bluuebunny/crossref_metadata_2025_split huggingface dataset:
Nanopore sequencing with unique molecular identifiers enables accurate mutation analysis and haplotyping in the complex Lipoprotein(a) KIV-2 VNTR
Authors: Amstler Stephan , Streiter Gertraud , Pfurtscheller Cathrin , Forer Lukas , Di Maio Silvia , Weissensteiner Hansi , Paulweber Bernhard , Schönherr Sebastian , Kronenberg Florian , Coassin Stefan 
Published: March 2024

AbstractBackgroundRepetitive genome regions, such as variable number of tandem repeats (VNTR) or short tandem repeats (STR), are major constituents of the uncharted dark genome and evade conventional sequencing approaches. The protein-codingLPAkringle IV type-2 (KIV-2) VNTR (5.6 kb per unit, 1-40 units per allele) is a medically highly relevant example with a particularly intricate structure, multiple haplotypes, intragenic homologies and an intra-VNTR STR. It is the primary regulator of plasma lipoprotein(a) [Lp(a)] concentrations, an important cardiovascular risk factor. However, despite Lp(a) variance is mostly genetically determined, Lp(a) concentrations vary widely between individuals and ancestries. This VNTR region hides multiple causal variants and functional haplotypes.MethodsWe evaluated the performance of amplicon-based nanopore sequencing with unique molecular identifiers (UMI-ONT-Seq) for SNP detection, haplotype mapping, VNTR unit consensus sequence generation and copy number estimation via coverage-corrected haplotypes quantification in the KIV-2 VNTR. We used 15 human samples and low-level mixtures (0.5% to 5%) of KIV-2 plasmids as a validation set. We then applied UMI-ONT-Seq to extract KIV-2 VNTR haplotypes in 48 multi-ancestry 1000-Genome samples and analyzed at scale a poorly characterized STR within the KIV-2 VNTR.ResultsUMI-ONT-Seq detected KIV-2 SNPs down to 1% variant level with high sensitivity, specificity and precision (0.977±0.018; 1.000±0.0005; 0.993±0.02) and accurately retrieved the full-length haplotype of each VNTR unit. Human variant levels were highly correlated with next-generation sequencing (R2=0.983) without bias across the whole variant level range. Six reads per UMI produced sequences of each KIV-2 unit with Q40-quality. The KIV-2 repeat number determined by coverage-corrected unique haplotype counting was in close agreement with droplet digital PCR (ddPCR), with 70% of the samples falling even within the narrow confidence interval of ddPCR. We then analyzed 62,679 intra-KIV-2 STR sequences and identified ancestry-specific STR patterns. Finally, we characterized the KIV-2 haplotype patterns across multiple ancestries.ConclusionsUMI-ONT-Seq accurately retrieves the SNP haplotype and precisely quantifies the VNTR copy number of each repeat unit of the complex KIV-2 VNTR region across multiple ancestries. This study utilizes the KIV-2 VNTR, presenting a novel and potent tool for comprehensive characterization of medically relevant complex genome regions at scale.
The community of Marine Alveolate parasites in the Atlantic inflow to the Arctic Ocean is structured by season, depth and water mass
Authors: Egge Elianne , Vaulot Daniel , Larsen Aud , Edvardsen Bente 
Published: March 2024

AbstractThe marine alveolates (MALVs) are a highly diverse group of parasitic dinoflagellates, which may regulate populations of a wide range of hosts, including other dinoflagellates, copepods and fish eggs. Knowledge on their distribution and ecological role is still limited, as they are difficult to study with morphological methods. In this work, we describe the taxonomic composition, seasonal- and depth distribution of MALVs in the Arctic Ocean west and north of Svalbard, based on metabarcoding data from five cruises. We recovered amplicon sequence variants (ASVs) representing all major groups previously described from environmental sequencing studies (Dino-Groups I-V), with Dino-Groups I and II being the most diverse. The community was structured by season, depth, and water mass. In the epipelagic zone, the taxonomic composition varied strongly by season, however there was also a difference between Arctic and Atlantic water masses in winter. The spring and summer epipelagic communities were characterized by a few dominating ASVs, which were present in low proportions during winter and in mesopelagic summer samples, suggesting that they proliferate under certain conditions, e.g., when specific hosts are abundant. The mesopelagic samples were more similar across sampling months, and may harbor parasites of deep-dwelling organisms, little affected by season.
Element accumulation in the tracheal and bronchial cartilages of monkeys
Authors: Azuma Cho , Oishi Takao , Tohno Yoshiyuki , Ke Lining , Zhao Xiao-zhen , Minami Takeshi , Horii-Hayashi Noriko , Inoue Koichi 
Published: March 2024

AbstractCompositional changes in the tracheal and bronchial cartilages can affect respiratory ventilation and lung function. We aimed to elucidate element accumulation in the tracheal and bronchial cartilages of monkeys and divided it into four sites: tracheal, tracheal bifurcation, left bronchial, and right bronchial cartilages. The elemental content was analyzed using inductively coupled plasma atomic emission spectrometry.The average calcium content was two to three times higher in the tracheal cartilage than in the other three cartilages. The trends of phosphorus and zinc were similar to those of calcium. The average calcium, phosphorus, and zinc contents were the highest in the tracheal cartilage and decreased in the following order: the left bronchial, right bronchial, and tracheal bifurcation cartilages. These findings revealed that differences existed in element accumulation between different sites within the same airway cartilage and that calcium, phosphorus, and zinc accumulation mainly occurred in the tracheal cartilage.A substantial direct correlation was observed between age and calcium content in the tracheal and bronchial cartilages and all such monkeys with high calcium content were > four years of age. These results suggest that calcium accumulation occurs in the tracheal and bronchial cartilages after reaching a certain age.An extremely substantial direct correlation was observed between calcium and phosphorus contents in the tracheal and bronchial cartilages. This finding is similar to the previously published calcium and phosphorus correlations in several other cartilages, suggesting that the calcium and phosphorus contents of cartilage exist in a certain ratio.
Juvenile Atlantic Sturgeon Survival and Movement in Proximity to an Active Cutterhead Suction Dredge
Authors: Balazik Matthew , Clarke Douglas 
Published: March 2024

AbstractDuring 2019 and 2020, 268 (30-71cm fork length) juvenile Atlantic Sturgeon were captured and released in proximity to an active cutterhead suction dredge among three sites in the James River, Virginia. Of these captures, 30 were implanted with acoustic tags and telemetry was used to track their movements. Three juveniles telemetry tagged prior to this project were also detected moving within dredge operations. Cumulatively, tagged juveniles made at least 125 passes of the dredging operations with no evidence of detrimental impact in terms of survival and all were detected following the cessation of dredging. Juveniles were captured, presumed feeding, around 100m from the dredge in areas that could easily be avoided if the dredge created a stressful environment. No significant differences in catch-per-unit-effort were found when trawl catch was compared to a reference location or when monitoring gill netting catch 100m down current of a dredge over a month-long period at one of the sites. These results suggest a finding of very low risk of entrainment, migratory blockage or avoidance within 100m of an active cutterhead suction dredge by juvenile Atlantic Sturgeon.
Intermittent protein restriction elevates food intake and plasma ghrelin in male mice
Authors: Volcko K.L , Taghipourbibalan H. , McCutcheon J.E. 
Published: March 2024

AbstractLow-protein diets affect body weight, body composition, food intake, and food preferences in mice. Furthermore, single periods of protein restriction can have lasting effects on these parameters. We sought to examine the effect of multiple, short, bouts of protein restriction, relative to long-term maintenance on either a control (NR) or protein-restricted (PR) diet. We found that male mice experiencing intermittent protein restriction (IPR) were indistinguishable from NR mice in terms of body weight and composition, but had food intake and plasma ghrelin as high as mice on PR diet, even when they were returned to control diet. This was not found in female mice. The results of this experiment highlight the importance of diet history on food intake and ghrelin levels in male mice, and the difference in how PR diet might affect male and female mice.
Metformin treatment results in distinctive skeletal muscle mitochondrial remodeling in rats with different intrinsic aerobic capacities
Authors: Bubak Matthew P. , Davidyan Arik , O’Reilly Colleen L. , Mondal Samim A. , Keast Jordan , Doidge Stephen M. , Borowik Agnieszka K. , Taylor Michael E. , Volovičeva Evelina , Kinter Michael T. , Britton Steven L. , Koch Lauren G. , Stout Michael B. , Lewis Tommy L. , Miller Benjamin F. 
Published: March 2024

AbstractThe rationale for the use of metformin as a treatment to slow aging was largely based on data collected from metabolically unhealthy individuals. For healthspan extension metformin will also be used in periods of good health. To understand potential context specificity of metformin treatment on skeletal muscle, we used a rat model (HCR/LCR) with a divide in intrinsic aerobic capacity. Outcomes of metformin treatment differed based on baseline intrinsic mitochondrial function, oxidative capacity of the muscle (gastroc vs soleus), and the mitochondrial population (IMF vs SS). Metformin caused lower ADP-stimulated respiration in LCRs, with less of a change in HCRs. However, a washout of metformin resulted in an unexpected doubling of respiratory capacity in HCRs. These improvements in respiratory capacity were accompanied by mitochondrial remodeling that included increases in protein synthesis and changes in morphology. Our findings raise questions about whether the positive findings of metformin treatment are broadly applicable.
Exposure to live saprophyticLeptospirabefore challenge with a pathogenic serovar prevents severe leptospirosis and promotes kidney homeostasis
Authors: Kundu Suman , Shetty Advait , Gomes-Solecki Maria 
Published: March 2024

ABSTRACTPrevious studies demonstrated thatLeptospira biflexa, a saprophytic species, triggers innate immune responses in the host during early infection. This raised the question of whether these responses could suppress a subsequent challenge with pathogenicLeptospira. We inoculated C3H/HeJ mice with a single or a double dose ofL. biflexabefore challenge with a pathogenic serovar,L. interrogansserovar Copenhageni FioCruz (LIC). Pre-challenge exposure toL. biflexadid not prevent LIC dissemination and colonization of the kidney. However, it rescued weight loss and mouse survival thereby mitigating disease severity. Unexpectedly, there was correlation between rescue of overall health (weight gain, higher survival, lower kidney fibrosis marker ColA1) and higher shedding of LIC in urine. This stood in contrast to theL. biflexaunexposed LIC challenged control. Immune responses were dominated by increased frequency of effector T helper (CD4+) cells in spleen, as well as significant increases in serologic IgG2a. Our findings suggest that exposure to live saprophyticLeptospiraprimes the host to develop Th1 biased immune responses that prevent severe disease induced by a subsequent challenge with a pathogenic species. Thus, mice exposed to live saprophyticLeptospirabefore facing a pathogenic serovar may withstand infection with far better outcomes. Furthermore, a status of homeostasis may have been reached after kidney colonization that helps LIC complete its enzootic cycle.SignificancePrevious evidence of host innate immunity induced by live saprophyticLeptospirain mice led us to posit that these responses might mitigate leptospirosis severity upon a subsequent challenge with a pathogenic serovar. In this study, we validated our hypothesis. This is important for development of novel strategies to control leptospirosis and for understanding the epidemiologic risk factors of this and other infectious diseases transmitted by direct contact between pathogen and host. Unexpectedly, these studies also show that there is a correlation between kidney health afterL. interrogansinfection (less fibrosis marker ColA1) and higher shedding of this spirochete in urine. This suggests that a status of homeostasis may be reached after kidney colonization byL. interrogansthat helps the spirochete fulfill its enzootic cycle.
Decentralizing genetic testing for biodiversity monitoring and biosurveillance with the Nucleic Acid Barcode Identification Tool (NABIT) and Molecular Development Kit (MDK)
Authors: Holmes HR , Winters M , Fang C , Fotouhi G , Mercader J , Fox DA , Bunje PME , Dehgan A 
Published: March 2024

AbstractThe escalating threats to biodiversity, public health, and food security posed by emerging infectious diseases and illegal wildlife trafficking requires novel approaches to biosurveillance. This paper introduces two innovations developed to address these multifaceted challenges: the Nucleic Acid Barcode Identification Tool (NABIT) and the Molecular Development Kit (MDK).The NABIT is a handheld, battery-powered device that enables genetic tests to be performed at the point of contact by non-technical users, creating a critical bridge between centralized laboratories and the field by reducing barriers to accessible and routine genetic testing. Verification testing and validation results for the NABIT and the lyophilized assays used with it demonstrate key performance parameters, including sample preparation, detection sensitivity, and stability of field-ready assays after 17 months without refrigeration.The MDK complements the NABIT by providing a framework for third-party development and deployment of field-ready genetic assays. Similar to software development kits (SDKs), the MDK offers documentation, software tools, and NABIT hardware to accelerate the development of new assays, enabling early detection strategies and minimizing future losses. Crucially, the MDK empowers scientists worldwide to contribute to a new ecosystem for wildlife genetics and biosurveillance by developing their own field-ready tests for the NABIT.In summary, the NABIT and MDK present the potential for a paradigm shift in biosurveillance, ecosystem monitoring, and biodiversity conservation, enabling decentralized genetic testing, early disease detection, and rapid response to protect sensitive ecosystems, public health, and food security.
Metabolic Vulnerabilities of Temozolomide-Resistant Glioblastoma Cells: Implications for Targeted Therapies and Overcoming Chemoresistance
Authors: Amereh Meitham , Seyfoori Amir , Shojaei Shahla , Lane Sarah , Zhao Tian , Shokrollahi Mahdieh , Lum Julian , Walter Patrick , Akbari Mohsen 
Published: March 2024

AbstractChemoresistance is a major clinical challenge in the management of glioblastoma (GB), making it difficult to achieve long-term success with traditional treatments. Therefore, there is a need for the development of novel drugs. We explored the metabolic vulnerabilities of temozolomide (TMZ)-resistant GB and their potential implications for targeted therapies. In monolayer and tumoroid cultures, we found elevated reliance on oxidative phosphorylation in TMZ-resistant cells. Notably, iron reduction in TMZ-resistant cells reduced viability and proliferation, upregulated hypoxia-inducible factor 1-α (Hif1-α) expression, induced autophagy, inhibited autophagic flux, and increased reactive oxygen species (ROS) generation, indicating the significance of iron in metabolic vulnerabilities of these cells. Hypoxic cells showed acquired resistance to iron chelation compared to their normoxic state, suggesting an adaptive mechanism associated to hypoxia. Viability, size, and invasion were reduced in TMZ-resistant tumoroids. Additionally, we reported IC50 for the combination of TMZ with a range of DFO and DFP, making the combination therapy a promising drug candidate to improve therapeutic treatments.TeaserCombining iron reduction and chemotherapy in drug-resistant glioblastoma cells enhances therapeutic outcomes.
Do seabirds dream of artificial lights? Understanding light preferences of Procellariiformes
Authors: Atchoi Elizabeth , Mitkus Mindaugas , Machado Biana , Medeiros Valter , Garcia Sofia , Juliano Manuela , Bried Joël , Rodríguez Airam 
Published: March 2024

ABSTRACTSeabirds, and particularly fledglings of burrow-nesting species, are greatly impacted by light pollution. During their inaugural flights from colony to sea, fledglings become grounded after encountering artificial light. Such groundings, or fallout events, affect many fledglings each year. To mitigate this light induced mortality, rescue programs have been implemented for decades in many locations worldwide. Despite the notoriety of fallouts, the contributing behavioural and biological factors remain mostly unknown. How do the mechanisms of light attraction and light avoidance interact or how do they manifest in different groups (e.g., age, personality, populations), or light pollution levels, remain open questions. We tested behavioural preferences of Cory’s shearwaterCalonectris borealisfledglings, rescued after being grounded in urban areas, and of breeding adults, for contrasting light sources. Fledglings and adults were exposed to one of the three treatments in an experimental y-maze set-up: white light versus no-light, blue versus red light, and a control with no-light on each arm of the y-maze. Both age groups have shown preferences for the no-light arms and the red light arm. The preference for longer wavelengths and darker environments, along with slower responses by fledglings, suggest that close range light pollution appears to cause disorientation in seabirds. Our study helps to clarify the behavioural components of fallouts and provides further evidence on the disruptive effects of nocturnal artificial light on sensitive species.
Gut Microbiome-Driven Metabolites Influence Skin Pigmentation in TYRP1 Mutant Oujiang Color Common Carp
Authors: Mandal Roland Nathan , Ke Jing , Kanika Nusrat Hasan , Hou Xin , Zhang Zhiyi , Zhang Penghui , Chen Huifan , Zeng Chunxiao , Chen Xiaowen , Wang Jun , Wang Chenghui 
Published: March 2024

AbstractThe gut microbiome is one of the major regulators of the gut-skin axis and is partly regulated by host genetics. In the present study, using comparative high-throughput omics data on CRISPR/Cas9-mediatedTYRP1mutant and wild-color common carp populations, we quantified the proportion of inter-individual variation in the skin transcriptome and blood metabolome by genetic architecture and gut microbiomes. We found 525 differential metabolites (DMs) and 45 differential gut microbial genera inTYRP1mutant fishes relative to the wild type. Through interaction analysis and causal mediation analyses, we revealed that the TYRP1-mutant derived genetic background may exert an inflammatory Acinetobacter - Leukotrience-C4 and – Spermine metabolic pathway under the regulation of an anti-inflammatory cardio-vascular genetic network underlying the upregulating expression ofCOMT,PLG,C2,C3,F10,TDO2,MHC1, andSERPINF2gene for evolving unusual coffee-like color phenotype. This unique network appears to underlie the “coffee-like” color phenotype. We propose that theCOMT-mediated causal effect of the unusual gut microbiome on the atypical skin gene expression patterns through the gut-skin metabolic pathway.Article SummaryR.N. Mandal et al. report on the causal effect of gut microbiome-driven metabolites on the expression pattern of regulatory genes underlying an unusual color phenotype. It suggests that TYRP1 Mutation may rise an unusual inflammatory gut microbiome-skin metabolic pathway that may be balanced by an anti-inflammatory cardio-vascular genetic network leading to unique coloration in Oujiang Color Common Carp.
FACS-Sortable Triple Emulsion Picoreactors for Screening Reactions in Biphasic Environments
Authors: Thompson Samuel , Zhang Yanrong , Yang Zijian , Nichols Lisa A. , Fordyce Polly M. 
Published: March 2024

ABSTRACTBiphasic environments can enable successful chemical reactions where any single solvent results in poor substrate solubility or poor catalyst reactivity. For screening biphasic reactions at high-throughput, a platform based on microfluidic double emulsions could use widely available FACS (Fluorescence Activated Cell Sorting) machines to screen millions of picoliter reactors in a few hours. However, encapsulating biphasic reactions within double emulsions to form FACS-sortable droplet picoreactors requires optimized solvent phases and surfactants to produce triple emulsion droplets that are stable over multi-hour assays and compatible with desired reaction conditions. This work demonstrates such FACS-sortable triple emulsion picoreactors with a fluorocarbon shell and biphasic octanol-in-water core. First, surfactants were screened to stabilize octanol-in-water emulsions for the picoreactor core. With these optimized conditions, stable triple emulsion picoreactors were produced (>70% of droplets survived to 24 hours), and the ability to produce protein in the biphasic core was demonstrated via cell-free protein synthesis. Finally, triple emulsion picoreactors were sorted based on fluorescence using commercial FACS sorters at >100 Hz with 75-80% of droplets recovered. These triple emulsion picoreactors have potential for future screening bead-encoded catalyst libraries, including enzymes such as lipases for biofuel production.
Age-related behavioral resilience in smartphone touchscreen interaction dynamics
Authors: Ceolini Enea , Ridderinkhof K. Richard , Ghosh Arko 
Published: March 2024

AbstractWe experience a life that is full of ups and downs. The ability to bounce back after adverse life events such as the loss of a loved one or serious illness declines with age, and such isolated events can even trigger accelerated aging. How humans respond to common day-to-day perturbations is less clear. Here, we infer the aging status from smartphone behavior by using a decision tree regression model trained to accurately estimate the chronological age based on the dynamics of touchscreen interactions. Individuals (N = 280, 21 to 83 years of age) expressed smartphone behavior that appeared younger on certain days and older on other days through the observation period that lasted up to ∼4 years. We captured the essence of these fluctuations by leveraging the mathematical concept of critical transitions and tipping points in complex systems. In most individuals, we find one or more alternative stable aging states separated by tipping points. The older the individual, the lower the resilience to forces that push the behavior across the tipping point into an older state. Traditional accounts of aging based on sparse longitudinal data spanning decades suggest a gradual behavioral decline with age. Taken together with our current results, we propose that the gradual age-related changes are interleaved with more complex dynamics at shorter timescales where the same individual may navigate distinct behavioral aging states from one day to the next. Real-world behavioral data modeled as a complex system can transform how we view and study aging.