bluuebunny/crossref_metadata_2025_split huggingface dataset:
Forest growth resistance and resilience to the 2018-2020 drought depend on tree diversity and mycorrhizal type
Authors: Sachsenmaier Lena , Schnabel Florian , Dietrich Peter , Eisenhauer Nico , Ferlian Olga , Quosh Julius , Richter Ronny , Wirth Christian 
Published: January 2024

AbstractThe frequency of consecutive drought years is predicted to increase due to climate change. These droughts have strong negative impacts on forest ecosystems. Mixing tree species is proposed to increase the drought resistance and resilience of tree communities. However, this promising diversity effect has not yet been investigated under extreme drought conditions and in the context of complementary mycorrhizal associations and their potential role in enhancing water uptake.Here, we investigate whether tree diversity promotes growth resistance and resilience to extreme drought and whether drought responses are modulated by mycorrhizal associations. We used inventory data (2015 – 2021) of a young tree diversity experiment in Germany, manipulating tree species richness (1, 2, 4 species) and mycorrhizal type (communities containing arbuscular mycorrhizal (AM) or ectomycorrhizal (EM) tree species, or both). For all tree communities, we calculated basal area increment (BAI) in the periods before, during, and after the drought and used the concepts of resistance and resilience to quantify growth responses to drought.We found strong growth declines during the extreme 2018-2020 drought for most of the tree communities. Contrary to our hypothesis, we did not find that tree species richnessper secan buffer the negative impacts of extreme drought on tree growth. However, while for EM communities, drought resistance, and resilience decreased with tree species richness, they increased for AM communities and communities comprising both mycorrhizal types. We highlight that among various tree species mixtures, only those with mixed mycorrhizal types outperformed their respective monocultures during and after drought. Further, under extreme drought, the community tends to segregate into “winner” and “loser” tree species in terms of diversity, indicating a potential intensification of competition.While we cannot disentangle the underlying mechanisms, or clarify the role of mycorrhiza during drought, our findings suggest that mixtures of mycorrhizal types within tree communities could help safeguard forests against increasing drought frequency.Synthesis: Drought resistance and resilience of tree communities depend on tree diversity and mycorrhizal association types. Mixing tree species with diverse mycorrhizal types holds promise for forest restoration in the face of climate change.
Cross-species genomic survey reveals a single origin of the soft-shelled turtles
Authors: Li Wei , Zhu Junxian , Gao Zijian , Ji Liqin , Liu Yanchao , Liu Haiyang , Liu Xiaoli , Hong Xiaoyou , Wei Chengqing , Chen Jiehu , Chen Chen , Zhu Xinping 
Published: January 2024

AbstractTurtles have a have a complicated sex determination system; however, Trionychidae species, as a unique group, have evolved a conserved genetic sex determination, which provides an excellent case to study the evolution of environmental sex determination to genetic sex determination. Analysis of the chromosome-level genome assembly, construction of the first sex chromosomes of Trionychidae, and embryonic transcriptome revealed thatP. sinensishas a ZW-type sex determination system, and that the key sex-determining genes, includingDmrt1,Amh,Foxl2, etc., and their homologs, are not located on the sex chromosomes, which rejects the involvement ofDmrt1’s SDGs or dosage compensation effect in the sex determination ofP. sinensisZW system and also indicates that the ZW chromosomes in birds, turtles, frogs, and fishes originated from different chromosome pairs in the common ancestors. Subsequently, comparative genomic studies demonstrated that a conserved ZW-type sex determination system exists in Trionychidae species, and inferred that their sex chromosomes originate from the same chromosome pair of the common ancestor. More importantly, we found a single origin of the sex chromosomes in Trionychidae species, approximately 56 million years ago, which is highly coincident with the Paleocene-Eocene thermal maximum, PETM, event. Therefore, we hypothesize that the PETM event and the loss of embryonic self-thermal regulation are two critical dynamics that drive the adaptive evolution of sex chromosomes for the common ancestor of Trionychidae species in response to extreme temperature changes. Finally, we link the ancestral sex chromosome origin time, the species divergence time, the PETM event, and the continental plate movements to paint a picture of a single origin and radiation route for extant Trionychidae species. Collectively, our findings provide novel insights into the mechanisms of sex determination inP. sinensis, and the single origin of sex chromosomes and species in extant soft-shelled turtles.
Peptidoform analysis of IP-MS data allows detection of differentially present bait proteoforms
Authors: Kourtis Savvas , Cianferoni Damiano , Serrano Luis , Sdelci Sara 
Published: January 2024

AbstractWhile it is recognised that protein functions are determined by their proteoform state, such as mutations and post-translational modifications, methods to determine their differential abundance between conditions are limited. Here, we present a novel workflow for classical immunoprecipitation coupled to mass spectrometry (IP-MS) data that focuses on identifying differential peptidoforms of the bait protein between conditions, providing additional information about protein function.
YamOmics: A comprehensive data resource on yam multi-omics
Authors: Liu Jinding , Wang Mengda , Zhao Yi , Shen Danyu , Yang Qingxiang , Yang Tiegang , Yin Jianmei , He Longfei , Dou Daolong 
Published: January 2024

AbstractYams (Dioscorea spp.) are a highly important class of horticultural crops, serving as a staple food for millions of people in Africa and contributing significantly to food security. They are also widely cultivated in East Asia as medicinal herbs, bringing substantial economic incomes. Diverse omics data play a pivotal role in advancing yam research and breeding. However, these data are often scattered, lacking in systematic organization and analysis, which underscores the need for centralized and comprehensive data management. In view of this, we gathered extensive omics data and developed the Yam Omics Database (YamOmics;https://biotec.njau.edu.cn/yamdb). The database currently offers a vast and diverse range of omics data, covering genomic, transcriptomic and plastomic data from 41 distinct yam species, along with detailed records of genomic variants from ∼1000 germplasms, and gene expression profiles from ∼200 samples. Additionally, the database features thorough annotations, encompassing aspects like genome synteny, ortholog groups, signaling pathways, gene families and protein interactions. To support yam basic biology and breeding research, it is also equipped with a suite of user-friendly online tools, including PCR primer design, CRISPR design, expression analysis, enrichment analysis, and kinship analysis tools.
Erythrocyte TLR9 is upregulated in metabolic associated fatty liver disease, and is linked to an inflammatory immunometabolic signature
Authors: Papadopoulos Charalampos , Mimidis Konstantinos , Tentes Ioannis , Anagnostopoulos Konstantinos 
Published: January 2024

ABSTRACTMetabolic associated fatty liver disease (MAFLD) consists of lipid accumulation in the liver. Lipotoxicity, supported by aberrant amino acid metabolism, induces TLR9 upregulation, and activation, driving inflammation. Relatively, erythrocyte TLR9 activation leads to membrane rearrangement, surface CD47 loss, and pro-inflammatory erythrophagocytosis. Erythrocyte surface protein loss is accompanied by chemokine release. In addition, CD47 binds circulating TSP-1, a molecule controlling arginine and glutamine metabolism, along with metabolic inflammation. Based on these, we speculated that in MAFLD, lipotoxicity would drive erythrocyte TLR9 upregulation and activation, leading to immunometabolic remodeling.Twenty-four patients (15 men and 9 women) with MAFLD and 9 healthy controls (4 men and 5 women) were enrolled. Erythrocytes were isolated from EDTA-containing blood. Protein levels were measured in erythrocyte lysates (triton X-100 0.01% v/v) or plasma with enzyme-linked immunosorbent assays, whereas lipids and enzyme activities were measured in erythrocyte hemoglobin-free membranes by a semi-quantitative thin layer chromatography and assay kits, respectively.The levels of TLR9 were increased (p=0.002) and positively correlated with sphingosine levels, albeit not statistically significantly (p=0.060). The erythrocyte membrane PC/PE ratio was decreased (p=0.002) and inversely correlated to TLR9 levels. Erythrocyte TLR9 levels correlated inversely with CD47, and positively with MCP-1 release. TSP-1 was decreased in MAFLD erythrocytes (p=0.0017) and correlated positively with CD47 and negatively with TLR9 levels. In vitro, erythrocytes of MAFLD patients bound less TSP-1 molecules. Erythrocytes of MAFLD patients also exhibit decreased arginase-1 protein (p=0.009) and activity (p=0.042). Glutaminase activity was increased, albeit to not statistically significantly different levels (p=0.25). The levels of CD35 were not different (p=0.65), excluding the role of erythrocyte aging for explaining these events.In MAFLD patients, erythrocyte TLR9 is upregulated and is associated with erythrocyte sphingolipid and glycerophospholipid perturbation, CD47 loss, MCP1 release, reduced TSP-1 scavenging, decreased arginase and increased glutaminase.
Repeated horizontal acquisition of lagriamide-producing symbionts in Lagriinae beetles
Authors: Uppal Siddharth , Waterworth Samantha C. , Nick Alina , Vogel Heiko , Flórez Laura V. , Kaltenpoth Martin , Kwan Jason C. 
Published: January 2024

AbstractMicrobial symbionts associate with multicellular organisms on a continuum from facultative associations to mutual codependency. In some of the oldest intracellular symbioses there is exclusive vertical symbiont transmission, and co-diversification of symbiotic partners over millions of years. Such symbionts often undergo genome reduction due to low effective population sizes, frequent population bottlenecks, and reduced purifying selection. Here, we describe multiple independent acquisition events of closely related defensive symbionts followed by genome erosion in a group of Lagriinae beetles. Previous work inLagria villosarevealed the dominant genome-eroded symbiont of the genusBurkholderiaproduces the antifungal compound lagriamide and protects the beetle’s eggs and larvae from antagonistic fungi. Here, we use metagenomics to assemble 11 additional genomes of lagriamide-producing symbionts from seven different host species within Lagriinae from five countries, to unravel the evolutionary history of this symbiotic relationship. In each host species, we detected one dominant genome-erodedBurkholderiasymbiont encoding the lagriamide biosynthetic gene cluster (BGC). Surprisingly, however, we did not find evidence for host-symbiont co-diversification, or for a monophyly of the lagriamide-producing symbionts. Instead, our analyses support at least four independent acquisition events of lagriamide-encoding symbionts and subsequent genome erosion in each of these lineages. By contrast, a clade of plant-associated relatives retained large genomes but secondarily lost the lagriamide BGC. In conclusion, our results reveal a dynamic evolutionary history with multiple independent symbiont acquisitions characterized by high degree of specificity. They highlight the importance of the specialized metabolite lagriamide for the establishment and maintenance of this defensive symbiosis.
Reduced hybrid survival in a migratory divide between songbirds
Authors: Blain Stephanie A. , Justen Hannah C. , Easton Wendy , Delmore Kira E. 
Published: January 2024

AbstractMigratory divides, hybrid zones between populations that use different seasonal migration routes, are hypothesized to contribute to speciation. Specifically, relative to parental species, hybrids at divides are predicted to exhibit (1) intermediate migratory behavior and (2) reduced fitness as a result. We provide the first direct test of the second prediction here with one of the largest existing avian tracking datasets, leveraging a divide between Swainson’s thrushes where the first prediction is supported. Using detection rates as a proxy for survival, our results supported the migratory divide hypothesis with lower survival rates for hybrids than parental forms. This finding was juvenile-specific (vs. adults), suggesting selection against hybrids is stronger earlier in life. Reduced hybrid survival was not explained by selection against intermediate phenotypes or negative interactions among phenotypes. Additional work connecting specific features of migration is needed, but these patterns provide strong support for migration as an ecological driver of speciation.
Atypia of Undetermined Significance and ThyroSeq v3 Positive Call Rates as Quality Control Metrics for Cytology Laboratory Performance
Authors: Mejia-Mejia Odille , Bravo-Gonzalez Andres , Sanchez-Avila Monica , Tjendra Youley , Santoscoy Rodrigo , Drews-Elger Katherine , Zuo Yiqin , Arias-Abad Camilo , Gomez Carmen , Garcia-Buitrago Monica , Nadji Mehrdad , Jorda Merce , Velez-Torres Jaylou M. , Ruiz-Cordero Roberto 
Published: January 2024

AbstractBackgroundThe Bethesda system (TBS) for reporting thyroid cytopathology recommends an “atypia of undetermined significance (AUS)” rate of 10%. Recent data suggest that this category might be overused when the rate of cases with molecular positive results is low. As a quality metric, we calculated the AUS and positive call rates for our cytology lab and each cytopathologist.MethodsA retrospective analysis of all thyroid cytology cases in a 4.5-year period was performed. Cases were stratified by TBS category, and molecular testing results were collected for indeterminate categories. The AUS rate was calculated for each cytopathologist (CP) and the laboratory. The molecular positive call rate (PCR) was calculated with and without the addition ofcurrently negativeto thepositiveresults obtained from the ThyroSeq report.Results7,535 cases were classified asnon-diagnostic7.6%,benign69%,AUS17.5%,follicular neoplasm / suspicious for follicular neoplasm1.4%,suspicious for malignancy0.7 %, andmalignant3.8%. The AUS rate for each cytopathologist ranged from 9.9-36.8%. The overall PCR for the cytology laboratory was 24% (range 13-35.6% per CP). When including cases withcurrently negativeresults, the PCR increased to 35.5% for the cytology laboratory (range 13-42.6% per CP). Comparison analysis indicates a combination of overcalling benign cases and, less frequently, under calling of higher TBS category cases.ConclusionsThe AUS rate in the context of PCR is a useful metric to assess cytology laboratory and cytopathologists’ performance. Continuous feedback on this metric could help improve the overall quality of reporting thyroid cytology.
Polyploid genome assembly ofCardamine chenopodiifolia
Authors: Emonet Aurélia , Awad Mohamed , Tikhomirov Nikita , Vasilarou Maria , Pérez-Antón Miguel , Gan Xiangchao , Novikova Polina , Hay Angela 
Published: January 2024

AbstractBackgroundCardamine chenopodiifoliais an amphicarpic plant that develops two fruit morphs, one above and the other below ground. Above-ground fruit disperse their seeds by explosive coiling of the fruit valves, while below-ground fruit are non-explosive. Amphicarpy is a rare trait that is associated with polyploidy inC. chenopodiifolia. Studies into the development and evolution of this trait are currently limited by the absence of genomic data forC. chenopodiifolia.ResultsWe produced a chromosome-scale assembly of the octoploidC. chenopodiifoliagenome using high-fidelity long read sequencing with the Pacific Biosciences platform. We successfully assembled 32 chromosomes and two organelle genomes with a total length of 597.2 Mbp and an N50 of 18.8 kbp (estimated genome size from flow cytometry: 626 Mbp). We assessed the quality of this assembly using genome-wide chromosome conformation capture (Omni-C) and BUSCO analysis (97.1% genome completeness). Additionally, we conducted synteny analysis to infer thatC. chenopodiifolialikely originated via allo-rather than auto-polyploidy and phased one of the four sub-genomes.ConclusionsThis study provides a draft genome assembly forC. chenopodiifolia, which is a polyploid, amphicarpic species within the Brassicaceae family. This genome offers a valuable resource to investigate the under-studied trait of amphicarpy and the origin of new traits by allopolyploidy.
Systemic delivery of a splice-switching oligonucleotide heteroduplex corrects splicing in central nervous system and muscle in spinal muscular atrophy mice
Authors: Halloy François , Ahlskog Nina , Wood Matthew 
Published: January 2024

ABSTRACTOligonucleotide therapeutics are an established class of drugs for the treatment of genetic disorders. Their clinical development is challenging, however, as they typically distribute poorly to extra-hepatic tissues after systemic injection. Here we tested the heteroduplex oligonucleotide (HDO) platform for systemic delivery ofSMN2splice-switching oligonucleotides of 2’-O-methoxyethyl phosphorothioate or phosphorodiamidate morpholino oligomer chemistries. We first showed that splice-switching HDO cargoes correctSMN2splicing in cells derived from spinal muscular atrophy (SMA) patients, and validated extra-hepatic activity in spinal cord and muscle in a mouse model of SMA following systemic delivery. Our study raises prospects for delivery of nusinersen, the 2’-O-methoxylethyl phosphorothioate oligonucleotide therapy approved for SMA and currently delivered by intrathecal injection, by systemic injection exploiting the HDO chemistry platform. Our findings also suggest that oligonucleotide drugs lacking convincingin vivoefficacy in muscle tissue could be delivered effectively by the HDO technology.
Evaluating the effect of denoising submillimeter auditory fMRI data with NORDIC
Authors: Faes Lonike K. , Lage-Castellanos Agustin , Valente Giancarlo , Yu Zidan , Cloos Martijn A. , Vizioli Luca , Moeller Steen , Yacoub Essa , De Martino Federico 
Published: January 2024

AbstractFunctional magnetic resonance imaging (fMRI) has emerged as an essential tool for exploring human brain function. Submillimeter fMRI, in particular, has emerged as a tool to study mesoscopic computations. The inherently low signal-to-noise ratio (SNR) at submillimeter resolutions warrants the use of denoising approaches tailored at reducing thermal noise – the dominant contributing noise component in high resolution fMRI. NORDIC PCA is one of such approaches, and has been benchmarked against other approaches in several applications. Here, we investigate the effects that two versions of NORDIC denoising have on auditory submillimeter data. As investigating auditory functional responses poses unique challenges, we anticipated that the benefit of this technique would be especially pronounced. Our results show that NORDIC denoising improves the detection sensitivity and the reliability of estimates in submillimeter auditory fMRI data. These effects can be explained by the reduction of the noise-induced signal variability. However, we also observed a reduction in the average response amplitude (percent signal), which may suggest that a small amount of signal was also removed. We conclude that, while evaluating the effects of the signal reduction induced by NORDIC may be necessary for each application, using NORDIC in high resolution auditory fMRI studies may be advantageous because of the large reduction in variability of the estimated responses.
Neuroinflammation underlies the development of social stress induced cognitive deficit in sickle cell disease
Authors: DeVeaux S’Dravious A. , Vyshnya Sofiya , Propsom Katherine , Gbotosho Oluwabukola T. , Singh Asem S. , Horning Robert Z. , Sharma Mihika , Jegga Anil G. , Niu Liang , Botchwey Edward A. , Hyacinth Hyacinth I. 
Published: January 2024

AbstractCognitive deficit is a debilitating complication of SCD with multifactorial pathobiology. Here we show that neuroinflammation and dysregulation in lipidomics and transcriptomics profiles are major underlying mechanisms of social stress-induced cognitive deficit in SCD. Townes sickle cell (SS) mice and controls (AA) were exposed to social stress using the repeat social defeat (RSD) paradigm concurrently with or without treatment with minocycline. Mice were tested for cognitive deficit using novel object recognition (NOR) and fear conditioning (FC) tests. SS mice exposed to RSD without treatment had worse performance on cognitive tests compared to SS mice exposed to RSD with treatment or to AA controls, irrespective of their RSD or treatment disposition. Additionally, compared to SS mice exposed to RSD with treatment, SS mice exposed to RSD without treatment had significantly more cellular evidence of neuroinflammation coupled with a significant shift in the differentiation of neural progenitor cells towards astrogliogenesis. Additionally, brain tissue from SS mice exposed to RSD was significantly enriched for genes associated with blood-brain barrier dysfunction, neuron excitotoxicity, inflammation, and significant dysregulation in sphingolipids important to neuronal cell processes. We demonstrate in this study that neuroinflammation and lipid dysregulation are potential underlying mechanisms of social stress-related cognitive deficit in SS mice.Key PointsNeuroinflammation and lipid dysfunction are potential underlying mechanisms of social stress-related cognitive deficit in SCD patients.Mitigating or ameliorating the impact of cognitive deficits in SCD needs to consider the biological changes already created by exposure to social stress.Novelty of our FindingsWe show for the first time, that neuroinflammation along with changes in the brain lipidome and transcriptome, are underlying biological mechanism contributing to the development and potentially progression of cognitive impairment among sickle cell patients. These findings also provide for the first time, a mechanistic basis for an earlier reported observation of a higher likelihood of having lower intelligence quotient scores among children with sickle cell disease exposed to social stress in the form of low parental socioeconomic status.
Alzheimer’s disease-linked risk alleles elevate microglial cGAS-associated senescence and neurodegeneration in a tauopathy model
Authors: Carling Gillian K. , Fan Li , Foxe Nessa R. , Norman Kendra , Ye Pearly , Wong Man Ying , Zhu Daphne , Yu Fangmin , Xu Jielin , Yarahmady Allan , Chen Hao , Huang Yige , Amin Sadaf , Zacharioudakis Emmanouil , Chen Xiaoying , Holtzman David M. , Mok Sue-Ann , Gavathiotis Evripidis , Sinha Subhash C. , Cheng Feixiong , Luo Wenjie , Gong Shiaoching , Gan Li 
Published: January 2024

SUMMARYThe strongest risk factors for Alzheimer’s disease (AD) include the χ4 allele of apolipoprotein E (APOE), theR47Hvariant of triggering receptor expressed on myeloid cells 2 (TREM2), and female sex. Here, we combineAPOE4andTREM2R47H(R47H) in femaleP301Stauopathy mice to identify the pathways activated when AD risk is the strongest, thereby highlighting disease-causing mechanisms. We find that theR47Hvariant induces neurodegeneration in femaleAPOE4mice without impacting hippocampal tau load. The combination ofAPOE4andR47Hamplified tauopathy-induced cell-autonomous microglial cGAS-STING signaling and type-I interferon response, and interferon signaling converged across glial cell types in the hippocampus.APOE4-R47Hmicroglia displayed cGAS- and BAX-dependent upregulation of senescence, showing association between neurotoxic signatures and implicating mitochondrial permeabilization in pathogenesis. By uncovering pathways enhanced by the strongest AD risk factors, our study points to cGAS-STING signaling and associated microglial senescence as potential drivers of AD risk.