bluuebunny/crossref_metadata_2025 huggingface dataset:
Regulation of secondary hair follicle cycle in cashmere goats by miR-877-3p targeting IGFBP5 gene
Authors: Wu Cuiling , Yuan Liang , Cao Wenzhi , Ye Xiaofang , Ma Xiaolin , Qin Chongkai , Li Bin , Yu Fei , Fu Xuefeng
Published: October 2023

Cashmere, a highly valuable animal product derived from cashmere goats, holds significant economic importance. MiRNAs serve as crucial regulators in the developmental processes of mammalian hair follicles. Understanding the regulation of miRNAs during the hair follicle cycle is essential for enhancing cashmere quality. In this investigation, we employed high-throughput sequencing technology to analyze the expression profiles of miRNAs in the secondary hair follicles of Jiangnan cashmere goats at different stages. Through bioinformatics analysis, we identified differentially expressed miRNAs (DE miRNAs). The regulatory relationships between miRNAs and their target genes were verified using multiple techniques, including RT-qPCR, western blot, Dual-Luciferase Reporter, and CKK-8 assays. Our findings revealed the presence of 193 DE miRNAs during various stages of the hair follicle cycle in Jiangnan cashmere goats. Based on the previously obtained mRNA data, the target genes of DE miRNA were predicted, and 1,472 negative regulatory relationships between DE miRNAs and target genes were obtained. Notably, the expression of chi-miR-877-3p was down-regulated during the telogen (Tn) phase compared to the anagen (An) and catagen (Cn) phases, while the IGFBP5 gene exhibited up-regulation. Further validation experiments confirmed that overexpression of chi-miR-877-3p in dermal papilla cells suppressed IGFBP5 gene expression and facilitated cell proliferation. The results of this study provide novel insights for analyzing the hair follicle cycle.
Effects of early weaning on the reproductive performance of suckled Nelore cows in the subsequent breeding season
Authors: Nishimura Thiago Kan , da Silva Amanda Guimarães , Abitante Gabriela , Dahlen Carl Robertson , Goulart Rodrigo Silva , Zamudio Germán Darío Ramírez , Luz Silva Saulo , Santana Miguel Henrique de Almeida , Saran Netto Arlindo , Leme Paulo Roberto , Pugliesi Guilherme
Published: October 2023

This study aimed to evaluate the effects of early weaning (EW) on body composition, hormone concentrations and metabolites, and reproductive performance of Nelore cows in the subsequent breeding season (BS). Suckled cows that became pregnant by timed-AI (TAI) in the 2020-BS were exposed in 2021 to early weaning at 150 d (27 primiparous [PRI] and 74 multiparous [MUL]) or conventional weaning (CW) at 240 d postpartum (30 PRI and 77 MUL). Body weight (BW) and body condition score (BCS) were determined at 2020-BS, EW, CW, prepartum, and 2021-BS. Blood samples were collected at EW, CW, prepartum (54.75 ± 0.56 d prepartum), and 2021-TAI and assayed for insulin-like growth factor-1 (IGF-I), non-esterified fatty acid (NEFA), and β-hydroxybutyrate (BHB) concentrations. In 2021-BS, cows were exposed to a P4/E2-based protocol for TAI at day 0 (D0), and a second TAI was performed at D22 in females detected with luteolysis (D20) by Doppler ultrasound. The presence of corpus luteum (CL) on D10, estrous expression, and dominant follicle (DF) diameter, and blood perfusion (BP) on D2 and D0 were determined. Data were analyzed by ANOVA or logistic regression of SAS as a 2 × 2 factorial with main factors of parity (PRI or MUL) and weaning strategy (EW or CW). An interaction of parity and weaning strategy was not observed (P > 0.1), but the weight (kg) and BCS were greater (P < 0.05) in MUL cows at the five timepoints, and EW cows were heavier than CW at the moment of CW (541 vs. 493 kg; and 5.3 vs. 4.3), prepartum (551 vs. 506 kg; and 5.2 vs. 4.4) and 2021-BS (475 vs. 450 kg; and 4.5 vs. 3.7). Plasma urea concentration at 2021-BS was greater (P = 0.01) for PRI than for MUL. A parity-by-time interaction was observed (P ≤ 0.05) for concentrations of IGF-I, NEFA, and BHB. PRI cows had greater (P ≤ 0.05) concentrations of IGF-I at EW and greater (P ≤ 0.05) prepartum concentrations of NEFA and BHB than MUL cows. The proportion of cows with CL at D10 was not affected (P > 0.1) by weaning but was greater (P < 0.05) in MUL than in PRI cows (40.4 vs. 15.7%). The diameter of DF and proportion of BP on D0 were greater (P < 0.05) in EW cows than in CW cows. The pregnancy rate (P/AI, %) at the first TAI was greater (P < 0.05) in EW cows (60% vs. 45%), whereas no difference (P > 0.1) was observed at the second TAI. Cumulative P/AI (first and second TAIs) was greater (P < 0.05) in EW cows (81% vs. 63%). In conclusion, weaning at 150 d in Nelore cattle is a strategy to successfully recover the parous cow’s body condition and to improve pregnancy success in the next BS, regardless of the cow’s parity order.
Incidence and outcome of pseudoprogression after radiation therapy in glioblastoma patients: A cohort study
Authors: Blakstad Hanne , Mendoza Mireles Eduardo Erasmo , Heggebø Liv Cathrine , Magelssen Henriette , Sprauten Mette , Johannesen Tom Børge , Vik-Mo Einar Osland , Leske Henning , Niehusmann Pitt , Skogen Karoline , Helseth Eirik , Emblem Kyrre Eeg , Brandal Petter
Published: October 2023

Background

Differentiating post-radiation MRI changes from progressive disease (PD) in glioblastoma (GBM) patients represents a major challenge. The clinical problem is two-sided; avoid termination of effective therapy in case of pseudoprogression (PsP) and continuation of ineffective therapy in case of PD. We retrospectively assessed the incidence, management, and prognostic impact of PsP and analyzed factors associated with PsP in a GBM patient cohort.

Methods

Consecutive GBM patients diagnosed in the South-Eastern Norway Health Region from 2015 to 2018 who had received RT and follow-up MRI were included. Tumor, patient, and treatment characteristics were analyzed in relationship to re-evaluated MRI examinations at 3 and 6 months post-radiation using Response Assessment in Neuro-Oncology criteria.

Results

A total of 284 patients were included in the study. PsP incidence 3 and 6 months post-radiation was 19.4% and 7.0%, respectively. In adjusted analyses, methylated O6-methylguanine-DNA methyltransferase (MGMT) promoter and the absence of neurological deterioration were associated with PsP at both 3 (p < .001 and p = .029, respectively) and 6 months (p = .045 and p = .034, respectively) post-radiation. For patients retrospectively assessed as PD 3 months post-radiation, there was no survival benefit of treatment change (p = .838).

Conclusions

PsP incidence was similar to previous reports. In addition to the previously described correlation of methylated MGMT promoter with PsP, we also found that absence of neurological deterioration significantly correlated with PsP. Continuation of temozolomide courses did not seem to compromise survival for patients with PD at 3 months post-radiation; therefore, we recommend continuing adjuvant temozolomide courses in case of inconclusive MRI findings.
A Pilot Study Examining Feasibility and Initial Efficacy of Remotely Delivered Cognitive Adaptation Training
Authors: Velligan Dawn I , Li Feiyu , Sebastian Veronica , Kennedy Cory , Mintz Jim
Published: October 2023

Cognitive Adaptation Training (CAT) is an evidence-based treatment that uses environmental supports including signs, text messages, checklists, smart pill containers, and the organization of belongings to bypass cognitive and motivational impairments and to cue adaptive behavior in the home or work environment. We developed and tested a remote version of CAT to make the treatment available more broadly. Because CAT is focused on working with the individual in their home environment to establish supports, CAT may not be as easy to translate into an effective virtual treatment as talk-therapies. Fifty-six members of managed care were assigned to or given their treatment preference for CAT or Remote CAT (R-CAT) for 6 months. In-person or virtual pill counts were conducted monthly and assessments of habit-formation, symptoms, functioning, and satisfaction were administered every 2 months by independent raters. Analyses using mixed models with repeated measures focused on pre-planned evaluations of within-group change. Adherence improved significantly in R-CAT, functioning improved significantly in CAT and both groups improved significantly on measures of habit-formation and symptoms across 6 months. Higher functioning individuals appeared to choose R-CAT. Satisfaction with treatment was very high in both groups. R-CAT appears to be a potentially effective treatment, particularly for medication follow-though. However, in contrast to decades of previous research, fewer than 20% of eligible Medicaid recipients agreed to participate in the study. This may have been due to recruitment during and immediately post-pandemic.
A phylogeny with divergence-time estimation of planthoppers (Hemiptera: Fulgoroidea) based on mitochondrial sequences
Authors: Wang Wenqian , Meng Rui , Huang Yixin , Fang Wei , Zhang Huan , Liu Huizhen , Stroiński Adam , Bourgoin Thierry , Qin Daozheng
Published: October 2023

The planthopper superfamily Fulgoroidea (Hemiptera: Fulgoromorpha) currently includes more than 14 000 described species in about 21 extant families. Despite multiple studies attempted, based on morphological characters or DNA sequence data, the phylogeny of this superfamily remains unsatisfactorily resolved. Here we reconstruct the phylogenetic relationship among the families of this superfamily based on the whole mitogenome sequences from 113 species representing 17 planthopper families and three families as outgroups, in which 41 species of Fulgoroidea were sequenced for this study. The phylogenetic trees were reconstructed based on three different datasets, both by maximum likelihood (ML, IQtree) and Bayesian inference (BI, MrBayes, and PhyloBayes). The tree topologies of ML and BI analyses were quite similar with only a few differences in some clades. The phylogenetic results showed that Cixiidae and Delphacidae were placed as sister-taxa at the base of this superfamily; the clade Fulgoridae + Dictyopharidae appeared younger than the Meenoplidae + Kinnaridae one, Derbidae and Achilidae were more recently derived than Fulgoridae + Dictyopharidae without depicting a monophyletic unit, and Tropiduchidae and Acanaloniidae appeared as sister-taxa. The divergence-time estimation analysis shows that most planthoppers underwent relatively rapid radiation during the Jurassic and Cretaceous. Divergence time between Cixiidae and Delphacidae can be traced back to the Middle Jurassic; Meenoplidae, Fulgoridae, and Issidae originated in the Lower Cretaceous; Lophopidae and Eurybrachidae can be traced to the Upper Cretaceous. This paper reconstructs the cladogram of Fulgoroidea based on more comprehensive mitogenome sequences so far, which could provide new clues for a better understanding of the evolution of this superfamily. However, the taxa sampling appears insufficient to address controversial groups in Fulgoroidea.
Transcriptomic analysis of PADI4 target genes during multi-lineage differentiation of embryonic stem cells
Authors: Singh Anup Kumar , Khan Soumen , Moore Daniel , Andrews Simon , Christophorou Maria A.
Published: October 2023

During mammalian embryo development, pluripotent epiblast cells diversify into the three primary germ layers, which will later give rise to all fetal and adult tissues. These processes involve profound transcriptional and epigenetic changes that require precise coordination. Peptidylarginine deiminase IV (PADI4) is a transcriptional regulator that is strongly associated with inflammation and carcinogenesis but whose physiological roles are less well understood. We previously found that
Padi4
expression is associated with pluripotency. Here, we examined the role of PADI4 in maintaining the multi-lineage differentiation potential of mouse embryonic stem (ES) cells. Using bulk and single-cell transcriptomic analyses of embryoid bodies (EBs) derived from
Padi4
knock-out (
Padi4-KO
) mouse ES cells, we find that PADI4 loss impairs mesoderm diversification and differentiation of cardimyocytes and endothelial cells. Additionally,
Padi4
deletion leads to concerted downregulation of genes associated with polarized growth, sterol metabolism and the extracellular matrix (ECM). This study indicates a requirement for
Padi4
in the specification of the mesodermal lineage and reports the
Padi4
associated transcriptome, providing a platform for understanding the physiological functions of
Padi4
in development and homeostasis.

This article is part of the Theo Murphy meeting issue ‘The virtues and vices of protein citrullination’.
Protein citrullination: inhibition, identification and insertion
Authors: Barasa Leonard , Thompson Paul R.
Published: October 2023

Protein citrullination is a post-translational modification (PTM) that is catalysed by the protein arginine deiminase (PAD) family of enzymes. This PTM involves the transformation of an arginine residue into citrulline. Protein citrullination is associated with several physiological processes, including the epigenetic regulation of gene expression, neutrophil extracellular trap formation and DNA damage-induced apoptosis. Aberrant protein citrullination is relevant to several autoimmune and neurodegenerative diseases and certain forms of cancer. PAD inhibitors have shown remarkable efficacy in a range of diseases including rheumatoid arthritis (RA), lupus, atherosclerosis and ulcerative colitis. In RA, anti-citrullinated protein antibodies can be detected prior to disease onset and are thus a valuable diagnostic tool for RA. Notably, citrullinated proteins may serve more generally as biomarkers of specific disease states; however, the identification of citrullinated protein residues remains challenging owing to the small 1 Da mass change that occurs upon citrullination. Herein, we highlight the progress made so far in the development of pan-PAD and isozyme selective inhibitors as well as the identification of citrullinated proteins and the site-specific incorporation of citrulline into proteins.

This article is part of the Theo Murphy meeting issue ‘The virtues and vices of protein citrullination’.
The effects of sport-specific training on individuals action strategies while avoiding a virtual player approaching on a 45° angle while completing a secondary task
Authors: Thompson Brooke J. , Cinelli Michael E.
Published: October 2023

Sports provide varying scenarios where athletes must interact with and avoid opposing players in dynamic environments. As such, sport-specific training can improve one’s ability to integrate visual information which may result in improved collision avoidance behaviours. However, improved visuomotor capabilities are highly task dependent (i.e., athletes must be tested in sport-specific settings). The current study examined whether sport-specific training influenced individuals’ collision avoidance behaviours during a sport-specific task in virtual reality. Untrained young adults (N=21, 22.9±1.9 yrs, 11 males) and specifically trained athletes (N=18, 20±1.5 yrs, 7 males) were immersed in a virtual environment and were instructed to walk along a 7.5m path towards a goal located along the midline. Two virtual players positioned 2.83m to the left and right of the midline approached participants on a 45° angle at one of three speeds: 0.8x, 1.0x, or 1.2x each participant’s average walking speed. Participants were instructed to walk to a goal without colliding with the virtual players while performing a secondary task; reporting whether a shape changed above either of the virtual players’ heads. Results revealed that athletes had a higher percentage of correct responses on the secondary task compared to untrained young adults. However, there was no group differences in the average time to first avoidance or average minimum clearance, but athletes were more variable in their avoidance behaviours. Findings from this study demonstrate that athletes may be more adaptive in their behaviours and may perform better on attentionally demanding tasks in dynamic environments.
Extracellular vesicles from patients with coronary artery disease (CAD) demonstrate enhanced pro-coagulatory activity
Authors: Soyama Shin , Zhou Ruihan , Whyte Abigail , Mark Sharon , Dymott Leanne , Brunton Mark , Fischer Roman , Hester Svenja , McKenna Charlie , Ruparelia Neil , Yaqoob Parveen , Allen-Redpath Keith
Published: October 2023

Aims

Extracellular vesicles (EVs) carry unique repertoires of biologically active cargo that hold promise as novel biomarkers and future interventional targets for cardiovascular diseases (CVDs). However, it is unclear as to how the number, location, cellular origin, and size of these EVs within the circulation relate to the development of CVDs such as coronary artery disease (CAD). The current study compared these novel markers in arterial and venous blood samples in individuals undergoing coronary assessment with angiography.. EVs were then characterized from those presenting with and without CAD.

Methods and Results

Arterial and venous blood samples were collected from individuals with confirmed CAD following coronary angiography and a matched cohort in whom there was no evidence of disease. EV fractions were isolated from 500µL of platelet free plasma (PFP) by size exclusion chromatography. EVs were analyzed by Nanoparticle Tracking Analysis and flow cytometry to characterize number, size and cellular origin. A thrombin generation assay was used to assess the pro-coagulatory activity of the isolated circulating EVs. Proteomics was used to determine the protein cargo carried within the EVs.

Coagulatory activity of EVs isolated from CAD patients was significantly higher in when compared to controls, although the numbers of EVs did not differ. There were higher numbers of endothelial-derived EVs in arterial blood compared with venous blood. Linear regression models revealed that plasma triacylglycerol concentration and age independently predicted circulating EV numbers in CAD patients. Proteomics revealed several proteins associated with coagulation upregulated in patients with CAD.

Conclusions

Although the absolute numbers of EVs in CAD patients were not elevated, EVs in CAD patients had greater pro-coagulant activity, highlighting a potentially important role for EVs in the pathogenesis of CAD.

Clinical Perspective

What is new?

CAD patients displayed a greater EV-induced thrombin generation capability when compated to those with no disease.

The proteomic profile of arterial-derived EVs in patients with CAD demonstrated several proteins associated with coagulation that may be a risk factor for developing a future event.

What are the clinical implications?

The identification of EVs in patients with CAD with upregulated coagulation proteins may be a novel biomarker for the development of future events and may identify a high risk patient group that may benefit for more aggressive cardiovascular risk intervention.
Reinforcement learning in Parkinson’s disease is not associated with inflammatory tone
Authors: Tichelaar Jorryt G. , Verbeek Marcel M. , Kersten Iris , Cools Roshan , Helmich Rick C.
Published: October 2023

Parkinson’s disease (PD) is associated with large variability in the development and severity of both motor and nonmotor symptoms, including depression and impulse control disorder. Neuroinflammation might contribute to this heterogeneity, given its association with dopaminergic signalling, neuropsychiatric symptoms, and reward versus punishment learning. Here, we assessed the effect of inflammatory tone on probabilistic reinforcement learning and impulse control disorders in PD. We measured computational learning model-based neural reward prediction error and expected value signals in frontostriatal circuity during reinforcement learning using functional MRI. In addition, we acquired cerebral spinal fluid of 74 PD patients and screened for 13 inflammatory factors, including our primary marker of interest IL-6, previously implicated in reward learning signaling in the ventral striatum. In contrast to our prediction, we found no association between inflammatory tone and any of the behavioural or neural reinforcement learning parameters. Furthermore, we did we not find any correlation between inflammatory tone and depressive or impulsive PD symptoms. Exploratory analyses revealed a negative association between MCP-1 and reward prediction error signals in the ventral striatum, an observation that should be replicated in future work. The null findings might reflect the fact that measurements were taken ON medication, or that our sample consists of an early disease stage cohort that may be too small to detect these effects, or that IL-6 is a suboptimal marker for inflammatory tone, or a combination of these factors.
IL-1β–mediated inflammatory signaling drives ineffective erythropoiesis in early-stage myelodysplastic syndromes
Authors: Adema Vera , Ganan-Gomez Irene , Ma Feiyang , Rodriguez-Sevilla Juan Jose , Chien Kelly , Yang Hui , Thongon Natthakan , Kanagal-Shamanna Rashmi , Loghavi Sanam , Montalban-Bravo Guillermo , Hammond Danielle , Gu Yiqian , Tan Roselyn , Tan Lin , Lorenzi Philip , Al-Atrash Gheath , Clise-Dwyer Karen , Bejar Rafael , Pellegrini Matteo , Garcia-Manero Guillermo , Colla Simona
Published: October 2023

Myelodysplastic syndromes (MDS) are a group of incurable hematopoietic stem cell (HSC) neoplasms characterized by peripheral blood cytopenias and a high risk of progression to acute myeloid leukemia. MDS represent the final stage in a continuum of HSCs’ genetic and functional alterations and are preceded by a premalignant phase, clonal cytopenia of undetermined significance (CCUS). Dissecting the mechanisms of CCUS maintenance may uncover therapeutic targets to delay or prevent malignant transformation.

Here, we demonstrate thatDNMT3AandTET2mutations, the most frequent mutations in CCUS, induce aberrant HSCs’ differentiation towards the myeloid lineage at the expense of erythropoiesis by upregulating IL-1β–mediated inflammatory signaling and that canakinumab rescues red blood cell transfusion dependence in early-stage MDS patients with driver mutations inDNMT3AandTET2.

This study illuminates the biological landscape of CCUS and offers an unprecedented opportunity for MDS intervention during its initial phase, when expected survival is prolonged.
The Identification of IL-4 as a Regulator of Chimeric Antigen Receptor T Cell Exhaustion
Authors: Stewart Carli M. , Siegler Elizabeth L. , Sakemura R. Leo , Cox Michelle J. , Huynh Truc , Kimball Brooke , Mai Long , Can Ismail , Manriquez Roman Claudia , Yun Kun , Sirpilla Olivia , Girsch James H. , Ogbodo Ekene , Ismail Wazim , Gaspar Maia Alexandre , Budka Justin , Kim Jenny , Scholler Nathalie , Mattie Mike , Filosto Simone , Kenderian Saad S.
Published: October 2023

Durable response to chimeric antigen receptor T (CART) cell therapy remains limited in part due to CART cell exhaustion. We investigated the regulation of CART cell exhaustion with three independent approaches including: a genome-wide CRISPR knockout screen using a validatedin vitromodel for exhaustion, RNA and ATAC sequencing on baseline and chronically stimulated CART cells, and RNA and ATAC sequencing on pre-infusion CART cell products from responders and non-responders in the ZUMA-1 clinical trial. Each of these approaches identified IL-4 as a key regulator of CART cell dysfunction. Further, when CART cells were treated with IL-4, they developed signs of exhaustion, but when CART cells were treated with an IL-4 monoclonal antibody, they showed improved antitumor efficacy and reduced signs of exhaustion in preclinical models. Therefore, our study identified both a novel role for IL-4 on CART cells and the improvement of CART cell therapy through IL-4 neutralization.

Statement of Significance

Identifying regulators of CART cell exhaustion will not only enhance the field’s understanding of therapeutic failure, but it will also provide avenues to enhance CART cell efficacy. This study reveals both a novel role for IL-4 in exhaustion and a strategy to improve CART cell activity through IL-4 neutralization.
Induced pluripotent stem cell derived pericytes respond to endogenous mediators of proliferation and contractility
Authors: King Natalie E. , Courtney Jo-Maree , Brown Lachlan S. , Fortune Alastair J. , Blackburn Nicholas B. , Fletcher Jessica L. , Cashion Jake M. , Talbot Jana , Pébay Alice , Hewitt Alex W. , Morris Gary P. , Young Kaylene M. , Cook Anthony L. , Sutherland Brad A.
Published: October 2023

Background

Pericytes are multifunctional contractile cells that reside on capillaries. Pericytes are critical regulators of cerebral blood flow and blood-brain barrier function, and pericyte dysfunction may contribute to the pathophysiology of human neurological diseases including Alzheimers disease, multiple sclerosis, and stroke. Induced pluripotent stem cell (iPSC)-derived pericytes (iPericytes) are a promising tool for vascular research. However, it is unclear how iPericytes functionally compare to primary human brain vascular pericytes (HBVPs). We differentiated iPSCs into iPericytes of either the mesoderm or neural crest lineage using established protocols. We compared iPericyte and HBVP morphologies, quantified gene expression by qPCR and bulk RNA sequencing, and visualised pericyte protein markers by immunocytochemistry. To determine whether the gene expression of neural crest iPericytes, mesoderm iPericytes or HBVPs correlated with their functional characteristicsin vitro, we quantified EdU incorporation following exposure to the key pericyte mitogen, platelet derived growth factor (PDGF)-BB and, contraction and relaxation in response to the vasoconstrictor endothelin-1 or vasodilator adenosine, respectively. iPericytes were morphologically similar to HBVPs and expressed canonical pericyte markers. However, iPericytes had 1864 differentially expressed genes compared to HBVPs, while there were 797 genes differentially expressed between neural crest and mesoderm iPericytes. Consistent with the ability of HBVPs to respond to PDGF-BB signalling, PDGF-BB enhanced and PDGF receptor-beta inhibitors impaired iPericyte proliferation. Administration of endothelin-1 led to iPericyte contraction and adenosine led to iPericyte relaxation, of a magnitude similar to the response evoked in HBVPs. We determined that neural crest iPericytes were less susceptible to PDGFR beta inhibition, but responded most robustly to vasoconstrictive meditators. iPericytes express pericyte-associated genes and proteins and, exhibit an appropriate physiological response upon exposure to a key endogenous mitogen or vasoactive mediators. Therefore, the generation of functional iPericytes would be suitable for use in future investigations exploring pericyte function or dysfunction in neurological diseases.
Impact of whole-genome duplications on structural variant evolution in the plant genusCochlearia
Authors: Hämälä Tuomas , Moore Christopher , Cowan Laura , Carlile Matthew , Gopaulchan David , Brandrud Marie K. , Birkeland Siri , Loose Matthew , Kolář Filip , Koch Marcus A. , Yant Levi
Published: October 2023

Polyploidy, the result of whole-genome duplication (WGD), is a major driver of eukaryote evolution. All angiosperms have undergone ancient WGDs, and today stable polyploids account for a substantial portion of both wild and domesticated plant species. Despite its centrality in evolution, WGD is a hugely disruptive mutation, and we still lack a clear understanding of its fitness consequences. Here, we study whether WGD results in greater diversity of genomic structural variants (SVs) and how this influences evolutionary dynamics in nature. Using a set of long-read sequenced samples from the plant genusCochlearia(Brassicaceae), which contains diploids and a recent ploidy series up to octoploid, we show that masking of recessive mutations due to WGD has led to a substantial and progressive accumulation of genic SVs across four ploidy levels. Such SVs likely constitute a genetic load and thus reduce the adaptive potential of polyploid populations. However, this SV accumulation also provides a rich pool of standing genetic variation upon which selection may act in novel environments. By constructing a graph-based pangenome forCochlearia, we identify SVs in hundreds of samples and study the genomic basis of environmental adaptation. We find putatively beneficial SVs involved in pathogen resistance, root development, and salt tolerance, many of which are unique to polyploids. Finally, we explore the adaptive landscapes of SVs and SNPs, identify geographical regions where SVs make novel contributions to adaptive variation, and predict that the role of SVs in environmental adaptation increases due to rapid climate change.
Polyploidy is widespread in Microsporidia
Authors: Khalaf Amjad , Jaron Kamil S. , Blaxter Mark L. , Lawniczak Mara K. N.
Published: October 2023

Microsporidia are obligate intracellular eukaryotic parasites with an extremely broad host range. They have both economic and public health importance. Ploidy in microsporidia is variable, with a few species formally identified as diploid and one as polyploid. Given the increase in the number of studies sequencing microsporidian genomes, it is now possible to assess ploidy levels across all currently-explored microsporidian diversity. We estimate ploidy for all microsporidian datasets available on the Sequence Read Archive (SRA) using k-mer-based analyses, and demonstrate that polyploidy is widespread in Microsporidia, and that ploidy change is dynamic in the group. Using genome-wide heterozygosity estimates, we also show that polyploid microsporidian genomes are relatively homozygous, and we discuss the implications of these findings on the timing of polyploidisation events and their origin.

Author Summary

Microsporidia are single-celled intracellular parasites, distantly related to fungi, that can infect a broad range of hosts, from humans all the way to protozoans. Exploiting the wealth of microsporidian genomic data available, we use k-mer based analyses to assess ploidy status across the group. Understanding a genome’s ploidy is crucial in order to assemble it effectively, and may also be relevant for better understanding a parasite’s behaviour and life cycle. We show that tetraploidy is present in at least six species in Microsporidia, and that these polyploidisation events are likely to have occurred independently. We discuss why these findings may be paradoxical, given that Microsporidia, like other intracellular parasites, have extremely small, reduced genomes.
Revisiting the origins of theSobemovirusgenus: a case for ancient origins of plant viruses
Authors: Ghafari Mahan , Somera Merike , Sarmiento Cecilia , Niehl Annette , Hébrard Eugénie , Tsoleridis Theocharis , Ball Jonathan , Moury Benoît , Lemey Philippe , Katsourakis Aris , Fargette Denis
Published: October 2023

The discrepancy between short- and long-term rate estimates, known as the time-dependent rate phenomenon (TDRP), poses a challenge to extrapolating evolutionary rates over time and reconstructing evolutionary history of viruses. The TDRP reveals a decline in evolutionary rate estimates with the measurement timescale, explained empirically by a power-law rate decay, notably observed in animal and human viruses. A mechanistic evolutionary model, the Prisoner of War (PoW) model, has been proposed to address TDRP in viruses. Although TDRP has been studied in animal viruses, its impact on plant virus evolutionary history remains largely unexplored. Here, we investigated the consequences of TDRP in plant viruses by applying the PoW model to reconstruct the evolutionary history of sobemoviruses, plant pathogens with significant importance due to their impact on agriculture and plant health. Our analysis showed that theSobemovirusgenus dates back over four million years, indicating an ancient origin. We found evidence that supports deep host jumps to Poaceae, Fabaceae, and Solanaceae occurring between tens to hundreds of thousand years ago, followed by specialization. Remarkably, the TDRP-corrected evolutionary history of sobemoviruses was extended far beyond previous estimates that had suggested their emergence during the Neolithic period. By incorporating sequences collected through metagenomic analyses, the resulting phylogenetic tree showcases increased genetic diversity, reflecting a deep history of sobemovirus species with major radiation events taking place during the Neolithic period, suggesting rapid diversification in that period. Our findings make a case for the possibility of deep evolutionary origins of plant viruses.
Stability of Genomic Imprinting and X-Chromosome Inactivation in the Aging Brain
Authors: Mancino Samantha , Seneviratne Janith , Mupo Annalisa , Krueger Felix , Oxley David , Eckersley-Maslin Melanie A , da Rocha Simão Teixeira
Published: October 2023

Epigenetic drift is a hallmark of aging that contributes to the irreversible decline in organismal fitness ultimately leading to aging-related diseases. Epigenetic modifications regulate the cellular memory of the epigenetic processes of genomic imprinting and X-chromosome inactivation to ensure monoallelic expression of imprinted and X-linked genes. Whether epigenetic drift affects maintenance of genomic imprinting and X-chromosome inactivation has not been comprehensively studied. Here, we investigate the allele-specific transcriptional and epigenetic signatures of the aging brain, by comparing juvenile and old hybrid mice obtained from C57BL/6J (BL6) & CAST/EiJ (CAST) reciprocal crosses, with an emphasis on the hippocampus (HCP). We confirm that the aged HCP shows an increase of DNA hydroxymethylation, a sign of epigenetic drift, and a typical aging transcriptional signature. Genomic imprinting was found to be largely unaffected with stable parent-of-origin-specific DNA methylation in HCP, but also other brain regions such as the cerebellum (CB), nucleus accumbens, hypothalamus and prefrontal cortex. Consistently, transcriptomics analysis confirmed unaltered imprinting expression in the aged HCP. An exception are three novel non-coding transcripts (B230209E15Rik,Ube2nlandA330076H08Rik) at the Prader-Willi syndrome/Angelman syndrome (PWS/AS) imprinted locus which lose strict monoallelic expression during aging. Like imprinting, X-chromosome inactivation was remarkably stable with no signs of aging-driven skewing or relaxation of monoallelic expression of X-linked genes. Our study provides a valuable resource for evaluating monoallelic expression in the aging brain and reveals that, despite epigenetic drift during aging, genomic imprinting and X-chromosome inactivation remain predominantly stable throughout the process of physiological aging in the mouse brain.
DNA damaged-induced phosphorylation of a viral replicative DNA helicase results in inhibition of DNA replication through attenuation of helicase function
Authors: Homiski Caleb , Dey-Rao Rama , Shen Shichen , Qu Jun , Melendy Thomas
Published: October 2023

A major function of the DNA damage responses (DDRs) that act during the replicative phase of the cell cycle is to inhibit initiation and elongation of DNA replication. The polyomavirus SV40 is an important model system for studying human DNA replication and DDRs due to its heavy reliance on host factors for viral DNA replication, and the arrest of SV40 DNA replication in response to DDR activation. The inhibition of SV40 DNA replication following DDR activation is associated with enhanced DDR kinase phosphorylation of SV40 Large T-antigen (LT), the viral origin-binding protein and DNA helicase. NetPhos prediction of LT phosphorylation on multiple sites were confirmed by mass spectroscopy, including a highly conserved DDR kinase site, T518. In cell-based DNA replication assays expression of the phosphomimetic mutant form of LT at T518 (T518D) resulted in dramatically decreased levels of SV40 DNA replication; while LT-dependent transcriptional activation was unaffected. WT and LT T518D were subsequently expressed, purified, and analyzedin vitrofor assessment of biochemical function. In concordance with the cell-based data, reactions using SV40 LT-T518D, but not T518A, showed dramatic inhibition of SV40 DNA replication. Importantly, the LT T518D mutation did not affect critical LT protein interactions or its ATPase function, but showed decreased helicase activity on long, but not very short, DNA templates. These results suggest that DDR phosphorylation at T518 inhibits SV40 DNA replication by impeding LT helicase activity, thereby slowing the DNA replication fork. This is consistent with the slowing of cellular replication forks following DDR and may provide a paradigm for another mechanism for how DNA replication forks can be slowed in response to DDR, by phosphorylation of DNA helicases.
Probiotic neoantigen delivery vectors for precision cancer immunotherapy
Authors: Redenti Andrew , Im Jongwon , Redenti Benjamin , Li Fangda , Rouanne Mathieu , Sheng Zeren , Sun William , Gurbatri Candice R. , Huang Shunyu , Komaranchath Meghna , Jang YoungUk , Hahn Jaeseung , Ballister Edward R. , Vincent Rosa L. , Vardoshivilli Ana , Danino Tal , Arpaia Nicholas
Published: October 2023

Microbial systems have been synthetically engineered to deploy therapeutic payloadsin vivo1–4. With emerging evidence that bacteria naturally home to tumors5–7and modulate anti-tumor immunity8,9, one promising application is the development of bacterial vectors as precision cancer vaccines10–12. In this study, we engineered probioticE. coliNissle 1917 (EcN) as an anti-tumor vaccination platform optimized for enhanced production and cytosolic delivery of neoepitope-containing peptide arrays, with increased susceptibility to blood clearance and phagocytosis. These features enhance both safety and immunogenicity, achieving a system which drives potent and specific T cell–mediated anti-cancer immunity that effectively controls or eliminates tumor growth and extends survival in advanced murine primary and metastatic solid tumors. We demonstrate that the elicited anti-tumor immune response involves extensive priming and activation of neoantigen-specific CD4+and CD8+T cells, broader activation of both T and NK cells, and a reduction of tumor-infiltrating immunosuppressive myeloid and regulatory T and B cell populations. Taken together, this work leverages the advantages of living medicines to deliver arrays of tumor-specific neoantigen–derived epitopes within the optimal context to induce specific, effective, and durable systemic anti-tumor immunity.
SalmonellaTyphimurium employ spermidine to exert protection against ROS-mediated cytotoxicity and rewires host polyamine metabolism to ameliorate its survival in macrophages
Authors: Nair Abhilash Vijay , Singh Anmol , Rajamani R. S. , Chakravortty Dipshikha
Published: October 2023

Salmonellainfection involves a cascade of attacks and defence measures. After breaching the intestinal epithelial barrier,Salmonellais phagocytosed by the macrophages, inside which, the bacteria face multiple stresses and, consequently, employ appropriate countermeasures. We show that, inSalmonella, the polyamine spermidine activates a stress response mechanism by regulating critical antioxidant genes.SalmonellaTyphimurium mutants for spermidine transport and synthesis cannot mount an antioxidative response, resulting in high intracellular ROS levels. These mutants are also compromised in their ability to be phagocytosed by macrophages. Furthermore, it regulates a novel enzyme inSalmonella, Glutathionyl-spermidine synthetase (GspSA), which is known to prevent the oxidation of proteins inE.coli. Moreover, the spermidine mutants and the GspSA mutant show significantly reduced survival in the presence of hydrogen peroxidein vitro, and lesser organ burden in the mouse model ofSalmonellainfection. Conversely, in macrophages isolated fromgp91phox-/-mice, we observed a rescue in the attenuated fold proliferation previously observed upon infection. Interestingly,Salmonellaupregulates polyamine biosynthesis in the host through its effectors from SPI-1 and SPI-2, which also solves the mystery of the attenuated proliferation observed in spermidine transport mutants. Thus, inhibition of this pathway in the host abrogates the proliferation ofSalmonellaTyphimurium in macrophages. From a therapeutic perspective, inhibiting host polyamine biosynthesis using an FDA-approved chemopreventive drug, D,L-α-difluoromethylornithine (DFMO), reducesSalmonellacolonization and tissue damage in the mouse model of infection, while enhancing the survival of infected mice. Therefore, our work provides a mechanistic insight into the critical role of spermidine in stress resistance ofSalmonella. It also reveals a strategy of the bacteria in modulating host metabolism to promote their intracellular survival and shows the potential of DFMO to curb Salmonellainfection.
Replicated Functional Evolution in Cichlid Adaptive Radiations
Authors: Martinez Christopher M. , Corn Katherine A. , Williamson Sarah , Satterfield Darien , Roberts-Hugghis Alexus S. , Barley Anthony , Borstein Samuel R. , McGee Matthew D. , Wainwright Peter C.
Published: October 2023

Adaptive radiations highlight the mechanisms by which species and traits diversify and the extent to which these patterns are predictable. We used 1,110 high-speed videos of suction feeding to study functional and morphological diversification in 300 cichlid species from three African Great Lake radiations of varying ages (Tanganyika, Malawi and Victoria) and an older, spatially dispersed continental radiation in the Neotropics. Among African radiations, standing diversity was reflective of time. Morphological and functional variance in Lake Victoria, the youngest radiation, was a subset of that within Lake Malawi, which itself was nested within the older Tanganyikan radiation. However, functional diversity in Neotropical cichlids was often lower than in Lake Tanganyika, despite being at least 25 My older. These two radiations broadly overlapped, but each diversified into novel trait spaces not found in the youngest lake radiations. Evolutionary rates across radiations were inversely related to age, suggesting, at least for lake radiations, extremely rapid trait evolution at early stages. Despite this support for early bursts, other patterns of trait diversity were inconsistent with expectations of adaptive radiations. This work suggests that cichlid functional evolution has played out in strikingly similar fashion in different radiations, with contingencies eventually resulting in lineage-specific novelties.
A native phosphoglycolate salvage pathway of the synthetic autotrophic yeastKomagataella phaffii
Authors: Baumschabl Michael , Mitic Bernd M. , Troyer Christina , Hann Stephan , Ata Özge , Mattanovich Diethard
Published: October 2023

Synthetic autotrophs can serve as chassis strains for bioproduction from CO2as a feedstock to take measures against the climate crisis. Integration of the Calvin–Benson–Bassham (CBB) cycle into the methylotrophic yeastKomagataella phaffii(Pichia pastoris) enabled it to use CO2as the sole carbon source. The key enzyme in this cycle is ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) catalyzing the carboxylation step. However, this enzyme is error prone to perform an oxygenation reaction leading to the production of toxic 2-phosphoglycolate. Native autotrophs have evolved different recycling pathways for 2-phosphoglycolate. However, for synthetic autotrophs, no information is available for the existence of such pathways. Deletion ofCYB2in the autotrophicK. phaffiistrain led to the accumulation of glycolate, an intermediate in phosphoglycolate salvage pathways, suggesting that such a pathway is enabled by nativeK. phaffiienzymes.13C tracer analysis with labeled glycolate indicated that the yeast pathway recycling phosphoglycolate is similar to the plant salvage pathway. This orthogonal yeast pathway may serve as a sensor for RuBisCO oxygenation, and as an engineering target to boost autotrophic growth rates inK. phaffii.
Structural and quantum chemical basis for OCP-mediated quenching of phycobilisomes
Authors: Sauer Paul V. , Cupellini Lorenzo , Sutter Markus , Bondanza Mattia , Domínguez Martin María Agustina , Kirst Henning , Bína David , Koh Adrian Fujiet , Kotecha Abhay , Greber Basil J , Nogales Eva , Polívka Tomáš , Mennucci Benedetta , Kerfeld Cheryl A.
Published: October 2023

Cyanobacteria employ large antenna complexes called phycobilisomes (PBS) for light harvesting. However, intense light triggers non-photochemical quenching, where the Orange Carotenoid Protein (OCP) binds to PBS, dissipating excess energy as heat. The mechanism of efficiently transferring energy from phycocyanobilins in PBS to canthaxanthin in OCP remains insufficiently understood. Using advanced cryogenic-electron microscopy, we unveiled the OCP-PBS complex structure at 1.6-2.1 Å resolution, showcasing its inherent flexibility. Employing multiscale quantum chemistry, we disclosed the quenching mechanism. Identifying key protein residues, we clarified how canthaxanthin’s transition dipole moment in its lowest-energy dark state becomes large enough for efficient energy transfer from phycocyanobilins. Our energy transfer model offers a detailed understanding of the atomic determinants of light harvesting regulation and antenna architecture in cyanobacteria.

One sentence summary

High-resolution cryo-EM structure of the OCP-PBS complex reveals intrinsic motions and enables the atomic simulation of the quenching mechanism
Forward genetic screens identify mechanisms of resistance to small molecule lactate dehydrogenase inhibitors
Authors: Frank Anderson R , Vandiver Florentina , McFadden David G
Published: October 2023

Altered metabolism is a hallmark of cancer; however, it has been difficult to specifically target metabolism in cancer for therapeutic benefit. Cancers with genetically defined defects in metabolic enzymes constitute a subset of cancers where targeting metabolism is potentially accessible. Hürthle cell carcinoma of the thyroid (HTC) tumors frequently harbor deleterious mitochondrial DNA (mtDNA) mutations in subunits of complex I of the mitochondrial electron transport chain (ETC). Previous work has shown that HTC models with deleterious mtDNA mutations exhibit mitochondrial ETC defects that expose lactate dehydrogenase (LDH) as a therapeutic vulnerability. Here, we performed forward genetic screens to identify mechanisms of resistance to small molecule LDH inhibitors. We identified two distinct mechanisms of resistance: upregulation of an LDH isoform and a compound-specific resistance mutation. Using these tools, we demonstrate that the anti-cancer activity of LDH inhibitors in cell line and xenograft models of complex I-mutant HTC is through on-target LDH inhibition.