wrist postures when grasping an object at various orientations. By presenting an initial orientation prior to the grasping of an ambiguous orientation, we found that subjects become biased to select a grasp for the ambiguous target that would be most congruent with the initial, determinate orientation. However, when object motion is observed between the initial and target positions, the bias is reversed, i.e. subjects choose the alternate wrist posture. Furthermore, the bias strength was found to be independent of the motion magnitude, and persists even when greater decision time is allowed. We provide evidence that this bias effect is not a perceptual phenomenon, and suggest it is potentially a behavioural manifestation of inhibitory circuits that delay decisions in conditions of motor ambiguity.
14-3-3 binding motif phosphorylation disrupts Hdac4 organized condensates to stimulate cardiac reprogramming
Authors: Liu Liu , Lei Ienglam , Tian Shuo , Gao Wenbin , Guo Yijing , Li Zhaokai , Sabry Ziad , Tang Paul , Chen Y. Eugene , Wang Zhong
Published: November 2023

Cell fate conversion is associated with extensive epigenetic and post translational modifications (PTMs) and architectural changes of sub-organelles and organelles, yet how these events are interconnected remains unknown. We report here the identification of a phosphorylation code in 14-3-3 binding motifs (PC14-3-3) that greatly stimulates induced cardiomyocyte (iCM) formation from fibroblasts. PC14-3-3 was identified in pivotal functional proteins for iCM reprogramming, including transcription factors and epigenetic factors. Akt1 kinase and PP2A phosphatase were a key writer and eraser of the PC14-3-3 code, respectively. PC14-3-3 activation induces iCM formation with the presence of only Tbx5. In contrast, PC14-3-3 inhibition by mutagenesis or inhibitor-mediated code removal abolished reprogramming. We discovered that key PC14-3-3 embedded factors, such as Hdac4, Mef2c, Nrip1, and Foxo1, formed Hdac4 organized inhibitory nuclear condensates. Notably, PC14-3-3 activation disrupted Hdac4 condensates to promote cardiac gene expression. Our study suggests that sub-organelle dynamics regulated by a post-translational modification code could be a general mechanism for stimulating cell reprogramming and organ regeneration.

Highlights

A PC14-3-3 (phosphorylation code in 14-3-3 binding motifs) is identified in pivotal functional proteins, such as HDAC4 and Mef2c, that stimulates iCM formation.

Akt1 kinase and PP2A phosphatase are a key writer and a key eraser of the PC14-3-3 code, respectively, and PC14-3-3 code activation can replace Mef2c and Gata4 in cardiac reprogramming.

PC14-3-3 activation disrupts Hdac4 organized condensates which results in releasing multiple 14-3-3 motif embedded proteins from the condensates to stimulate cardiac reprogramming.

Sub-organelle dynamics and function regulated by a post-translational modification code could be a general mechanism in stimulating cell reprogramming and organ regeneration.

Graphic abstract