bluuebunny/crossref_metadata_2025 huggingface dataset:
“Two-Birds-One-Stone” Oral Nanotherapeutic Designed to Target Intestinal Integrins and Regulate Redox Homeostasis for Ulcerative Colitis Treatment
Authors: Huang Long , Hu Wei , Huang Long Qun , Zhou Qin Xuan , Song Zheng Yang , Tao Heng Yu , Xu Bing , Zhang Can Yang , Wang Yi , Xing Xin-Hui
Published: January 2024

Designing highly efficient orally administrated nanotherapeutics with specific inflammatory site-targeting functions in the gastrointestinal (GI) tract for ulcerative colitis (UC) management is a significant challenge. Straightforward and adaptable modular multifunctional nanotherapeutics represent groundbreaking advancements and are crucial to promoting broad application in both academic research and clinical practice. In this study, we focused on exploring a specific targeting modular and functional oral nanotherapy, serving as “one stone”, for the directed localization of inflammation and the regulation of redox homeostasis, thereby achieving effects against “two birds” for UC treatment. The designed nanotherapeutic agent OPNs@LMWH, which has a core-shell structure composed of oxidation-sensitive ε-polylysine nanoparticles (OPNs) in the core and low-molecular-weight heparin (LMWH) in the shell, exhibited specific active targeting effects and therapeutic efficacy simultaneously. We qualitatively and quantificationally confirmed that OPNs@LMWH possessed high integrin αM-mediated immune cellular uptake efficiency and preferentially accumulated in inflamed lesions. Compared with bare OPNs, OPNs@LMWH exhibited enhanced intracellular reactive oxygen species (ROS) scavenging and anti-inflammatory effects. After oral administration of OPNs@LMWH to mice with dextran sulfate sodium (DSS)-induced colitis, robust resilience was observed. OPNs@LMWH effectively ameliorated oxidative stress and inhibited the activation of inflammation-associated signalling pathways while simultaneously bolstering the protective mechanisms of the colonic epithelium. Overall, these findings underscore the compelling dual functionalities of OPNs@LMWH, which enable effective oral delivery to inflamed sites, thereby facilitating precise UC management.
Neutral speciation in realistic populations
Authors: Nelson Erik D.
Published: January 2024

de Aguiar et al. have shown that basic patterns of species diversity found in nature can be described by a neutral model of speciation in which species emerge simply as a consequence of local mating, and mate preference for genetic similarity. Their results have been cited as support for the neutral theory of biodiversity. However, because the mutation rates considered in their work are much larger than those experienced by living organisms, there is still some question as to whether speciation will occur in this type of model under realistic conditions. Here, I develop a variant of the neutral model that includes a realistic mechanism for organism dispersal. I explore speciation in the model for a class of mobile organisms (butterflies), and I find that speciation does occur under conditions consistent with butterfly populations, albeit on narrow landscapes. The model also appears to exhibit scaling behavior – specifically, if the model is “scaled up” by increasing the area of the landscape while holding its length to width ratio and population density constant, the number of species tends to an asymptotic value. The results suggest that it is possible to infer speciation patterns in large populations by simulating much smaller, computationally tractable populations.
Fall of giants: European diversity resistance to waterscape degradation and its potential continental drivers
Authors: Cunillera-Montcusí David , Borthagaray Ana-Inés , Bou Jordi , Arim Matías
Published: January 2024

Aquatic landscapes, or waterscapes, face severe threats from human activities propelling their deterioration. Waterscape degradation represents a main driver of the current diversity crisis, although its long-term consequences are difficult to quantify. In addition, the understanding of the potential effects of waterscape degradation on biodiversity at large spatial scales, such as biomes and continents, remains limited. In this work, we explore the potential trends in diversity decay in response to waterscape degradation across Europe to provide a first answer to these main threads. We reconstructed the European waterscape based on available satellite data and simulated diversity patterns using a coalescent metacommunity model run for several European ecoregions and considering nine dispersal abilities. Subsequently, we generated a gradient of waterscape degradation by systematically removing a percentage of available habitat and recalculating diversity metrics. For each ecoregion, dispersal ability, and degradation level we obtained a theoretical gamma diversity value. We synthesized the captured diversity decay trends in two parameters: the proportional decay rate and the collapsing rate, which respectively inform about the speed of diversity loss and its acceleration as waterscape degradation progresses. Finally, we mapped these parameters across Europe and related them with ecoregion structural descriptors (i.e. geographic location, water cover, connectivity, and size). Through this exercise, we could identify ecoregions’ sensitivities and their continental variation based on their diversity decay parameters. Connectivity and water cover emerged as primary descriptors of diversity decay, with more heterogeneous ecoregions generally exhibiting greater resistance to waterscape degradation. Our study provides a first order approximation to an urgently needed information: the continental-scale consequences of waterscape degradation for biodiversity. This data has the potential to improve conservation practices and facilitate the integration of innovative approaches in management, thereby enhancing our understanding of the consequences posed by one of the principal threats to freshwater diversity.
BATF controls IFN I production via DC-SCRIPT in plasmacytoid dendritic cells
Authors: Ali Shafaqat , Mann-Nüttel Ritu , Marson Marcel , Leiser Ben , Hoffe Jasmina , Dress Regine J. , Bhuyan Mahamudul Hasan , Petzsch Patrick , Köhrer Karl , Xu Haifeng C. , Lang Philipp A. , Zhang Shengbo , Chopin Michaël , Nutt Stephen L. , Alferink Judith , Scheu Stefanie
Published: January 2024

The basic leucine zipper ATF-like transcription factor (BATF) plays a pivotal role in coordinating various aspects of lymphoid cell biology, yet essential functions in dendritic cells (DCs) have not been reported. Here we demonstrate that BATF deficiency leads to increased interferon (IFN) I production in Toll-like receptor 9 (TLR9)-activated plasmacytoid dendritic cells (pDCs), while BATF overexpression has an inhibitory effect. BATF-deficient mice exhibit elevated IFN I serum levels early in lymphocytic choriomeningitis virus (LCMV) infection. Through ATAC-Seq analysis, BATF emerges as a pioneer transcription factor, regulating approximately one third of the known transcription factors in pDCs. Integrated transcriptomics and ChIP-Seq approaches identified the transcriptional regulator DC-SCRIPT as a direct target of BATF that suppresses IFN I promoter activity by interacting with the interferon regulatory factor 7 (IRF7). Genome-wide association study (GWAS) analyses further implicate BATF in pDC-mediated human diseases. Our findings establish a novel negative feedback axis in IFN I regulation in pDCs during anti-viral immune responses orchestrated by BATF and DC-SCRIPT, with broader implications for pDC and IFN I-mediated autoimmunity.
Immunogenicity of autologous and allogeneic human primary cholangiocyte organoids
Authors: Petrus-Reurer Sandra , Tysoe Olivia , Lei Winnie , Mairesse Maelle , Tan Thomas , Rehakova Sylvia , Mahbubani Krishnaa , Jones Julia , Brodie Cara , Han Namshik , Betts Catherine , Vallier Ludovic , Saeb-Parsy Kourosh
Published: January 2024

Primary human cells cultured in 3D organoid format have great promise as potential regenerative cellular therapies, but their immunogenicity has not yet been fully characterized. In this study, we usein vitroco-cultures andin vivohumanized mouse experimental models to examine the human immune response to autologous and allogeneic primary cholangiocyte organoids (PCOs). Our data demonstrate that PCOs upregulate the expression of HLA-I and HLA-II in inflammatory conditions. The immune response to allogeneic PCOs is driven by both HLA-I and HLA-II and is substantially ameliorated by donor-recipient HLA matching. Autologous PCOs induce a low-level immune infiltration into the graft site, while allogeneic cells display evolving stages of immune rejectionin vivo. Our findings have important implications for the design and clinical translation of autologous and allogeneic organoid cellular therapies.

ONE-SENTENCE SUMMARY

The immune response to human primary cholangiocyte organoids is ameliorated by donor-recipient HLA matching.
Short-chain fatty acid metabolites propionate and butyrate are unique epigenetic regulatory elements linking diet, metabolism and gene expression
Authors: Nshanian Michael , Gruber Joshua J. , Geller Benjamin S. , Chleilat Faye , Lancaster Samuel , White Shannon M. , Alexandrova Ludmila , Camarillo Jeannie Marie , Kelleher Neil L. , Zhao Yingming , Snyder Michael P.
Published: January 2024

The short-chain fatty acids (SCFA) propionate and butyrate have beneficial health effects, are produced in large amounts by microbial metabolism and have been identified as unique acyl lysine histone marks. In order to better understand the function of these modifications we used ChIP-seq to map the genome-wide location of four short-chain acyl histone marks H3K18pr, H3K18bu, H4K12pr and H4K12bu in treated and untreated colorectal cancer (CRC) and normal cells, as well as in mouse intestinesin vivo. We correlate these marks with open chromatin regions along with gene expression to access the function of the target regions. Our data demonstrate that propionate and butyrate bind and act as promoters of genes involved in growth, differentiation as well as ion transport. We propose a mechanism involving direct modification of specific genomic regions, by SCFA resulting in increased chromatin accessibility, and in case of butyrate, opposing effects on the proliferation of normal versus CRC cells.
Internalisation of integrin-bound extracellular matrix modulates invasive carcinoma cell migration
Authors: Martinez Montserrat Llanses , Nan Keqian , Bao Zhe , Bacchetti Rachele , Yuan Shengnan , Tyler Joe , Guezennec Xavier Le , Bard Frédéric A. , Rainero Elena
Published: January 2024

The interaction between cancer cells and the extracellular matrix (ECM) plays a pivotal role in tumour progression. While the extracellular degradation of ECM proteins has been well characterised, ECM endocytosis and its impact on cancer cell progression, migration and metastasis is poorly understood. ECM internalisation is increased in invasive breast cancer cells, suggesting it may support invasiveness. Here we developed a high-content screening assay to study ECM uptake. We identified that mitogen-activated protein kinase (MAPK) family members, MAP3K1 and MAPK11 (p38β), and the protein phosphatase 2 (PP2) subunit PPP2R1A were required for the internalisation of ECM-bound α2β1 integrin. Furthermore, α2β1 integrin was necessary for macropinocytosis of soluble dextran, identifying it as a novel and targetable regulator of macropinocytosis in cancer. Moreover, disruption of α2 integrin, MAP3K1, MAPK11 and PP2R1A-mediated ECM internalisation significantly impaired cancer cell migration and invasion in 2D and 3D culture systems. Finally, α2β1 integrin and MAP3K1 expression were significantly upregulated in pancreatic tumours and correlated with poor prognosis in pancreatic cancer patients. Strikingly, MAP3K1, MAPK11, PPP2R1A and α2 integrin expression were higher in chemotherapy-resistant tumours in breast cancer patients. Our results identified the α2β1 integrin/p38 signalling axis as a novel regulator of ECM endocytosis, which drives invasive migration and tumour progression.
Genomic database furnishes a spontaneous example of a functional Class II glycyl-tRNA synthetase urzyme
Authors: Patra Sourav Kumar , Douglas Jordan , Wills Peter R. , Bouckeart Remco , Betts Laurie , Qing Tang Guo , Carter Charles W.
Published: January 2024

The chief barrier to studies of how genetic coding emerged is the lack of experimental models for ancestral aminoacyl-tRNA synthetases (AARS). We hypothesized that conserved core catalytic sites could represent such ancestors. That hypothesis enabled engineering functional “urzymes” from TrpRS, LeuRS, and HisRS. We describe here a fourth urzyme, GlyCA, detected in an open reading frame from the genomic record of the arctic fox,Vulpes lagopus. GlyCA is homologous to a bacterial heterotetrameric Class II GlyRS-B. Alphafold2 predicted that the N-terminal 81 amino acids would adopt a 3D structure nearly identical to the HisRS urzyme (HisCA1). We expressed and purified that N-terminal segment. Enzymatic characterization revealed a robust single-turnover burst size and a catalytic rate for ATP consumption well in excess of that previously published for HisCA1. Time-dependent aminoacylation of tRNAGlyproceeds at a rate consistent with that observed for amino acid activation. In fact, GlyCA is actually 35 times more active in glycine activation by ATP than the full-length GlyRS-B α-subunit dimer. ATP-dependent activation of the 20 canonical amino acids favors Class II amino acids that complement those favored by HisCA and LeuAC. These properties reinforce the notion that urzymes represent the requisite ancestral catalytic activities to implement a reduced genetic coding alphabet.
Chromosome-levelde novogenome unveils the evolution ofGleditsia sinensisand thorns development
Authors: Xiao Dandan , Liu Jiahao , Wang Jing , Yang Yuzhang , Yang Xiaoqian , Yu Ruen , Wang Chun , Wang Yanwei , Liu Yanping , Fan Dingchen , Lin Furong
Published: January 2024

GleditsiaLinn is widely distributed in the world andGleditsia sinensisas an important Leguminosae specie, especially its thorns, has been used in the Chinese medicine as a chief ingredient for centuries. While the lack of genome database limits its in-depth research, especially genetic regulation and molecular developmental mechanism. In this investigation, a chromosome-levelde novogenome ofG. sinensiswas assembled through PacBio HiFi, Illumina sequencing as well as those from Hi-C, genetic mapping and K-mer analysis. TheG. sinensisharbors 786.13 Mb sized genome (contig N50=1.58 Mb, scaffold N50=51.53 Mb, 2n=28) with 36, 408 protein-coding genes. The full-length transcriptome sequencing of diverse tissues was performed to assist genome functional annotation. The comparative and evolutionary analysis unveiled thatG. sinensisdiverged from the Cretaceous period approximately 76.31 million years ago (Mya) and the close relationship betweenG. sinensisand other 8 Leguminosae species. The whole-genome duplication (WGD) analysis indicatedG. sinensisunderwent three WGD events and might go through another WGD event after differentiating from other Leguminosae plants. The Weighted Gene Coexpression Network Analysis based on phenotype and differentially expressed genes further demonstrated thatGsinMYBshould be involved in the development of thorns via regulating late thorn differentiation. This investigation provides a high level genome ofGleditsiafor Leguminosae species evolution comparison and functional elucidation and also key insights for further study on the molecular regulation mechanisms of the thorns development as a special abnormal stem organ in plants and the molecular breeding ofG. sinensis.
Delayed Healthcare Seeking and Associated Factors for Common Childhood Illnesses among Caregivers with Under-Five Children in Southwestern Ethiopia, 2023
Authors: Hunde Gamechu Atomsa , Fikadu Kalkidan , Demeke Tigist
Published: January 2024

Background

For under-five children, receiving timely and appropriate medical attention is crucial in preventing serious and fatal complications. Unfortunately, evidence shows that parents of young children frequently delay seeking care, contributing to the death of many kids before they even get to a medical facility.

Objectives

The study aimed to assess delay in healthcare seeking and associated factors for common childhood illnesses among caregivers with under-five children visiting Yem special woreda public health facilities, 2023.

Methods

A facility-based cross-sectional study was conducted among 333 caregivers of under-five children diagnosed with common childhood illnesses visiting Yem special woreda public health facilities. Systematic random sampling was employed and data collection was carried out using an interviewer-administered questionnaire. Delay was characterized as a long time (typically >24 hours) between disease onset and start of the necessary treatment. Data was entered using Epi Data version 4.7 and exported to Statistical Package for the Social Sciences version 25.0. Bi-variable and multivariable logistic regression analyses were conducted to identify the factors that influence the delay in healthcare seeking. Adjusted odds ratios with a 95% confidence interval were used to determine the associations. Statistically significant variables were identified based on a p-value < 0.05.

Results

A total of 326 caregivers participated in the study with a response rate of 98%. The proportion of delayed health care seeking was 74.5%. Child ≥ 12 months (AOR =1.99, 95% CI: 1.11-3.57), rural residence (AOR = 2.41, 95% CI: 1.35-4.28), no community health insurance (AOR = 1.91, 95% CI: 1.07-3.42), traditional treatment (AOR = 2.98, 95% CI: 1.46- 6.10), and self-medication at home first (AOR = 2.73, 95% CI: 1.32-5.63) and perceiving illness as mild (AOR= 2.64, 95% CI: 1.28-5.42) were factors associated with delayed healthcare seeking.

Conclusion and recommendation

The study showed delay in health care seeking for common childhood illnesses among caregivers was high. Hence, reducing delays necessitates the implementation of public education campaigns, collaboration with local organizations, and the provision of counseling for caregivers regarding childhood illnesses.
Effect of the Healing Fit program on sleep quality, stress, and concentration: a randomized controlled study
Authors: Kim Wonjong , Bae Iklyul , Kim Kiyong , Ju Wonheo
Published: January 2024

This study examined the usefulness for improving sleep quality of the Healing Fit program, which provides micro-electrical stimulation of the brain (transcranial electrical stimulation) and music therapy, in healthy adults who experienced sleep deprivation. A randomized controlled pretest–posttest design was used to evaluate effects on sleep quality, stress, and concentration. The study began after approval from the Institutional Review Board of Eulji University before conducting the study (EU22-90). Healing Fit was applied to the experimental group (n = 25) at a volume of 50 dB (about the level of normal conversation) for 30 min. Transcranial electrical stimulation intensity was set individually from 1 to 10 to the extent that the participant had no pain. Afterwards, interventions corresponding to learning, healing, and sleep music within Healing Fit were applied three times a day (30 min per session) for 14 days while participants continued their normal daily routines. The 25 control participants rested without any treatment for 30 min. Subjective/objective sleep quality, subjective/objective stress, concentration, and general characteristics were measured on day 1 of the experiment in both groups. Objective/subjective sleep quality was measured on day 7 and objective/subjective sleep quality, objective/subjective stress, and concentration were measured on day 14. The total sleep time, waking time after sleep onset, sleep efficiency, deep sleep, and subjective sleep quality were significantly better in the experimental group than in the control group. Objective and subjective stress decreased significantly in the experimental group compared to the control group, but there were no significant differences in autonomic nervous system activity. However, sympathetic and parasympathetic nervous system activity was balanced when Healing Fit was applied. There were no significant differences in concentration between groups; however, concentration tended to increase over time in the experimental group.

Clinical Trial Registration

Clinical Research Information Service (https://cris.nih.go.kr/; KCT0009045).
Insulin resistance assessed by short insulin tolerance test and its association with obesity and insulin resistance-related parameters in humans: A randomized trial
Authors: Hayashishita Akiko , Watanabe Taku , Suzuki Naoko , Nakaya Toshitaka , Sugimoto Ayako , Yokota Isao , Ohira Hiroshi , Nishimura Masaharu , Tsujino Ichizo
Published: January 2024

The aim of this study was to examine the association of insulin resistance (evaluated by the short insulin tolerance test [SITT]) with parameters related to obesity and insulin resistance. We prospectively recruited controls and patients with type 2 diabetes mellitus (T2DM), subjected them to the SITT, and calculated the K indices of the intravenous insulin tolerance test (KITT(iv)) and the subcutaneous insulin tolerance test (KITT(sc)). We compared KITT(iv) between the volunteers and patients, and examined its correlation with KITT(sc). We also examined the association of KITT(iv) with obesity, insulin resistance-related parameters, and the insulin dose required for glycemic control. A total of 24 participants (seven controls and 17 patients with T2DM) were studied. The mean KITT(iv) was significantly lower in patients with T2DM than in the controls (2.5%±2.1% vs. 4.5%±1.8%). In all participants, KITT(iv) was significantly correlated with the HOMA-IR values (r=−0.601, p<0.05) but not with KITT(sc) (p=0.62). KITT(iv) was correlated positively with the serum adiponectin concentration, but negatively with the visceral fat area and serum concentrations of tumor necrosis factor-α and branched-chain amino acids. In patients with T2DM, KITT(iv) and HOMA-IR values were significantly correlated with the total insulin dose required for glycemic control. Insulin resistance evaluated using intravenous insulin (KITT(iv)) was correlated with the HOMA-IR values, but not with the resistance evaluated using subcutaneous insulin (KITT(sc)). The degree of insulin resistance was associated with biomarkers, such as adiponectin, and with the dose of insulin required for glycemic control.
Contribution of parasite and host genotype to immunopathology of schistosome infections
Authors: Jutzeler Kathrin S. , Le Clec’h Winka , Chevalier Frédéric D. , Anderson Timothy J.C.
Published: January 2024

Background

The role of pathogen genotype in determining disease severity and immunopathology has been studied intensively in microbial pathogens including bacteria, fungi, protozoa, and viruses, but is poorly understood in parasitic helminths. The medically important blood flukeSchistosoma mansoniis an excellent model system to study the impact of helminth genetic variation on immunopathology. Our laboratory has demonstrated that laboratory schistosome populations differ in sporocyst growth and cercarial production in the intermediate snail host and worm establishment and fecundity in the vertebrate host. Here, we (i) investigate the hypothesis that schistosome genotype plays a significant role in immunopathology and related parasite life history traits in the vertebrate mouse host and (ii) quantify the relative impact of parasite and host genetics on infection outcomes.

Methods

We infected BALB/c and C57BL/6 mice with four different laboratory schistosome populations from Africa and the Americas. We quantified disease progression in the vertebrate host by measuring body weight and complete blood count (CBC) with differential over an infection period of 12 weeks. On sacrifice, we assessed parasitological (egg and worm counts, fecundity), immunopathological (organ measurements and histopathology), and immunological (CBC with differential and cytokine profiles) characteristics to determine the impact of parasite and host genetics.

Results

We found significant variation between parasite populations in worm numbers, fecundity, liver and intestine egg counts, liver and spleen weight, and fibrotic area, but not in granuloma size. Variation in organ weight was explained by egg burden and by intrinsic parasite factors independent of egg burden. We found significant variation between infected mouse lines in cytokines (IFN-γ, TNF-α), eosinophil, lymphocyte, and monocyte counts.

Conclusions

This study showed that both parasite and host genotype impact the outcome of infection. While host genotype explains most of the variation in immunological traits, parasite genotype explains most of the variation in parasitological traits, and both host and parasite genotype impact immunopathology outcomes.
Delineation of signaling routes that underlie differences in macrophage phenotypic states
Authors: Totu Tiberiu , Bossart Jonas , Hast Katharina , Li Chen , Rottmar Markus , Sobottka Bettina , Yu Guocan , Ayala-Nunez Vanesa , Buljan Marija
Published: January 2024

Macrophages represent a major immune cell type in tumor microenvironments, they exist in multiple functional states and are of a strong interest for therapeutic reprogramming. While signaling cascades defining pro-inflammatory macrophages are better characterized, pathways that drive polarization in immunosuppressive macrophages are incompletely mapped. Here, we performed an in-depth characterization of signaling events in primary human macrophages in different functional states using mass spectrometry-based proteomic and phosphoproteomic profiling. Analysis of direct and indirect footprints of kinase activities has suggested PAK2 and PKCα kinases as important regulators ofin vitroimmunosuppressive macrophages (IL-4/IL-13 or IL-10 stimulated). Network integration of these data with the corresesponding transcriptome profiles has further highlighted FOS and NCOR2 as central transcription regulators in immunosuppressive states. Furthermore, we retrieved single cell sequencing datasets for tumors from cancer patients and found that the unbiased signatures identified here through proteomic analysis were able to successfully separate pro-inflammatory macrophage populations in a clinical setting and could thus be used to expand state-specific markers. This study contributes to in-depth multi-omics characterizations of macrophage phenotypic landscapes, which could be valuable for assisting future interventions that therapeutically alter immune cell compartments.

Abstract Figure

Highlights

Global proteomic characterization of primary human macrophages in different states

Mapping of main signaling events through in-depth data analysis

PKCα and PAK2 kinases are important regulators of immunosuppressive macrophages

Proteomic signatures enable accurate detection of pro-inflammatory macrophages in patient tumors
Long-Term Potentiation Produces a Sustained Expansion of Synaptic Information Storage Capacity in Adult Rat Hippocampus
Authors: Samavat Mohammad , Bartol Thomas M. , Bromer Cailey , Hubbard Dusten D. , Hanka Dakota C. , Kuwajima Masaaki , Mendenhall John M. , Parker Patrick H. , Bowden Jared B. , Abraham Wickliffe C. , Sejnowski Terrence J. , Harris Kristen M.
Published: January 2024

Long-term potentiation (LTP) has become a standard model for investigating synaptic mechanisms of learning and memory. Increasingly, it is of interest to understand how LTP affects the synaptic information storage capacity of the targeted population of synapses. Here, structural synaptic plasticity during LTP was explored using three-dimensional reconstruction from serial section electron microscopy. Storage capacity was assessed by applying a new analytical approach, Shannon information theory, to delineate the number of functionally distinguishable synaptic strengths. LTP was induced by delta-burst stimulation of perforant pathway inputs to the middle molecular layer of hippocampal dentate granule cells in adult rats. Spine head volumes were measured as predictors of synaptic strength and compared between LTP and control hemispheres at 30 min and 2 hr after the induction of LTP. Synapses from the same axon onto the same dendrite were used to determine the precision of synaptic plasticity based on the similarity of their physical dimensions. Shannon entropy was measured by exploiting the frequency of spine heads in functionally distinguishable sizes to assess the degree to which LTP altered the number of bits of information storage. Outcomes from these analyses reveal that LTP expanded storage capacity; the distribution of spine head volumes was increased from 2 bits in controls to 3 bits at 30 min and 2.7 bits at 2 hr after the induction of LTP. Furthermore, the distribution of spine head volumes was more uniform across the increased number of functionally distinguishable sizes following LTP, thus achieving more efficient use of coding space across the population of synapses.

Significance

Establishing relationships between structure, function, and information storage capacity provides a new approach to assessing network strength from structural measurements. Long term potentiation (LTP) is a standard model for investigating synaptic mechanisms of learning and memory. Information is a retrievable quantity that is being stored in synapses as synaptic strength and is correlated with multiple structural components of synaptic strength. Structural synaptic plasticity was measured in 3D reconstructions from serial section electron microscopy of spine head volume, as a proxy for synapse strength, at 30 min and 2 hr after LTP induction. Outcomes indicate that LTP enhances information storage capacity for at least 2 hr by increasing the precision of the synaptic structure and expanding the range of synapse sizes.
Microsatellite break-induced replication generates highly mutagenized extrachromosomal circular DNAs
Authors: Gadgil Rujuta Yashodhan , Rider S. Dean , Shrestha Resha , Alhawach Venicia , Hitch David C. , Leffak Michael
Published: January 2024

Extrachromosomal circular DNAs (eccDNAs) are produced from all regions of the eucaryotic genome. In tumors, highly transcribed eccDNAs have been implicated in oncogenesis, neoantigen production and resistance to chemotherapy. Here we show that unstable microsatellites capable of forming hairpin, triplex, quadruplex and AT-rich structures generate eccDNAs when integrated at a common ectopic site in human cells. These non-B DNA prone microsatellites form eccDNAs by replication-dependent mechanisms. The microsatellite-based eccDNAs are highly mutagenized and display template switches to sister chromatids and to nonallelic chromosomal sites. High frequency mutagenesis occurs within the eccDNA microsatellites and extends bidirectionally for several kilobases into flanking DNA and nonallelic DNA. Mutations include mismatches, short duplications, longer nontemplated insertions and large deletions. Template switching leads to recurrent deletions and recombination domains within the eccDNAs. Template switching events are microhomology-mediated, but do not occur at all potential sites of complementarity. Each microsatellite exhibits a distinct pattern of recombination, microhomology choice and base substitution signature. Depletion of Rad51, the COPS2 signalosome subunit or POLη alter the eccDNA mutagenic profiles. We propose an asynchronous capture model based on break-induced replication from microsatellite-induced DNA breaks for the generation and circularization of mutagenized eccDNAs and genomic homologous recombination deficiency (HRD) scars.
Mitochondrial membrane potential regulates nuclear DNA methylation and gene expression through phospholipid remodeling
Authors: Mori Mateus Prates , Lozoya Oswaldo , Brooks Ashley M. , Grenet Dagoberto , Nadalutti Cristina A. , Ryback Birgitta , Huang Kai Ting , Hasan Prottoy , Hajnóczky Gyӧrgy , Santos Janine H.
Published: January 2024

Maintenance of the mitochondrial inner membrane potential (ΔΨM) is critical for many aspects of mitochondrial function, including mitochondrial protein import and ion homeostasis. While ΔΨM loss and its consequences are well studied, little is known about the effects of increased ΔΨM. In this study, we used cells deleted ofATPIF1, a natural inhibitor of the hydrolytic activity of the ATP synthase, as a genetic model of mitochondrial hyperpolarization. Our data show that chronic ΔΨM increase leads to nuclear DNA hypermethylation, regulating transcription of mitochondria, carbohydrate and lipid metabolism genes. Surprisingly, remodeling of phospholipids, but not metabolites or redox changes, mechanistically links the ΔΨM to the epigenome. These changes were also observed upon chemical exposures and reversed by decreasing the ΔΨM, highlighting them as hallmark adaptations to chronic mitochondrial hyperpolarization. Our results reveal the ΔΨM as the upstream signal conveying the mitochondrial status to the epigenome to regulate cellular biology, providing a new framework for how mitochondria can influence health outcomes in the absence of canonical dysfunction.

Highlights

Mitochondria hyperpolarization leads to nuclear DNA hypermethylation

DNA methylation regulates expression of mitochondrial and lipid metabolism genes

Phospholipid remodeling mediates the epigenetic effects of mitochondrial hyperpolarization
Little evidence for inbreeding depression for birth mass, survival and growth in Antarctic fur seal pups
Authors: Paijmans A.J. , Berthelsen A.L. , Nagel R. , Cristaller F. , Kröcker N. , Forcada J. , Hoffman J.I.
Published: January 2024

Inbreeding depression, the loss of offspring fitness due to consanguineous mating, is generally detrimental for individual performance and population viability. We therefore investigated inbreeding effects in a declining population of Antarctic fur seals at Bird Island, South Georgia. Here, localised warming has reduced the availability of the seal’s staple diet, Antarctic krill, leading to a temporal increase in the strength of viability selection against inbred offspring, which are increasingly failing to recruit into the adult breeding population. However, it remains unclear whether viability selection operates before or after nutritional independence at weaning. We therefore used microsatellite data from 884 pups and their mothers, and SNP array data from 100 mother-offspring pairs, to quantify the effects of individual and maternal inbreeding on three important neonatal fitness traits: birth mass, survival and growth. We did not find any clear or consistent effects of inbreeding on any of these traits. This suggests that viability selection filters inbred individuals out of the population as juveniles during the time window between weaning and recruitment. Our study brings into focus a poorly understood life-history stage and emphasises the importance of understanding the ecology and threats facing juvenile pinnipeds.
Intrinsically disordered regions regulate RhlE RNA helicase functions in bacteria
Authors: Hausmann Stéphane , Geiser Johan , Allen George Edward , Geslain Sandra Amandine Marie , Valentini Martina
Published: January 2024

RNA helicases—central enzymes in RNA metabolism— often feature intrinsically disordered regions (IDRs) that enable phase separation and complex molecular interactions. In the bacterial pathogenPseudomonas aeruginosa, the non-redundant RhlE1 and RhlE2 RNA helicases share a conserved REC catalytic core but differ in C-terminal IDRs. Here, we show how the IDR diversity defines RhlE RNA helicase specificity of function. Both IDRs facilitate RNA binding and phase separation, localizing proteins in cytoplasmic clusters. However, RhlE2 IDR is more efficient in enhancing REC core RNA unwinding, exhibits a greater tendency for phase separation, and interacts with the RNase E endonuclease, a crucial player in mRNA degradation. Swapping IDRs results in chimeric proteins that are biochemically active but functionally distinct as compared to their native counterparts. The RECRhlE1-IDRRhlE2chimera improves cold growth of arhlE1mutant, gains interaction with RNase E and affects a subset of both RhlE1 and RhlE2 RNA targets. The RECRhlE2-IDRRhlE1chimera instead hampers bacterial growth at low temperatures in the absence of RhlE1, with its detrimental effect linked to aberrant RNA droplets. By showing that IDRs modulate both protein core activities and subcellular localization, our study defines the impact of IDR diversity on the functional differentiation of RNA helicases.
Different metabolite profiles acrossPenicillium roquefortipopulations associated with ecological niche specialisation and domestication
Authors: Crequer Ewen , Coton Emmanuel , Cueff Gwennina , Cristiansen Johan V. , Frisvad Jens C. , de la Vega Ricardo Rodriguez , Giraud Tatiana , Jany Jean-Luc , Coton Monika
Published: January 2024

Fungi are known to produce many chemically diversified metabolites, yet their ecological roles are not always fully understood. The blue cheese making fungusPenicillium roquefortithrives in different ecological niches and is known to produce a wide range of metabolites, including mycotoxins. ThreeP. roquefortipopulations have been domesticated for cheese production and two populations thrive in other anthropized environments, i.e., spoiled food, lumber and silage. Here, we looked for differences in targeted and untargeted metabolite production profiles between populations using HPLC-HR-Q-TOF and UHPLC-Q-TOF-HR-MS/MS. The non-cheese populations produced several fatty acids and different terpenoids, lacking in cheese strains. The Termignon cheese population displayed intermediate metabolite profiles between cheese and non-cheese populations, as previously shown for other traits. The non-Roquefort population, the cheese population with the strongest domestication syndrome, produced the lowest quantities of measured metabolites, including known mycotoxins such as mycophenolic acid (MPA), andrastin A and PR toxin. Its inability to produce MPA was due to a deletion in thempaCgene, while a premature stop codon in ORF 11 of the PR toxin gene cluster explained its absence and the accumulation of its eremofortin A & B intermediates. In the Roquefort population, we detected no PR toxin nor eremofortins A or B, but found no indel or frameshift mutation, suggesting downregulation. Our results suggest that domesticated cheese populations were selected for lower toxin production while populations from other anthropized environments maintained high metabolite diversity, the bioactivities of these compounds being likely important in these ecological niches.
Droplet microfluidics for time-resolved serial crystallography
Authors: Stubbs Jack , Hornsey Theo , Hanrahan Niall , Esteban Luis Blay , Bolton Rachel , Malý Martin , Basu Shibom , Orlans Julien , de Sanctis Daniele , Shim Jung-uk , Stewart Patrick D. Shaw , Orville Allen M. , Tews Ivo , West Jonathan
Published: January 2024

Serial crystallography requires large numbers of microcrystals and robust strategies to rapidly apply substrates to initiate reactions in time-resolved studies. Here we report the use of droplet miniaturisation for the controlled production of uniform crystals, providing an avenue for controlled diffusion and synchronous reaction initiation. The approach was evaluated using two enzymatic systems, yielding 3-µm lysozyme crystals and 2-µm crystals of Pdx1, an Arabidopsis enzyme involved in vitamin B6 biosynthesis. A seeding strategy was used to overcome the improbability of Pdx1 nucleation occurring with diminishing droplet volumes. Convection within droplets was exploited for rapid crystal mixing with ligands. Mixing times of <2 milliseconds were achieved. Droplet microfluidics for crystal size engineering and rapid micromixing can be used to advance time-resolved serial crystallography.
Intestinal stearoyl-CoA desaturase-1 regulates energy balance via alterations in bile acid homeostasis
Authors: Burchat Natalie , Vidola Jeanine , Pfreundschuh Sarah , Sharma Priyanka , Rizzolo Daniel , Guo Grace L. , Sampath Harini
Published: January 2024

Background and Aims

Stearoyl-CoA desaturase-1 (SCD1) converts saturated fatty acids into monounsaturated fatty acids and plays an important regulatory role in lipid metabolism. Previous studies have demonstrated that mice deficient in SCD1 are protected from diet-induced obesity and hepatic steatosis due to altered lipid esterification and increased energy expenditure. Previous studies in our lab have shown that intestinal SCD1 modulates intestinal and plasma lipids and alters cholesterol metabolism. Here we investigated a novel role for intestinal SCD1 in the regulation of systemic energy balance.

Methods

To interrogate the role of intestinal SCD1 in modulating whole body metabolism, intestine-specificScd1knockout (iKO) mice were maintained on standard chow diet or challenged with a high-fat diet (HFD). Studies included analyses of bile acid content and composition, metabolic phenotyping including body composition, indirect calorimetry, glucose tolerance analyses, and assessment of bile acid signaling pathways.

Results

iKO mice displayed elevated plasma and hepatic bile acid content and decreased fecal bile acid excretion, associated with increased expression of the ileal bile acid uptake transporter,Asbt. These increases were associated with increased expression of TGR5 targets, includingDio2in brown adipose tissue and elevated plasma glucagon-like peptide-1 levels. Upon HFD challenge, iKO mice had reduced metabolic efficiency apparent through decreased weight gain despite higher food intake. Concomitantly, energy expenditure was increased, and glucose tolerance was improved in HFD-fed iKO mice.

Conclusion

Our results indicate that deletion of intestinal SCD1 has significant impacts on bile acid metabolism and whole-body energy balance, likely via activation of TGR5.
Divisome minimization shows that FtsZ and SepF can form an active Z-ring, and reveals BraB as a new cell division influencing protein inBacillus subtilis
Authors: Gulsoy Ilkay Celik , Saaki Terrens N. V. , Wenzel Michaela , Syvertsson Simon , Morimoto Taku , Hamoen Leendert W.
Published: January 2024

One of the aims of synthetic biology is the construction of a minimal cell. Since bacteria are the simplest life forms, they are the preferred blueprint for such a cell. In this study, we tried to find the minimal set of proteins required for division of a cell wall containing cell, using the bacterial model systemBacillus subtilis. Bacterial cytokinesis begins with polymerization of the tubulin homologue FtsZ at midcell into the Z-ring, which recruits the late cell division protein that synthesize the division septum. Assembly of FtsZ is carefully regulated, involving a dozen conserved cell division proteins. These proteins are not essential, but removing more than one is in many cases lethal. We made use of known suppressor mutations to find a gene deletion route that eventually enabled us to remove eight conserved cell division proteins: ZapA, MinC, MinJ, UgtP, ClpX, Noc, EzrA and FtsA. Only FtsZ and its membrane anchor SepF appeared to be required for Z-ring formation. Interestingly, SepF is also the FtsZ anchor in archaea, and both proteins may date back to the Last Universal Common Ancestor (LUCA). Curiously, viability was not greatly affected by the multiple deletions, although the frequency of cell division was considerably reduced. However, genome sequencing exposed the accumulation of several suppressor mutations, and revealed an unexpected cell division regulation function for the branched chain amino acid transporter BraB. The implications of these findings for the role of SepF in cell division, and the construction of a minimal cell division machinery are discussed.
Endoplasmic reticulum stress delays choroid development in theHCAR1knock-out mouse
Authors: Modaresinejad Monir , Yang Xiaojuan , Nezhady Mohammad Ali Mohammad , Zhu Tang , Bajon Emmanuel , Hou Xin , Tahiri Houda , Hardy Pierre , Rivera José Carlos , Lachapelle Pierre , Chemtob Sylvain
Published: January 2024

The sub-retina, composed of the choroid and the retinal pigment epithelium (RPE), bears a critical role in proper vision. In addition to phagocytosis of photoreceptor debris, the RPE shuttles oxygen and nutrients to the neuroretina. For their own energy production, RPE cells mainly rely on lactate, a major by-product of glycolysis. Lactate in turn is believed to convey most of its biological effects via the HCAR1 receptor. Here, we show that the lactate-specific receptor, HCAR1, is exclusively expressed in the RPE cells and thatHcar1−/−mice exhibit a substantially thinner choroid vasculature during development. Notably, the angiogenic properties of lactate on the choroid are impacted by the absence ofHcar1.Hcar1-deficient mice exhibit elevated endoplasmic reticulum (ER) stress along with eIF2α phosphorylation, a significant decrease in the global protein translation rate, and a lower proliferation rate of choroidal vasculature. Strikingly, inhibition of the Integrated Stress Response using an inhibitor of eIF2α phosphorylation (ISRIB) restores protein translation and rescues choroidal thinning. These results provide evidence that lactate signalling via HCAR1 is important for choroidal development/angiogenesis and highlight the importance of this receptor in establishing mature vision.
Identification and quantification of human relaxin proteins by immunoaffinity-mass spectrometry
Authors: Rais Yasmine , Drabovich Andrei P.
Published: January 2024

The human relaxins belong to the Insulin/IGF/Relaxin superfamily of peptide hormones, and their physiological function is primarily associated with reproduction. In this study, we focused on a prostate tissue-specific relaxin RLN1 (REL1_HUMAN protein), and a broader tissue specificity RLN2 (REL2_HUMAN). Due to their structural similarity, REL1 and REL2 proteins were collectively named a ‘human relaxin protein’ in previous studies and were exclusively measured by immunoassays. We hypothesized that the highly selective and sensitive immunoaffinity-selected reaction monitoring (IA-SRM) assays could reveal the identity and concentration of REL1 and REL2 in biological samples and facilitate evaluation of these proteins for diagnostic applications. RT-PCR revealed the high levels of RLN1 and RLN2 transcripts in prostate and breast cancer cell lines. However, no endogenous prorelaxin-1 or mature REL1 were detected by IA-SRM in numerous biological samples. IA-SRM assay of REL2 revealed its undetectable levels (<9 pg/mL) in control female and male sera, relatively high levels of REL2 in maternal sera (median 331 pg/mL, 120 patients), and a biphasic expression of REL2 across the gestational weeks. IA-SRM assays discovered potential cross-reactivity and false-positive measurements for relaxin immunoassays. The developed IA-SRM assays will facilitate investigation of physiological and pathological roles of REL1 and REL2 peptide hormones.