bluuebunny/crossref_metadata_2025 huggingface dataset:
A Flexible Framework for Assessing the Cumulative Effects of Offshore Wind Energy Activities and Other Pressures on Aerofauna
Authors: Ferguson Megan C. , Williams Kathryn A. , Goodale M. Wing , Adams Evan M. , Knaga Paul , Kingdon Katrien , Avery-Gomm Stephanie
Published: August 2024

The offshore wind energy (OSW) industry is pivotal for renewable energy transition and climate resiliency. However, OSW activities may negatively affect aerofauna, contributing to CE from human activities and natural processes. Cumulative effects assessments (CEA) are vital for informed planning and management of OSW activities during regional assessment, site selection, and site evaluation. To reduce impacts on aerofauna, OSW developments should be sited in areas that avoid or minimize cumulative effects (CE). This study presents a cohesive and flexible framework for assessing the CE from OSW activities, other human activities, and natural processes on aerofauna to support decision-making during the initial OSW planning phases. The framework uses a species-based approach, applicable to various receptors, and adapts to available information on ecology, socioeconomics, and pressures. The analytical strategy uses a CE metric to indicate the presence or magnitude of effects from all pressures on receptors. Spatially explicit optimization methods identify OSW site configurations that minimize a CE metric. The framework accommodates alternative pressure scenarios that include foreseeable future human activities and natural processes and can explore the sensitivity of the result to uncertain parameters. Given sufficient spatial information on receptor density, pressure magnitude, and cause-effect pathways, the spatial optimization algorithm can find solutions that minimize population-level impacts from CE. If this ideal standard cannot be achieved due to information gaps, alternative metrics may be used to inform the immediate decision-making process.
Anin vivoscreen identifies NAT10 as a master regulator of brain metastasis
Authors: Chen Jocelyn F , Xu Peng , Cai Wesley L , Chen Huacui , Wingrove Emily , Li Wenxue , Biancon Giulia , Zhang Meiling , Balabaki Amer , Krop Ethan D , Zhang Yangyi , Yin Mingzhu , Tebaldi Toma , Meier Jordan L , Westbrook Thomas F , Halene Stephanie , Liu Yansheng , Nguyen Don X , Yan Qin
Published: August 2024

Metastasis is the major cause of cancer-related deaths. Emerging evidence has shown that epigenetic regulation plays a fundamental role in cancer metastasis. To better understand the epigenetic regulation of metastasis, we conducted an in vivo shRNA screen for vulnerabilities of brain metastasis and identified N-acetyltransferase 10 (NAT10) as a driver of brain metastasis. Knockdown of NAT10 significantly restrains cancer cell proliferation and migrationin vitro, and tumor growth and brain metastasisin vivo. Structure-function analysis of NAT10 showed that its poorly characterized RNA helicase domain is critical for breast cancer cell growthin vitro, while its N-acetyltransferase domain is essential for primary tumor growth and brain metastasisin vivo. Integrative transcriptomic and proteomic analyses revealed key downstream effectors of NAT10, including PHGDH and PSAT1, two catalyzing enzymes for serine biosynthesis implicated in brain metastasis, and HSPA5, known to promote metastasis. We found that distant metastases of breast cancer, especially brain metastases express higher levels of NAT10, PHGDH, PSAT1, and HSPA5. Silencing PHGDH/PSAT1 or HSPA5 in metastatic breast cancer cells inhibits their ability to grow in the serine/glycine-limited condition or migrate, respectively, phenocopying the effects of NAT10 depletion. Moreover, NAT10 promotes the expression of PHGDH, PSAT1, and HSPA5 in its RNA helicase-dependent manner. These findings establish NAT10 as a master regulator of brain metastasis and shed light on the biological functions of its RNA helicase domain, nominating NAT10 as a target for treating metastatic diseases.
Data acquisition strategies to reduce cardiac-induced noise in brain maps of R2* and magnetic susceptibility
Authors: Raynaud Quentin , Dardano Thomas , Oliveira Rita , Di Domenicantonio Giulia , Kober Tobias , Roy Christopher W. , van Heeswijk Ruud B. , Lutti Antoine
Published: August 2024

Purpose

Cardiac pulsation increases the noise level in brain MR images. Maps of the transverse relaxation rate R2* and magnetic susceptibility (QSM) are particularly affected by cardiac-induced noise as they are computed from gradient-echo data acquired at multiple echo times. Here, we introduce two data acquisition strategies to mitigate the impact of cardiac-induced noise in brain maps of R2* and QSM.

Methods

The proposed strategies are based on the higher level of cardiac-induced noise near the k-space centre. Using a pseudo-spiral sampling trajectory, the first strategy allows for the acquisition of a specific number of averages at each k-space location, set from the local level of cardiac-induced noise. The second strategy synchronizes the acquisition with the cardiac cycle in real time. We compared in 10 healthy volunteers, the variability of data acquired across 4 repetitions and in the same session, using both strategies and with a standard linear trajectory.

Results

Compared to linear sampling, the pseudo-spiral trajectory reduced the variability of R2* and QSM maps across repetitions by 26/28/22% and 19/18/16% in the brainstem/cerebellum/whole brain, for a 14% increase in scan time. The pseudo-spiral sampling also reduced the level of aliasing artifacts from pulsating blood vessels. The cardiac-triggered trajectory did not reduce the variability of R2* or QSM maps.

Conclusion

Pseudo-spiral k-space trajectories can be designed to mitigate cardiac-induced noise in brain maps of the MRI parameters R2* and QSM. Synchronization of the acquisition with the cardiac cycle in real time did not lead to any reduction in cardiac-induced noise.
Evidence for belief updating in decision-variable space: past decisions with finer granularity attract future ones more strongly
Authors: Lee Heeseung , Lim Jaeseob , Lee Sang-Hun
Published: August 2024

Essential to adaptive intelligence is the ability to create mental spaces where knowledge from past experiences cumulates and integrates with newly acquired information. When engaged in decision-making tasks, humans are known to create such a space and therein form decision variables, which integrate task-essential information from multiple sources in a generalizable form. Much effort has focused on the cognitive and neural processes involved in forming decision variables. However, there is limited understanding of how decision variables, once formed, are utilized to adapt to the environment. Considering the abstract and generalizable nature of decision variables, we reason that decision-makers would benefit from shaping and updating probabilistic knowledge—known asbelief—within the decision-variable space. As one such belief updating, we hypothesize that an act of decision commitment restricts the current belief about the decision variable to a range of states corresponding to that decision. This implies that past decisions not only attract future ones but also exert a greater pull when those decisions are made with finer granularity—dubbed ‘the granularity effect.’ Here, we present the findings of seven psychophysical experiments that consistently confirm these implications while ruling out the stimulus and action space as potential loci of the granularity effect. Further, as a principled and unified account of the granularity effect and other history effects found in various perceptual tasks, we offer a Bayesian model where beliefs are updated separately in the stimulus and decision-variable spaces. Our work demonstrates how humans leverage the abstract and generalizable nature of the decision-variable space to effectively adapt to their surroundings, expanding the gamut of human intellect.
Angiotensin Converting Enzyme Hub Model of Peptide Flux Relating Calculated AT1 Receptor and Aldosterone Levels
Authors: Westwood Brian M. , Chappell Mark C.
Published: August 2024

Utilizing data from the Vitamin C, Thiamine, and Steroids in Sepsis (VICTAS) Trial, this hub model was developed to limit seventeen Renin-Angiotensin-Aldosterone System (RAAS) components as three entrance and four exits, to facilitate the calculation of a model as one egress unknown, the angiotensin type 1 (AT1) receptor. Following previous evidence relating renin levels to mortality, this study found controls were more like sepsis patients with levels < renin quartile 1 (Q1) for calculated AT1, while more like sepsis patients with renin levels > quartile 3 (Q4) for measured aldosterone levels. Additionally differential discrete correlate summation (DCS) analysis indicates AT1, aldosterone and renin as major hub nodes in this independent DCS model of metabolic data inputs.
Extracellular Vesicle-Associated Neutrophil Elastase Activates Hepatic Stellate Cells and Promotes Liver Fibrogenesis via ERK1/2 Pathway
Authors: Oshins Regina , Greenberg Zachary , Tai Yun-Ling , Zhao Derrick , Wang Xuan , Mehrad Borna , He Mei , Patel Ishan , Khartabil Laith , Zhou Huiping , Brantly Mark , Khodayari Nazli
Published: August 2024

Liver fibrosis associated with increased mortality is caused by activation of hepatic stellate cells and excessive production and accumulation of extracellular matrix in response to fibrotic insults. It has been shown that in addition to liver inflammation, systemic inflammation also contributes to liver fibrogenesis. A deeper understanding of mechanisms that control liver fibrotic response to intra- and extra-hepatic inflammation is essential to develop novel clinical strategies against this disease. Extracellular vesicles (EV) have been recognized as immune mediators that facilitate activation of hepatic stellate cells. In inflammatory diseases, activated neutrophils release neutrophil elastase (NE) bound to EV, which has been identified as a significant contributor to inflammation by promoting immune cell activation. Here, we aimed to explore the role of inflammation derived plasma EV-associated NE in liver fibrogenesis and its potential mechanisms. We show EV-associated NE induces activation, proliferation and migration of hepatic stellate cells by promoting activation of the ERK1/2 signaling pathway. This effect did not occur through EV without surface NE, and Sivelestat, a NE inhibitor, inhibited activation of the ERK1/2 signaling pathway mediated by EV-associated NE. Moreover, we found plasma EV-associated NE increases deposition of collagen1 and α-smooth muscle actin in the liver of a mouse model of liver fibrosis (Mdr2-/-). Notably, this effect does not occur in control mice without preexisting liver disease. These data suggest that EV-associated NE is a pro-fibrogenic factor for hepatic stellate cell activation via the ERK1/2 signaling pathway in pre-existing liver injuries. Inhibition of the plasma EV-associated NE in inflammatory conditions may be a therapeutic target for liver fibrosis in patients with inflammatory diseases.
Protein stability models fail to capture epistatic interactions of double point mutations
Authors: Dieckhaus Henry , Kuhlman Brian
Published: August 2024

There is strong interest in accurate methods for predicting changes in protein stability resulting from amino acid mutations to the protein sequence. Recombinant proteins must often be stabilized to be used as therapeutics or reagents, and destabilizing mutations are implicated in a variety of diseases. Due to increased data availability and improved modeling techniques, recent studies have shown advancements in predicting changes in protein stability when a single point mutation is made. Less focus has been directed toward predicting changes in protein stability when there are two or more mutations, despite the significance of mutation clusters for disease pathways and protein design studies. Here, we analyze the largest available dataset of double point mutation stability and benchmark several widely used protein stability models on this and other datasets. We identify a blind spot in how predictors are typically evaluated on multiple mutations, finding that, contrary to assumptions in the field, current stability models are unable to consistently capture epistatic interactions between double mutations. We observe one notable deviation from this trend, which is that epistasis-aware models provide marginally better predictions on stabilizing double point mutations. We develop an extension of the ThermoMPNN framework for double mutant modeling as well as a novel data augmentation scheme which mitigates some of the limitations in available datasets. Collectively, our findings indicate that current protein stability models fail to capture the nuanced epistatic interactions between concurrent mutations due to several factors, including training dataset limitations and insufficient model sensitivity.

Significance

Protein stability is governed in part by epistatic interactions between energetically coupled residues. Prediction of these couplings represents the next frontier in protein stability modeling. In this work, we benchmark protein stability models on a large dataset of double point mutations and identify previously overlooked limitations in model design and evaluation. We also introduce several new strategies to improve modeling of epistatic couplings between protein point mutations.
Fecal microbiota transplantation promotes immunotherapy sensitivity in refractory gastrointestinal cancer patients: open label, single-arm, single center, phase 1 study
Authors: Zhang Yifan , Xu Xiaomin , Wang Shulin , Yin Xiaochen , Zhang Bohan , Zhu Zhengnong , Ji Rujie , Zhu Jing , He Hermione , Cheng Siyuan , Han Zihan , Xie Tong , Zhang Xiaotian , Wang Yakun , Shen Si , Kou Yan , Bao Siyu , Liu Yingyu , Cao Baoran , Bonny Christophe , Segal Eran , Tan Yan , Shen Lin , Peng Zhi
Published: August 2024

Background

The discovery and therapeutic application of immune checkpoint inhibitors (ICIs) has significantly improved clinical outcomes in cancer treatment. However, the response rate is still low in gastrointestinal (GI) cancers. The gut microbiome’s impact on immune modulation is a promising area for enhancing ICI efficacy.

Methods

This study (NCT04130763) is an open label, single-arm, single center, phase 1 study assessing the safety and efficacy of fecal microbiota transplantation (FMT) from healthy donors in ten advanced GI cancer patients resistant to anti-PD-(L)1 treatment. Patients received initial FMT treatment via oral capsules, followed by a combination therapy phase, where maintenance FMT was paired with nivolumab at 3mg/kg every two weeks for six cycles. Serial biomarker assessments were conducted through both fecal and blood sampling.

Findings

The combination of FMT and anti-PD1 treatment was well tolerated with no serious adverse reactions observed among all 10 patients. The objective response rate was 20% and the disease control rate was 40%. The progression-free survival of these two responders were 15 and more than 19 months respectively. Clinical benefits were associated with colonization of donor-derived immunogenic microbes, and an activated immune status reflected by peripheral immune cell populations. Responder-enriched microbes interacted closely as a butyrate-functional guild, while non-responder-enriched microbes interacted sparsely and had higher fraction of oral-originated microbes. Donor-specific microbial traits that influence clinical efficacy of FMT were validated in an independent cohort.

Interpretation

The current study demonstrates the feasibility of FMT for ICI-refractory GI cancer patients and provides a foundation for live biotherapeutic product (LBP) development to enhance ICI efficacy.
Capacity and limitations of microfluidic flow to increase solute transport in three-dimensional cell cultures
Authors: Bonneuil Willy V. , Katiyar Neeraj , Tenje Maria , Bagheri Shervin
Published: August 2024

Culturing living cells in three-dimensional (3D) environments increases the biological relevance of laboratory experiments, but has the caveat of requiring solutes to overcome a diffusion barrier to reach the center of cellular constructs. We present a theoretical and numerical investigation that brings a mechanistic understanding of how microfluidicculture conditions, including chamber size, inlet fluid velocity, and spatial confinement, affect solute distribution within 3D cellular constructs. Contact with the culture chamber reduces the maximally achievable construct radius by 15%. In practice, finite diffusion and convection kinetics in the microfluidic chamber further lower that limit. The benefits of external convection are greater if transport rates across diffusion-dominated areas are high. Those are omnipresent and include the diffusive boundary layer growing from the fluid-construct interface and regions near corners where fluid is recirculating. Less convection is required to approach an ideal maximally-supplied state when diffusion within the constructs is slow. Our results contribute to defining the conditions where complete solute transport into an avascular 3D cell construct is achievable and demonstrate how flow velocity must evolve with construct radius in order to maintain a given solute penetration depth.
Tumor suppressor p53 controls thymic NKT17 development
Authors: Celli Sofia , Watanabe Masashi , Hodes Richard J.
Published: August 2024

The tumor suppressor p53 antagonizes tumorigenesis, notably including the suppression of T cell lymphomas while its role on physiological T cell biology including thymic T cell development has not been fully understood. Invariant natural killer T (iNKT) cells develop in the thymus as innate-like αβ-T cells which consist of NKT1, NKT2 and NKT17 subsets. We found that the tumor suppressor p53 regulates specifically thymic NKT17 development. p53 is highly expressed in NKT17 relative to other T cell populations. Loss of p53 in the T cell lineage resulted in increased thymic NKT17 cell number with retention of lineage specific cytokine production, while development of NKT1, NKT2 and conventional T cells was not affected. Of interest, γH2AX expression was higher in NKT17 than NKT1 and NKT2 at steady state, and it was further increased in p53-deficient NKT17, suggesting that NKT17 development involves selectively greater DNA damage or genomic instability and that p53 expression might be in response to these damage signals. Taken together, our results indicated that the tumor suppressor p53 is active in selectively controlling thymic NKT17 development, with absence of p53 leading to an increase in thymic NKT17 cells expressing high levels of DNA damage response.
Functional imaging and connectome analyses reveal organizing principles of taste circuits inDrosophila
Authors: Li Jinfang , Dhaliwal Rabiah , Stanley Molly , Junca Pierre , Gordon Michael D.
Published: August 2024

Taste is crucial for many innate and learned behaviors. In the fly, taste impacts feeding, oviposition, locomotion, mating, and memory formation, to name a few. These diverse roles may necessitate the apparent distributed nature of taste responses across different circuits in the fly brain, leading to complexity that has hindered attempts to deduce unifying principles of taste processing and coding. Here, we combine information from the whole brain connectome with functional calcium imaging to examine the neural representation of taste at early steps of processing. We find that the representation of taste quality remains largely segregated in cholinergic and GABAergic local interneurons (LNs) that are directly postsynaptic to taste sensory neurons of the labellum. Although some taste projection neurons (TPNs) projecting to superior protocerebrum receive direct inputs from sensory neurons, many receive primarily indirect taste inputs via cholinergic LNs. Moreover, we found that cholinergic interneurons appear to function as nodes to convey feedforward information to dedicated sets of morphologically similar TPNs. Examining a small number of representative TPNs suggests that taste information remains mostly segregated at this level as well. Together, these studies suggest a previously unappreciated logic in the organization of fly taste circuits.
TAF1-dependent transcriptional dysregulation underlies multiple sclerosis
Authors: Rodríguez-López Claudia , Hernández Ivó H. , Terrón-Bautista José , Agirre Eneritz , Lozano-Muñoz David , Pose-Utrilla Julia , García-Ortiz Inés , Lucas-Santamaría Miriam , Ruiz-Blas Irene , González-Bermejo María , Ortega María C. , Chara Juan C. , Martínez Zara , Pérez-Cerdá Fernando , Fransen Nina L. , Martínez-Jiménez Miriam , Sancho-González Beatriz , Pérez-Samartín Alberto , Kabbe Mukund , Zheng Chao , Casado-Barbero Marcos , Santos-Galindo María , Borroto Aldo , Alarcón Balbino , Clemente Diego , Toma Claudio , Matute Carlos , Cortés-Ledesma Felipe , Castelo-Branco Gonçalo , Lucas José J.
Published: August 2024

Multiple sclerosis (MS) is characterized by neuroinflammation and demyelination of the central nervous system (CNS), leading to disablility1, 2. Genetic variants that confer MS risk implicate genes involved in immune function3, while variants related to severity of the disease are associated with genes preferentially expressed within the CNS4. Current MS therapies decrease relapse rates by preventing immune-mediated damage of myelin, but they ultimately fail to slow long-term disease progression, which apparently depends on CNS intrinsic processes. The molecular events that trigger progressive MS are still unknown. Here we report that the C-terminal region of TAF1 (the scaffolding subunit of the general transcription factor TFIID) is underrepresented in postmortem brain tissue from individuals with MS. Furthermore, we demonstratein vivo,in genetically modified mice, that C-terminal alteration of TAF1 suffices to induce an RNA polymerase II (RNAPII)-elongation deficit that particularly affects oligodendroglial myelination-related genes and results in an MS-like brain transcriptomic signature, including increased expression of proinflammatory genes. This transcriptional profile is accompanied by CNS-resident inflammation, robust demyelination and MS-like motor phenotypes. We also identify numerous interactors of C-terminal TAF1 that participate in RNAPII-promoter escape, of which two show evidence for genetic association to MS3, 4. Our study reveals that TAF1 dysfunction converges with genetic susceptibility to cause transcriptional dysregulation in CNS cell types, such as oligodendrocytes, to ultimately trigger MS.
Using dynamic ultrasound to assess Achilles tendon mechanics during running: the effect on running pattern and muscle-tendon junction tracking
Authors: Schallig Wouter , Sloot Ytjanda , van der Schaaf Milou M. , Bus Sicco A.
Published: August 2024

Achilles tendon strain can be quantified using dynamic ultrasound, but its use in running is limited. Minimal effects on running pattern and acceptable test-retest reliability of muscle-tendon junction (MTJ) tracking are prerequisites for ultrasound use during running. We aimed to assess (i) the effect of wearing an ultrasound transducer on running pattern and (ii) the test-retest reliability of MTJ tracking during running. Sixteen long-distance runners (nine injury-free, seven with Achilles tendinopathy) ran at different speeds on an instrumented treadmill with a 10-camera system tracking skin-mounted retroreflective markers, first without and then with an ultrasound transducer attached to the lower leg to track the MTJ of the gastrocnemius medialis. Spatiotemporal parameters, joint kinematics and kinetics were compared between conditions using mixed ANOVAs and paired t-tests. MTJ tracking was performed manually twice by three raters in ten participants. Variability and standard error of measurement (SEM) quantified the inter- and intra-tester test-retest reliability. The running pattern was not affected by wearing the ultrasound transducer, except for significantly less knee flexion during midstance (1.6°) and midswing (2.9°) found when wearing the transducer. Inter-rater and intra-rater SEMs for MTJ tracking to assess the tendon strain (0.43%, and 0.56%, respectively) were about four times as low as between-group differences presented in literature. The minimal effects found on the running pattern and acceptable test-retest reliability indicates that dynamic ultrasound during running can be appropriately used to study Achilles tendon mechanics and thereby help improve our understanding of Achilles tendon behavior during running, injury development and recovery.
Dynamic alterations of dural and bone marrow B cells in an animal model of progressive multiple sclerosis
Authors: Florescu Alexandra , Zuo Michelle , Wang Angela A. , Champagne-Jorgensen Kevin , Noor Mohammed Ariyan , Ward Lesley A. , van Puijenbroek Erwin , Klein Christian , Gommerman Jennifer L.
Published: August 2024

In multiple sclerosis (MS), the leptomeninges (LM) are populated with immune cell aggregates that correlate with disease progression. The impact of LM inflammation on the adjacent dura is largely unknown. Using a mouse model of MS that induces brain LM inflammation and age-dependent disease progression, we found that encephalitogenic T cells and B220highB cells accumulate substantially in the brain LM and parenchyma of both young and aged mice, while the adjacent dura remains relatively inert. We also observed a population of anti-CD20 resistant B220lowB cells in the dura and bone marrow that virtually disappear at disease onset and accumulate in the brain of young mice concomitant with disease remission. In contrast, aged mice show a paucity of brain-resident B220lowB cells at the expense of class-switched B220highB cells concomitant with severe, chronic disease. In summary, dynamic changes in brain, LM and dural B cells are associated with age-dependent disease severity in an animal model of progressive MS.

Short Summary

Florescuet al. investigate the temporal accumulation of immune cells within distinct meningeal compartments in an animal model of progressive MS and uncover a population of anti-CD20 resistant dural B cells that remain in the brain parenchyma at disease remission.
Ecosystem stability relies on diversity difference between trophic levels
Authors: Liu Yizhou , Hu Jiliang , Gore Jeff
Published: August 2024

The stability of ecological communities has a profound impact on humans, ranging from individual health influenced by the microbiome to ecosystem services provided by fisheries. A long-standing goal of ecology is the elucidation of the interplay between biodiversity and ecosystem stability, with some ecologists warning of instability due to loss of species diversity while others arguing that greater diversity will instead lead to instability. Here, by considering a minimal two-level ecosystem with multiple predator and prey species, we show that stability does not depend on absolute diversity but rather on diversity differences between levels. We discovered that increasing diversity in either level first destabilizes but then stabilizes the community (i.e., a re-entrant stability transition). We therefore find that it is the diversity difference between levels that is the key to stability, with the least stable communities having similar diversities in different levels. An analytical stability criterion is derived, demonstrating quantitatively that the critical diversity difference is determined by the correlation between how one level affects another and how it is affected in turn. Our stability criterion also applies to consumer-resource models with other forms of interaction such as cross-feeding. Finally, we show that stability depends on diversity differences in ecosystems with three trophic levels. Our finding of a non-monotonic dependence of stability on diversity provides a natural explanation for the variety of diversity-stability relationships reported in the literature, and emphasizes the significance of level structure in predicting complex community behaviors.
Screening macrocyclic peptide libraries by yeast display allows control of selection process and affinity ranking
Authors: Linciano Sara , Mazzocato Ylenia , Romanyuk Zhanna , Vascon Filippo , Soler Lluc Farrera , Will Edward , Xing Yuyu , Chen Shiyu , Kumada Yoichi , Simeoni Marta , Scarso Alessandro , Cendron Laura , Heinis Christian , Angelini Alessandro
Published: August 2024

Macrocyclic peptides provide an attractive modality for drug development due to their ability to bind challenging targes, their small size, and amenability to powerfulin vitroevolution techniques such as phage or mRNA display. While these technologies proved capable of generating and screening extremely large libraries and yielded ligands to already many targets, they often do not identify the best binders within a library due to the difficulty of monitoring performance and controlling selection pressure. Furthermore, only a small number of enriched ligands can typically be characterised due to the need of chemical peptide synthesis and purification prior to characterisation. In this work, we address these limitations by developing a yeast display-based strategy for the generation, screening and characterisation of structurally highly diverse disulfide-cyclised peptides. Analysis and sorting by quantitative flow cytometry enabled monitoring the performance of millions of individual macrocyclic peptides during the screening process and allowed us identifying macrocyclic peptide ligands with affinities in the low micromolar to high picomolar range against five highly diverse protein targets. X-ray analysis of a selected ligand in complex with its target revealed optimal shape complementarity, large interaction surface, constrained peptide backbones and multiple inter- and intra-molecular interactions, rationalising the high affinity and exquisite selectivity. The novel technology described here offers a facile, quantitative and cost-effective alternative to rapidly and efficiently generate and characterise fully genetically encoded macrocycle peptide ligands with sufficiently good binding properties to even therapeutically relevant targets.
Temperature and Pressure Shaped the Evolution of Antifreeze Proteins in Polar and Deep Sea Zoarcoid Fishes
Authors: Bogan Samuel N. , Surendran Nathan , Hotaling Scott , Desvignes Thomas , Bista Iliana , Lins Luana S.F. , Eilertsen Mari H. , Le François Nathalie R. , Algayer Tait , Hamilton Scott L. , Frandsen Paul B. , Hoffmann Federico G. , Kelley Joanna L.
Published: August 2024

Antifreeze proteins (AFPs) have enabled teleost fishes to repeatedly colonize polar seas. Four AFP types have convergently evolved in several fish lineages. AFPs inhibit ice crystal growth and lower cellular freezing point. In lineages with AFPs, species inhabiting colder environments may possess more AFP copies. Elucidating how differences in AFP copy number evolve is challenging due to the genes’ tandem array structure and consequently poor resolution of these repetitive regions. Here we explore the evolution of type III AFPs (AFP III) in the globally distributed suborder Zoarcoidei, leveraging six new long-read genome assemblies. Zoarcoidei has fewer genomic resources relative to other polar fish clades while it is one of the few groups of fishes adapted to both the Arctic and Southern Oceans. Combining these new assemblies with additional long-read genomes available for Zoarcoidei, we conducted a comprehensive phylogenetic test of AFP III evolution and modeled the effects of thermal habitat and depth on AFP III gene family evolution. We confirm a single origin of AFP III via neofunctionalization of the enzyme sialic acid synthase B and show that AFP gains and losses were not only correlated with temperature, but also with depth, which reduces freezing point via pressure. Associations between the environment and AFP III copy number were driven by duplications of paralogs that were translocated out of the ancestral locus at which Zoarcoidei AFP arose. Our results reveal novel environmental effects on AFP evolution and demonstrate the value of high-quality genomic resources for studying how structural genomic variation shapes convergent adaptation.
Your Blood is Out for Delivery: Considerations of Shipping Time and Temperature on Degradation of RNA from Stabilized Whole Blood
Authors: Stefanovic Filip , Brown Lauren G. , MacDonald James , Bammler Theo , Rinchai Darawan , Nguyen Serena , Zeng Yuting , Shinkawa Victoria , Adams Karen , Chausabel Damien , Berthier Erwin , Haack Amanda J. , Theberge Ashleigh B.
Published: August 2024

Remote research studies are an invaluable tool for reaching populations in geographical regions with limited access to large medical centers or universities. To expand the remote study toolkit, we have previously developed homeRNA, which allows for at-home self-collection and stabilization of blood and demonstrated the feasibility of using homeRNA in high temperature climates. Here, we expand upon this work through a systematic study exploring the effects of high temperature on RNA integrity through in-lab and field experiments. Compared to the frozen controls (overall mean RIN of 8.2,n= 8), samples kept at 37°C for 2, 4, and 8 days had mean RINs of 7.6, 5.9, and 5.2 (n= 3), respectively, indicating that typical shipping conditions (∼2 days) yield samples suitable for downstream RNA sequencing. Shorter time intervals (6 hours) resulted in minimal RNA degradation (median RIN of 6.4,n= 3) even at higher temperatures (50°C) compared to the frozen control (mean RIN of 7.8,n= 3). Additionally, we shipped homeRNA-stabilized blood from a single donor to 14 different states and back during the summer with continuous temperature probes (7.1 median RIN,n= 42). Samples from all locations were analyzed with 3’ mRNA-seq to assess differences in gene counts, with the transcriptomic data suggesting that there was no preferential degradation of transcripts as a result of different shipping times, temperatures, and regions. Overall, our data support that homeRNA can be used in elevated temperature conditions, enabling decentralized sample collection for telemedicine, global health, and clinical research.
Benchmarking text-integrated protein language model embeddings and embedding fusion on diverse downstream tasks
Authors: Ko Young Su , Parkinson Jonathan , Wang Wei
Published: August 2024

Protein language models (pLMs) have traditionally been trained in an unsupervised manner using large protein sequence databases with an autoregressive or masked-language modeling training paradigm. Recent methods have attempted to enhance pLMs by integrating additional information, in the form of text, which are referred to as “text+protein” language models (tpLMs). We evaluate and compare six tpLMs (OntoProtein, ProteinDT, ProtST, ProteinCLIP, ProTrek, and ESM3) against ESM2, a baseline text-free pLM, across six downstream tasks designed to assess the learned protein representations. We find that while tpLMs outperform ESM2 in five out of six benchmarks, no tpLM was consistently the best. Thus, we additionally investigate the potential of embedding fusion, exploring whether the combinations of tpLM embeddings can improve performance on the benchmarks by exploiting the strengths of multiple tpLMs. We find that combinations of tpLM embeddings outperform single tpLM embeddings in five out of six benchmarks, highlighting its potential as a useful strategy in the field of machine-learning for proteins. To facilitate the practical application of embedding fusion, we outline a heuristic framework to efficiently identify the optimal combination of embeddings, reducing the exponential time complexity of an exhaustive combination search down to a manageable linear time complexity. Using our embedding fusion framework, we achieve state-of-the-art performances on the protein-protein interaction prediction and homologous sequence recovery tasks without any specific model adjustments or hyperparameter tuning. Our experiments suggest embedding fusion is a useful tool in the machine-learning for proteins toolbox. Lastly, this study highlights the potential of future research on additional strategies for maximizing the utility of pLMs.
Identification of a mesodermal progenitor for the pro-definitive angio-hematopoietic lineage
Authors: Lazarov Tomi , Loyher Pierre-Louis , Yang Hairu , Choo Zi-Ning , Deng Zihou , Nowotschin Sonja , Kuo Ying-Yi , Zhou Ting , Alberdi-Gonzalez Araitz , Stumm Ralf , Mass Elvira , Gomez Perdiguero Elisa , Hadjantonakis Anna-Katerina , Geissmann Frederic
Published: August 2024

Mammalian hematopoietic cells arise from mesodermal progenitors in a close developmental relationship with endothelium, and along three distinct cell lineages known as primitive, pro-definitive, and definitive hematopoiesis. However, the developmental hierarchy between mesodermal progenitors, endothelium, and blood cell lineages is incompletely understood. We report here the identification in mouse gastrula and human (h)iPSC cultures of a population of CXCR4+primitive streak stage mesodermal progenitors that give rise to yolk sac endothelium, blood islands, yolk sac hematopoiesis, and resident macrophages, corresponding to the pro-definitive lineage. Strikingy, this progenitor does not give rise to primitive erythropoiesis or to caudal endothelium and definitive hematopoiesis. Interestingly however, the pro-definitive progenitor population also gives rise to rostral endothelium that persists in adults. Finally, pro-definitive progenitor-derived endothelium is the first and main source of macrophages in embryo and hiPSC cultures, both directly and via previously described multipotent Erythro-Myeloid Progenitors. The identification and isolation of this mesodermal progenitor defines a revised pro-definitive angio-hematopoietic lineage and provides a framework for resident macrophage and endothelial differentiation relevant to disease pathophysiology and their manipulation for therapeutic purposes.

One sentence summary

Identification in gastrulating embryo and hiPSC cultures of a mesodermal progenitor for yolk sac and rostral endothelial cells, early macrophages, and Erythro-Myeloid Progenitors characterize pro-definitive hematopoiesis and provide a revised framework for early angio-hematopoietic development.

Graphical abstract

Schematic represents the progeny of angio-hematopoietic progenitors at the posterior primitive streak. Developmental timing of CXCR4 expression distinguishesi)CXCR4-primitive hematopoiesis,ii)Early CXCR4+angio-hematopoieticprogenitors (EXAP) (purple) whichexpressCXCR4 between E6.5 and E7.5 and give rise to rostral vessels and resident macrophages through YS hemogenic endothelium, andiii)late CXCR4+intraembryonic angio-hematopoietic progenitors (blue) which acquire expression of CXCR4 around E8 and give rise to definitive hematopoiesis through an intraembryonic hemogenic endothelium. Abbreviations: E (Mouse Embryonic Day); YS (Yolk Sac); Hemog. (Hemogenic); Endo. (Endothelium); Defi. (Definitive).
Effectiveness of Exercise Intervention in Preventing Active Arthritis Exacerbation in an SKG Mouse Model of Rheumatoid Arthritis
Authors: Ozone Kaichi , Kumagai Tatsunori , Arakawa Kouhei , Sugasawa Takehito , Gu Wenchao , Kawabata Sora , Shimada Naoki , Takahashi Haruna , Yoneno Moe , Minegishi Yuki , Takahata Kei , Sato Michiaki , Oka Yuichiro , Kanemura Naohiko
Published: August 2024

Objectives

To investigate the effects of low-intensity exercise on active arthritis in an SKG mouse model of human rheumatoid arthritis (RA) pathology.

Methods

Twenty-four female SKG mice were divided into three groups: ‘sedentary’ (control), ‘AR’ (induced arthritis), and ‘AREx’ (induced arthritis plus low-intensity exercise). Arthritis was induced via intraperitoneal administration of mannan. After a 2-week inflammation period, low-intensity treadmill exercise was performed only in the AREx group. Arthritis was assessed weekly during the rearing period. After 4 weeks of exercise, histological and bone morphometric analyses of the right ankle joint were performed. A histological analysis of the gastrocnemius muscle was also performed. Bulk mRNA sequencing was conducted on the left synovial membrane-fat pad (SM-FP) complex.

Results

The synovitis score showed no change; however, the arthritis score was significantly lower in the AREx group than in the AR group (p<0.05), indicating that low-intensity exercise suppressed arthritis exacerbation. The calcaneal and talar bone volumes decreased in the AR group, whereas the AREx group showed no significant change. In the SM-FP complex tissue, the gene expression of inflammatory cytokines decreased in the AREx group compared with the AR group, particularly the suppression of IL6/Jak/Stat3. Immunohistochemical analysis revealed significantly decreased expression of pro-inflammatory cytokines and increased expression of anti-inflammatory cytokines in the synovium of the AREx group compared with the AR group (p<0.05).

Conclusion

Low-intensity exercise therapy for active RA showed anti-inflammatory and suppressive effects on arthritis exacerbation in SKG mice, a mouse model of human RA pathology.

Key messages

Exercise had an anti-inflammatory effect on SKG mice, a mouse model of rheumatoid arthritis.

Exercise suppresses pro-inflammatory cytokine pathways such as IL6/Jak/Stat3 signalling in the synovial-fat complex tissue.

Exercise therapy is effective in improving the pathophysiology of active rheumatoid arthritis.
A Dimeric SINE Discovered in Shrew Mole is Structurally Similar to Primate Alu
Authors: Kosushkin Sergey A. , Vassetzky Nikita S. , Borodulina Olga R. , Kramerov Dmitri A.
Published: August 2024

Families of Short Interspersed Elements (SINEs) originate from tRNA, 5S rRNA, and 7SL RNA molecules in the genomes of multicellular organisms. Families of 7SL RNA-derived SINEs are very rare; however, they have been best studied in primates and rodents. The rodent B1 SINE is a monomeric element, whereas the primate Alu is composed of two 7SL RNA-derived monomers.We found that in contrast to other members of the family Talpidae (moles), which possess a tRNA-derived Tal SINE, the shrew moleUropsilus graciliscontains 280,000 genomic copies of the previously unknown 7SL RNA-derived Urop SINE. Like Alu, Urop consists of two monomers connected by an A-rich linker. The origin of the Urop monomers, like that of the Alu and B1 monomers, was mediated by several essentially identical events - a long central deletion in the 7SL RNA, dimerization, and/or internal duplication. Urop copies can be divided into three subfamilies (a, b, and c), the latter being the most numerous and recent. Urop_c has more copies with poly(A) tails longer than 50 compared to other L1-mobilized SINEs. Urop and Alu illustrate an independent emergence in the evolutionary history of highly similar SINEs.
Mammalian retinal specializations for high acuity vision evolve in response to both foraging strategies and morphological constraints
Authors: Kopania Emily E. K. , Clark Nathan L.
Published: August 2024

Vision is a complex sensory system that requires coordination among cellular and morphological traits, and it remains unclear how functional relationships among traits interact with ecological selective pressures to shape the evolution of vision. Many species have specialized high visual acuity regions in the retina defined by patterns of ganglion cell density, which may evolve in response to ecological conditions. For example, ganglion cell density can increase radially towards the center of the retina to form an area centralis, which is thought to improve acuity towards the center of the visual field in predators. Another example is the horizontal streak, where ganglion cells are dense across the center of the retina, which is thought to be beneficial in horizon-dominated habitats. At the morphological level, many have proposed that predation selects for high orbit convergence angles, or forward-facing eyes. We tested these hypotheses in a phylogenetic framework across eutherian mammals and only found support for the association between the horizontal streak and horizon-dominated habitats. We also tested if retinal specializations evolve in response to orbit convergence angles. We found that horizontal streaks were associated with side-facing eyes, which may both facilitate panoramic vision. Previous studies observed that some species with side-facing eyes have an area centralis shifted towards the temporal side of the retina, such that the high acuity region would project forward, but this relationship had not been tested quantitatively. We found that the temporal distance of the area centralis from the center of the retina was inversely correlated with orbit convergence, as predicted. Our work shows a strong relationship between orbit convergence and retinal specializations. We find support that both visual ecology and functional interactions among traits play important roles in the evolution of some ocular traits across mammals.
Bats from the Colombian Caribbean Reveal a new subtype of Influenza A (H18N12)
Authors: Echeverri-De la Hoz Daniel , Martínez-Bravo Caty , Gastelbondo-Pastrana Bertha , Rivero Ricardo , Lopez Yesica , Hoyos Richard , Alemán Maira , Garay Evelin , Bertel Valeria , Arrieta Germán , Ramírez Juan David , Mattar Salim
Published: August 2024

Influenza viruses have an excellent capacity for mutation and adaptation in mammalian hosts, which makes them viruses of medical and veterinary importance. Influenzaviruses have been studied mainly in birds but minor in bats. It is unknown whether Chiroptera are reservoirs of influenza viruses. However, circulation in bats showed molecular divergence from H17N10 (Guatemala) and H18N11 (Peru), and they were designated as new subtypes. The study aimed to characterize the influenza A virus detected in the fishing batNoctilio albiventris. A surveillance study of pathogens of public health interest was carried out; rectal samples were taken from four fishing bats (N. albiventris) captured in Talaigua Nuevo, Bolívar, Colombia. The samples were sequenced by NGS using DNBseq (MGI-G50®) and analyzed with bioinformatics tools. Eight viral contigs associated with the Orthomyxoviridae family were obtained. The identified segments showed around 90% similarity with H18N11, except for the neuraminidase (N). The phylogenetic analysis of the N protein showed the appearance of a basal branch to the N11 subtype, and the molecular clock indicates that it does not share a recent common ancestor. 3D modeling indicates that the N protein ofN. albiventrispresents three mutations (K363R, T242K, and I139V) near the hypothetical active site of the protein. These mutations potentially increase the interaction with the HLA-DR of bats, which could have significant implications for the virus’s behavior. The phylogenetic, evolutionary, and antigenic divergence of the N protein ofN. albiventrissuggests a new subtype called H18N12. Its role as a pathogen must be studied.