bluuebunny/crossref_metadata_2025_split huggingface dataset:
Thermoregulation and Diurnal Roost Selection of Boreal Bats During Pre-Hibernation Period
Authors: Suominen Kati M. , Fritzén Niclas R. , Fjelldal Mari A. , Blomberg Anna S. , Viljamaa Minna J.K. , Lilley Thomas M. 
Published: May 2024

AbstractLiving in a seasonal environment poses challenges for small mammals, such as bats, reliant on insects as their primary food source. Bats may adeptly navigate these energetic challenges by reducing their metabolism and body temperature, entering a state of torpor. Particularly during the winter, bats remain torpid for extended periods, but are dependent on sufficient energy reserves to survive until spring. With the onset of autumn and declining temperature, bats face the challenge of building their fat deposits during a time of decreasing food availability. Bats may therefore transition to cooler roosts to initiate torpor, thereby reducing energy expenditure. However, little is still known about torpor use or roost selection by bats in autumn. This study explores the factors influencing roost selection and torpor use and –duration in two bat species during this critical transition period between the breeding and overwintering season. We show that date in autumn is a stronger driver of torpor use than prevailing ambient temperature, and that bats employ specific strategies in which they first increase daytime torpor use before also increasing the use of night-time torpor during the pre- hibernation fattening period, most likely to facilitate rapid fat accumulation. Notably, bats commenced night-time torpor use after spending entire days in torpor. These findings underscore the dynamic nature of torpor and the energy-saving strategies employed during the crucial pre- hibernation period, marking the transition from summer to winter.
SETBP1 Haploinsufficiency and Related Disorders Clinical and Neurobehavioral Phenotype Study
Authors: Oyler Haley O. , Hudac Caitlin M. , Chung Wendy K. , Snyder LeeAnne G. , Robertson Stephanie , Srivastava Siddharth , Geye Trina 
Published: May 2024

AbstractTo comprehensively investigate the neurodevelopmental profile and clinical characteristics associated with SETBP1 haploinsufficiency disorder (SETBP1-HD) and SETBP1-related disorders (SETBP1-RD). We reported genetic results on 34 individuals, with behavior and clinical data from 22 with SETBP1-HD and 5 with SETBP1-RD, by assessing results from medical history interviews and standardized adaptive, clinical, and social measures provided from Simons Searchlight. All individuals with SETBP1-HD and SETBP1-RD exhibited neurological impairments including intellectual disability/developmental delay (IDD), attention- deficit/hyperactivity disorder, autism spectrum disorder, and/or seizures, as well as speech and language delays. While restricted interests and repetitive behaviors present challenges, a relative strength was observed in social motivation within both cohorts. Individuals with SETBP1-RD reported a risk for heart issues and compared to SETBP1-HD greater risks for orthopedic and somatic issues with greater difficulty in bowel control. Higher rates for neonatal feeding difficulties and febrile seizures were reported for individuals with SETBP1-HD. Additional prominent characteristics included sleep, vision, and gastrointestinal issues, hypotonia, and high pain tolerance. This characterization of phenotypic overlap (IDD, speech challenges, autistic and attention deficit traits) and differentiation (somatic and heart issue risks for SETBP1-RD) between the distinct neurodevelopmental disorders SETBP1-HD and SETBP1- RD is critical for medical management and diagnosis.
UBR1 Promotes Sex-Dependent ACE2 Ubiquitination in Hypertension
Authors: Elgazzaz Mona , Lakkappa Navya , Berdasco Clara , Mohan Uma Priya , Nuzzo Anna , Restivo Luke , Martinez Alexa , Scarborough Amy , Guidry Jessie J. , Sriramula Srinivas , Xu Jiaxi , Daoud Hisham , Mendiola Plá Michelle A. , Bowles Dawn E. , Beyer Andreas M. , Mauvais-Jarvis Franck , Yue Xinping , Filipeanu Catalin M. , Lazartigues Eric 
Published: May 2024

AbstractBackgroundAngiotensin (Ang)-II impairs the function of the antihypertensive enzyme ACE2 by promoting its internalization, ubiquitination and degradation thus contributing to hypertension. However, few ACE2 ubiquitination partners have been identified and their role in hypertension remains unknown.MethodsProteomics and bioinformatic analysis were used to identify ACE2 ubiquitination partners in the brain, heart, and kidney from Ang-II-infused C57BL6/J mice from both sexes and validated the interaction between UBR1 and ACE2 in cells. Central and peripheral UBR1 knockdown was then performed in male mice to investigate its role in the maintenance of hypertension.ResultsProteomics analysis from hypothalamus identified UBR1 as a potential E3 ligase promoting ACE2 ubiquitination. Enhanced UBR1 expression, associated with ACE2 reduction, was confirmed in various tissues from hypertensive male mice and human samples. Treatment of endothelial and smooth muscle cells with testosterone, but not 17β-estradiol, confirmed a sex-specific regulation of UBR1. In vivo silencing of UBR1 using chronic administration of small interference RNA resulted in the restoration of ACE2 levels in hypertensive males. A transient decrease in blood pressure following intracerebroventricular, but not systemic, infusion was also observed. Interestingly, UBR1 knockdown increased the brain activation of Nedd4-2, an E3 ligase promoting ACE2 ubiquitination and reduced expression of SGK1, the kinase inactivating Nedd4-2. Conclusions: These data demonstrate that UBR1 is a novel ubiquitin ligase targeting ACE2 in hypertension. UBR1 and Nedd4-2 E3 ligases appear to work synergistically to ubiquitinate ACE2. Targeting of these ubiquitin ligases may represent a novel strategy to restore ACE2 compensatory activity in hypertension.
LOW-COST PELVIC PHANTOM PROTOTYPE WITH MATERIALS RESEMBLING HUMAN TISSUES
Authors: Coya Javiera García , Meier Catalina Nazar , Herrera TM Marco Jiménez , TM Ricardo Castillo V. 
Published: May 2024

ABSTRACTIntroductionPhantoms are elements used in radiological services for quality control tests. In the case of equipment with ionizing radiation, quality control tests focus on image quality and dosimetry. These phantoms are made with materials that resemble human tissues internally but are high-cost and difficult to access for radiology services.ObjectivesTo design a methodology for creating an anthropomorphic radiology phantom with materials correlating to human tissues of the pelvis for various uses, using Hounsfield Units (HU) as a comparison.MethodologyData from 34 female patients with bone pelvis exams were collected. HU was measured in bone, muscle, and adipose tissue of the hip. Simultaneously, HU of different material mixtures was measured to correlate data between patients and materials for the creation of a right hip phantom.ResultsHU values of the materials match human tissues except for adipose tissue, which is slightly increased. The costs for phantom creation were low.Discussion and ConclusionHU estimates of materials and human tissue mostly align with those estimated in the sample and reported in the literature, achieving the creation of a low-cost phantom easily accessible for institutions or educational centers requiring quality, dosimetry, or educational tests.
Quantification of rose rosette emaravirus (RRV) titers in eriophyoid mites: insights into viral dynamics and vector competency
Authors: Druciarek Tobiasz , Rojas Alejandro , Tzanetakis Ioannis 
Published: May 2024

AbstractUnderstanding the interaction between rose rosette emaravirus (RRV) and its vectors is pivotal in addressing the epidemic outbreak of rose rosette disease. This study employed quantitative real-time RT-PCR to assess RRV genome copy numbers inPhyllocoptes fructiphilusandP. adalius, providing insights into the viral dynamics and vector competency. Our findings suggest active virus replication withinP. fructiphilus, a confirmed vector species, unlikeP. adalius, highlighting its non-vector status. Furthermore, the study highlights the variability in virus concentration in mites over time, underlining possible developmental stage-specific response and influence of mite lifestyle on RRV retention and replication. This research is the first step in understanding the virus-mite interactome, which is essential for developing effective management strategies against rose rosette disease.
Staphylococcal aconitase expression during iron deficiency is controlled by an sRNA-driven feedforward loop and moonlighting activity
Authors: Barrault Maxime , Chabelskaya Svetlana , Coronel-Tellez Rodrigo H. , Toffano-Nioche Claire , Jacquet Eric , Bouloc Philippe 
Published: May 2024

ABSTRACTPathogenic bacteria employ complex systems to cope with metal ion shortage conditions and propagate in the host. IsrR is a regulatory RNA (sRNA) whose activity is decisive for optimumS. aureusfitness upon iron starvation and for full virulence. IsrR down-regulates several genes encoding iron-containing enzymes to spare iron for essential processes. Here we report that IsrR regulates the tricarboxylic acid (TCA) cycle by controlling aconitase (CitB), an iron-sulfur cluster-containing enzyme, and its transcriptional regulator, CcpE. This IsrR-dependent dual-regulatory mechanism provides an RNA-driven feedforward loop, underscoring the tight control required to prevent aconitase expression. Beyond its canonical enzymatic role, aconitase becomes an RNA-binding protein with regulatory activity in iron-deprived conditions, a feature that is conserved inS. aureus. Aconitase not only negatively regulates its own expression, but also impacts the enzymes involved in both its substrate supply and product utilization. This moonlighting activity concurrently upregulates pyruvate carboxylase expression, allowing it to compensate for the TCA cycle deficiency associated with iron scarcity. These results highlight the cascade of complex posttranscriptional regulations controllingS. aureuscentral metabolism in response to iron deficiency.
Subtle alteration in transcriptional memory governs the lineage-level cell cycle duration heterogeneities of mammalian cells
Authors: Charan Kajal , Kar Sandip 
Published: May 2024

AbstractCell cycle duration heterogeneities within a malignant tumor significantly reduce the therapeutic efficacy of cancer treatment. However, identifying factors governing such heterogeneities remains challenging. Here, we demonstrate that correlated fluctuations of the inherited transcription rates during cell cycle progression in combination with the random resetting of them during mitosis are sufficient to account for the experimentally observed cell cycle duration correlation patterns for daughter-daughter, mother-daughter, and cousin-cousin cell lineage pairs. The model elucidates that the variations in the transcriptional inheritance pattern dictate the extent of the cousin-mother inequality phenomenon. It further predicts that the longer the cell cycle duration, the lower will be the lineage pair correlations. However, higher S-G2-M phase duration will only increase daughter-daughter and mother-daughter correlations, hence, reducing the extent of cousin-mother inequality. Overall, the model shows how alteration of the inherited transcriptional fluctuations across lineages finetunes the lineage-level heterogeneities.
A Near Infrared Fluorescent Nanosensor for Spatial and Dynamic Measurements of Auxin, Indole-3-Acetic Acid,in Planta
Authors: Khong Duc Thinh , Vu Kien Van , Sng Benny Jian Rong , Choi Ian Kin Yuen , Porter Thomas K. , Cui Jianqiao , Gong Xun , Wang Song , Nguyen Nguyen Hoai , Ang Mervin , Park Minkyung , Lew Tedrick Thomas Salim , Loh Suh In , Ahsim Riza , Chin Hui Jun , Singh Gajendra Pratap , Chan-Park Mary B. , Chua Nam-Hai , Strano Michael S. , Jang In-Cheol 
Published: May 2024

AbstractAuxins, particularly indole-3-acetic acid (IAA), is a phytohormone critical for plant growth, development, and response to environmental stimuli. Despite its importance, there is a lack of species-independent sensors that allow direct and reversible detection of IAA. Herein, we introduce a novel near infrared fluorescent nanosensor for spatial and temporal measurement of IAAin plantausing Corona Phase Molecular Recognition. The IAA nanosensor shows high specificity to IAAin vitroand was validated to localize and function in plant cells. The sensor works across different plant species without optimization and allows visualization of dynamic changes to IAA distribution and movement in leaf tissues. The results highlighted the utility of IAA nanosensor for understanding IAA dynamicsin planta.
Downregulations of mRNA expressions in theEPAS1andEGLN1: Unraveling a genetic mechanism for high-altitude hypoxia adaptation in Sherpa highlanders
Authors: Droma Yunden , Yue Fengming , Ota Masao , Kobayashi Nobumitsu , Kitaguchi Yoshiaki , Hanaoka Masayuki 
Published: May 2024

AbstractSherpa highlanders exhibit unique hypoxia-tolerant traits, likely evolved through natural selection in response to high-altitude conditions. Previous research has implicatedEPAS1andEGLN1in this adaptation, but their functional mechanisms remain unclear. This study aims to elucidate these mechanisms by exploring mRNA expressions ofEPAS1andEGLN1in Sherpa highlanders. Field investigations enrolled 54 healthy Sherpa highlanders and 25 non-Sherpa lowlanders in Namche Bazaar (3,440 m) and Kathmandu (1,300 m), respectively. Venous blood was collected for erythropoietin (EPO) measurements,EPAS1andEGLN1mRNA expression analyses, and genotyping of single nucleotide polymorphisms (SNPs) rs13419896 and rs4953354 inEPAS1, as well as rs1435166 and rs2153364 SNPs inEGLN1.Comparative analyses were conducted on these elements between highlanders and lowlanders. Despite decreased SpO2in Sherpa highlanders, EPO concentrations did not elevate at high altitudes. TheEPAS1andEGLN1 mRNA expressions were significantly lower in Sherpa highlanders compared to non-Sherpa lowlanders. Moreover, genotype distributions and allele frequencies of rs13419896 and rs4953354 inEPAS1, as well as rs1435166 and rs2153364 inEGLN1, differed significantly between Sherpa highlanders and non-Sherpa lowlanders. Analyses of the relative mRNA expressions ofEPAS1andEGLN1by the SNPs suggested that the rs13419896/G and rs4953354/A alleles inEPAS1, as well as the rs1435166/G and rs2153364/A alleles inEGLN1,have down-regulatory effects on the gene mRNA expressions in Sherpa highlanders, contributing to inhibiting the EPO hypoxia response and exhibiting hypoxia-tolerant EPO levels in Sherpa highlanders. Natural selection, driven by high-altitude hypoxia, has encouraged adaptive evolution in Sherpa highlanders, including modifications inEPAS1andEGLN1genes. This evolutionary process leads to the downregulation of gene mRNA expressions, effectively tempering EPO responses to hypoxia and thereby enabling adaptation to high-altitude environments.
Improving allele-specific epigenomic signal coverage by10-foldusing Hidden Markov Modeling and Machine Learning
Authors: Dumont Emmanuel LP , Janati Ali , Bhattacharya Moumita , Jeannin Jean-Baptiste , Do Catherine 
Published: May 2024

AbstractAllele-specific epigenomic signals refer to differences in epigenomic patterns between the two copies, or “alleles,” of a DNA region inherited from each parent. Epigenomic patterns are defined as alterations of the DNA sequence (e.g., chemical) without modifying the underlying DNA sequence (which would be referred to as “mutations”). Mapping allele-specific epigenomic signals across a genome is crucial, as some can influence gene expression, disease susceptibility, and developmental processes. However, identifying allele-specific epigenomic patterns across an entire genome is limited by the average read length (50-150 nucleotides) of short-read sequencing technologies, which are the most widely-used and affordable whole genome sequencing methods, and by the 99.9% similarity in the DNA sequences inherited from each parent. These limitations restrict the assessment of allele-specific signals to approximately 10% of the genome, potentially overlooking critical regulatory regions. In this paper, we present a highly effective machine-learning approach based on variational hidden Markov modeling, which enables the detection of allele-specific epigenomic signals across the entire genome, resulting in a 10-fold improvement in genomic coverage compared to state-of-the-art methods. We demonstrate our method on DNA methylation, a critical epigenomic regulatory signal.
Generation length of the world’s amphibians and reptiles
Authors: Mancini G. , Santini L. , Cazalis V. , Ficetola F. , Meiri S. , Roll U. , Silvestri S. , Pincheira-Donoso D. , Di Marco M. 
Published: May 2024

AbstractVariation in life histories influences demographic processes from adaptive changes to population declines leading to extinction. Among life history traits, generation length offers a critical feature to forecast species’ demographic trajectories such as population declines (widely used by the IUCN Red List of Threatened Species) and adaptability to environmental change over time. Therefore, estimates of generation length are crucial to monitor demographic stability or future change in highly threatened organisms, particularly ectothermic tetrapods (amphibians and reptiles) – which rank among the most threatened groups – but for which uncertainty in future impacts remains high. Despite its importance, generation length for amphibians and reptiles is largely missing. Here, we aimed to fill-in this gap by modeling generation lengths for amphibians, squamates and testudines as a function of species size, climate, life history, and phylogeny using generalized additive models and phylogenetic generalized least squares. We obtained estimates of generation lengths for 4,543 (52%) amphibians, 8,464 (72%) squamates and 118 (32%) testudines. Our models performed well for most families, for example Bufonidae in amphibians, Lacertidae and Colubridae in squamates and Geoemydidae in testudines, while we found high uncertainty around the prediction of a few families, notably Chamaeleonidae. Species’ body size and mean temperature were the main predictors of generation length in all groups. Although our estimates are not meant to substitute robust and validated measurements from field studies or natural history museums, they can help reduce existing biases in conservation assessments until field data will be comprehensively available.
Single-cell proteomics reveals decreased abundance of proteostasis and meiosis proteins in advanced maternal age oocytes
Authors: Galatidou S , Petelski A , Pujol A , Lattes K , Latorraca L B , Fair T , Popovic M , Vassena R , Slavov N , Barragan M 
Published: May 2024

ABSTRACTAdvanced maternal age is associated with a decline in oocyte quality, which often leads to reproductive failure in humans. However, the mechanisms behind this age-related decline remain unclear. To gain insights into this phenomenon, we applied plexDIA, a multiplexed, single-cell mass spectrometry method, to analyze the proteome of oocytes from both young women and women of advanced maternal age. Our findings primarily revealed distinct proteomic profiles between immature fully grown germinal vesicle and mature metaphase II oocytes. Importantly, we further show that a woman’s age is associated with changes in her oocyte proteome. Specifically, when compared to oocytes obtained from young women, advanced maternal age oocytes exhibited lower levels of the proteasome and TRiC complex, as well as other key regulators of proteostasis and meiosis. This suggests that aging adversely affects the proteostasis and meiosis networks in human oocytes. The proteins identified in this study hold potential as targets for improving oocyte quality and may guide future studies into the molecular processes underlying oocyte aging.
Applying nutritional ecology to optimize diets of crickets raised for food and feed
Authors: Muzzatti Matthew J , Harrison Sarah J. , McColville Emily R. , Brittain Caelyn T. , Brzezinski Hunter , Manivannan Sujitha , Stabile Cassandra C. , MacMillan Heath A. , Bertram Susan M. 
Published: May 2024

AbstractIncreasing yield is a primary goal of mass insect rearing for food and feed, and diet shapes insect life history traits important to yield, such as survival, development time, and body size at adulthood. Little is known about how developmental macronutrient intake impacts survival, growth, and adult body size of mass reared insects. Here, we applied the nutritional geometry framework and reared individual tropical house crickets (Gryllodes sigillatus) from hatch to adulthood on a wide range of protein:carbohydrate diets. We measured weekly food consumption, survival, development time to adulthood, and adult body size and mass, and calculated a yield metric to extrapolate our individual-level results and predict how diet influences yield at the mass rearing level. Yield was maximized on a 3P:1Cdiet, as crickets fed this diet were most likely to develop into adults and grew maximum mass and body size. When provided with a choice between diets, crickets selected a relatively balanced 1.05P:1Cdiet throughout development, but males consumed 17% more protein than females. Our results represent a crucial first step towards determining the optimal standard feed formulation required to maximize cricket farming yield.
Virulence evolution: thinking outside of the host
Authors: Silva Luís M. , Koella Jacob C. 
Published: May 2024

AbstractThe main theory of the evolution of virulence relies on a trade-off between virulence and transmission rate. However, it has been difficult to measure the required trade-off. A recent transmission decomposition framework explains this might be due to a lack of information about the parasite’s survival in the environment outside the hosts, where the parasite finds itself during transmission between hosts. In this study, we used parasite lines ofVavraia culiciswith varying levels of virulence upon infecting their host, the mosquitoAnopheles gambiae, to explore the interaction between parasite-driven virulence within its host and its survival outside of the host. Our findings showed that parasite lines with greater virulence and growth within their hosts had a cost in their intrinsic ability to withstand the environment, irrespective of temperature. These results underscore the importance of considering the full context of transmission and other parasite fitness traits in studying and predicting the evolution and spread of infectious diseases.
Widespread adaptive evolution in the photosystems of angiosperms provides new insight into the evolution of photosystem II repair
Authors: Robbins Elizabeth HJ , Kelly Steven 
Published: May 2024

AbstractOxygenic photosynthesis generates the initial energy source which fuels nearly all life on earth. At the heart of the process are the photosystems, pigment binding multi-protein complexes that catalyse the first step of photochemical conversion of light energy into chemical energy. Here, we investigate the molecular evolution at single residue resolution of the plastid-encoded subunits of the photosystems across 773 angiosperm species. We show that despite an extremely high level of conservation, 7% of residues in the photosystems, spanning all photosystem subunits, exhibit hallmarks of adaptive evolution. Throughin silicomodelling of these adaptive substitutions we uncover the impact of these changes on the properties of the photosystems, focussing on their effects on co-factor binding and the formation of inter-subunit interfaces. We further reveal that evolution has repeatedly destabilised the interaction photosystem II and its D1 subunit, thereby reducing the energetic barrier for D1 turn-over and photosystem repair. Together, these results provide new insight into the trajectory of photosystem evolution during the radiation of the angiosperms.