bluuebunny/crossref_metadata_2025_split huggingface dataset:
Registration of sugar beet genetic stocks FC308 (PI701378) and FC309 (PI700990)
Authors: Todd Olivia E , Nielson Amy L , Fenwick Ann , Hanson Linda E , Richardson Kelley L , Dorn Kevin M 
Published: May 2023

AbstractSugar beet (Beta vulgarisL.) genetic stock lines FC308 (PI701378) and FC309 (PI700990) are two highly homozygous and phenotypically homogenous sources of resistance to two sugar beet pests. FC308 is resistant to sugar beet cyst nematode (Heterodera schachtii), but susceptible to Fusarium yellows, while FC309 is Fusarium yellows resistant, but sugar beet cyst nematode susceptible. These two populations were developed by the USDA-ARS in Fort Collins, CO, derived from unreleased USDA-ARS Salinas germplasm lines. Multiple field and greenhouse trials for Fusarium yellows and nematode resistance confirmed the uniform phenotypes of both lines for each disease. To enable molecular breeders to rapidly screen proprietary markers in silico, gene space assemblies for each line were also developed. Genome sequencing of individual plants from each line, as well as pooled sequencing of sub-populations of both lines indicated fixation of a previously reported genetic variant linked to sugar beet cyst nematode resistance in FC308. However, two previously reported variants linked to Fusarium resistance appear to be unlinked to the resistance found in FC309. Collectively, these two new genetic stocks should prove useful as sources of resistance to Fusarium yellows and sugar beet cyst nematode, as model genetic backgrounds for studying plant-pathogen interactions, and for mapping the resistance genes present in these lines.
A severe bottleneck impacted the genomic structure of egg-eating cichlids
Authors: Imamoto Minami , Nakamura Haruna , Aibara Mitsuto , Hatashima Ryo , Itoh Takehiko , Nikaido Masato 
Published: May 2023

AbstractThe explosive adaptive radiation of Haplochromine cichlids in Lake Victoria, East Africa, produced 500 endemic species within only 15,000 years. A paedophage or an egg-eater is considered a unique example of trophic adaptation. Many field studies reported that more than 200 cichlids have extinct due to the upsurge of Nile perch, a carnivorous species introduced to the lake in the 1950s. Especially, piscivorous cichlids like paedophages were critically damaged by Nile perch predation. Here, we performed a genome-wide evolutionary study of the paedophages in Lake Victoria to understand their past demographic events and phylogenetic relationships. We discovered evidence of a recent, short-period, and severe bottleneck in a paedophage “matumbi hunter”. Interestingly, the signature of a strong bottleneck, as observed in matumbi hunter, was not detected in other species including paedophagus species. In addition, it was revealed that the population size of matumbi hunter started to decline 30 years ago and recover from 20 to 10 years ago, corresponding to the time of both disappearance and resurgence of Lake Victoria Haplochromines were reported. Although population structure analyses showed that matumbi hunter is composed of a unique genetic component, phylogenetic analyses supported its strong monophyly with other paedophagus species. These results suggest that the paedophages originated only once in Lake Victoria followed by the decline of genetic diversity in matumbi hunter. This study succeeded to demonstrate the demographic events triggered by invasive species and associated genomic consequences of the unique trophic group, promoting a holistic understanding of adaptive radiation.
Tomato CYP94C1 terminates jasmonate signaling during fruit ripening by inactivating bioactive jasmonoyl-L-isoleucine
Authors: Yang Tianxia , Deng Lei , Sun Chuanlong , Ali Muhammad , Wu Fangming , Zhai Huawei , Xu Qian , Xin Peiyong , Chu Jinfang , Huang Tingting , Li Chang-Bao , Li Chuanyou 
Published: May 2023

ABSTRACTRipe fruits are more susceptible to necrotrophic pathogens than unripe fruits. Although this phenomenon is widespread across different fruit species and results in substantial economic losses, the underlying mechanism is still poorly understood. Previous studies revealed that ethylene (ET) is a key signal controlling climacteric fruit ripening and that jasmonate (JA) regulates plant resistance to necrotrophs. We investigated the function of tomato cytochrome P450 94 (CYP94) family genes in JA signaling and report here that ET-mediated ripening suppresses JA-mediated defense by promoting the deactivation of bioactive JA-Ile. ETHYLENE-INSENSITIVE 3 (EIN3)/EIN3-LIKE (EIL) transcription factors directly activatedCYP94C1to convert JA-Ile to its inactive form 12-COOH-JA-Ile, thereby terminating JA signaling during fruit ripening. Mutation ofCYP94C1led to increased resistance of ripe fruits to the necrotrophic pathogenBotrytis cinereawithout affecting the ripening process. Additionally, the master transcription factor MYC2 directly activated two other CYP94 membersCYP94B1andCYP94B2to convert JA-Ile to its less active form 12-OH-JA-Ile, thereby attenuating JA signaling in wounded leaves. Simultaneous mutation ofCYP94B1andCYP94B2increased the resistance of leaves toB. cinerea. Thus, differences in the expression and enzymatic activities ofCYP94family gene members precisely control JA-mediated defense responses in tomato.
On the mechanical origins of waving, coiling and skewing inArabidopsis thalianaroots
Authors: Porat Amir , Tekinalp Arman , Bhosale Yashraj , Gazzola Mattia , Meroz Yasmine 
Published: May 2023

By masterfully balancing directed growth and passive mechanics, plant roots are remarkably capable of navigating complex heterogeneous environments to find resources. Here we present a theoretical and numerical framework which allows us to interrogate and simulate the mechanical impact of solid interfaces on the growth pattern of plant organs. We focus on the well-known waving, coiling and skewing patterns exhibited by roots ofArabidopsis thalianawhen grown on inclined surfaces, serving as a minimal model of the intricate interplay with solid substrates. By modelling growing slender organs as Cosserat rods that mechanically interact with the environment, our simulations verify hypotheses of waving and coiling arising from the combination of active gravitropism and passive root-plane responses. Skewing is instead related to intrinsic twist due to cell file rotation. Numerical investigations are outfitted with an analytical framework that consistently relates transitions between straight, waving, coiling and skewing patterns with substrate tilt angle. Simulations are found to corroborate theory and recapitulate a host of reported experimental observations, thus providing a systematic approach for studyingin silicoplant organs behavior in relation to their environment.SignificancePlant roots exhibit an exceptional ability to navigate in heterogeneous soil environments while overcoming obstacles. Our study combines theory and experimental observations to interrogate and simulate the mechanical impact of obstacles on organ growth. As a test case we focus on well-known observations of waving, coiling and skewing growth patterns ofArabidopsis thalianaroots grown on inclined substrates. Overall, our study explains a broad set of experimental observations through the minimal ingredients of gravitropism and passive mechanics. Our numerical framework provides anin silicolaboratory, yielding quantitative insight into the dynamics of growing organs at the intersection of active processes and passive mechanics, applicable beyond plants to any slender growing system, from neurons or fungal hyphae to novel soft robots.
Altered glucose utilization and disrupted mitochondrial homeostasis in CD4+T cells from HIV-positive women on combination anti-retroviral therapy
Authors: Akiso Matrona , Ameka Magdalene , Naidoo Kewreshini K , Langat Robert , Kombo Janet , Sikuku Delories , Ndung’u Thumbi , Altfeld Marcus , Anzala Omu , Mureithi Marianne 
Published: May 2023

AbstractBackgroundFor optimal functionality, immune cells require a robust and adaptable metabolic program that is fueled by dynamic mitochondrial activity. In this study, we investigate the metabolic alterations occurring in immune cells during HIV infection and antiretroviral therapy by analyzing the uptake of metabolic substrates and mitochondrial homeostasis. By delineating changes in immune cell metabolic programming during HIV, we may identify novel potential therapeutic targets to improve antiviral immune responses.MethodsWhole blood was drawn from HIV uninfected female volunteers and women with chronic HIV infection on combination antiretroviral therapy. Peripheral blood mononuclear cells-derived immune cells were directly incubated with different fluorescent markers: FITC-2-NBDG (2-[N-(7-nitrobenz-2-oxa-1,3-diazol-4-yl) amino]-2-deoxy-D-glucose), FITC-BODIPY (4,4-Difluoro-5,7-Dimethyl-4-Bora-3a,4a-Diaza-s-Indacene-3-Hexadecanoic Acid), FITC-MitoTracker Green and APC-MitoTracker Deep Red. The uptake of glucose and fats and the mitochondrial mass and potential were measured using flow cytometry. All values are reported quantitatively as geometric means of fluorescence intensity.ResultsDuring chronic HIV infection, cellular uptake of glucose increases in HIV+dendritic cells (DCs) in particular. CD4+T cells had the lowest uptake of glucose and fats compared to all other cells regardless of HIV status, while CD8+T cells took up more fatty acids. Interestingly, despite the lower utilization of glucose and fats in CD4+T cells, mitochondrial mass increased in HIV+CD4+T cells compared to HIV negative CD4+T-cells. HIV+CD4+T cells also had the highest mitochondrial potential.ConclusionsSignificant disparities in the utilization of substrates by leukocytes during chronic HIV/cART exist. Innate immune cells increased utilization of sugars and fats while adaptive immune cells displayed lower glucose and fat utilization despite having a higher mitochondrial activity. Our findings suggest that cART treated HIV-infected CD4+T cells may prefer alternative fuel sources not included in these studies. This underscores the importance of understanding the metabolic effects of HIV treatment on immune function.
Nematostella vectensisexemplifies the exceptional expansion and diversity of opsins in the eyeless Hexacorallia
Authors: McCulloch Kyle J , Babonis Leslie S , Liu Alicia , Daly Christina M , Martindale Mark Q , Koenig Kristen M 
Published: May 2023

AbstractBackgroundOpsins are the primary proteins responsible for light detection in animals. Cnidarians (jellyfish, sea anemones, corals) have diverse visual systems that have evolved in parallel with bilaterians (squid, flies, fish) for hundreds of millions of years. Medusozoans (e.g. jellyfish, hydroids) have evolved eyes multiple times, each time independently incorporating distinct opsin orthologs. Anthozoans (e.g. corals, sea anemones,) have diverse light-mediated behaviors and, despite being eyeless, exhibit more extensive opsin duplications than medusozoans. To better understand the evolution of photosensitivity in animals without eyes we increased anthozoan representation in the phylogeny of animal opsins and investigated the large but poorly characterized opsin family in the sea anemoneNematostella vectensis.ResultsWe analyzed genomic and transcriptomic data from 16 species of cnidarians to generate a large opsin phylogeny (708 sequences) with the largest sampling of anthozoan sequences to date. We identified 29 opsins fromN. vectensis(NvOpsins) with high confidence, using transcriptomic and genomic datasets. We found that lineage-specific opsin duplications are common across Cnidaria, with anthozoan lineages exhibiting among the highest numbers of opsins in animals. To establish putative photosensory function ofNvOpsins, we identified canonically conserved protein domains and amino acid sequences essential for opsin function in other animal species. We show high sequence diversity amongNvOpsinsat sites important for photoreception and transduction, suggesting potentially diverse functions. We further examined the spatiotemporal expression ofNvOpsinsand found both dynamic expression of opsins during embryonic development and sexually dimorphic opsin expression in adults.ConclusionsThese data show that lineage-specific duplication and divergence has led to expansive diversity of opsins in eyeless cnidarians, suggesting opsins from these animals may exhibit novel biochemical functions. The variable expression patterns of opsins inN. vectensissuggest opsin gene duplications allowed for a radiation of unique sensory cell types with tissue-and stage-specific functions. This diffuse network of distinct sensory cell types could be an adaptive solution for varied sensory tasks experienced in distinct life history stages in Anthozoans.
Praziquantel inhibitsCaenorhabditis elegansdevelopment and species-wide differences might be cct-8-dependent
Authors: Wit Janneke , Dilks Clayton M. , Zhang Gaotian , Kim Guisbert Karen S. , Zdraljevic Stefan , Guisbert Eric , Andersen Erik C. 
Published: May 2023

ABSTRACTAnthelmintic drugs are used to treat parasitic roundworm and flatworm infections in humans and other animals.Caenorhabditis elegansis an established model to investigate anthelmintics used to treat roundworms. In this study, we useC. elegansto examine the mode of action and the mechanisms of resistance against the flatworm anthelmintic drug praziquantel (PZQ), used to treat trematode and cestode infections. We found that PZQ inhibited development and that this developmental delay varies by genetic background. Interestingly, both enantiomers of PZQ are equally effective againstC. elegans, but only the left-handed PZQ (S-PZQ) is effective against schistosome infections. We conducted a genome-wide association mapping with 74 wildC. elegansstrains to identify a region on chromosome IV that is correlated with differential PZQ susceptibility. Five candidate genes in this region:cct-8, znf-782, Y104H12D.4, Y104H12D.2, andcox-18, might underlie this variation. The genecct-8, a subunit of the protein folding complex TRiC, has variation that causes a putative protein coding change (G226V), which is correlated with reduced developmental delay. Gene expression analysis suggests that this variant correlates with slightly increased expression of bothcct-8andhsp-70. Acute exposure to PZQ caused increased expression ofhsp-70, indicating that altered TRiC function might be involved in PZQ responses. To test if this variant affects development upon exposure to PZQ, we used CRISPR-Cas9 genome editing to introduce the V226 allele into the N2 genetic background (G226) and the G226 allele into the JU775 genetic background (V226). These experiments revealed that this variant was not sufficient to explain the effects of PZQ on development. Nevertheless, this study shows thatC. eleganscan be used to study responses to PZQ to identify mode of action and resistance mechanisms. Additionally, we show that the TRiC complex requires further evaluation for PZQ responses inC. elegans.
The health impact of wood dust in Kijishi: Yamanaka Kijishi Study
Authors: Nakao Yuki , Okada Kazuhiro , Goto Yasuhiro , Matsuda Yosuke , Fujimoto Kiyohiko , Okuhara Yoshiyasu 
Published: May 2023

ABSTRACTObjectivesIt is well known that exposure to wood dust can cause Sinonasal carcinomas (SNC) and various respiratory diseases such as allergies. Japanese woodturners called kijishi work in an environment where wood dust is generated from lathes, and they are considered at risk for various diseases. However, there is a dearth of research on the health impacts of wood dust on kijishi. The purpose of this study is to understand the real situation of kijishi that are exposed to wood dust.MethodsA questionnaire survey was conducted with 20 kijishi. We measured the amounts of wood dust two experienced kijishi were exposed to during a typical woodturning session.ResultsApproximately half the participants exhibited allergic symptoms such as rhinitis; however, this rate was equivalent to the result of the Japan Comprehensive Survey of Living Conditions 2019. SNC was not observed in any of the participants. The level of exposure to wood dust was low, that is, inhalable dust was 0.03 mg/m3, and total dust 0.22 mg/m3. The measured values were very low compared to the Occupational Safety and Health Administration (OSHA), National Institute for Occupational Safety and Health (NIOSH), American Conference of Governmental Industrial Hygienist (ACGIH), and Health and Safety Executive Control of Substances Hazardous to Health (HSE COSHH) standards.ConclusionsWe concluded that constant ventilation during woodturning reduces exposure to wood dust, thereby preventing harm to the health of kijishi to a considerable extent.
The indirect relationship between sleep and cognition in the PREVENT Cohort: Identifying targets for intervention
Authors: Tari Benjamin , Yehuda Michael Ben , Laurell Axel Anders Stefan , Ritchie Karen , Dauvilliers Yves , Ritchie Craig , Lawlor Brian , Naci Lorina , Terrera Graciela Muniz , Malhotra Paresh A. , Watermeyer Tam , Dudas Robert , Underwood Benjamin R. , O’Brien John T. , Raymont Vanessa , Koychev Ivan 
Published: May 2023

AbstractIntroductionAs the global population ages, the economic, societal, and personal burdens associated with worsening cognition and dementia onset are growing. It is therefore becoming ever more critical to understand the factors associated with cognitive decline. One such factor is sleep. Adequate sleep has been shown to maintain cognitive function and protect against the onset of chronic disease, whereas sleep deprivation has been linked to cognitive impairment and the onset of depression and dementia.ObjectivesHere, we aim to identify and explore mechanistic links between several sleep parameters, depressive symptoms and cognition in a cohort of middle-aged adults.MethodsWe investigated data from the PREVENT dementia programme via structural equation modelling to illustrate links between predictor variables, moderator variables, and two cognitive constructs (i.e., Executive Function and Memory).ResultsOur model demonstrated that sleep quality, and total hours of sleep were related to participants’ depressive symptoms, and that, participant apathy was related to higher scores on the Epworth Sleepiness and Lausanne NoSAS Scales. Subsequently, depressive symptoms, but not sleep or apathy ratings, were associated with Executive Function.ConclusionsWe provide evidence for an indirect relationship between sleep and cognition mediated by depressive symptoms in a middle-aged population. Our results provide a base from which cognition, dementia onset, and potential points of intervention, may be better understood.
Deep brain stimulation modulates directional limbic connectivity in major depressive disorder
Authors: Fridgeirsson Egill A. , Bergfeld I.O. , de Kwaasteniet B.P. , Luigjes J. , van Laarhoven J. , Notten P. , Beute G. , van den Munckhof P. , Schuurman P.R. , Denys D.A.J.P. , van Wingen G.A. 
Published: May 2023

AbstractDeep brain stimulation (DBS) is being investigated as treatment for patients with refractory major depressive disorder (MDD). However, little is known about how DBS exerts its antidepressive effects. Here, we investigated whether ventral anterior limb of the internal capsule (vALIC) stimulation modulates a limbic network centered around the amygdala in patients with treatment resistant MDD.Nine patients underwent resting state functional magnetic resonance imaging (fMRI) before DBS surgery and after one year of treatment. In addition, they were scanned twice within two weeks during the subsequent double blind crossover phase with active and sham treatment. Eleven matched controls underwent fMRI scans at same time intervals to account for test-retest effects. The imaging data was investigated with functional connectivity analysis and dynamic causal modelling (DCM).Results showed that one year of DBS treatment was associated with increased functional connectivity of the left amygdala with precentral cortex and left insula along with decreased bilateral connectivity between nucleus accumbens and ventromedial prefrontal cortex. No changes in functional connectivity were observed during the crossover phase. Effective connectivity analyses using DCM revealed widespread amygdala-centric changes between pre-surgery and one year follow-up, while the crossover phase was associated with insula-centric changes between active and sham stimulation.These results suggest that vALIC DBS results in complex rebalancing of the limbic network involved in emotion, reward and interoceptive processing.
A protocol for a critical realist systematic synthesis of interventions to promote pupils’ wellbeing by improving the school climate in Low- and Middle-Income Countries
Authors: Abbott Pamela , Shanks Rachel , Stanley Isabel , D’Ambruoso Lucia 
Published: May 2023

AbstractIntroductionThe review described in this protocol will be the first critical realist review of the literature reporting on the impact of interventions to promote pupils’ wellbeing by improving the school climate in Low- and Middle-Income Countries. The review is being carried out to inform the programme theory for a critical realist evaluation of a whole school mindfulness intervention in Ethiopia and Rwanda to improve pupils’ mental wellbeing. Our initial programme theory hypothesises that pupils’ (and teachers’) responses to the mindfulness intervention as well as changing the behaviour and attitudes of individual pupils and teachers, will change the ‘school climate’ in ways that have a positive impact on mental wellbeing. This literature review will facilitate the identification of mechanisms for change working at the level of the whole school climate, something which is only infrequently discussed in evaluations of mindfulness interventions.Methods and analysisA critical realist review methodology will be used to provide a causal interdisciplinary understanding of how school climate can promote the wellbeing of pupils. This will be done through a systematic literature review and extrapolating context, agency, intervention, mechanisms, and outcome configurations and synthesising these to provide a conceptual understanding of the impact of interventions to improve school climate.DiscussionThe review findings will inform a critical realist evaluation of a mindfulness intervention in schools that we will be carrying out. The findings from the review will enable us to focus more precisely and transparently on what policymakers and other stakeholders need to know about how school climate changes due to introducing mindfulness to the curriculum and how this impacts pupils’ wellbeing [and for which pupils]. We will publish the findings from the review in academic and professional publications, policy briefs, workshops, conferences, and social media.PROSPERO registration numberCRD42023417735