bluuebunny/crossref_metadata_2025 huggingface dataset:
KNUCKLES regulates floral meristem termination by controlling auxin distribution and cytokinin activity
Authors: Wang Guangling , Wu Zhiyue , Sun Bo
Published: November 2024

The termination of floral meristem (FM) activity is essential for the normal development of reproductive floral organs. During this process, KNUCKLES (KNU), a C2H2-type zinc finger protein, crucially regulates FM termination by directly repressing the expression of both the stem cell identity gene WUSCHEL (WUS) and the stem cell marker gene CLAVATA3 (CLV3) to abolish the WUS-CLV3 feedback loop required for FM maintenance. In addition, phytohormones auxin and cytokinin are involved in FM regulation. However, whether KNU modulates auxin and cytokinin activities for FM determinacy control remains unclear. Here, we show that the auxin distribution and the cytokinin activity mediated by KNU in Arabidopsis (Arabidopsis thaliana) promote the termination of FM during stage 6 of flower development. Mutation of KNU leads to altered distribution of auxin and cytokinin in the FM of a stage 6 floral bud. Moreover, KNU directly represses the auxin transporter gene PIN-FORMED1 (PIN1) and the cytokinin biosynthesis gene ISOPENTENYLTRANSFERASE7 (IPT7) via mediating H3K27me3 deposition on these 2 loci to regulate auxin and cytokinin activities. Our study presents a molecular regulatory network that elucidates how the transcriptional repressor KNU integrates and modulates the activities of auxin and cytokinin, thus securing the timed FM termination.
Pummelo fruit extract (Citrus maxima) reduces oxidative damage in peripheral blood of obese patients
Authors: Nunes Vinícius Tejada , Gonçalves Itamar Luís , Schmitt Elizandra Gomes , Schreiner Gênifer Erminda , dos Santos Laura Smolski , de Moura Sarmento Silvia Muller , Pereira Camila Berny , da Costa Escobar Piccoli Jacqueline , Manfredini Vanusa , Denardin Cristiane Casagrande
Published: November 2024

Objectives

To verify the level of oxidation of biomolecules in the peripheral blood of obese patients before and after incubation with the pummelo pulp extract at 25 mg/mL.

Methods

This investigation included 241 individuals, distributed across the following groups: control (n = 69; 30 men and 39 women); pre-obesity (n = 78; 29 men and 49 women); level I obesity (n = 62; 20 men and 42 women); and level II or III obesity (n = 32; 11 men and 21 women).

Results

TBARS and MN levels were significantly altered by incubation with pummelo extract in both genders and in all the groups according to their obesity level. Another alteration in the antioxidant profile of the samples was a significant increase in vitamin C levels observed after incubation with pummelo extract in all experimental groups.

Conclusions

The aqueous extract of pummelo pulp showed in vitro biological activity against the oxidation of biomolecules, suggesting that its bioactive compounds may bring health benefits of obese patients.
Is therapeutic plasma exchange effective in leptospirosis-associated severe pulmonary haemorrhagic syndrome? A systematic review
Authors: Bandara J M R P , Rosairo A , Ranasinghe G S , De Silva T D , Gawarammana I B
Published: November 2024

Leptospirosis is a re-emerging zoonosis fast becoming a global burden. Pulmonary haemorrhages are a deadly complication, with case fatality rates >50%. Systemic vasculitis is thought to be the pathological process responsible for pulmonary haemorrhages and therapeutic plasma exchange (TPE) is one of the treatments offered. This systematic review aims to evaluate the effectiveness of TPE in managing leptospirosis-associated severe pulmonary haemorrhagic syndrome (SPHS). A systematic review was conducted using the Preferred Reporting Items for Systematic Reviews and Meta-Analysis protocol. The search used Medical Subject Headings in PubMed with keywords ‘Leptospirosis’ OR ‘Leptospira’ OR ‘Weil disease’ AND ‘plasmapheresis’ OR ‘plasma exchange’ AND ‘pulmonary haemorrhage’ OR ‘alveolar haemorrhage’. The search was widened to include the Google Scholar database. The review was confined to English-language articles and focused on primary research studies. Nineteen articles were considered for analysis. There were no randomized controlled trials. A non-randomized trial and a retrospective cohort documented recovery following adjuvant TPE treatment. Most case reports mention significant improvement and complete recovery following administration of TPE. One case reported the death of a patient despite treatment. However, this review revealed a lack of strong evidence endorsing the routine application of TPE as a therapeutic intervention for cases of SPHS. Thus we recommend the initiation of a well-structured randomized controlled trial to ensure an accurate assessment of the efficacy of TPE.
Emergence of Omicron FN.1 a descendent of BQ.1.1 in Botswana
Authors: Choga Wonderful T , Gustani-Buss Emanuele , Tegally Houriiyah , Maruapula Dorcas , Yu Xiaoyu , Moir Monika , Zuze Boitumelo J L , James San Emmanuel , Ndlovu Nokuthula S , Seru Kedumetse , Motshosi Patience , Blenkinsop Alexandra , Gobe Irene , Baxter Cheryl , Manasa Justen , Lockman Shahin , Shapiro Roger , Makhema Joseph , Wilkinson Eduan , Blackard Jason T , Lemey Phillipe , Lessells Richard J , Martin Darren P , de Oliveira Tulio , Gaseitsiwe Simani , Moyo Sikhulile
Published: November 2024

Botswana, like the rest of the world, has been significantly impacted by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). In December 2022, we detected a monophyletic cluster of genomes comprising a sublineage of the Omicron variant of concern (VOC) designated as B.1.1.529.5.3.1.1.1.1.1.1.74.1 (alias FN.1, clade 22E). These genomes were sourced from both epidemiologically linked and unlinked samples collected in three close locations within the district of Greater Gaborone. In this study, we assessed the worldwide prevalence of the FN.1 lineage, evaluated its mutational profile, and conducted a phylogeographic analysis to reveal its global dispersal dynamics. Among approximately 16 million publicly available SARS-CoV-2 sequences generated by 30 September 2023, only 87 were of the FN.1 lineage, including 22 from Botswana, 6 from South Africa, and 59 from the UK. The estimated time to the most recent common ancestor of the 87 FN.1 sequences was 22 October 2022 [95% highest posterior density: 2 September 2022—24 November 2022], with the earliest of the 22 Botswana sequences having been sampled on 7 December 2022. Discrete trait reconstruction of FN.1 identified Botswana as the most probable place of origin. The FN.1 lineage is derived from the BQ.1.1 lineage and carries two missense variants in the spike protein, S:K182E in NTD and S:T478R in RDB. Among the over 90 SARS-CoV-2 lineages circulating in Botswana between September 2020 and July 2023, FN.1 was most closely related to BQ.1.1.74 based on maximum likelihood phylogenetic inference, differing only by the S:K182E mutation found in FN.1. Given the early detection of numerous novel variants from Botswana and its neighbouring countries, our study underscores the necessity of continuous surveillance to monitor the emergence of potential VOCs, integrating molecular and spatial data to identify dissemination patterns enhancing preparedness efforts.
Mathematical comparison of protocols for adapting a bacteriophage to a new host
Authors: Bull James J , Krone Stephen M
Published: November 2024

Interest in phage therapy—the use of bacterial viruses to treat infections—has increased recently because of the rise of infections with antibiotic-resistant bacteria and the failure to develop new antibiotics to treat those infections. Phages have shown therapeutic promise in recent work, and successful treatment minimally requires giving the patient a phage that will grow on their infecting bacterium. Although nature offers a bountiful and diverse supply of phages, there have been a surprising number of patient infections that could not be treated with phages because no suitable phage was found to kill the patient’s bacterium. Here, we develop computational models to analyze an alternative approach to obtaining phages with new host ranges—directed evolution via laboratory propagation of phages to select mutants that can grow on a new host. The models separately explore alternative directed evolution protocols for phage variants that overcome three types of bacterial blocks to phage growth: a block in adsorption, temperate phage immunity to superinfection, and abortive infection. Protocols assume serial transfer to amplify pre-existing, small-effect mutants that are initially rare. Best protocols are sensitive to the nature of the block, and the models provide several insights for enhancing success specific to each case. A common result is that low dilution rates between transfers are beneficial in reducing the mutant growth rate needed to ascend. Selection to overcome an adsorption block is insensitive to many protocol variations but benefits from long selection times between transfers. A temperate phage selected to grow on its lysogens can evolve in any of three phenotypes, but a common protocol favors the desired changes in all three. Abortive infection appears to be the least amenable to evolving phage growth because it is prone to select phages that avoid infection.
Adjusting adjustments: Using external data to estimate the impact of different confounder sets on published associations.
Authors: Ahern Thomas P. , Collin Lindsay J. , MacLehose Richard F. , Littenberg Benjamin , Haines Laura , Bonnett Michaela , Asmussen Fanny Børne , Chen Jennifer , Lash Timothy L.
Published: November 2024

Background:

A 2013 meta-analysis observed a protective association between overweight BMI (versus normal BMI) and all-cause mortality that was particularly strong in people aged ≥65. Estimates informing this meta-analysis were highly heterogeneous, and critics raised insufficient or inappropriate confounder adjustment in many studies as an explanation for the protective summary association. Using this topic as an example, we demonstrate a novel approach for external adjustment of individual studies for a uniform and sufficient confounder set before meta-analysis.

Methods:

We abstracted summary data on the 33 associations comprising the age ≥65 stratum of the 2013 meta-analysis. Using an external dataset (NHANES III), we derived covariates used in each study’s multivariable model of the overweight–mortality association. We then calculated a bias factor to quantify the direction and magnitude of displacement of the ratio measure of association after changing from the original adjustment set to a sufficient adjustment set. After applying bias factors to adjust original associations, we compared summary results from random effects meta-analyses with and without such adjustment.

Results:

We reproduced the original meta-analysis of overweight–mortality estimates among older participants and found a protective association similar to that reported in 2013 (summary RR=0.88, 95% CI: 0.84, 0.92, I2=38.4%). After we simulated uniform adjustment of all 33 associations for a minimally sufficient confounder set (age, sex, and smoking status), the meta-analysis showed a similar summary association (summary RR=0.90, 95% CI: 0.86, 0.94), but with reduced heterogeneity (I2=34.6%).

Conclusion:

Simulated uniform adjustment for a sufficient confounder set may improve rigor and promote consensus in meta-analysis.
Comparison of Colorado Needle Electrocautery and Traditional Scalpel for Lower Eyelid Blepharoplasty Incision: A Randomized Controlled Trial
Authors: Pruksapong Chatchai , Jankajorn Suttisun , Burusapat Chairat , Attainsee Akaradech , Wanichjaroen Nutthapong , Wongprakob Nuttadon , Siriwattana Kolid
Published: November 2024

Background:

Lower eyelid blepharoplasty is one of the most popular aesthetic procedures. Electrocautery provides a hemostatic benefit for skin incision; however, its effect on scar cosmesis remains unclear, particularly in Asian skin types. We compared the Colorado needle electrocautery (pure-cutting mode) versus the traditional scalpel in terms of efficacy, complications, and cosmetic outcomes.

Methods:

A prospective intraindividual randomized controlled trial was conducted to compare the efficacy of Colorado needle electrocautery and scalpel in lower blepharoplasty. The study outcomes were scar quality at different times until 1 year postoperatively, bleeding during incision, and postoperative ecchymosis. Scar quality was evaluated using 3 standard scar ratings: the Vancouver Scar Scale, Patient and Observer Scar Assessment Scale, and Hollander wound evaluation scale.

Results:

The study included 25 patients, and the electrocautery side had less blood loss during incision than the scalpel side (2.6 ± 0.65 versus 5.28 ± 0.68 sticks; P < 0.001). The electrocautery side had less postoperative ecchymosis (P < 0.001); however, 1-year scar quality was not statistically significant between the groups.

Conclusions:

Colorado needle electrocautery pure-cutting mode can be an alternative to the traditional scalpel for lower eyelid blepharoplasty skin incision because of long-term scar quality. Electrocautery also has hemostatic benefits, leading to a decrease in intraoperative and postoperative bleeding.
The Small Finger Reverse Ulnar Digital Artery Hypothenar Palmar Perforator Flap: An Anatomical Study With Clinical Examples
Authors: Kunda Nicholas , Cai Steven B. , Dagum Alexander B.
Published: November 2024

Background:

Local flaps are commonly used for reconstruction of digital soft-tissue defects. There remains a paucity of options available for small finger volar and dorsal soft-tissue defects distal to the proximal interphalangeal joint. The purpose of this study was to analyze perforators along the hypothenar palmar region arising from the artery of the ulnar side of the small finger as it comes off the superficial palmar arch for consistency and potential to be used for perforator-based flap reconstruction of soft-tissue defects and joint coverage of the small finger.

Methods:

Four cadaveric upper extremities were injected with Microfil silicone injection compound. Dissection was performed from the superficial palmar arch to the ulnar digital artery of the small finger, and perforators were identified and analyzed for consistency and utility. Flap elevation was performed based on these perforators in a small finger reverse ulnar digital artery fashion.

Results:

All cadaveric dissections showed a suitable perforator pattern along the hypothenar palmar region with a minimum of 5 perforators available from which to base a flap to address dorsal and volar defects of the small finger. Two clinical examples are presented confirming the viability and utility of this flap.

Conclusions:

A detailed anatomic study with 2 clinical examples of this retrograde pedicle island flap is presented. The small finger reverse ulnar digital artery hypothenar palmar–based perforator flaps are a viable option with a reliable perforator pattern, providing a functional solution for reconstruction of soft-tissue defects and joint coverage of the small finger.
Collaborative Section-Based DNP Project Faculty Workload Model
Authors: Hubbell Sara , Dodson Crystal , Sigmon Lorie , Parker Diane , Young Susan , Culp-Roche Amanda , Reardon Lecia , Duea Stephanie , Wax Erin , O’Brien Coleen , Ford Shannon
Published: November 2024

Background:

The Doctor of Nursing Practice (DNP) degree culminates in the DNP project, a scholarly project aimed at enhancing health care systems aligned with national standards. While DNP projects are valued, they pose challenges due to resource-intensive demands including faculty time and effort.

Problem:

Faculty workload models related to DNP projects have not kept pace with increasing enrollment and program expectations.

Approach:

Consistent with national standards, a large public university convened a task force to examine faculty workload relative to DNP projects and to devise a more equitable and realistic model.

Outcomes:

Task force output led to the creation of the Collaborative Section-Based Faculty Workload Model that resulted in increases in faculty satisfaction, retention, and student mentorship, while maintaining DNP project rigor.

Conclusions:

The Collaborative Section-Based Faculty Workload Model responds to the challenge of balancing DNP project oversight with increasing time demands on faculty and increasing enrollment.
Histological Evaluation of Mandibular Bone After Mandibular Outer Cortex Osteotomy: The Role of the Periosteum
Authors: Cheng Wenjie , Liu Wei , Gui Lai
Published: November 2024

Objective:

This study investigates the role of the periosteum in the repair and reconstruction process post-osteotomy using histological analysis to provide insights for pediatric craniofacial surgery.

Methods:

Twenty-four 3-month-old miniature pigs were divided into 2 groups. Group I: left mandibular outer cortex and periosteum resection + right mandibular outer cortex resection with periosteum preserved. Group II: left mandibular outer cortex and periosteum resection + no surgery on the right side. Excised the incision skin, bilateral masseter muscles, condyles, and mandible at 4, 12, and 24 weeks postoperatively for hematoxylin-eosin staining and immunohistochemical staining of osteoprotegerin, receptor activator for nuclear factor kappa B ligand, bone morphogenetic protein-4, Ki-67, caspase-3, CD3, and CD19.

Results:

Hematoxylin-eosin staining showed no significant differences between the left and right incision skin, masseter muscles, and condyles. The periosteum-preserved side showed better bone healing. Immunohistochemical staining showed early osteogenesis and osteoclast activity on the periosteum-resected side were significantly lower than on the periosteum-preserved side, but gradually enhanced during late-stage healing.

Conclusion:

The periosteum factor is one of the main reasons for mandibular deviation after mandibular outer cortex osteotomy. The periosteum has a dual role in promoting osteogenesis and limiting excessive bone growth.
Use of Botulinum Toxin Type A in the Open Reduction of a Mandibular Fracture in a Patient With Cerebral Palsy
Authors: Kim Rah Yoon , Lee Chang Jun , Yoo Gyeol
Published: November 2024

Patient compliance is essential for stabilizing mandibular fractures and ensuring successful outcomes. However, uncontrollable movement disorders can greatly complicate the overall management. This case discusses the management of a mandibular body fracture in a 46-year-old male with dyskinetic cerebral palsy, without using maxillomandibular fixation. The patient fell from a wheelchair, resulting in a mandibular body fracture. He received open reduction and internal fixation, but maxillomandibular fixation was not feasible due to his condition. Severe bruxism led to excessive contractions of the masseter muscle, which complicated recovery. The patient underwent 2 revision surgeries, along with botulinum toxin injections and muscle relaxants. Three months after the final surgery, the patient recovered without complications, and radiographic follow-up confirmed proper fixation. This case demonstrates that for patients with dyskinetic cerebral palsy, combining open reduction and internal fixation with botulinum toxin injections can effectively manage mandibular body fractures and lead to successful healing.
Clarifying the Relationship Between Orbito-Zygomatic and Mandibular Dysmorphology in Treacher Collins Syndrome
Authors: Wu Meagan , Barnett Sarah L. , Massenburg Benjamin B. , Friedman Leigh M. , Ng Jinggang J. , Romeo Dominic J. , Barrero Carlos E. , Swanson Jordan W. , Bartlett Scott P. , Taylor Jesse A.
Published: November 2024

Introduction:

This study aims to clarify the relationship between orbito-zygomatic and mandibular dysmorphology as well as their associations with the most frequently observed craniofacial anomalies in patients with Treacher Collins syndrome (TCS).

Methods:

The authors retrospectively reviewed patients with TCS who presented between 2000 and 2023. Patients were included if they had at least one computed tomography scan performed before skeletal reconstruction along with clinical photographs. Serial scans were used to grade degrees of orbito-zygomatic and mandibular dysmorphology using previously published severity scales.

Results:

Ninety hemi-skulls were evaluated among 35 patients at an average age of 5.7±5.6 years. There was a significant positive correlation between the severity of orbito-zygomatic and mandibular hypoplasia (r=0.294, P=0.005). Greater severity of orbito-zygomatic hypoplasia was positively correlated with down-slanting palpebral fissures (r=0.461, P<0.001), ectropion (r=0.381, P<0.001), ptosis (r=0.327, P=0.002), eyelash problems (r=0.268, P=0.011), and eyelid coloboma (r=0.104, P<0.001). Greater severity of mandibular hypoplasia was correlated with intubation or tracheostomy as a neonate (r=0.519, P<0.001), NG tube or gastrotomy (r=0.355, P<0.001), cleft lip and/or palate (r=0.349, P<0.001), and microtia (r=0.304, P=0.004).

Conclusions:

The authors found a positive correlation between (1) severity of orbito-zygomatic and mandibular dysmorphology, (2) severity of orbito-zygomatic hypoplasia and the presence of periorbital deficiencies, and (3) severity of mandibular hypoplasia and history of oropharyngeal airway compromise in patients with TCS. Given the morbidity risk and surgical burden associated with these dysmorphologies, early identification of and anticipation for a greater number of aesthetic and functional challenges based on the severity of underlying skeletal deficiencies is critical.
Impact of Bariatric Surgery on Complications After Prolapse Surgery
Authors: Le Neveu Margot , Marra Emily , Rhodes Stephen , Sheyn David
Published: November 2024

Importance

Obesity is a risk factor for pelvic organ prolapse (POP) and independently associated with perioperative complications following prolapse surgery. Although weight loss surgery (WLS) may lead to weight loss and mitigate obesity-related comorbidities, it is associated with chronic malabsorption, which may also lead to increased perioperative complications. There have been no studies evaluating the impact of prior WLS on POP surgery outcomes.

Objective

This study aimed to describe the effect of WLS on complications after POP surgery.

Study Design

We performed a retrospective cohort study of patients with obesity who underwent POP surgery and compared outcomes between those with and without a prior history of WLS. Data were procured from the Premier U.S. National Database between January 2000 and March 2020.

Results

Of 22,905 surgical procedures performed for POP, 542 (2.2%) previously underwent WLS with a median of 30 months between procedures (IQR, 15–51). The WLS group had higher rates of postoperative mesh erosion at 3 months (3.0% vs 1.5%, P = 0.0079) and 12 months (3.1% vs 1.8%, P = 0.04) and had higher hematoma incidence (1.7% vs 0.68%, P = 0.014). After adjusting for covariates, WLS was not associated with increased probability of infectious (OR, 0.94; 95% CI, 0.67–1.27) or noninfectious morbidity (OR, 1.06; 95% CI, 0.59–1.75). Rates of recurrent prolapse resulting in surgery were similar between groups (1.7% vs 1.3%, P = 0.56), and time interval between WLS and POP surgical procedures did not affect rates of complications.

Conclusion

WLS does not appear to increase the risk of perioperative complications following surgery for POP.
The extended ‘common cause’: causal links between punctuated evolution and sedimentary processes
Authors: Polly P. David
Published: November 2024

The common-cause hypothesis says that factors regulating the sedimentary record also exert macroevolutionary controls on speciation, extinction, and biodiversity. I show through computational modeling that common cause factors can, in principle, also control microevolutionary processes of trait evolution. Using Bermuda and its endemic land snailPoecilozonites, I show that the glacial-interglacial sea level cycles that toggle local sedimentation between slow pedogenesis and rapid eolian accumulation could also toggle evolution rates between long slow phases associated with large geographic ranges and short rapid phases associated with small, fragmented ranges and “genetic surfing” events. Patterns produced by this spatially driven process are similar to the punctuated equilibria patterns that Gould inferred from the fossil record of Bermuda, but without speciation or true stasis. Rather, the dynamics of this modeled system mimic a two-rate Brownian motion process (even though the rate parameter is technically constant) in which the contrast in rate and duration of the phases makes the slower one appear static. The link between sedimentation and microevolution in this model is based on a sediment-starved island system, but the principles may apply to any system where physical processes jointly control the areal extents of sedimentary regimes and species distributions.

Non-Technical Summary

The history of life is known from the fossils preserved in the geological record. The common-cause hypothesis suggests that processes like mountain building and sea-level change can affect both the structure of the geological record and species diversity. Using the snails of Bermuda as an example, this paper develops a computational model to show that sea level cycles could affect morphological evolution within species, not just species diversity. As sea level rose on Bermuda, the available snail habitat would have become smaller and more fragmented, which would be expected to drive rapid bursts of genetic drift (the random component of evolutionary change). When sea level fell, the snails’ habitat would have expanded and coalesced, resulting in slower rates of evolution because the total population size would increase. This process would produce an uneven cycle of rapid and slow evolution similar to what paleontologist Steven Gould observed in the fossil snails of Bermuda and led him to propose the theory of punctuated equilibria. While these simulations are focused specifically on an island system, the principles are applicable to other situations suggesting that geological and evolutionary processes may be linked in more ways than previously understood.
Ox-LDL induces a non-inflammatory response enriched for coronary artery disease risk in human endothelial cells
Authors: Jiang Jiahao , Hiron Thomas K. , Chalisey Anil , Malhotra Yashaswat , Agbaedeng Thomas , O’Callaghan Chris A.
Published: November 2024

Oxidised low-density lipoprotein cholesterol (ox-LDL) is critical in the initiation and progression of atherosclerosis. While excessive atherogenic lipids in the arterial intima can trigger endothelial dysfunction in advanced lesions, the response of endothelial cells to ox-LDL in the early stages of atherogenesis remains unclear. Here, we conducted a comprehensive, genome-wide multi-omics characterisation of the cellular response to ox-LDL in primary human aortic endothelial cells (HAECs). Our results reveal that the exposure of HAECs to ox-LDL leads to pathogenic changes in metabolism, transcriptome and epigenome, but in the absence of a typical inflammatory endothelial phenotype. An integrative analysis implicates the role of AP-1, NFE-2 and CEBP transcription factors in regulating ox-LDL-induced transcription. We further demonstrate that ox-LDL activates endothelial cell migration through the epigenomic rewiring of transcription factor binding. Notably, these ox-LDL-induced dynamic binding sites are enriched for the genetic risk of coronary artery disease, enabling the discovery of the gene-environment interaction of rs62172376 and ox-LDL at theCALCRL/TFPIlocus. Collectively, our findings provide an unbiased understanding of the transcriptional regulation in endothelial cells in response to ox-LDL, together with its interaction with the genetic element of coronary artery disease.
A floor-field model of tau-taxol competition explains tau envelope dynamics on taxol-stabilized microtubules
Authors: Chevalier Carole , Siahaan Valerie , Grover Rahul , Diez Stefan , Santen Ludger
Published: November 2024

Tau is a microtubule-associated protein (MAP) that is highly expressed in neurons. Recent in-vitro studies have shown that tau molecules can segregate into cohesive ‘envelopes’ on paclitaxel (taxol) stabilized microtubules. These envelopes act as selective barriers gating the motor transport and protecting microtubules against the action of severing enzymes. However, the mechanisms underlying the formation of these envelopes remain unclear. Recent in vitro reconstitution assays revealed that the formation of tau envelopes induces a compaction of the underlying microtubule lattice, whereas taxol binding induces lattice expansion, indicating competitive binding between tau and taxol on microtubules. In this study, we use physical modeling to investigate how this competition between tau and taxol regulates the formation of tau envelopes. Our model includes static and dynamic floor-fields, concepts adapted from pedestrian dynamics. By comparing our simulation results with experimental data, we demonstrate that tau-taxol competition on the microtubule lattice is sufficient to explain the features of the formation and disassembly of tau envelopes. Notably, tau-tau interactions are not necessary to account for the steadiness of these envelopes.
Dendritic cells accelerate CAR T cells in irradiated tumors through chimeric synapses
Authors: Navarre Sophia , Ishibashi Maki , Nair Achuth , Reyes-Torres Ivan , Belabed Meriem , Halasz Laszlo , Park Matthew D. , Mattiuz Raphaël , Ounadjela Merouane , Gunset Gertrude , Mansilla-Soto Jorge , Feucht Judith , Cabriolu Annalisa , Berichel Jessica Le , Eyquem Justin , Brown Brian , Merad Miriam , Sadelain Michel , Ahmed Jalal
Published: November 2024

The persistence of adoptively transferred T cells is vital for anti-tumor efficacy. Chimeric antigen receptor (CAR) T cells can persist indefinitely when delivered to patients with B cell cancers and can confer long-term remission. For patients with solid tumors, however, sustaining CAR T cell activity remains a major challenge. This has been attributed in part to the immune microenvironment within solid tumors, though the contribution of specific immune subsets to resistance to CAR T cells is not clear. Here we resolve how the immunology of irradiated tumors dramatically enhances persistence and efficacy of CAR T cells targeted to advanced lung metastases in a syngeneic mouse model. Remarkably, CAR T cell persistence depended critically on dendritic cells (DC) that underwent trogocytic “antigen-dressing” of tumor target antigens and stimulated CAR T cells through the chimeric receptor. Furthermore, tumor irradiation increased antigen-dressing onto DCs. In the absence of functional DCs, CAR T cell activity in irradiated tumor was short-lived and tumors relapsed. These findings establish a critical mechanism through which DCs maintain the CAR T cell pool in irradiated tumors, thus supporting translation of this approach to advance CAR T cell therapy for solid tumors.
Machine learning application to predict binding affinity between peptide containing non-canonical amino acids and HLA0201
Authors: Jiang Shan , Su Zhaoqian , Bloodworth Nathaniel , Liu Yunchao , Martina Cristina , Harrison David G. , Meiler Jens
Published: November 2024

Class 1 major histocompatibility complexes (MHC-I), encoded by the highly polymorphic HLA-A, HLA-B, and HLA-C genes in humans, are expressed on all nucleated cells. Both self and foreign proteins are processed to peptides of 8 to 10 amino acids, loaded into MCH-1 within the endoplasmic reticulum and then presented on the cell surface. Foreign peptides presented in this fashion activate CD8+ T cells and their immunogenicity correlates with their affinity for the MHC-1 binding groove. Thus, predicting antigen binding affinity for MHC-I is a valuable tool for identifying potentially immunogenic antigens. While quite a few predictors for MHC-I binding exist, there are no currently available tools that can predict antigen/MHC-I binding affinity for antigens with explicitly labeled post-translational modifications or unusual/non-canonical amino acids (NCAAs). However, such modifications are increasingly recognized as critical mediators of peptide immunogenicity. In this work, we propose a machine learning application that quantifies the binding affinity of epitopes containing NCAAs to MHC-I and compares its performance with other commonly used regressors. Our model demonstrates robust performance, with 5-fold cross-validation yielding an R2value of 0.477 and a root-mean-square error (RMSE) of 0.735, indicating strong predictive capability for peptides with NCAAs. This work provides a valuable tool for the computational design and optimization of peptides incorporating NCAAs, potentially accelerating the development of novel peptide-based therapeutics with enhanced properties and efficacy.
The antimycotic 5-fluorocytosine is a virulence inhibitor of uropathogenicEscherichia coliand eradicates biofilm-embedded bacteria synergizing with β-lactams
Authors: Ravishankar Srikanth , Conte Antonietta Lucia , Carrasco Aliaga Stacy Julisa , Baldelli Valerio , Nielsen Karen Leth , Conte Maria Pia , Landini Paolo , Rossi Elio
Published: November 2024

Objectives

Biofilm increases bacterial antibiotic tolerance, posing a challenge for treating biofilm-associated infections in clinical settings. 5-fluorocytosine (5-FC), an FDA-approved antifungal and antitumor drug, has been shown to inhibit virulence factor production and biofilm formation in Gram-negative bacteria. This work aims to determine whether 5-FC antivirulence and antibiofilm activity are preserved in clinicalE. coliisolates and to test possible synergies with antibiotics in treating preformed biofilm.

Methods

5-FC ability to inhibit biofilm formation, disrupt mature biofilm, and modulate virulence determinants was tested on uropathogenicE. coli(UPEC) clinical strains using the Crystal Violet-based biofilm adhesion and minimum biofilm eradication concentration assays. Gene expression was measured by RT-qPCR. The effect on bacterial viability within preformed biofilm was monitored using fluorescein diacetate and by determining colony-forming units in biofilm treated with or without 5-FC and specific antibiotics. Bladder epithelial cell cultures were used to assess the effect of 5-FC on UPEC adherence and cytotoxicity.

Results

5-FC inhibited biofilm formation in all tested UPEC strains. Gene expression analysis suggested that 5-FC concurrently inhibits the expression of genes encoding curli fibers, a major adhesion factor inE. coli, as well as other virulence determinants such as secreted toxins and type I and P fimbriae. Accordingly, 5-FC reduced UPEC adherence to epithelial cells and promoted host cell survival. Although 5-FC could not disrupt preformed biofilm, combining 5-FC with β-lactams drastically reduced the viability of biofilm-resident bacteria.

Conclusions

5-FC shows antibiofilm and antivirulence activity against uropathogenicE. colistrains by reducing the expression of several virulence factors and the overall UPEC pathogenic potential. In combination with β-lactams, 5-FC eradicates bacteria within mature biofilms, which are known to be highly refractory to antibiotic treatment. Our data suggest that 5-FC is an excellent candidate for preventing and treating bacterial infections associated with recalcitrant biofilms.
Pupillometry and Whole-Brain c-Fos Mapping Uncover Multimodal Mirror Mechanisms in Emotional Contagion Networks of Mice
Authors: Caldarelli Matteo , Zucca Stefano , Viglione Aurelia , Stella Alessandra , Nisar Rida , Sagona Giulia , Papini Ester Maria , Carrara Fabio , Bovetti Serena , Mazziotti Raffaele , Pizzorusso Tommaso
Published: November 2024

Emotional contagion (ECo) represents a fundamental form of empathy. In this study, we used pupillometry to quantify ECo by assessing pupil responses of a mouse watching another mouse receive a tail shock. Pupil dilation effectively measured both direct and vicarious emotional response thresholds at the individual level through psychometric curve analysis. The pupillary ECo response diminished when the observer could not see the demonstrator, suggesting a multisensory process involving vision. Viewing videos of tail-shocked mice was sufficient to elicit a pupil response in the observer. Whole-brain c-Fos mapping revealed a broad network of 88 brain regions activated during ECo, with all areas activated in the demonstrator also engaged in the observer. Additionally, in certain brain regions, correlated activation was detected between each observer-demonstrator pair, indicating that ECo promotes a shared neural state. These findings advance our understanding of the neural basis of empathy, with implications for analyzing neuropsychiatric disorder models.
Three-dimensional tissue strain measurement using a row-column array during biaxial testing of excised ventricular myocardium
Authors: Navy Xavier , Sheng Zhiyu , Kim Kang , Cormack John M.
Published: November 2024

Objective

To implement and validate a 3D volume imaging sequence and 3D strain estimation procedure for enhanced biaxial mechanical testing of excised ventricular myocardium.

Methods

One right- and one left-ventricular excised porcine myocardium specimens were tested using dual-loading protocol quasi-static biaxial mechanical testing. During biaxial testing, volume ultrasound images were acquired using a row-column addressed array probe using a synthetic aperture imaging sequence. Volume ultrasound images were used to compute tissue deformation using 3D correlation-based ultrasound speckle tracking. Ultrasound-derived tissue strains were validated against repeated measurements using typical standard optical camera imaging of the surface deformation of the specimen.

Results

Synthetic aperture imaging with the RCA yielded artifact-free and uniform ultrasound speckle for high-fidely speckle tracking of tissue deformation. Ultrasound-derived tissue strain is in good agreement with ground-truth camera-derived surface strain measurements (root-mean-square error is 1.6% strain).

Conclusion

High-fidelity 3D strain measurement with ultrasound imaging is accurate and can enhance biomechanical insights from biaxial experimentation, especially in large tissues such as porcine and human myocardium where assumptions of plane stress and incompressibility may not apply.
Reconstitution of SPO11-dependent double-strand break formation
Authors: Zheng Zhi , Zheng Lyuqin , Arter Meret , Liu Kaixian , Yamada Shintaro , Ontoso David , Kim Soonjoung , Keeney Scott
Published: November 2024

Homologous meiotic recombination starts with DNA double-strand breaks (DSBs) generated by SPO11 protein1. SPO11 is critical for meiosis in most species but the DSBs it makes are also dangerous because of their mutagenic2and gametocidal3potential, so cells must foster SPO11’s beneficial functions while minimizing its risks4. SPO11 mechanism and regulation remain poorly understood. Here we report reconstitution of DNA cleavage in vitro with purified recombinant mouse SPO11 bound to its essential partner TOP6BL. Similar to their yeast orthologs5,6, SPO11– TOP6BL complexes are monomeric (1:1) in solution and bind tightly to DNA. Unlike in yeast, however, dimeric (2:2) assemblies of mouse SPO11–TOP6BL cleave DNA to form covalent 5′ attachments requiring SPO11 active site residues, divalent metal ions, and SPO11 dimerization. Surprisingly, SPO11 can also manifest topoisomerase activity by relaxing supercoils and resealing DNA that it has nicked. Structure modeling with AlphaFold37illuminates the protein-DNA interface and suggests that DNA is bent prior to cleavage. Deep sequencing of in vitro cleavage products reveals a rotationally symmetric base composition bias that partially explains DSB site preferences in vivo. Cleavage is inefficient on complex DNA substrates, partly because SPO11 is readily trapped in DSB-incompetent (presumably monomeric) binding states that exchange slowly. However, cleavage is improved by using substrates that favor DSB-competent dimer assembly, or by fusing SPO11 to an artificial dimerization module. Our results inform a model in which intrinsically feeble dimerization restrains SPO11 activity in vivo, making it exquisitely dependent on accessory proteins that focus and control DSB formation so that it happens only at the right time and the right places.
TIRE-seq: an Integrated Sample Extraction and Transcriptomics Workflow for High Throughput Perturbation Studies
Authors: O’Keeffe Piper , Nouri Yasmin , Saw Hui Shi , Moore Zachery , Baldwin Tracey M. , Olechnowicz Sam W.Z. , Jabbari Jafar S. , Squire David McG , Leslie Stephen , Wang Changqing , You Yupei , Ritchie Matthew E. , Cross Ryan S. , Jenkins Misty R. , Audiger Cindy , Naik Shalin H. , Whittle James R. , Freytag Saskia , Best Sarah A. , Hickey Peter F. , Amann-Zalcenstein Daniela , Bowden Rory , Brown Daniel V.
Published: November 2024

RNA sequencing (RNA-seq) is widely used in biomedical research, advancing our understanding of gene expression across biological systems. Traditional methods require upstream RNA extraction from biological inputs, adding time and expense to workflows. We developed TIRE-seq (Turbocapture Integrated RNA Expression Sequencing) to address these challenges. TIRE-seq integrates mRNA purification directly into library preparation, eliminating the need for a separate extraction step. This streamlined approach reduces turnaround time, minimizes sample loss, and improves data quality. A comparative study with the widely used Prime-seq protocol demonstrates TIRE-seq’s superior sequencing efficiency with crude cell lysates as inputs. TIRE-seq’s utility was demonstrated across three biological applications. It captured transcriptional changes in stimulated human T cells, revealing activation-associated gene expression profiles. It also identified key genes driving murine dendritic cell differentiation, providing insights into lineage commitment. Lastly, TIRE-seq analyzed the dose-response and time-course effects of temozolomide on patient-derived neurospheres, identifying differentially expressed genes and enriched pathways linked to the drug’s mechanism of action. With its simplified workflow and high sequencing efficiency, TIRE-seq offers a cost-effective solution for large-scale gene expression studies across diverse biological systems.
Cardiac electrical abnormalities in a mouse model of left ventricular non-compaction cardiomyopathy
Authors: Fernandes Vítor S. , Caballero Ricardo , Siguero-Álvarez Marcos , Papoutsi Tania , Gimeno Juan Ramón , Delpón Eva , de la Pompa José Luís
Published: November 2024

Mutations inMINDBOMB 1(MIB1), encoding an E3 ubiquitin ligase of the NOTCH signaling pathway, cause left ventricular noncompaction cardiomyopathy (LVNC) in mice and humans, increasing the risk of arrhythmia and left ventricular dysfunction. This study aimed to investigate the effect ofMIB1mutations on cardiac electrical activity. We examined maleMib1flox;Tnnt2Cremice, a disease model of LVNC, and wildtype littermates on the C57BL/6J genetic background. Our results demonstrate that the gap-junction protein connexin43 was delocalized from the intercalated disks to the lateral long axis ofMib1flox;Tnnt2Crecardiomyocytes. Cardiomyocyte electrophysiology revealed an increase in the Na (INa) peak density at potentials between –50 and –30 mV inMib1flox;Tnnt2Cremice, with no changes in INaactivation or inactivation kinetics.Mib1flox;Tnnt2Crecardiomyocytes also showed decreases in outward K+peak currents and currents at the end of depolarizing pulses at potentials ≥−10 mV and ≥−20 mV, respectively, and this was accompanied by a lower charge density at ≥−20 mV. Action potential duration was increased inMib1flox;Tnnt2Crecardiomyocytes. The cardiac stress, induced by swimming endurance training or β-adrenergic stimulation with isoproterenol, increases QTc duration inMib1flox;Tnnt2Cremice, accompanied by a decrease in T-wave amplitude and area. Swimming endurance training decreased heart rate in wildtype andMib1flox;Tnnt2Cremice but was unaffected by long-term isoproterenol treatment. These mouse findings are in agreement with an increased QTc duration found in LVNC patients carryingMIB1mutations. These results provide insight into the outcomes of LVNC and relate its pathogenicity to impaired ventricular repolarization.
TaxSEA: an R package for rapid interpretation of differential abundance analysis output
Authors: Ryan Feargal J.
Published: November 2024

Microbial communities are essential regulators of ecosystem function, with their composition commonly assessed through DNA sequencing. Most current tools focus on detecting changes among individual taxa (e.g., species or genera), however in other omics fields, such as transcriptomics, enrichment analyses like Gene Set Enrichment Analysis (GSEA) are commonly used to uncover patterns not seen with individual features. Here, we introduce TaxSEA, an R package for taxon set enrichment analysis. TaxSEA integrates taxon sets from five public microbiota databases (BugSigDB, MiMeDB, GutMGene, mBodyMap, and GMRepoV2) to assess whether disease signatures, metabolite producers, or previously reported associations are enriched or depleted in a metagenomic dataset of interest. In-silico assessments show TaxSEA is accurate across a range of set sizes. When applied to differential abundance analysis output from Inflammatory Bowel Disease and Type 2 Diabetes metagenomic data, TaxSEA outperforms current tools and can rapidly identify changes in functional groups corresponding to known associations. We also show that TaxSEA is robust to the choice of differential abundance (DA) analysis package. In summary, TaxSEA enables researchers to efficiently contextualize their findings within the broader microbiome literature, facilitating rapid interpretation and advancing understanding of microbiome–host and environmental interactions.
CTCF depletion decouples enhancer-mediated gene activation from chromatin hub formation during cellular differentiation
Authors: Karpinska Magdalena A. , Zhu Yi , Ghazvini Zahra Fakhraei , Ramasamy Shyam , Barbieri Mariano , Cao T. B. Ngoc , Varahram Natalie , Aljahani Abrar , Lidschreiber Michael , Papantonis Argyris , Oudelaar A. Marieke
Published: November 2024

Enhancers and promoters interact in 3D chromatin structures to regulate gene expression. Here, we characterize the mechanisms that drive the formation of these structures and their function in gene regulation in a lymphoid-to-myeloid transdifferentiation system. Based on analyses at base-pair resolution, we demonstrate a close correlation between binding of regulatory proteins, formation of chromatin interactions, and gene expression. Integration of multi-way interaction analyses and computational modeling shows that tissue-specific gene loci are organized into chromatin hubs, characterized by cooperative interactions between multiple enhancers, promoters, and CTCF-binding sites. Depletion of CTCF strongly impairs the formation of these structures. However, the effects of CTCF depletion on gene expression are modest and can be explained by rewired enhancer-promoter interactions. This demonstrates an instructive role for enhancer-promoter interactions in gene regulation that is independent of cooperative interactions in chromatin hubs. Together, these results contribute to a mechanistic understanding of the structure-function relationship of the genome during cellular differentiation.