bluuebunny/crossref_metadata_2025 huggingface dataset:
Regulation of abscisic acid receptor mRNA stability: Involvement of microRNA5628 in PYL6 transcript decay
Authors: Vieira João G P , Duarte Gustavo T , Barrera-Rojas Carlos H , Matiolli Cleverson C , Viana Américo J C , Campos Raphael de A , Canesin Lucas E D , Vicentini Renato , Nogueira Fabio T S , Vincentz Michel
Published: December 2024

Phytohormone signaling is fine-tuned by regulatory feedback loops. The phytohormone abscisic acid (ABA) plays key roles in plant development and abiotic stress tolerance. PYRABACTIN RESISTENCE 1/PYR1-LIKE/REGULATORY COMPONENT OF ABA RECEPTOR (PYR/PYL/RCAR) receptors sense ABA, and in turn, ABA represses their expression. Conversely, ABA induces expression of Type 2C PROTEIN PHOSPHATASES (PP2C) genes, which negatively regulate the ABA signaling pathway. This regulatory feedback scheme is likely important for modulating ABA signaling. Here, we provide insight into the mechanisms underlying the ABA-induced repression of PYR/PYL/RCAR expression in Arabidopsis (Arabidopsis thaliana). ABA time course analyses revealed strong and sustained repression of PYR/PYL/RCARs, suggesting that receptor gene regulation is an important step in resetting the ABA signaling pathway. Cordycepin-induced transcription inhibition showed that PYL1/4/5/6 mRNA destabilization is involved in the ABA-induced repression of these genes. Furthermore, genetic evidence indicated that decapping may play a role in PYL4/5/6 mRNA decay. We also provide evidence that the Arabidopsis-specific microRNA5628 (miR5628), which is transiently induced by the ABA core signaling pathway, guides PYL6 transcript cleavage in response to ABA. After cleavage, the resulting 5′- and 3′-cleaved fragments of PYL6 mRNA may be degraded by the XRN4 exoribonuclease. miR5628 is an evolutionary novelty that may enhance PYL6 mRNA degradation, along with decapping and XRN4 activity. Thus, regulating the stability of PYR/PYL/RCAR transcripts maintains ABA signaling homeostasis.
Characterizing the Clinical Trajectory and Predicting Persistence and Deterioration of Attenuated Psychotic Symptoms in Ultra-High-Risk Individuals
Authors: Wannan Cassandra , Scott Isabelle , Dwyer Dominic , Clark Scott R , Hartmann Simon , Ye Rochelle Ruby , Amminger G Paul , Yuen Hok Pan , Lavoie Suzie , Markulev Connie , Schaefer Miriam R , Hartmann Jessica A , Mossaheb Nilufar , Schlögelhofer Monika , Smesny Stefan , Hickie Ian B , Berger Gregor , Chen Eric Y H , de Haan Lieuwe , Nieman Dorien H , Nordentoft Merete , Riecher-Rössler Anita , Verma Swapna , Thompson Andrew , Yung Alison R , Kerr Melissa , Spark Jessica , Wallis Nicky , Polari Andrea , McGorry Patrick D , Nelson Barnaby
Published: December 2024

Background

Almost 40% of individuals at ultra-high risk (UHR) for psychosis experience persistent attenuated psychotic symptoms (APS) yet it is unclear (1) whether they share overlapping clinical and functional outcomes compared to individuals who transition to psychosis, (2) when symptom and functioning trajectories begin to diverge between UHR individuals with different clinical outcomes, and (3) whether non-remission (persistent APS or transition) can be predicted using baseline and/or longitudinal data.

Study Design

Participants were drawn from 2 randomized clinical trials: Neurapro (n = 220; discovery sample) and STEP (n = 180; external validation sample). First, 12–24 month symptoms and functioning were compared between UHR individuals with persistent APS, sustained remission, or transition to psychosis. Next, short-term changes in symptoms and functioning were compared between groups to determine timepoints at which trajectories began to diverge. Finally, we used support vector machines to predict non-remission (persistent APS or transition) vs sustained remission using data from baseline, 6-month follow-up, and combined baseline and 6-month follow-up.

Results

Individuals with persistent APS had substantially poorer outcomes compared to those who remitted, and more closely resembled individuals who later transitioned to psychosis. Despite few baseline differences between groups, clinical and functional trajectories of the persistent APS and transition groups rapidly diverged from those who remitted. Prediction of non-remission was poor using baseline data but improved substantially when using 6-month follow-up or combined baseline-6-month data.

Conclusions

Ultra-high-risk individuals with persistent APS display similar clinical and functional trajectories to transitioned cases, suggesting that more intensive and sustained intervention is required for this subgroup. However, prospective identification of individuals with poor clinical outcomes (ie, persistence or deterioration of attenuated psychotic symptoms) may require longitudinal monitoring of symptom and functioning trajectories for several months.
Development and Validation of a Brief Age-Normed Screening Tool for Subthreshold Psychosis Symptoms in Youth
Authors: Calkins Monica E , Ered Arielle , Moore Tyler M , White Lauren K , Taylor Jerome , Moxam Alexander B , Ruparel Kosha , Wolf Daniel H , Satterthwaite Theodore D , Kohler Christian G , Gur Ruben C , Gur Raquel E
Published: December 2024

Background and Hypothesis

Improvements in screening tools for early subthreshold psychosis symptoms are needed to facilitate early identification and intervention efforts, especially given the challenges of rapidly differentiating age-appropriate experiences from potential early signs of emerging psychosis. Tools can be lengthy and time-consuming, impacting their utility and accessibility across clinical settings, and age-normed data are limited. To address this gap, we sought to develop and validate a brief, empirically derived, age-normed, subthreshold psychosis screening tool, for public use.

Study Design

Computerized adaptive test simulation was used to derive a 5-item short form with age norm equivalencies from a 12-item PRIME-Screen-Revised (PRIME-12) administered to 7053 youth (Mage = 15.8, SD = 2.7; 54% female; 33% Black). Concurrent validity was assessed (n = 758) using contemporaneous administration of the PRIME-5 and the Structured Interview for Prodromal Syndromes. Comparability of criterion-related validity of the PRIME-5, PRIME-12, and Scale of Prodromal Symptoms (SOPS) was assessed by relating scores to psychosis-risk-relevant criteria. Finally, self-report versus assessor-administered PRIME total scores were compared (n = 131) to assess their concurrent validity.

Study Results

Correlations among PRIME-5, PRIME-12, and SOPS were comparable and moderate, supporting their convergent validity. The PRIME-5 also showed comparable criterion-related validity, demonstrating similar relationships with psychosis-risk indicators as the other tools. Self-reported and assessor-administered PRIME-5 were moderately correlated.

Conclusions

Public availability of a brief, age-normed, and validated screening tool—which can be assessor or self-administered—will expedite and improve early identification of youth (age 11 and older) at risk for psychosis.
NK cell cytotoxicity towards pluripotent stem cells and their neural progeny: impacts of activating and inhibitory receptors and KIR/HLA mismatch
Authors: Henden Camilla , Fjerdingstad Hege B , Bjørnsen Elisabeth G , Thiruchelvam-Kyle Lavanya , Daws Michael R , Inngjerdingen Marit , Glover Joel C , Dissen Erik
Published: December 2024

Pluripotent stem cells provide opportunities for treating injuries and previously incurable diseases. A major concern is the immunogenicity of stem cells and their progeny. Here, we have dissected the molecular mechanisms that allow natural killer (NK) cells to respond to human pluripotent stem cells, investigating a wide selection of activating and inhibitory NK cell receptors and their ligands. Reporter cells expressing the activating receptor NKG2D responded strongly to embryonic stem (ES) cell lines and induced pluripotent stem (iPS) cell lines, whereas reporter cells expressing the activating receptors NKp30, NKp46, KIR2DS1, KIR2DS2 and KIR2DS4 did not respond. Human ES and iPS cells invariably expressed several ligands for NKG2D. Expression of HLA-C and HLA-E was lacking or low, insufficient to trigger reporter cells expressing the inhibitory receptors KIR2DL1, -2DL2 or -2DL3. Similar results were obtained for the pluripotent embryonic carcinoma cell lines NTERA-2 and 2102Ep, and also iPS cell-derived neural progenitor cells. Importantly, neural progenitor cells and iPS cell-derived motoneurons also expressed B7H6, the ligand for the activating receptor NKp30. In line with these observations, IL-2 stimulated NK cells showed robust cytotoxic responses to ES and iPS cells as well as to iPS cell-derived motoneurons. No significant differences in cytotoxicity levels were observed between KIR/HLA matched and mismatched combinations of NK cells and pluripotent targets. Together, these data indicate that pluripotent stem cells and their neural progeny are targets for NK cell killing both by failing to sufficiently express ligands for inhibitory receptors and by expression of ligands for activating receptors.
Can pension fund design increase pension savings? Evidence from a conjoint experiment in six European countries
Authors: Fernández Juan J , Gonzales Sara , James Hayley , Wiß Tobias
Published: December 2024

In times of welfare state retrenchment, occupational pension savings become essential for ensuring adequate retirement income. We know that individuals’ socioeconomic characteristics and a country’s characteristics matter for the level of occupational pension plan (OPP) savings. However, there is a gap in knowledge regarding how pension fund design affects pension savings. This paper fills this gap by examining the influence of OPP characteristics on the willingness of individuals to increase their contribution level. We analyze a conjoint experiment embedded in an online representative survey conducted in Austria, Denmark, Germany, Ireland, The Netherlands, and Spain. The plans differed across seven attributes. The results indicate that (i) past financial returns, (ii) the structure of the OPP board, and (iii) board responsiveness to participants’ demands have the strongest effects, followed by current (iv and v) contributions by employees and employers and (vi) environmental, social, and governance (ESG) policies. The type of (vii) tools used to inform participants proves unrelated to OPP selection.
Corticospinal excitability is not facilitated by observation of asymmetric walking on a split-belt treadmill in humans
Authors: Kitamura Masaya , Ishikura Tadao , Kamibayashi Kiyotaka
Published: December 2024

The present study aimed to investigate changes in corticospinal excitability (CSE) by observing unnatural walking patterns on a treadmill with different left and right belt speeds. Fifteen healthy adults watched video clips (10 s each) of walking under the tied condition (left and right treadmill belt speeds are the same), walking during the initial and late periods under the split-belt condition (left and right treadmill belt speeds are different), and the static fixation cross (control condition) in random order. The step lengths of the actor in the walking clips were almost symmetric under the tied condition and during the late period under the split-belt condition but largely asymmetric during the initial period under the split-belt condition. We recorded the motor-evoked potential (MEP) of the left tibialis anterior muscle during the observation of video clips by delivering transcranial magnetic stimulation to the right primary motor cortex. The MEP amplitude was significantly higher when observing walking under the tied condition and walking during the late period under the split-belt condition than the control condition. However, the MEP amplitudes during the observation of walking during the initial period under the split-belt condition and the control condition were not significantly different. These results indicate that observation of symmetric walking, even under the split-belt condition, facilitates CSE, whereas observation of unnatural asymmetric walking does not. Therefore, it is suggested that familiarity with observed movements affects CSE even in the observation of semi-automatic movements such as walking.
Swallows with sexually dimorphic tails have higher speciation rates
Authors: Hasegawa Masaru
Published: December 2024

Sexual selection can promote speciation in theory, but macroevolutionary studies have reported mixed results. A possible explanation for this inconsistency is the difficulty of choosing appropriate proxies of sexual selection. Here, by focusing on swallows and allies (Aves: Hirundinidae), I examined whether or not a classic example of sexually selected trait, long outermost tail feathers, explains speciation rate in this clade. Long tails have been repeatedly shown to be intersexually selected in manipulative experiments, which is further corroborated by a series of macroevolutionary studies, thereby validating their use as a proxy of sexual selection. I found that hirundines with sexually dimorphic tail length have a significantly higher speciation rate than those with sexually monomorphic tail length. Extinction rate was estimated to be small with no detectable difference between them, and thus hirundines with sexually dimorphic tail length, but not those with sexually monomorphic tail length, have a positive net diversification rate. When sexual dimorphism in tail length was replaced with sexual dimorphism in wing length or sexual plumage dichromatism, neither explained speciation and extinction rates. Furthermore, evolutionary changes in the extent of sexual tail dimorphism (and those in the extent of male outermost tail exaggeration) was significantly positively associated with speciation rate. Taken together, the current study demonstrated the importance of choosing appropriate proxies (or “targets”) of sexual selection in studies on the macroevolutionary patterns of speciation. Using a classic, unidimensional sexual trait (i.e., long tail), I demonstrated a strong macroevolutionary support that divergence of intersexually selected traits promotes speciation.
Deficiency of DDI2 suppresses liver cancer progression by worsening cell survival conditions
Authors: Liu Keli , Hu Shaofan , Wufuer Reziyamu , Zhang Qun , Qiu Lu , Zhang Zhengwen , Wang Meng , Zhang Yiguo
Published: December 2024

The levels of reactive oxygen species (ROS) and the extent of ensuing DNA damage significantly influence cancer initiation and progression. Of crucial importance, the aspartate protease DDI2 has been proposed to play a pivotal role in monitoring intracellular ROS levels (to trigger oxidative eustress or distress), as well as in the oxidative DNA damage repair, through redox homeostasis-determining factor Nrf1 (encoded byNFE2L1). However, the specific role of DDI2 in the multi-step process resulting in the development and progression of liver cancer remains elusive to date. In the present study, we employed the CRISPR/Cas9 gene editing system to create two nuanced lines ofDDI2knockout (i.e.,DDI2−/−andDDI2insG/−) from liver cancer cells. Subsequent experiments indicate that the knockout ofDDI2leads to increased ROS levels in hepatoma cells by downregulating two major antioxidant transcription factors Nrf1 and Nrf2 (encoded byNFE2L2), exacerbating endogenous DNA damages caused by ROS and not-yet-identified factors, thereby inhibiting cell proliferation and promoting apoptosis, and ultimately hinderingin vivomalignant growth of xenograft tumor cells. Conversely, the restoration of DDI2 expression reverses the accumulation of ROS and associated DNA damage caused byDDI2knockout, eliminating the subsequent inhibitory effects ofDDI2deficiency on bothin vitroandin vivogrowth of liver cancer cells. Collectively, these findings demonstrate thatDDI2deficiency impedes liver tumor growth by disrupting its survival environment, suggesting that DDI2 may serve as a novel therapeutic target for anti-cancer strategies aimed at modulating ROS or DNA damage processes.
Computational Modeling of Effects ofPKP2Gene Therapy on Ventricular Conduction Properties in Arrhythmogenic Cardiomyopathy
Authors: Ostini Alessio , Kléber André G. , Rudy Yoram , Saffitz Jeffrey E. , Kucera Jan P.
Published: December 2024

Background

Patients with arrhythmogenic cardiomyopathy (ACM) due to pathogenic variants inPKP2, the gene for the desmosomal protein plakophilin-2, are being enrolled in gene therapy trials designed to replace the defective allele via adeno-associated viral (AAV) transduction of cardiac myocytes. Evidence from experimental systems and patients indicates that ventricular myocytes inPKP2ACM have greatly reduced electrical coupling at gap junctions and reduced Na+current density. In previous AAV gene therapy trials, <50% of ventricular myocytes have generally been transduced.

Methods

We used established computational models of ventricular cell electrophysiology to define the effects of varying levels of successful gene therapy on conduction in patients withPKP2ACM. Conduction velocity and development of conduction block were analyzed in tissue constructs composed of cells with levels of electrical coupling and Na+current density observed in experimental studies.

Results

We observed a non-linear relationship between conduction velocity and the proportion of transduced cells. Conduction velocity increased only modestly when up to 40% of myocytes were transduced. Conduction block did not occur in tissue constructs with moderate levels of uncoupling (0.10 or 0.15 of normal) as this degree of coupling was sufficient to allow electrotonic current to pass through diseased cells. Thus, low levels of transduction, likely to occur in phase 1 clinical trials, do not appear to pose a major safety concern. However, our models did not incorporate potential effects of fibrosis and immune signaling, both of which will presumably be present inPKP2ACM patients undergoing gene therapy.

Conclusions

The extent of successful ventricular myocyte transduction anticipated to be achieved inPKP2AAV gene therapy trials will likely not restore conduction velocity to levels sufficient to decrease risk of reentrant arrhythmias.

What is Known

-

Patients with arrhythmogenic cardiomyopathy due to pathogenic variants inPKP2(the gene for the desmosomal protein plakophilin-2) are now being enrolled in gene therapy trials.

-

Experimental and clinical observations indicate that patients with arrhythmogenic cardiomyopathy have slow ventricular conduction with a propensity to conduction block due to source-sink mismatch.

-

<50% of ventricular myocytes are usually transduced after adeno-associated viral gene therapy.

What the Study Adds

-

At anticipated levels of successful transduction of ventricular myocytes, little change in conduction velocity will be achieved in patients with arrhythmogenic cardiomyopathy due to variants inPKP2.

-

Higher levels of transduction could produce conditions that increase risk of conduction block, especially in the presence of areas of non-conducting fibrofatty scar tissue.
Cnot4 heterozygosity attenuates high fat diet-induced obesity in mice and impairs PPARγ-mediated adipocyte differentiation
Authors: Yamaguchi Tomokazu , Hoshizaki Midori , Imai Yumiko , Yamamoto Tadashi , Kuba Keiji
Published: December 2024

Adipocyte differentiation is crucial for formation and expansion of white adipose tissue and is also associated with the pathologies of obesity. CNOT4 is an E3 ubiquitin ligase and also contains RNA binding domain. In mammals CNOT4 has been suggested to interact with CCR4-NOT complex, a major executor of mRNA poly(A) shortening. While several subunits within the CCR4-NOT complex were shown to be involved in obesity and energy metabolism, the roles of CNOT4 in obesity remain unexplored. In this study, we generated and analyzed Cnot4 knockout mice and found that Cnot4 heterozygous (Cnot4 Het) mice exhibit resistance to high fat diet-induced obesity, including significant reduction in adipose tissue mass and hepatic lipid depots. However, Cnot4 Het did not affect mRNA expression of metabolic genes as well as serum lipid levels or glucose tolerance. Mechanistically, Cnot4 Het fibroblasts significantly reduced the capability of differentiation into adipocytes and down-regulated adipogenic gene expression compared to wild type fibroblasts. Heterozygous deletion of Cnot4 down-regulated the transcriptional activity of PPARγ, thereby suppressing up-regulation of adipocyte marker gene expression in response to rosiglitazone, a PPARγ agonist. These results suggest that CNOT4 mediates adipocyte differentiation during formation and growth of adipose tissue partly through positively regulating transcriptional activity of PPARγ.
Optogenetic inhibition quenches the integration of sensory input in the cortex
Authors: Manuel Ambrosone , Elena Montagni , Francesco Resta , Lorenzo Curti , Guido Mannaioni , Alessio Masi , Saverio Pavone Francesco , Anna Letizia Allegra Mascaro
Published: December 2024

Significance

Many fundamental processes of brain computation, such as sensory perception and motor control, heavily rely on the mesoscopic dynamics of activity across the cerebral cortex. Manipulating mesoscale activity and observing its effects across multiple brain regions is crucial for understanding the causal link between cortical dynamics and behavior.

Objective

The goal of this study was to develop a novel all-optical system that allows inhibition of excitatory neurons while simultaneously monitoring cortical responses at arbitrary sites across the entire dorsal cortex of mice.

Methods

We combined wide-field imaging and optogenetics to create a mesoscale all-optical approach, enabling simultaneous monitoring and manipulation of cortical activity using light. Intravenous injection of two PHP.eB AAVs enabled the whole-brain co-expression of the red-shifted calcium indicator jRCaMP1b and the inhibitory actuator stGtACR2, with stable expression over several weeks. This system was calibrated, and the effects of inhibition on sensory responses were tested.

Results

Increasing laser power progressively reduced spontaneous activity at the site of irradiation. A single 5-second pulse on the barrel field cortex significantly decreased the amplitude of sensory-evoked responses, not only in the stimulated region but across the entire stimulated hemisphere.

Conclusions

This novel all-optical system enables targeted inhibition while concurrently monitoring mesoscale cortical activity. It provides insights into the dynamics of cortical circuits and offers a milestone for investigating the causal links between neuronal activity and behavior. Future research can use this tool to address sensory responsiveness impairments in neurological and neuropsychiatric disorders.
Multimodal normative modeling in Alzheimer’s Disease with introspective variational autoencoders
Authors: Kumar Sayantan , Qiu Peijie , Yang Braden , Bani Abdalla , Payne Philip R.O , Sotiras Aristeidis
Published: December 2024

Normative models in neuroimaging learn patterns of healthy brain distributions to identify deviations in disease subjects, such as those with Alzheimer’s Disease (AD). This study addresses two key limitations of variational autoencoder (VAE)-based normative models: (1) VAEs often struggle to accurately model healthy control distributions, resulting in high reconstruction errors and false positives, and (2) traditional multimodal aggregation methods, like Product-of-Experts (PoE) and Mixture-of-Experts (MoE), can produce uninformative latent representations. To overcome these challenges, we developed a multimodal introspective VAE that enhances normative modeling by achieving more precise representations of healthy anatomy in both the latent space and reconstructions. Additionally, we implemented a Mixture-of-Product-of-Experts (MOPOE) approach, leveraging the strengths of PoE and MoE to efficiently aggregate multimodal information and improve abnormality detection in the latent space. Using multimodal neuroimaging biomarkers from the Alzheimer’s Disease Neuroimaging Initiative (ADNI) dataset, our proposed multimodal introspective VAE demonstrated superior reconstruction of healthy controls and outperformed baseline methods in detecting outliers. Deviations calculated in the aggregated latent space effectively integrated complementary information from multiple modalities, leading to higher likelihood ratios. The model exhibited strong performance in Out-of-Distribution (OOD) detection, achieving clear separation between control and disease cohorts. Additionally, Z-score deviations in specific latent dimensions were mapped to feature-space abnormalities, enabling interpretable identification of brain regions associated with AD pathology.
Targeted KRASG12Vdegradation elicits efficient and durable lung adenocarcinoma regressionin vivo
Authors: Martín Alberto , García-Pérez Inés M. , José Sonia San , Rojo Pep , Riego-Mejías Carlos , Teodosio Cristina , Barbosa Bárbara MG. , Sánchez-Zarzalejo Carolina , Folch-I-Casanovas Ignasi , Caballol Antonia Odena , Jarió Sònia , Entrialgo Rodrigo , Nokin Marie-Julie , Loa Diana , Guruceaga Elizabeth , Attolini Camille Stephan-Otto , Ambrogio Chiara , Villanueva Alberto , Vicent Silvestre , Riera Antoni , Santamaría David , Mayor-Ruiz Cristina
Published: December 2024

Recent drug discovery breakthroughs led to the approval of KRASG12Cinhibitors in lung adenocarcinoma (LUAD). Unfortunately, clinical responses remain limited due to rapid resistance onset. Proteolysis-targeting chimeras (PROTACs) have emerged as promising alternatives to traditional inhibition. However, there is limited mechanistic understanding of KRAS degradationin vivo. Here, we developed a preclinical LUAD mouse model and demonstrated that targeted oncogenic KRAS degradation induces rapid tumor regression. Transcriptional, histological, and immunophenotypic analyses revealed a substantial remodeling of the tumor microenvironment. Notably, disease relapse observed during long-term degrader treatment stems from proteolysis machinery dysregulation, indicating resistance mechanisms distinct from those reported upon KRAS inhibition. Our findings highlight the therapeutic potential of KRAS degradation in LUAD, offering insights into cell-intrinsic and extrinsic mechanisms driving durable antitumor responses and supporting further clinical exploration.

SIGNIFICANCE

Given the short duration of the clinical responses to KRAS inhibitors, complementary therapies are a dire medical need. Our preclinical findings endorse KRAS degradation as a therapeutic alternative in LUAD, where cell-intrinsic and extrinsic mechanisms drive tumor regression and durable therapeutic responses.
Future climate and land use change will equally impact global terrestrial vertebrate diversity
Authors: Hari Chantal , Hickler Thomas , Hof Christian , Reyer Christopher P.O. , Vanderkelen Inne , Voskamp Alke , Biber Matthias F. , Fischer Markus , Davin Édouard L.
Published: December 2024

Aim

Terrestrial biodiversity is impacted by both climate and land use change. Yet, future biodiversity projections have rarely considered these two drivers in combination. In this study, we aim to assess the individual and combined impact of future climate and land use change on global terrestrial vertebrate diversity under a “sustainability” (SSP1-RCP2.6) and an “inequality” (SSP4-RCP6.0) scenario.

Location

Global land, excluding Antarctica.

Time period

1995, 2080

Major taxa studied

Amphibians, birds, and mammals.

Methods

We combined global climate-driven species distribution model (SDM) projections of 13903 vertebrates (amphibians, birds and mammals) with future and present land use projections from the Land Use Harmonization 2 (LUH2) project. We refined the SDM outputs by the habitat requirements of each species using a land use filtering approach. We then analyzed future species richness changes globally, per region and per land-use category and also looked at taxon-specific effects.

Results

Under both scenarios, decreases in future species richness dominate at low and mid-latitudes with climate and land use change playing an equally important role. Land use change can be either an alleviating (SSP1-RCP2.6) or an exacerbating (SSP4-RCP6.0) factor of climate-induced biodiversity loss. Sub-Saharan Africa is projected to become a high-risk area for future land use-driven biodiversity loss under the “inequality” scenario. Under SSP1-RCP2.6, forested and non-forested land areas increase, while SSP4-RCP6.0 leads to higher rates of deforestation and pasture expansion. Mammals experience the largest climate-driven losses, affecting 56.4% of land area under SSP4-RCP6.0, while amphibians are particularly vulnerable to land use-driven losses, especially under SSP4-RCP6.0.

Main conclusions

Generally, our results suggest that both climate and land use pressures on biodiversity will be highest in lower latitudes which harbor the highest levels of biodiversity.
A simplified two-plasmid system for orthogonal control of mammalian gene expression using light-activated CRISPR effector
Authors: Garimella Shruthi S. , Minami Shiaki A. , Khanchandani Anusha N. , Schaffer Susannah R. , Shah Priya S.
Published: December 2024

Background

Optogenetic systems use light-responsive proteins to control gene expression with the “flip of a switch”. One such tool is thelightactivatedCRISPReffector (LACE) system. Its ability to regulate gene expression in a tunable, reversible, and spatially resolved manner makes it attractive for many applications. However, LACE relies on delivery of four separate components on individual plasmids, which can limit its use. Here, we optimize LACE to reduce the number of plasmids needed to deliver all four components.

Results

The two-plasmid LACE (2pLACE) system combines the four components of the original LACE system into two plasmids. Following construction, the behavior of 2pLACE was rigorously tested using optogenetic control of enhanced green fluorescent protein (eGFP) expression as a reporter. We optimized the ratio of the two plasmids, measured activation as a function of light intensity, and determined the frequency of the light to activate the maximum fluorescence. Overall, the 2pLACE system showed a similar dynamic range, tunability, and activation kinetics as the original four plasmid LACE (4pLACE) system. Interestingly, 2pLACE also had less variability in activation signal compared to 4pLACE.

Conclusions

This simplified system for optogenetics will be more amenable to biotechnology applications where variability needs to be minimized. By optimizing the LACE system to use fewer plasmids, 2pLACE becomes a flexible tool in multiple research applications.
Eosinophils restrict CRC metastasis by inhibiting pro-tumorigenic SPP1+macrophage differentiation
Authors: Handler Kristina , Raju Deeksha , Gurtner Alessandra , Dalessi Tosca , Brügger Michael D. , Crepaz Daniel , Esposito Cinzia , Trajanoski Zlatko , Münz Christian , Scharl Michael , Valenta Tomas , Piscuoglio Salvatore , Fazilaty Hassan , Arnold Isabelle C.
Published: December 2024

Eosinophils, traditionally associated with allergic responses, have emerged as critical immune modulators in colorectal cancer (CRC). Here, we reveal that eosinophils actively shape the tumor microenvironment and influence metastatic progression. Using comprehensive transcriptomics analysis of human CRC and a murine orthotopic tumor model, we identify a conserved tumor-specific eosinophil signature and activation profile. Despite their declining presence in advanced CRC, eosinophils suppress metastatic dissemination by counteracting the pro-tumorigenic functions of SPP1+macrophages – a subset linked to immune exclusion and tumor metastasis. Mechanistically, eosinophils respond to tumor-derived signals and inhibit macrophage differentiation into SPP1+cells. Eosinophil depletion exacerbates peritoneal tumor spread. These findings highlight the pivotal role of eosinophils in restraining late-stage CRC progression and unveil a novel eosinophil–macrophage axis as potential therapeutic targets.
PacBio genome assembly ofOlea europaeaL. subsp.europaeacultivars ‘Frantoio’ and ‘Leccino’ reveal main structural differences in key genes related to salt stress
Authors: Sebastiani Luca , Sarfraz Iqra , Francini Alessandra , Celii Mirko , Wing Rod A. , Zuccolo Andrea
Published: December 2024

We present two high-quality genome assemblies forOlea europaeaL. cultivars ‘Frantoio’ and ‘Leccino’ leveraging PacBio HiFi sequencing to achieve approximately 30× genome coverage for each cultivar. The assemblies span 1.18 Gbp and 1.43 Gbp with contig N50 values of 1.78 Mbp and 45.88 Mbp for ‘Frantoio’ and ‘Leccino’ respectively. BUSCO analysis revealed a great genome completeness (∼97.9%), surpassing many of earlierOlea europaeaassemblies and is in par with the most recent one. Repetitive content accounted for ∼67.5% in ‘Frantoio’ and ∼70.8% in ‘Leccino’ with long terminal repeats (LTRs) dominating. Notably, a tandem repeat family, Satellite 1, represented ∼16.9% and ∼8.6% of the ‘Leccino’ and ‘Frantoio’ genomes, respectively. The structural variant (SV) analysis was done with a particular focus on those associated with nine key gene families involved in salinity tolerance and identified cultivar-specific genomic differences, emphasizing the diversity within domesticated olives. This comprehensive analysis provides valuable resources for studying olive genome evolution, domestication, and genetic improvement, underscoring the utility of long-read sequencing for resolving complex genomic features.
StayRose: a photostable StayGold derivative red-shifted by genetic code expansion
Authors: Scott Will , Ivorra-Molla Esther , Akhuli Dipayan , Massam-Wu Teresa , Cook Jonathan , Song Lijiang , Mishima Masanori , Crow Allister , Balasubramanian Mohan K.
Published: December 2024

Photobleaching of fluorescent proteins often limits the acquisition of high-quality images in microscopy. StayGold, a novel dimeric green fluorescent protein recently monomerised through sequence engineering, addresses this challenge with its high photostability. There is now focus on producing different colour StayGold derivatives to facilitate concurrent tagging of multiple targets. The unnatural amino acid 3-aminotyrosine has previously been shown to red-shift super folder GFP upon incorporation into its chromophore via genetic code expansion. Here we apply the same strategy to red-shift StayGold through substitution of Tyrosine-58 with 3-aminotyrosine. The resultant red fluorescent protein, StayRose, shows 530 nm excitation and 588 nm emission peaks, shifting from the 497 nm and 504 nm excitation and emission peaks of StayGold. StayRose also retains the favourable photostability of StayGold and can be similarly monomerised using mutations at the dimer interface. A high-resolution crystal structure of StayRose confirms the modified structure of the amino-chromophore within an unperturbed 3D fold. Although reliant on genetic code expansion, StayRose provides an important step towards developing red-shifted StayGold derivatives.
Comparison of imaging-based single-cell resolution spatial transcriptomics profiling platforms using formalin-fixed, paraffin-embedded tumor samples
Authors: Ozirmak Lermi Nejla , Molina Ayala Max , Hernandez Sharia , Lu Wei , Khan Khaja , Serrano Alejandra , Lubo Idania , Hamana Leticia , Tomczak Katarzyna , Barnes Sean , Dou Jinzhuang , Liang Qingnan , Team RTI , Raso Maria Gabriela , Tang Ximing , Jiang Mei , Sanchez-Espiridion Beatriz , Weissferdt Annikka , Heymach John , Zhang Jianjun , Sepesi Boris , Cascone Tina , Tsao Anne , Altan Mehmet , Mehran Reza , Gibbons Don , Wistuba Ignacio , Haymaker Cara , Chen Ken , Solis Soto Luisa M.
Published: December 2024

Imaging-based spatial transcriptomics (ST) is evolving rapidly as a pivotal technology in studying the biology of tumors and their associated microenvironments. However, the strengths of the commercially available ST platforms in studying spatial biology have not been systematically evaluated using rigorously controlled experiments. In this study, we used serial 5-m sections of formalin-fixed, paraffin-embedded surgically resected lung adenocarcinoma and pleural mesothelioma tumor samples in tissue microarrays to compare the performance of the single cell ST platforms CosMx, MERFISH, and Xenium (uni/multi-modal) platforms in reference to bulk RNA sequencing, multiplex immunofluorescence, GeoMx Digital Spatial Profiler, and hematoxylin and eosin staining data for the same samples. In addition to objective assessment of automatic cell segmentation and phenotyping, we performed pixel-resolution manual evaluation of phenotyping to carry out pathologically meaningful comparison between ST platforms. Our study detailed the intricate differences between the ST platforms, revealed the importance of parameters such as tissue age and probe design in determining the data quality, and suggested reliable workflows for accurate spatial profiling and molecular discovery.
Discovery of an on-pathway protein folding intermediate illuminates the kinetic competition between folding and misfolding
Authors: Luan Qing , Clark Patricia L.
Published: December 2024

Our current understanding of protein folding is based predominantly on studies of small (<150 aa) proteins that refold reversibly from a chemically denatured state. As protein length increases, the competition between off-pathway misfolding and on-pathway folding likewise increases, creating a more complex energy landscape. Little is known about how intermediates populated during the folding of larger proteins affect navigation of this more complex landscape. Previously, we reported extremely slow folding rates for the 539 aa β-helical passenger domain of pertactin (P.69T), including conditions that favor the formation of a kinetically trapped, off-pathway partially folded state (PFS). The existence of an on-pathway intermediate for P.69T folding was speculated but its characterization remained elusive. In this work, we exploited the extremely slow kinetics of PFS unfolding to develop a double-jump “denaturant challenge” assay. With this assay, we identified a transient unfolding intermediate, PFS*, that adopts a similar structure to PFS, including C-terminal folded structure and a disordered N-terminus, yet unfolds much more quickly than PFS. Additional experiments revealed that PFS* also functions as an on-pathway intermediate for P.69T folding. Collectively, these results support a two-step, C-to-N-terminal model for P.69T folding: folding initiates in the C-terminus with the rate-limiting formation of the transient on-pathway PFS* intermediate, which sits at the junction of the kinetic competition between folding and misfolding. Notably, processive folding from C-to-N-terminus also occurs during C-to-N-terminal translocation of P.69T across the bacterial outer membrane. These results illuminate the crucial role of kinetics when navigating a complex energy landscape for protein folding.
Sub-clustering, marker identification and multi-omics integration influenced by protoplasting in plant scRNA-seq data analysis
Authors: Yao Jie , Shang Nianmin , Chen Hongyu , Hu Yurong , Zhu Qian-Hao , Fan Longjiang , Ye Chuyu , Chu Qinjie
Published: December 2024

Single-cell RNA sequencing (scRNA-seq) technology is a powerful tool for exploring cell heterogeneity and lineage dynamics, revealing complex mechanisms driving tissue function and development. However, plant cell’s rigid cell walls require a protoplasing step, an enzymatic process that can introduce biases. The impact of protoplasting on plant scRNA-seq data remains poorly understood. In this study, we analyzed gene expression patterns from bulk RNA-seq of various plant tissues before and after protoplasting. Cell-type specific protoplasting effects were discovered in different plant tissues. Protoplasting-related biases were found to distort clustering, marker gene identification, and multi-omics integration. By calculating protoplasted scores based on gene expression, we identified and mitigated protoplasting effects, enabling the accurate clustering and annotation of tobacco BY-2 cells and identification of cell-cycle-related genes. Our findings underscore the importance of assessing and correcting for protoplasting biases in plant scRNA-seq data analysis, offering new insights for more accurate data interpretation and biological discovery.
High-Throughput Targeted Drug Screening for NF1-associated High-Grade Gliomas with ATRX Deficiency
Authors: Dubey Swati , Rai Simran , Guillen Fabiola , Iyer Ajeeth , Aung Su , Yuan Ming , Eberhart Charles G. , Rodriguez Fausto J
Published: December 2024

Neurofibromatosis type 1 (NF1)-associated high-grade gliomas (HGGs) harboring ATRX mutations exhibit an aggressive clinical phenotype, driven by heightened genomic instability and metabolic reprogramming. Existing therapies, including chemotherapy and radiotherapy, are limited by resistance mechanisms and formation of secondary malignancy, underscoring the need for novel therapeutic strategies. Here, we report the results of a high-throughput screening of 10,000 small molecules aimed at identifying compounds selectively targeting vulnerabilities associated with concurrent ATRX and NF1 loss. Among the screened compounds, K784-6195 (ChemDiv ID) emerged as a promising candidate, exhibiting marked selective cytotoxicity in NF1-associated glioma cell lines with ATRX deficiency (IC50 = 4.84 µM). In comparison, wild-type ATRX sporadic glioma cell lines (U251) exhibited significantly reduced sensitivity to K784-6195 (IC50 = 37.03 µM). However, ATRX knockout U251 glioma cells recapitulating concurrent ATRX and NF1 loss exhibited heightened susceptibility to K784-6195 (IC50 = 20-23 µM) compared to their wild-type counterpart. Metabolomic analysis revealed that K784-6195 treatment impairs metabolic pathways, including the pentose phosphate pathway, glutamine metabolism, and redox homeostasis, leading to oxidative stress and impaired cell survival. These findings highlight K784-6195 as a promising candidate for therapeutic development, offering a targeted approach for the treatment of NF-1 associated HGGs with ATRX deficiency.
Molecular and spatial analysis of ganglion cells on retinal flatmounts: diversity, topography, and perivascularity
Authors: Tsai Nicole Y. , Nimkar Kushal , Zhao Mengya , Lum Matthew R. , Yi Yujuan , Garrett Tavita R. , Wang Yixiao , Toma Kenichi , Caval-Holme Franklin , Reddy Nikhil , Ehrlich Aliza T. , Kriegstein Arnold R. , Do Michael Tri H. , Sivyer Benjamin , Shekhar Karthik , Duan Xin
Published: December 2024

Diverse retinal ganglion cells (RGCs) transmit distinct visual features from the eye to the brain. Recent studies have categorized RGCs into 45 types in mice based on transcriptomic profiles, showing strong alignment with morphological and electrophysiological properties. However, little is known about how these types are spatially arranged on the two-dimensional retinal surface—an organization that influences visual encoding—and how their local microenvironments impact development and neurodegenerative responses. To address this gap, we optimized a workflow combining imaging-based spatial transcriptomics (MERFISH) and immunohistochemical co-staining on thin flatmount retinal sections. We used computational methods to registeren facesomata distributions of all molecularly defined RGC types. More than 75% (34/45) of types exhibited non-uniform distributions, likely reflecting adaptations of the retina’s anatomy to the animal’s visual environment. By analyzing the local neighborhoods of each cell, we identified perivascular RGCs located near blood vessels. Seven RGC types are enriched in the perivascular niche, including members of intrinsically photosensitive RGC (ipRGC) and direction-selective RGC (DSGC) subclasses. Orthologous human RGC counterparts of perivascular types - Melanopsin-enriched ipRGCs and ON DSGCs - were also proximal to blood vessels, suggesting their perivascularity may be evolutionarily conserved. Following optic nerve crush in mice, the perivascular M1-ipRGCs and ON DSGCs showed preferential survival, suggesting that proximity to blood vessels may render cell-extrinsic neuroprotection to RGCs through an mTOR-independent mechanism. Overall, our work offers a resource characterizing the spatial profiles of RGC types, enabling future studies of retinal development, physiology, and neurodegeneration at individual neuron type resolution across the two-dimensional space.
Implications of diabetes mellitus on pathophysiology of Tuberculosis: Role of AGE-RAGE Axis and Glycated Proteins
Authors: Panda Sudhasini , Singh Alankrita , Seelan Diravya M , Arora Alisha , Dagar Gunjan , Ethayathulla Abdul S , Luthra Kalpana , Mohan Anant , Vikram Naval K , Gupta Neeraj Kumar , Singh Mayank , Singh Archana
Published: December 2024

Chronic hyperglycemia in diabetes mellitus promotes the formation of advanced glycation end products (AGEs) via non-enzymatic glycation of plasma proteins. AGEs and their receptor RAGE are central to diabetic complications, as they activate inflammatory pathways and oxidative stress. We studied the AGE-RAGE axis in uncontrolled diabetic individuals having pulmonary TB (PTB+DM), uncontrolled diabetic individuals with no infection (DM), and pulmonary TB patients (PTB). Levels of AGEs and RAGE were measured across these groups and compared to controls. The results showed significantly higher AGEs and RAGE levels in the diabetic milieu, reflecting chronic hyperglycemia. These AGEs were shown to be associated with impaired macrophage function, evidenced by reduced phagocytic capacity. Increased AGEs correlated with disease severity in tuberculosis patients co-affected by diabetes, indicating compromised immune responses. RAGE expression also showed a higher trend in TB patients, although not statistically significant, potentially influencing infection outcomes. Glycated calmodulin was also elevated in diabetic and TB-diabetes comorbid patients and negatively correlated with nitric oxide (NO) levels, suggesting that calmodulin glycation hinders NO production in diabetic conditions. Molecular dynamic studies revealed that glycosylation disrupts calmodulin’s interaction with inducible nitric oxide synthase (iNOS), potentially explaining the decreased NO levels in TB-diabetes comorbid patients. These findings underscore the detrimental impact of AGEs and RAGE in diabetic immune dysregulation, highlighting the need for therapeutic strategies to mitigate their effects on macrophage function and restore immune responses.

Highlights

We conducted this study to examine how hyperglycemia-driven AGEs and RAGE contribute to immune dysfunction and disease severity in diabetic and TB-diabetes patients.

High AGEs and RAGE impairs macrophage function, decreasing phagocytic capacity and worsening disease severity in TB-diabetes comorbidity.

Glycosylation disrupts calmodulin’s interaction with iNOS, contributing to lower NO levels and weakened immune responses in TB-diabetes comorbidity.

The AGE-RAGE axis should be studied further for these comorbid conditions to assess and improve macrophage function and restore immune responses.
Eq-DIAGNOBATCH, a Shiny application for topical product equivalence with batch effect and multivariate outlier analysis
Authors: Monleón-Getino Toni , Ocaña Jordi
Published: December 2024

The Eq-DIAGNOBATCH application presented here complements a previous theoretical article about establishing the equivalence of topical products in a parallel linear model, accounting for a batch effect or not. This application provides a very simple way of carrying out the equivalence test for this type of situation, efficiently obtaining the estimates of the parameters of interest (equivalence intervals, geometric mean ratio, and variance components), and allowing calculations to be performed assuming a batch effect or not. It also examines the statistical implications of the presence of outliers in the sample, from both a univariate and multivariate point of view. The operation and mode of use of Eq-DIAGNOBATCH are presented, including examples related with the quality and equivalence of topical products and bioequivalence analysis. Some of these examples come from the literature and others from real-life industry case studies.