bluuebunny/crossref_metadata_2025 huggingface dataset:
Surgical Second Opinion for Pancreatic Cancer Patients
Authors: Quinn Patrick L , Nikahd Melica , Saiyed Shah , Heifetz Addie , Bath Natalie M , Hyer J Madison , Cloyd Jordan M , Jain Shikha , Ejaz Aslam
Published: September 2024

BACKGROUND:

Due to the complexity of pancreatic surgery, patients diagnosed with pancreatic ductal adenocarcinoma (PDAC) may seek out the opinion of more than 1 surgeon. Little is known regarding how second surgical opinions impact the likelihood of pancreatectomy and perioperative outcomes. Our study aimed to determine the impact of obtaining second surgical opinions on pancreatectomy rates and to assess its impact on surgical outcomes.

STUDY DESIGN:

Patients who were diagnosed with PDAC between 2013 and 2020 were identified using 100% Medicare Inpatient and Outpatient Standard Analytic Files. Data collected included the number of surgeons consulted and geographic region. Receipt of pancreatectomy and perioperative outcomes were compared between patients who received only 1 and more than 1 surgical consultation.

RESULTS:

Of 116,072 patients diagnosed with PDAC, 10,640 (9.2%) underwent pancreatectomy. A total of 4,913 (4.2%) patients received a second surgical opinion, of whom 1,906 (17.9%) patients underwent pancreatectomy after the second opinion visit. Patients receiving a second surgical opinion were more likely to undergo pancreatectomy (adjusted odds ratio 6.17; 95% CI 5.78 to 6.59). Patients who received a second opinion and underwent surgery had equivalent length of stay and complication rates compared to those who underwent surgery without seeking a second opinion (both p > 0.05).

CONCLUSIONS:

Among Medicare patients who underwent pancreatectomy for pancreatic cancer, approximately 1 in 7 patients received a second surgical opinion. Further research is needed to determine how patient motivations, referral patterns, disease characteristics, and treatments all interplay to affect clinical outcomes for patients undergoing pancreatectomy for PDAC.
FLIMPA: A versatile software for Fluorescence Lifetime Imaging Microscopy Phasor Analysis
Authors: Kapsiani Sofia , Läubli Nino F. , Ward Edward N. , Shehata Mona , Kaminski Clemens F. , Kaminski Schierle Gabriele S.
Published: September 2024

Fluorescence lifetime imaging microscopy (FLIM) is an advanced microscopy technique capable of providing a deeper understanding of the molecular environment of a fluorophore. While FLIM data were traditionally analysed through the exponential fitting of the fluorophores’ emission decays, the use of phasor plots is increasingly becoming the preferred standard. This is due to their ability to visualise the distribution of fluorescent lifetimes within a sample, offering insights into molecular interactions in the sample without the need for model assumptions regarding the exponential decay behaviour of the fluorophores. However, so far most researchers have had to rely on commercial phasor plot software packages, which are closed-source and rely on proprietary data formats. In this paper, we introduce FLIMPA, an opensource, stand-alone software for phasor plot analysis that provides many of the features found in commercial software, and more. FLIMPA is fully developed in Python and offers advanced tools for data analysis and visualisation. It enhances FLIM data comparison by integrating phasor points from multiple trials and experimental conditions into a single plot, while also providing the possibility to explore detailed, localised insights within individual samples. We apply FLIMPA to introduce a cell-based assay for the quantification of microtubule depolymerisation, measured through fluorescence lifetime changes of SiR-tubulin, in response to various concentrations of Nocodazole, a microtubule depolymerising drug relevant to anti-cancer treatment.
IL-27 neutralization to modulate the tumor microenvironment and increase immune checkpoint immunotherapy efficacy
Authors: Papargyris Loukas , Glaziou Quentin , Basset Laetitia , d’Almeida Sènan , Pignon Pascale , Jabrane-Ferrat Nabila , Blanquart Christophe , Delneste Yves , Tabiasco Julie
Published: September 2024

Tumor-associated macrophages (TAMs) accumulate in the majority of solid tumors, producing inflammatory cytokines and growth factors involved in tumor maintenance. They have recently emerged as targets for restoring an effective antitumor response and limiting tumor growth. In the present study, we investigated the potential of IL-27 neutralization to modify macrophage polarization and thus the tumor immune microenvironment.

We monitored the effect of IL-27 neutralization on human macrophages and in vivo in a murine colon adenocarcinoma model.

In this study, we demonstrated the importance of IL-27 in the generation of human immunoregulatory macrophages. Mechanistically, IL-27 neutralization reduced the immunosuppressive properties of macrophages. These modifications led to a reduction in the ability of macrophages to inhibit the function of CD4+and CD8+T cells. Furthermore, in vivo neutralization of IL-27 reduced MC38 tumor growth. Collectively, we uncovered the role of IL-27 in the immunosuppressive tumor microenvironment. IL-27 neutralization thus appears as a promising strategy to target macrophages in immunosuppressive TME and improve the clinical efficacy of immunotherapy protocols.
Validation of a refined protocol for mouse oral glucose tolerance testing without gavage
Authors: Pye Katherine R. , Lantier Louise , Ayala Julio E. , Beall Craig , Ellacott Kate L.J.
Published: September 2024

A glucose tolerance test (GTT) is routinely used to assess glucose homeostasis in clinical settings and in preclinical research studies using rodent models. The procedure assesses the ability of the body to clear glucose from the blood in a defined time after a bolus dose. In the human clinical setting, glucose is ingested via voluntary consumption of a glucose-sweetened drink. Typically, in the rodent GTT oral gavage (gavage-oGTT) or (more commonly) intraperitoneal injection (IPGTT) are used to administer the glucose bolus. Although used less frequently, likely due to investigator technical and experience barriers, the former is the more physiologically relevant as it integrates the gastrointestinal tract (GI), including release of key incretin hormones. However, orally gavaging glucose in the GTT is also not without its limitations: gavaging glucose straight into the stomach bypasses potentially critical early glucose-sensing via the mouth (cephalic phase) and associated physiological responses. Furthermore, gavaging is stressful on mice, and this by itself can increase blood glucose levels. We have developed and validated a refined protocol for mouse oral GTT which uses a voluntary oral glucose dosing method, micropipette-guided drug administration (MDA), without the need for water deprivation. This approach is simple and non-invasive. It is less stressful for the mice, as evidenced by lower circulating corticosterone levels 10 minutes after glucose-dosing compared to oral gavage. This is significant for animal and investigator welfare, and importantly minimising the confounding effect of stress on mouse glucose homeostasis. Using a randomised cross-over design, we have validated the MDA approach in the oGTT against oral gavage in male and female C57BL/6J and C57BL/6N mice. We show the ability of this method to detect changes in glucose tolerance in diet-induced obese animals. Compared to oral gavage there was lower inter-animal variation in the MDA-oGTT. In addition to being more representative of the human procedure, the MDA-oGTT is easy and has lower barriers to adoption than the gavage oGTT as it is non-invasive and requires no specialist equipment or operator training. The MDA-oGTT a more clinically representative, accessible, and refined replacement for the gavage-oGTT for mouse metabolic phenotyping, which is simple yet overcomes significant deficiencies in the current standard experimental approaches.
Pharmacological Inhibition of Epac1 Protects against Pulmonary Fibrosis by Blocking FoxO3a Neddylation
Authors: Jankowski Katherine , Lemay Sarah E , Lozano-ojalvo Daniel , Perez Rodriguez Leticia , Sauvaget Mélanie , Breuils-Bonnet Sandra , Formoso Karina , Jagana Vineeta , Zhang Shihong , Milara Javier , Cortijo Julio , Turnbull Irene C. , Provencher Steeve , Bonnet Sebastien , Orchando Jordi , Lezoualc’h Frank , Bisserier Malik , Hadri Lahouaria
Published: September 2024

Background

Idiopathic Pulmonary fibrosis (IPF) is characterized by progressive scarring and fibrosis within the lungs. There is currently no cure for IPF; therefore, there is an urgent need to identify novel therapeutic targets that can prevent the progression of IPF. Compelling evidence indicates that the second messenger, cyclic adenosine monophosphate (cAMP), inhibits lung fibroblast proliferation and differentiation through the classical PKA pathway. However, the contribution of theexchangeprotein directlyactivated bycAMP 1 (Epac1) to IPF pathophysiological processes is yet to be investigated.

Objective

To determine the role of the cAMP-binding protein Epac1 in the progression of IPF.

Methods

We used lung samples from IPF patients or healthy controls, mouse lung samples, or lung fibroblast isolated from a preclinical mouse model of PF induced by bleomycin intratracheal injection. The effect of bleomycin (BLM) treatment was determined in Epac1 knock-out mice or wild-type littermates. Epac1 expression was modulatedin vitroby using lentiviral vectors or adenoviruses. The therapeutic potential of the Epac1-selective pharmacological inhibitor, AM-001, was testedin vivoandin vitro,using a bleomycin mouse model of PF and anex vivoprecision-cut lung slices (PCLs) model of human lung fibrosis.

Results

Epac1 expression was increased in the lung tissue of IPF patients, in IPF-diseased fibroblasts and in BLM-challenged mice. Furthermore, Epac1 genetic or pharmacological inhibition with AM-001 decreased normal and IPF fibroblast proliferation and the expression of profibrotic markers, αSMA, TGF-β/SMAD2/3, and interleukin-6 (IL-6)/STAT3 signaling pathways. Consistently, blocking Epac1 protected against BLM-induced lung injury and fibrosis, suggesting a therapeutic effect of Epac1 inhibition on PF pathogenesis and progression. Global gene expression profiling revealed a decrease in the key components of the profibrotic gene signature and neddylation pathway in Epac1-deficient lung fibroblasts and IPF human-derived PLCs. Mechanistically, the protective effect of Epac1 inhibition against PF development involves the inhibition of FoxO3a neddylation and its subsequent degradation by NEDD8, and in part, by limiting the proliferative capacity of lung-infiltrating monocytes.

Conclusions

We demonstrated that Epac1 is an important regulator of the pathological state of fibroblasts in PF and that small molecules targeting Epac1 can serve as novel therapeutic drugs against PF.
Dissecting earthworm diversity in tropical rainforests
Authors: Goulpeau Arnaud , Hedde Mickaël , Ganault Pierre , Lapied Emmanuel , Maggia Marie-Eugénie , Marcon Eric , Decaëns Thibaud
Published: September 2024

Tropical rainforests are among the most emblematic ecosystems in terms of biodiversity. However, our understanding of the structure of tropical biodiversity is still incomplete, particularly for certain groups of soil organisms such as earthworms, whose importance for ecosystem functioning is widely recognised. This study aims at determining the relative contribution of alpha and beta components to earthworm regional diversity at a hierarchy of nested spatial scales in natural ecosystems of French Guiana. For this, we performed a hierarchical diversity partitioning of a large dataset on earthworm communities, in which DNA barcode-based operational taxonomic units (OTUs) were used as species surrogates. Observed regional diversity comprised 256 OTUs. We found that alpha diversity was lower than predicted by chance, regardless of the scale considered. Community-scale alpha diversity was on average 7 OTUs. Beta diversity among remote landscapes was higher than expected by chance, explaining as much as 87% of regional diversity. This points to regional mechanisms as the main driver of species diversity distribution in this group of organisms with low dispersal capacity. At more local scales, multiplicative beta diversity was higher than expected by chance between habitats, while it was lower than expected by chance between communities in the same habitat. This highlights the local effect of environmental filters on the species composition of communities. The calculation of a Chao 2 index predicts that as much as 1,700 species could be present in French Guiana, which represents a spectacular increase compared with available checklists, and calls into question the commonly accepted estimates of global number of earthworm species.
Optimization of rearingTranseius montdorensisunder laboratory conditions
Authors: Nguyen Hung , Nguyen Binh , Mainali Bishwo , Maselko Maciej
Published: September 2024

The global application ofTranseius montdorensis(Acari: Phytoseiidae) as a biological control agent across various protected crops has proven effective against a range of insect pests like thrips and whiteflies, as well as pest mites like broad mites and russet mites. Optimization of rearingT. montdorensisunder laboratory conditions is crucial for further studies of this species to improve their application in Integrated Pest Management (IPM) programs. Here, we evaluated the development and reproduction ofT. montdorensiswhen fed on four different diets, including cattail pollen (Typha latifolia), living dried fruit mites (Carpoglyphus lactis), frozenC. lactiseggs, and a mixed diet of frozenC. lactiseggs andT. latifoliapollen. Females consuming the mixed diet exhibited superior total fecundity and daily oviposition rate, along with the highest intrinsic rate of increase (rm) and net productive rate (R0) among all diets tested. The immature period was significantly longer for mites on a diet of livingC. lactiscompared to those on other diets. Importantly, utilizing frozenC. lactiseggs andT. latifoliapollen mitigates the risk of infestation and contamination from the living dried fruit mites, which is important for laboratory and field settings when releasing the predator colonies. Our findings not only present an optimized rearing method for predatory mites under laboratory conditions but also suggest potential broader applications for enhancing the effectiveness and sustainability of biological control strategies across various agroecosystems and reducing dependency on chemical pesticides.
Design and immunogenicity of an HIV-1 clade C pediatric envelope glycoprotein stabilized by multiple platforms
Authors: Kumar Sanjeev , del Moral-Sánchez Iván , Singh Swarandeep , Newby Maddy L. , Allen Joel D. , Bijl Tom P. L. , Vaghani Yog , Jing Liang , Ortlund Eric A. , Crispin Max , Patel Anamika , Sanders Rogier W. , Luthra Kalpana
Published: September 2024

Various design platforms are available to stabilize soluble HIV-1 envelope (Env) trimers, which can be used as antigenic baits and vaccine antigens. However, stabilizing HIV-1 clade C trimers can be challenging. Here, we stabilized an HIV-1 clade C trimer based on an Env isolated from a pediatric elite-neutralizer (AIIMS_329) using multiple platforms, including SOSIP.v8.2, ferritin nanoparticles (NP) and an I53-50 two-component NP, followed by characterization of their biophysical, antigenic, and immunogenic properties. The stabilized 329 Envs showed binding affinity to trimer-specific HIV-1 broadly neutralizing antibodies (bnAbs), with negligible binding to non-neutralizing antibodies (non-nAbs). Negative-stain electron microscopy (nsEM) confirmed the native-like conformation of the Envs. Multimerization of 329 SOSIP.v8.2 on ferritin and two-component I53-50 NPs improved the overall affinity to HIV-1 bnAbs and immunogenicity in rabbits. These stabilized HIV-1 clade C 329 Envs demonstrate the potential to be used as antigenic baits and as components of multivalent vaccine candidates in future.
Melanocortin-4 receptor antagonist TCMCB07 alleviates chemotherapy-induced anorexia and weight loss
Authors: Zhu Xinxia , Potterfield Russell , Gruber Kenneth A. , Zhang Emma , Newton Samuel , Norgard Mason A. , Levasseur Peter R. , Bai Peng , Chen Xu , Gu Qingyang , Grossberg Aaron J. , Marks Daniel L.
Published: September 2024

Cancer patients undergoing chemotherapy often experience anorexia and weight loss that significantly deteriorates overall health, reduces treatment tolerance and quality of life, and worsens oncologic outcomes. There are currently few effective therapeutic options to mitigate these side effects. The central melanocortin system, which plays a pivotal role in regulating appetite and energy homeostasis, presents a logical target for treating anorexia and weight loss. In this preclinical study, we evaluated the efficacy of TCMCB07, a synthetic antagonist of the melanocortin-4 receptor, in mitigating anorexia and weight loss in several rat models of chemotherapy: cisplatin, 5-fluorouracil, cyclophosphamide, vincristine, doxorubicin, and a combination of irinotecan and 5-fluorouracil. Our results indicate that peripheral administration of TCMCB07 improved appetite, stabilized body weight, preserved fat and heart mass, and slightly protected lean mass after multiple cycles of chemotherapy. Furthermore, combining TCMCB07 with a growth differentiation factor 15 antibody enhanced treatment effectiveness. Similar effects from TCMCB07 treatment were observed in a rat tumor model following combination chemotherapy. No significant adverse effects nor increased chemotherapy-related toxicities were observed with TCMCB07 treatment. These findings suggest that peripheral administration of TCMCB07 holds promise as a therapeutic approach for alleviating chemotherapy-induced anorexia and weight loss, potentially benefiting numerous patients undergoing chemotherapy.

Graphical abstract
An Experimental Test of Local Adaptation in Native and Introduced Populations of an Ectomycorrhizal Fungus,Suillus luteus
Authors: Allen Brooke M. , Vilgalys Rytas J. , Hoeksema Jason D.
Published: September 2024

After species introductions and subsequent invasions, organisms often encounter intense selection pressures from biotic and abiotic aspects of novel environments, driving rapid evolutionary changes that potentially lead to local adaptation. This study aimed to investigate how invasion has influenced symbiotic interactions through rapid evolution in exotic isolates of the ectomycorrhizal (EcM) fungusSuillus luteus, which was co-introduced with obligately symbiotic pine trees into the Southern Hemisphere. We conducted a cross-inoculation experiment testing the compatibility of sympatric and allopatric pairings between pines and isolates ofS. luteusfrom native and introduced populations. Our results showed that plant and fungal performance were substantially affected by these pairings, largely supporting a hypothesis of local maladaptation. Several performance metrics indicated stronger outcomes in allopatric pairings compared to sympatric ones. This suggests that fungal isolates may have evolved traits that are less beneficial or even somewhat harmful to their local host plants. These findings highlight the complex dynamics of coevolution and emphasize the necessity of considering both local adaptation and maladaptation in understanding species interactions.
Characterizing the connection between Parkinson’s disease progression and healthcare utilization
Authors: Fitzsimmons Lane , Frau Francesca , Bozzi Sylvie , Chandross Karen J. , Beaulieu-Jones Brett K.
Published: September 2024

Background and Objectives

Parkinson’s disease (PD) progression can be characterized in terms of healthcare utilization by analyzing clinical events across different stages of disease.

Methods

PD progression was measured by the Hoehn & Yahr (H&Y) clinical rating scale and clinical events at each stage were evaluated. Natural language processing and a large language model were used to extract H&Y values from real-world data enabling a larger cohort than manually collected studies, and multi-state hidden Markov models were used for H&Y progression likelihood.

Results

Within the one year, most patients in H&Y stages 2-5 remained in the same stage. Stage transitions, when they occurred, were most frequently to the next higher stage. Higher H&Y stages were associated with discharges into long term care and higher rates of additional clinical events.

Conclusions

Stratifying key clinical events by H&Y score demonstrates the increases of health care utilization and economic burden with PD severity. Modelling the progression likelihood establishes a progression timeline and emphasizes the unmet need to identify treatment options that stop or slow these transitions.
A rapid, inexpensive, culture-free, universal bacterial identification system using internal transcribed spacer targeting primers: a proof-of-principle study
Authors: Asthana Vishwaratn , Nieves Erika Martínez , Bugga Pallavi , Smith Clara , Dunn Tim , Narayanasamy Satish , Dickson Robert P. , VanEpps J. Scott
Published: September 2024

Techniques for bacterial detection and identification can be characterized as either untargeted and taxonomically broad or targeted and taxonomically narrow. Untargeted techniques (e.g., culture and sequencing) are time-consuming and/or expensive while targeted techniques (polymerase chain reaction; PCR) can be faster and less expensive but require a strong pre-test suspicion of the potential organism to choose the correct test. We have developed a universal bacterial identification system that is as taxonomically broad as culture and amplicon sequencing but as fast, easy, and affordable as PCR. The platform utilizes a unique universal polymerase chain reaction (PCR) primer set that targets the internal transcribed spacer (ITS) regions between conserved bacterial genes, creating a distinguishable electrophoretic pattern for each bacterial species. Bioinformatic simulation demonstrates that at least 45 commonly isolated pathogenic species can be uniquely identified from a single set of PCR primers using this approach. We experimentally confirmed these predictions on seven representative human pathogens, including gram-negatives and gram-positives, aerobes and anaerobes, and spore formers. Withouta prioriknowledge of the organism, this system can rapidly identify the unique pattern generated by multiple species in a single reaction. Using quantitative PCR, the system can also determine the corresponding concentration of the organism in question. We also show that the primers are resilient to human DNA contamination at physiologic concentrations, eliminating the need for complex and time intensive extraction methods. Proof-of-principle testing on actual clinical specimens demonstrate that this assay can identify more than twice the species as current multiplex PCR assays (e.g., BioFire) using only one universal primer pair in a single PCR reaction, providing results in <3 hours for <$20 without bioinformatic turnaround time.

SIGNIFICANCE STATEMENT

This paper describes a novel bacterial identification system that is as taxonomically broad as culture and amplicon sequencing but as fast, easy, and affordable as PCR. The assay covers more than twice the species as the leading multiplex PCR assays but uses only one universal primer pair in a single PCR reaction. It is resilient to human genomic contamination precluding the need for timely or costly methods to clear human DNA. This approach represents a major advancement in the decades-long struggle to rapidly and accurately identify bacteria.
DNA polymerase theta-mediated DNA repair is a functional dependency and therapeutic vulnerability in DNMT3A deficient leukemia cells
Authors: Le Bac Viet , Vekariya Umeshkumar , Toma Monika M , Nieborowska-Skorska Margaret , Caron Marie-Christine , Gozdecka Malgorzata , Haydar Zayd , Walsh Martin , Ghosh Jayashri , Vaughan-Williams Elaine , Podszywalow-Bartnicka Paulina , Kukuyan Anna-Mariya , Ziolkowska Sylwia , Hadzijusufovic Emir , Chandramouly Gurushankar , Piwocka Katarzyna , Pomerantz Richard , Vassiliou George S , Huntly Brian JP , Valent Peter , Bellacosa Alfonso , Masson Jean-Yves , Gupta Gaorav P , Challen Grant A , Skorski Tomasz
Published: September 2024

Myeloid malignancies carrying somatic DNMT3A mutations (DNMT3Amut) are usually resistant to standard therapy. DNMT3Amut leukemia cells accumulate toxic DNA double strand breaks (DSBs) and collapsed replication forks, rendering them dependent on DNA damage response (DDR). DNA polymerase theta (Polθ), a key element in Polθ-mediated DNA end-joining (TMEJ), is essential for survival and proliferation of DNMT3Amut leukemia cells. Polθ is overexpressed in DNMT3Amut leukemia cells due to abrogation of PARP1 PARylation-dependent UBE2O E3 ligase-mediated ubiquitination and proteasomal degradation of Polθ. In addition, PARP1-mediated recruitment of the SMARCAD1-MSH2/MSH3 repressive complex to DSBs was diminished in DNMT3Amut leukemia cells which facilitated loading of Polθ on DNA damage and promoting TMEJ and replication fork restart. Polθ inhibitors enhanced the anti-leukemic effects of mainstream drugs such as FLT3 kinase inhibitor quizartinib, cytarabine and etoposide in vitro and in mice with FLT3(ITD);DNMT3Amut leukemia. Altogether, Polθ is an attractive target in DNMT3Amut hematological malignancies
Free fatty acids accelerate β-cell death in type 1 diabetes
Authors: Elliott Emily C. , Sakar Soumyadeep , Bramer Lisa , Burnet Meagan , Kim Young-Mo , Yi Xiaoyan , Estevao Igor L. , Rewers Marian , Cambronne Xiaolu A. , Vehik Kendra , Arrojo e Drigo Rafael , Metz Thomas O. , Eizirik Decio L. , Webb-Robertson Bobbie-Jo M. , Mirmira Raghavendra G. , Nakayasu Ernesto S.
Published: September 2024

Type 1 diabetes (T1D) results from autoimmune destruction of the insulin producing pancreatic β cells. The body’s lipid metabolism is strongly regulated during this process but there is a need to understand how this regulation contributes to the β-cell death. Here, we show that fatty acids are released from plasma lipoproteins in children during islet autoimmunity, prior to T1D onset. These fatty acids (FFAs) enhanced cytokine-mediated apoptosis in cultured insulin-producing cells by downregulating the production of nicotinamide adenosine dinucleotide (NAD) via its salvage pathway, as well as deregulated central carbon metabolism and impaired levels of ATP. Downregulation of the NAD salvage pathway and central carbon metabolism enzymes were further observed during T1D development, supporting that the pathways for NAD and energy production are compromisedin vivo. Our findings show that fatty acids are released during islet autoimmunity, accelerating disease development through impaired NAD metabolism.
Transcranial magnetic stimulation of dorsomedial prefrontal cortex for cocaine use disorder: A pilot study
Authors: Webber Heather E. , Hong L. Elliot , Quevedo João , Weaver Michael F. , Schmitz Joy M. , Lane Scott D.
Published: September 2024

Cocaine use disorder (CUD) is a difficult-to-treat condition with no FDA-approved medications. Recent work has turned to brain stimulation methods to help rectify hypofrontality and dopamine reward system changes often observed in individuals with CUD. Preliminary studies using transcranial magnetic stimulation (TMS) have demonstrated promising results, but there is room for optimization of the stimulation site, stimulation pattern, and identification of relevant biomarkers of TMS effects. The current pilot study aimed to test the feasibility, safety, and preliminary effects of a double-blind, sham-controlled, cross-over, acute design using intermittent theta burst stimulation to dorsomedial prefrontal cortex (dmPFC) on electroencephalogram (EEG) as intermediate outcome assessment in CUD patients. This small pilot enrolled five individuals with moderate-to-severe CUD for feasibility and proof-of-concept. Participants completed safety, psychometric, and EEG measures before and after receiving two sessions of active or sham TMS to dmPFC on two separate days. All five participants completed all the study tasks and found the TMS to be tolerable. The side effects were minimal and consistent with an acute TMS design. Visible changes were observed in the electrical activity of the brain during a monetary guessing task, while minimal changes in psychometric measures were observed. These results indicate the feasibility and safety of the current approach and suggest that dmPFC is a viable target for treating CUD. Future work should expand upon these findings in a randomized controlled clinical trial.
Integrative modeling in the age of machine learning: a summary of HADDOCK strategies in CAPRI rounds 47-55
Authors: Reys Victor , Giulini Marco , Cojocaru Vlad , Engel Anna , Xu Xiaotong , Roel-Touris Jorge , Geng Cunliang , Ambrosetti Francesco , Jiménez-García Brian , Jandova Zuzana , Koukos Panagiotis I. , van Noort Charlotte , Teixeira Joao M. C. , van Keulen Siri C. , Réau Manon , Honorato Rodrigo V. , Bonvin Alexandre M.J.J.
Published: September 2024

The HADDOCK team participated in CAPRI rounds 47-55 as both server, manual predictor, and scorers. Throughout these CAPRI rounds, we used a plethora of computational strategies to predict the structure of protein complexes. Of the 10 targets comprising 24 interfaces, we achieved acceptable or better models for 3 targets in the human category and 1 in the server category. Our performance in the scoring challenge was slightly better, with our simple scoring protocol being the only one capable of identifying an acceptable model for Target 234. This result highlights the robustness of the simple, fully physics-based HADDOCK scoring function, especially when applied to highly flexible antibody-antigen complexes. Inspired by the significant advances in machine learning for structural biology and the dramatic improvement in our success rates after the public release of Alphafold2, we identify the integration of classical approaches like HADDOCK with AI-driven structure prediction methods as a key strategy for improving the accuracy of model generation and scoring.
Mechanical Profiling of Biopolymer Condensates through Acoustic Trapping
Authors: Nakajima Kichitaro , Sneideris Tomas , Good Lydia L. , Erkamp Nadia A. , Ogi Hirotsugu , Knowles Tuomas P. J.
Published: September 2024

Characterizing the mechanical properties of single colloids is a central problem in soft matter physics. It also plays a key role in cell biology through biopolymer condensates, which function as membraneless compartments. Such systems can also malfunction, leading to the onset of a number of diseases, including many neurodegenerative diseases; the functional and pathological condensates are commonly differentiated by their mechanical signature. Probing the mechanical properties of biopolymer condensates at the single particle level has, however, remained challenging. In this study, we demonstrate that acoustic trapping can be used to profile the mechanical properties of single condensates in a contactless manner. We find that acoustic fields exert the acoustic radiation force on condensates, leading to their migration to a trapping point where acoustic potential energy is minimized. Furthermore, our results show that the Brownian motion fluctuation of condensates in an acoustic potential well is an accurate probe for their bulk modulus. We demonstrate that this framework can detect the change in the bulk modulus of polyadenylic acid condensates in response to changes in environmental conditions. Our results show that acoustic trapping opens up a novel path to profile the mechanical properties of soft colloids at the single particle level in a non-invasive manner with applications in biology, materials science, and beyond.
Most Beefalo cattle have no detectable bison genetic ancestry
Authors: Shapiro Beth , Oppenheimer Jonas , Heaton Michael P , Kuhn Kristen L , Green Richard E , Blackburn Harvey D , Smith Timothy PL
Published: September 2024

Hybridization is common among lineages in the genusBos, often mediated through human management for the selection of adaptive or desirable traits. A recent example is the American Beefalo cattle breed, which was developed in the 1970s and defined as a hybrid between American bison (Bison bison) and cattle (Bos taurus). The American Beefalo Association typically require ⅜ bison ancestry to qualify as Beefalo. Here, we sought to characterize admixed ancestry among Beefalo as a component of a larger project to understand the role of hybridization in shaping present-day diversity in bison and cattle. We generated genomic data from 50 historical and present-day Beefalo and bison hybrids, including several important founding animals, as well as from 10 bison originating from commercial herds that represent potential sources of bison ancestry in Beefalo. We found that most Beefalo did not contain detectable bison ancestry. No individual Beefalo within our data set satisfies the ancestry requirements specified by the American Beefalo Association (ABA), although several Beefalo had smaller proportions of bison ancestry (2-18%). Some beefalo had detectable indicine cattle ancestry (2-38%), suggesting that hybridization of taurine and zebu cattle may contribute to morphological similarity between some Beefalo and bison. Overall, ancestry profiles of Beefalo and bison hybrid genomes are consistent with repeated backcrossing to either parental species rather than the breeding between hybrids themselves, implying significant barriers to gene flow between bison and cattle. Our results call into question the ⅜ bison ancestry targeted by the breed association and demonstrate the value of genomic information in examining claims of interspecies gene flow amongBosspecies.
Directional Cell-to-cell Transport in Plant Roots
Authors: Jacquier Léa , Fiorenza Celeste , Robe Kevin , Han Jian-Pu , Cléard Fabienne , Fuchs Christelle , Ramakrishna Priya , Loubéry Sylvain , Lefebvre-Legendre Linnka , Barberon Marie
Published: September 2024

Cell-to-cell communication is critical for multicellular organisms. In plants, plasmodesmata—cytoplasmic channels—enable molecular transport between adjacent cells. In roots, this transport is predicted to be essential in nutrient acquisition and delivery to the vasculature. We demonstrate that plasmodesmatal transport persists in differentiated roots, despite apoplastic barriers such as Casparian strips and suberin lamellae in the endodermis, suggesting plasmodesmata as the sole pathway for water and nutrient flow at this stage. We also reveal a developmental switch in plasmodesmata function resulting in an unidirectional transport in differentiated roots. A genetic screen identified mutations that disrupt this directionality, leading to bidirectional transport. These mutations correlate with larger plasmodesmatal apertures, linked to defects in pectin composition and cell wall organization. This discovery underscores the role of plasmodesmatal aperture regulation and pectin in controlling directional transport. Our findings provide insights into plasmodesmata function and their regulation in roots.
A long shelf-life melon created via CRISPR/Cas9 RNP-basedin plantagenome editing
Authors: Sasaki Kentaro , Mimida Naozumi , Nonaka Satoko , Ezura Hiroshi , Imai Ryozo
Published: September 2024

We developed a non-culture and DNA-free genome editing technique for melon using in plant Particle Bombardment (iPB-RNP). The method was employed to create CmACO1 mutants. One of the mutant lines exhibited an extended shelf life due to ethylene deficiency during fruit ripening. As no cell culture step is involved, the iPB-RNP method is expected to overcome limitations associated with conventional genome editing, such as genotype dependency and somatic variations. Thus, this methodology holds significant potential for application in commercial melon breeding and across a wide range of Cucurbitaceae species.
A transcontinental experiment elucidates (mal)adaptation of a cosmopolitan plant to climate in space and time
Authors: Albano Lucas J. , Bastias Cristina C. , Estarague Aurélien , Hendrickson Brandon T. , Innes Simon G. , King Nevada , Patterson Courtney M. , Tudoran Amelia , Vasseur François , Puentes Adriana , Violle Cyrille , Kooyers Nicholas J. , Johnson Marc T. J.
Published: September 2024

Climate change and the global spread of invasive species are two of the most significant threats to biodiversity. Both of these phenomena subject populations to novel conditions, either in space (species invasion) or in time (climate change), yet the role of adaptation in how populations respond to these rapid environmental shifts is poorly understood. We conducted a large-scale trans-continental common garden experiment using white clover (Trifolium repens, Fabaceae) to test if adaptive evolution to spatiotemporal variation in climate could contribute to the ecological success of one of the most widespread invasive plant species in the world. Individuals from 96 populations ofTrifolium repens(white clover) from both its native (Europe) and introduced (North America) ranges were planted into four experimental common gardens located in northern (Uppsala, Sweden) and southern (Montpellier, France) Europe, and northern (Mississauga, Canada) and southern (Louisiana, USA) North America. We recorded plant sexual and clonal fitness in each common garden and assessed whether the strength of local adaptation differed between the native and introduced ranges and whether populations are rapidly adapting to climate change. Results show that local adaptation was only evident when populations were transplanted into common gardens located in the same range (native or introduced) from which they originated and was driven by stronger selection (due to climatic factors rather than herbivory) at lower latitudes in both ranges. Our results indicate that rapid local adaptation across a large latitudinal gradient has occurred inT. repenspopulations in less than 400 years since its introduction to North America. However, we find evidence of an adaptation lag in the northern common garden in the introduced range, with plants from historically slightly warmer climates exhibiting the greatest fitness. These findings support two major conclusions: 1) white clover can rapidly adapt to spatial variation in climate in its introduced range as well as the native range, and 2) despite rapid adaptation to novel ranges, introduced white clover populations are not keeping pace with rapid climate change. Overall, our results provide insight into the role of adaptation in facilitating the ecological success of invasive species in a rapidly changing world.
Effect of oral contraceptive consumption timing on substrate metabolism, cognition, and exercise performance in females: a randomised controlled trial
Authors: Martin D , Bargh M , Pennington K
Published: September 2024

The pharmacokinetic profile of oral contraceptives (OCs) results in an acute, transient increase in circulating synthetic reproductive hormones. The aim of this study was to examine the effects of acute OC ingestion on cognitive function, substrate metabolism and exercise performance. Sixteen combined OC (30µg ethinyl oestradiol and 150mg Levonorgestrel) users ingested either their OC or placebo (PLA) in a randomised, double-blind, crossover manner. After 60 minutes, participants completed tests of verbal memory and verbal fluency, followed by sub-maximal treadmill exercise for 6 minutes at 60% lactate threshold (LT) and 90% LT where respiratory exchange ratio (RER), carbohydrate oxidation, fat oxidation, heart rate (HR), rating of perceived exertion (RPE), felt arousal and feeling scale were recorded. Participants then completed an incremental ramp test to exhaustion to assess time to exhaustion (TTE) and peak oxygen uptake (VO2peak), before ingesting the pill corresponding to the condition, they were not in. RER, arousal and feeling scale were all significantly lower in the OC condition compared to PLA (all P < 0.05) with no difference in HR, carbohydrate oxidation, fat oxidation, RPE, TTE or VO2peak (all P > 0.05). Verbal fluency score was significantly higher in the OC condition compared to PLA (P < 0.05), with no differences between conditions for any aspect of verbal memory (all P < 0.05). Combined OC ingestion acutely affects substrate metabolism, affective responses to exercise and verbal fluency. The timing of OC ingestion should be considered in relation to aspects of physiological function.

Key findings

Ingestion of a combined oral contraceptive (OC) results in a transient increase in circulating synthetic reproductive hormones.

The altered reproductive hormone profile affects substrate metabolism and affective responses to exercise.

Cognitive performance in a verbal fluency task is also improved post OC ingestion.

The within-day timing of OC ingestion can be manipulated to affect aspects of physiology, which may have implications for athletes, exercises and the general population, in addition to interpretation of prior research using OCs.
Meta-SAIGE: Scalable and Accurate Meta-Analysis for Rare Variants
Authors: Park Eunjae , Nam Kisung , Jeong Seokho , Keat Karl , Kim Dokyoon , Bansal Vikas , Zhou Wei , Lee Seunggeun
Published: September 2024

A meta-analysis is a practical approach to increasing the power of rare variant tests by combining summary statistics from multiple cohorts. However, existing methods for rare variant meta-analysis often fail to correctly control type I error rates when analyzing low-prevalence binary traits and are computationally intensive when analyzing many phenotypes. This paper introduces Meta-SAIGE, a novel approach for rare variant meta-analyses that addresses these challenges. Meta-SAIGE reduces type I error inflation through precise estimation of the distribution of test statistics and allows the reuse of the linkage disequilibrium (LD) matrix across phenotypes, significantly improving computational efficiency for phenome-wide analyses. Simulation studies using UK Biobank whole-exome sequencing (WES) genotypes demonstrate that Meta-SAIGE effectively controls type I error rates and yields power similar to that of pooled individual-level data through SAIGE-GENE+. A meta-analysis of UK Biobank and All of Us WES data for 83 low prevalence disease phenotypes identified 237 associations. Notably, 80 of these associations were not significant in either dataset alone, underscoring the power of our meta-analysis.
Cas9AEY (Cas9-facilitated Homologous Recombination Assembly of non-specific Escherichia coli yeast vector) method of constructing large-sized DNA
Authors: ma xiaoshu , yang lei , ye hua
Published: September 2024

Saccharomyces cerevisiae is widely used in DNA assembly due to their efficient homologous recombination [1], but DNA assembly through yeast recombination in vivo usually requires the vector to have the ability to replicate in yeast. The CRISPR-Cas9 system can efficiently edit DNA [2,3], and the system can also be used for DNA editing of plasmids. In this paper, a yeast universal element is selected, which can be inserted into the vector, so that the vector can replicate in yeast cells, and then the intermediate plasmid containing yeast universal element can be obtained by recombination in yeast. At the same time, a pCas-SmR plasmid was designed in this paper. After Donor DNA is added, the CRISPR-Cas9 system can accurately and efficiently knock out the yeast universal element in the intermediate plasmid, remove the pCas-SmR plasmid through sucrose screening, and finally obtain a pure plasmid. Saccharomyces cerevisiae cells are widely used in DNA assembly due to their efficient homologous recombination [1], but DNA assembly through yeast recombination in vivo usually requires the vector to have the ability to replicate in yeast. The CRISPR-Cas9 system can efficiently edit DNA [2,3], and the system can also be used for DNA editing of plasmids. In this paper, a yeast universal element is selected, which can be inserted into the vector, so that the vector has the ability to replicate in yeast cells, and then the intermediate plasmid containing yeast universal element can be obtained by recombination in yeast. At the same time, a pCas-SmR plasmid was designed in this paper. After Donor DNA is added, the CRISPR-Cas9 system can accurately and efficiently knock out the yeast universal element in the intermediate plasmid, remove the pCas-SmR plasmid through sucrose screening, and finally obtain a pure knocked out plasmid.
The LOTUS-domain containing protein PpLDCP3 controls germline and dispersal unit formation in the moss Physcomitrium patens
Authors: Kermanov Anton , Becker Jorg D.
Published: September 2024

Dispersal is crucial for the survival and thriving of plant populations, yet the mechanisms of dispersal unit formation are poorly understood. LOTUS domain-containing proteins are essential for animal reproduction, promoting cell cycle control, transposon silencing, and transgenerational inheritance in the germline. In this study, we demonstrate that the formation of dispersal units, sperm and spores, in the model moss Physcomitrium patens relies on the novel LOTUS domain-containing protein 3 (PpLDCP3). Ppldcp3 knock-out mutants revealed pleiotropic phenotypes in both gametogenesis and sporogenesis. Ppldcp3 sperm were rarely released and appeared to be partially non-viable, leading to fewer sporophytes produced. Sporophyte development in Ppldcp3 was impaired, resulting in abnormal dehiscence of spores, which were incapable of germinating. Fluorescent reporter lines revealed the presence of PpLDCP3 in developing gametangia. Within the premature egg cell and ventral canal cell of archegonia, PpLDCP3 was identified as a component of cytoplasmic fluorescent foci, which we interpret as P-bodies. This suggests a role for PpLDCP3 in RNA metabolism, analogous to animal LDCPs. Moreover, bioinformatic predictions indicate PpLDCP3 as a downstream player of WOX13 and bHLH transcription factors. We conclude that PpLDCP3 is integrated into evolutionary conserved mechanisms of dispersal unit formation in land plants.
Differential translocation of bacteriophages across the intestinal barrier in health and Crohn’s disease
Authors: Douadi Clara , Theodorou Ilias , Lamy-Besnier Quentin , Schiettekatte Olivier , Sbardella Yanis , Brot Loïc , Costantini Paolo Emidio , Saporetti Roberto , Danielli Alberto , Calvaresi Matteo , De Paepe Marianne , Sokol Harry , Garcia-Weber Diego , Carrière Véronique , Thenet Sophie , De Sordi Luisa
Published: September 2024

Impaired intestinal barrier function is a major feature of Crohn’s disease (CD), leading to exacerbated inflammation in response to the microbiota. In this context, the translocation of intestinal bacteriophages (phages) and their effects on the host have been little investigated. We used phage fluorescence imaging coupled with ex-vivo and in-vitro models that mimic physiological and inflammatory conditions and found that phages can translocate across the intestinal barrier without disrupting its integrity. Although the translocation rate across the intestinal epithelium depended on phage morphology and the condition of the barrier, these factors did not influence the crossing of phage across the vascular endothelium. Virome analysis confirmed that viral sequences shared between blood and stool samples are more abundant in CD patients than healthy subjects, indicating that a barrier defect facilitates phage translocation from the gut to the bloodstream.