bluuebunny/crossref_metadata_2025 huggingface dataset:
Integrative assessment of the transcriptome and virome of the poultry red mite Dermanyssus gallinae
Authors: Ribeiro José M , Hartmann David , Bartošová-Sojková Pavla , Debat Humberto , Moos Martin , Šimek Petr , Fara Jiří , Palus Martin , Kučera Matěj , Hajdušek Ondřej , Sojka Daniel , Kopáček Petr , Perner Jan
Published: May 2022

Dermanyssus gallinae is a blood-feeding mite that parasitises on wild birds and farmed poultry. The D. gallinae mite has a short life cycle of fewer than two weeks from the egg to an egg-laying female. The remarkably swift processing of blood, together with the capacity to blood-feed in most developmental stages, makes this mite a highly debilitating pest. We have constructed developmental stage-specific transcriptomes, through Illumina RNA-seq, to mine the repertoire of protein-encoding mRNA transcripts, products of which participate in key processes that ensure the success of blood digestion, rapid ontogeny, and immunity. As a result of high reproductive capacity, the prevalence of D. gallinae in egg-producing poultry farms globally causes significant economic losses. Acaricides that are used to limit the reproduction of D. gallinae mites target cys-loop ion channels, which are widely shared across the phylogeny of invertebrates. To catalogue a comprehensive list of potential invertebrate-specific ion channels, we have constructed and analysed an additional RNA-seq library of D. gallinae micro-dissected midguts, a tissue with direct exposure to host blood and potential anti-parasitics. We phylogenetically defined groups of cys-loop proteins and probed their sensitivity to selected acaricides. Ultimately, we have catalogued all assembled transcripts and their expression values in a hyper-linked excel sheet with available sequences of individual contigs. The transcriptomic data were complemented by mass-spectrometry (MS)-based metabolite identification and by viability assays using selected inhibitors applied either by microinjection or through artificial membrane feeding. Additionally, we have described the RNA-virome of D. gallinae and identified a novel virus dubbed Red Mite Quaranjavirus 1.
Multiple routes of adaptation to high levels of CIN and aneuploidy in budding yeast
Authors: Clarke Matthew N. , Marsoner Theodor , Alonso Y Adell Manuel , Ravichandran Madhwesh C. , Campbell Christopher S.
Published: May 2022

Both an increased frequency of chromosome missegregation (chromosomal instability) and the presence of an abnormal complement of chromosomes (aneuploidy) are hallmarks of cancer. Paradoxically, both chromosomal instability and aneuploidy are also associated with substantial decreases in cellular fitness. To better understand how cells are able to adapt to high levels of chromosomal instability, we previously examined yeast cells that were deleted of the gene BIR1, a member of the chromosomal passenger complex (CPC). The CPC is an essential regulator of chromosome segregation fidelity. We found bir1Δ cells quickly adapted by acquiring specific combinations of beneficial aneuploidies. However, targeted mutations of specific genes were notably absent in the short term. In this study, we monitored these yeast strains for longer periods of time to determine how cells adapt to high levels of both CIN and aneuploidy in the long term. We identify suppressor mutations that mitigate the chromosome missegregation phenotype. The mutated proteins fall into four main categories: outer kinetochore subunits, members of the SCFCdc4 complex, the mitotic kinase Mps1, and a member of the CPC itself. These mutants function in two distinct ways, as mutations in the outer kinetochore suppress Bir1 deletion indirectly by destabilizing connections between the chromosomes and the mitotic spindle, whereas the other three categories of mutations affect the CPC directly. As a consequence of the accumulation of suppressor point mutations, overall levels of aneuploidy decreased. These experiments demonstrate a timeline of adaptation to high rates of CIN wherein cells first acquire specific aneuploidies that suppress the CIN phenotype, next develop point mutations that more specifically target the source of CIN, and finally reduce the level of aneuploidy to relieve the fitness burden placed by aneuploidy on the cell.
Fluid extraction from the left-right organizer uncovers mechanical properties needed for symmetry breaking
Authors: Sampaio Pedro , Pestana Sara , Guerrero Adán , Telley Ivo A. , Smith David. J. , Lopes Susana S.
Published: May 2022

Humans and other vertebrates define body axis left-right asymmetry in the early stages of embryo development (Shiratori and Hamada, 2006). The mechanism behind left-right establishment is not fully understood (Mizuno et al., 2020; Maerker et al., 2021; Minegishi et al., 2021). Symmetry breaking occurs in a dedicated organ called the left-right organizer (LRO) and involves motile cilia generating fluid-flow therein. However, it has been a matter of debate whether the process of symmetry breaking relies on a chemosensory or a mechanosensory mechanism (Shinohara et al., 2012). Novel tailored manipulations for LRO fluid extraction in living zebrafish embryos allowed us to pinpoint a decisive developmental period for breaking left-right symmetry during development. The shortest critical time-window was narrowed to one hour and characterized by a mild counterclockwise flow. The experimental challenge consisted in emptying the LRO of its fluid, abrogating simultaneously flow force and chemical determinants. Our findings revealed an unprecedented recovery capacity of the embryo to re-fil and re-circulate new LRO fluid. The embryos that later developed laterality problems were found to be those that had lower anterior angular velocity and thus less anterior-posterior heterogeneity. Aiming to test if this led to differential endocytosis of any molecular determinant, we replaced the LRO fluid by a physiological buffer. Despite some transitory flow homogenization, laterality defects were absent unless viscosity was altered demonstrating that symmetry breaking does not depend on the nature of the fluid content but rather relies on fluid mechanics. Altogether, we conclude that mechanosensing is the likely mechanism to govern left-right early establishment.
Improved assessments of milk microbiota composition via sample preparation and DNA extraction methods
Authors: Xue Zhengyao , Marco Maria L.
Published: May 2022

Although bacterial detection by 16S rRNA gene amplicon DNA sequencing is now a widely-applied technique, standardized methods for sample preparation and DNA extraction are needed to ensure accuracy, reproducibility, and scalability for automation. To develop these methods for bovine milk, we assembled a bacterial cell mock community (BCMC) containing bacterial species commonly found in milk. Variations to the following methods were examined: BCMC enumeration method (colony enumeration or microscopy), sample volume (200 μl to 30 ml), sample storage condition (frozen in PBS or 25% glycerol or exposure to freeze-thaw cycles), cell lysis method (bead-beating, vortex, enzymatic), and DNA extraction procedure (MagMAX Total, MagMAX CORE, and MagMAX Ultra 2.0, with and without either Proteinase K or RNase A). Cell enumeration by microscopy was shown to be more accurate for quantification of the BCMC contents. We found that least 10 mL (≥ 104 cells in high quality milk) is needed for reproducible bacterial detection by 16S rRNA gene amplicon DNA sequencing, whereas variations in storage conditions caused minor differences in the BCMC. For DNA extraction and purification, a mild lysis step (bead-beating for 10 s at 4 m/s or vortexing at 1800 rpm for 10 s) paired with the MagMAX Total kit and Proteinase K digestion provided the most accurate representation of the BCMC. These approaches were confirmed to provide similar results in commercial milk samples. Overall, variations in cell lysis methods conferred the greatest changes to milk microbiota composition and therefore should be optimized for sample type.
Glucagon-Like Peptide-1 Receptor Activation Stimulates PKA-Mediated Phosphorylation of Raptor and this Contributes to the Weight Loss Effect of Liraglutide
Authors: Le Thao D. V. , Liu Dianxin , Besing Gai-Linn K. , Raghavan Ritika , Ellis Blair J. , Ceddia Ryan P. , Collins Sheila , Ayala Julio E.
Published: May 2022

The canonical target of the glucagon-like peptide-1 receptor (GLP-1R), Protein Kinase A (PKA), has been shown to stimulate mechanistic Target of Rapamycin Complex 1 (mTORC1) by phosphorylating the mTOR-regulating protein Raptor at Ser791following β-adrenergic stimulation. The objective of these studies is to test whether GLP-1R agonists similarly stimulate mTORC1 via PKA phosphorylation of Raptor at Ser791and whether this contributes to the weight loss effect of the therapeutic GLP-1R agonist liraglutide. We measured phosphorylation of the mTORC1 signaling target ribosomal protein S6 in Chinese Hamster Ovary cells expressing GLP-1R (CHO-Glp1r) treated with liraglutide in combination with PKA inhibitors. We also assessed liraglutide-mediated phosphorylation of the PKA substrate RRXS*/T* motif in CHO-Glp1r cells expressing Myc-tagged wild-type (WT) Raptor or a PKA-resistant (Ser791Ala) Raptor mutant. Finally, we measured the body weight response to liraglutide in WT mice and mice with a targeted knock-in of PKA-resistant Ser791Ala Raptor. Liraglutide increased phosphorylation of S6 and the PKA motif in WT Raptor in a PKA-dependent manner but failed to stimulate phosphorylation of the PKA motif in Ser791Ala Raptor in CHO-Glp1r cells. Lean Ser791Ala Raptor knock-in mice were resistant to liraglutide-induced weight loss but not setmelanotide-induced (melanocortin-4 receptor-dependent) weight loss. Diet-induced obese Ser791Ala Raptor knock-in mice were not resistant to liraglutide-induced weight loss; however, there was weight-dependent variation such that there was a tendency for obese Ser791Ala Raptor knock-in mice of lower relative body weight to be resistant to liraglutide-induced weight loss compared to weight-matched controls. Together, these findings suggest that PKA-mediated phosphorylation of Raptor at Ser791contributes to liraglutide-induced weight loss.
How does data structure impact cell-cell similarity? Evaluating the influence of structural properties on proximity metric performance in single cell RNA-seq data
Authors: Watson Ebony Rose , Mora Ariane , Fard Atefeh Taherian , Mar Jessica Cara
Published: May 2022

Accurately identifying cell populations is paramount to the quality of downstream analyses and overall interpretations of single-cell RNA-seq (scRNA-seq) datasets but remains a challenge. The quality of single-cell clustering depends on the proximity metric used to generate cell-to-cell distances. Accordingly, proximity metrics have been benchmarked for scRNA-seq clustering, typically with results averaged across datasets to identify a highest performing metric. However, the ‘best-performing’ metric varies between studies, with the performance differing significantly between datasets. This suggests that the unique structural properties of a scRNA-seq dataset, specific to the biological system under study, has a substantial impact on proximity metric performance. Previous benchmarking studies have omitted to factor the structural properties into their evaluations. To address this gap, we developed a framework for the in-depth evaluation of the performance of 17 proximity metrics with respect to core structural properties of scRNA-seq data, including sparsity, dimensionality, cell population distribution and rarity. We find that clustering performance can be improved substantially by the selection of an appropriate proximity metric and neighbourhood size for the structural properties of a dataset, in addition to performing suitable pre-processing and dimensionality reduction. Furthermore, popular metrics such as Euclidean and Manhattan distance performed poorly in comparison to several lessor applied metrics, suggesting the default metric for many scRNA-seq methods should be re-evaluated. Our findings highlight the critical nature of tailoring scRNA-seq analyses pipelines to the system under study and provide practical guidance for researchers looking to optimise cell similarity search for the structural properties of their own data.
Metatranscriptomic comparison of viromes in endemic and introduced passerines in New Zealand
Authors: French Rebecca K. , Filion Antoine , Niebuhr Chris N. , Holmes Edward C.
Published: May 2022

New Zealand has many endemic passerine birds vulnerable to emerging infectious diseases. Yet little is known about viruses in passerines, and in some countries, including New Zealand, the virome of wild passerines has received little research attention. Using metatranscriptomic sequencing we characterised the virome of New Zealand endemic and introduced species of passerine. Accordingly, we identified 34 possible avian viruses from cloacal swabs of 12 endemic and introduced bird species not showing signs of disease. These included a novel siadenovirus, iltovirus and avastrovirus in the Eurasian blackbird (Turdus merula, an introduced species), song thrush (Turdus philomelos, introduced) and silvereye (Zosterops lateralis, introduced), respectively. This is the first time novel viruses from these genera have been identified in New Zealand, likely reflecting prior undersampling. It also represents the first identification of an iltovirus and siadenovirus in blackbirds and thrushes globally. These three viruses were found only in introduced species and may pose a risk to endemic species if they were to jump species boundaries, particularly the iltoviruses and siadenoviruses that have a prior history of disease associations. Further virus study and surveillance is needed in New Zealand avifauna, particularly inTurduspopulations and endemic species.
A within-host model of SARS-CoV-2 infection
Authors: Carruthers Jonathan , Xu Jingsi , Finnie Thomas , Hall Ian
Published: May 2022

Within-host models have been used to successfully describe the dynamics of multiple viral infections, however, the dynamics of SARS-CoV-2 virus infection remain poorly understood. A greater understanding of how the virus interacts with the host can contribute to more realistic epidemiological models and help evaluate the effect of antiviral therapies and vaccines. Here, we present a within-host model to describe SARS-CoV-2 viral dynamics in the upper respiratory tract of individuals enrolled in the UK COVID-19 Human Challenge Study. Using this model, we investigate the viral dynamics and provide timescales of infection that independently verify key epidemiological parameters important in the management of an epidemic. In particular, we estimate that an infected individual is first capable of transmitting the virus after approximately 2.1 days, remains infectious for a further 8.3 days, but can continue to test positive using a PCR test for up to 27 days.
Crop management shapes the diversity and activity of DNA and RNA viruses in the rhizosphere
Authors: Muscatt George , Hilton Sally , Raguideau Sebastien , Teakle Graham , Lidbury Ian D. E. A. , Wellington Elizabeth M. H. , Quince Christopher , Millard Andrew , Bending Gary D. , Jameson Eleanor
Published: May 2022

Background

The rhizosphere is a hotspot for microbial activity and contributes to ecosystem services including plant health and biogeochemical cycling. The activity of microbial viruses, and their influence on plant-microbe interactions in the rhizosphere, remains undetermined. Given the impact of viruses on the ecology and evolution of their host communities, determining how soil viruses influence microbiome dynamics is crucial to build a holistic understanding of rhizosphere functions.

Results

Here, we aimed to investigate the influence of crop management on the composition and activity of bulk soil, rhizosphere soil, and root viral communities. We combined viromics, metagenomics, and metatranscriptomics on soil samples collected from a 3-year crop rotation field trial of oilseed rape (Brassica napus L.). By recovering 1,059 dsDNA viral populations and 16,541 ssRNA bacteriophage populations, we expanded the number of underexplored Leviviricetes genomes by > 5 times. Through detection of viral activity in metatranscriptomes, we uncovered evidence of “Kill-the-Winner” dynamics, implicating soil bacteriophages in driving bacterial community succession. Moreover, we found the activity of viruses increased with proximity to crop roots and identified that soil viruses may influence plant-microbe interactions through the reprogramming of bacterial host metabolism. We have provided the first evidence of crop rotation-driven impacts on soil microbial communities extending to viruses. To this aim, we present the novel principal of “viral priming”, which describes how the consecutive growth of the same crop species primes viral activity in the rhizosphere through local adaptation.

Conclusions

Overall, we reveal unprecedented spatial and temporal diversity in viral community composition and activity across root, rhizosphere soil and bulk soil compartments. Our work demonstrates that the roles of soil viruses need greater consideration to exploit the rhizosphere microbiome for food security, food safety, and environmental sustainability.
The ciliopathy protein CCDC66 controls mitotic progression and cytokinesis by promoting microtubule nucleation and organization
Authors: Batman Umut , Deretic Jovana , Firat-Karalar Elif Nur
Published: May 2022

Precise spatiotemporal control of microtubule nucleation and organization is critical for faithful segregation of cytoplasmic and genetic material during cell division and signaling via the primary cilium in quiescent cells. Microtubule-associated proteins (MAPs) govern assembly, maintenance, and remodeling of diverse microtubule arrays. While a set of conserved MAPs are only active during cell division, an emerging group of MAPs acts as dual regulators in dividing and non-dividing cells. Here, we elucidated the nonciliary functions and molecular mechanism of action of the ciliopathy-linked protein CCDC66, which we previously characterized as a regulator of ciliogenesis in quiescent cells. We showed that CCDC66 dynamically localizes to the spindle poles, the bipolar spindle, the spindle midzone, the central spindle and the midbody in dividing cells and interacts with the core machinery of centrosome maturation and MAPs involved in cell division. Loss-of-function experiments revealed its functions during mitotic progression and cytokinesis. Specifically, CCDC66 depletion resulted in defective spindle assembly and positioning, kinetochore fiber stability, chromosome alignment in metaphase as well as central spindle and midbody assembly and organization in anaphase and cytokinesis. Notably, CCDC66 regulates mitotic microtubule nucleation via noncentrosomal and centrosomal pathways via recruitment of gamma-tubulin to the spindle poles and the spindle. Additionally, CCDC66 bundles microtubulesin vitroand in cells by its C-terminal microtubule-binding domain. Phenotypic rescue experiments showed that the microtubule and centrosome-associated pools of CCDC66 individually or cooperatively mediate its mitotic and cytokinetic functions. Collectively, our findings identify CCDC66 as a multifaceted regulator of the nucleation and organization of the diverse mitotic and cytokinetic microtubule arrays and provides new insight into nonciliary defects that underlie ciliopathies.
The germline factor DDX4 contributes to the chemoresistance of small cell lung cancer cells
Authors: Noyes Christopher , Kitajima Shunsuke , Li Fengkai , Suita Yusuke , Miriyala Saradha , Isaac Shakson , Ahsan Nagib , Knelson Erik , Vajdi Amir , Tani Tetsuo , Thai Tran C. , Xu Derek , Murai Junko , Tapinos Nikos , Takahashi Chiaki , Barbie David A. , Yajima Mamiko
Published: May 2022

Human cancers often re-express germline factors, yet their mechanistic role in oncogenesis and cancer progression remains unknown. Here we demonstrate that DDX4, a germline factor and RNA helicase conserved in all multicellular organisms, contributes to epithelial mesenchyme transition (EMT)-like features and cisplatin resistance in small cell lung cancer (SCLC) cells. DDX4 depletion in H69AR and SHP77 cell lines decreased motility and resistance to cisplatin, whereas its overexpression increased these features. Proteomic analysis suggests that DDX4 upregulates metabolic protein expression related to DNA repair and immune/inflammatory response, suggesting its fundamental function may be in regulating cellular metabolism. Consistent with these trends in cell lines, DDX4 depletion compromised in vivo tumor development while its overexpression enhanced tumor growth even after cisplatin treatment in nude mice. Although the DDX4 expression level in somatic tumors is generally low compared to that in the germline, the relatively higher DDX4 expression in SCLC patients correlates with decreased survival and shows increased expression of EMT and cisplatin resistance markers. Taken together, we conclude that DDX4 influences the survival of SCLC patients by altering cellular metabolism in response to environmental cues such as drug treatments. This fundamental function of DDX4 as a germline factor might be applicable in other cancer types that express DDX4 and may serve as a key to combat specific tumors that are highly resistant to treatments.

Highlights

DDX4 contributes to cellular motility and drug resistance in SCLC cells.

DDX4-overexpression globally alters the proteome and suppresses cytokine production.

DDX4 promotes tumorigenesis and drug resistance in vitro and in vivo.

DDX4 expression correlates with survival in SCLC patients and with immune/inflammatory response both in cell lines and patient samples.
A phased chromosome-level genome and full mitochondrial sequence for the dikaryotic myrtle rust pathogen, Austropuccinia psidii
Authors: Edwards Richard J , Dong Chongmei , Park Robert F , Tobias Peri A
Published: May 2022

The fungal plant pathogen Austropuccinia psidii is spreading globally and causing myrtle rust disease symptoms on plants in the family Myrtaceae. A. psidii is dikaryotic, with two nuclei that do not exchange genetic material during the dominant phase of its life-cycle. Phased and scaffolded genome resources for rust fungi are important for understanding heterozygosity, mechanisms of pathogenicity, pathogen population structure and for determining the likelihood of disease spread. We have assembled a chromosome-level phased genome for the pandemic biotype of A. psidii and, for the first time, show that each nucleus contains 18 chromosomes, in line with other distantly related rust fungi. We show synteny between the two haplo-phased genomes and provide a new tool, ChromSyn, that enables efficient comparisons between chromosomes based on conserved genes. Our genome resource includes a fully assembled and circularised mitochondrial sequence for the pandemic biotype.
High-Throughput Global Phosphoproteomic Profiling Using Phospho Heavy-Labeled-Spiketide FAIMS Stepped-CV DDA (pHASED)
Authors: Staudt Dilana E. , Murray Heather C. , Skerrett-Byrne David A. , Smith Nathan D. , Jamaluddin Muhammad F. , Kahl Richard G.S. , Duchatel Ryan J. , Germon Zacary , McLachlan Tabitha , Jackson Evangeline R. , Findlay Izac J. , Kearney Padraic S. , Mannan Abdul , McEwen Holly P. , Douglas Alicia M. , Nixon Brett , Verrills Nicole M. , Dun Matthew D.
Published: May 2022

Global high-throughput profiling of oncogenic signaling pathways by phosphoproteomics is increasingly being applied to cancer specimens. Such quantitative unbiased phosphoproteomic profiling of cancer cells identifies oncogenic signaling cascades that drive disease initiation and progression; pathways that are often invisible to genomics sequencing strategies. Therefore, phosphoproteomic profiling has immense potential for informing individualized anti-cancer treatments. However, complicated and extensive sample preparation protocols, coupled with intricate chromatographic separation techniques that are necessary to achieve adequate phosphoproteomic depth, limits the clinical utility of these techniques. Traditionally, phosphoproteomics is performed using isobaric tagged based quantitation coupled with TiO2 enrichment and offline prefractionation prior to nLC-MS/MS. However, the use of isobaric tags and offline HPLC limits the applicability of phosphoproteomics for the analysis of individual patient samples in real-time. To address these limitations, here we have optimized a new protocol, phospho-Heavy-labeled-spiketide FAIMS Stepped-CV DDA (pHASED). pHASED maintained phosphoproteomic coverage yet decreased sample preparation time and complexity by eliminating the variability associated with offline prefractionation. pHASED employed online phosphoproteome deconvolution using high-field asymmetric waveform ion mobility spectrometry (FAIMS) and internal phosphopeptide standards to provide accurate label-free quantitation data. Compared with our traditional tandem mass tag (TMT) phosphoproteomics workflow and optimized using isogenic FLT3-mutant acute myeloid leukemia (AML) cell line models (n=18/workflow), pHASED halved total sample preparation, and running time (TMT=10 days, pHASED=5 days) and doubled the depth of phosphoproteomic coverage in real-time (phosphopeptides = 7,694 pHASED, 3,861 TMT). pHASED coupled with bioinformatic analysis predicted differential activation of the DNA damage and repair ATM signaling pathway in sorafenib-resistant AML cell line models, uncovering a potential therapeutic opportunity that was validated using cytotoxicity assays. Herein, we optimized a rapid, reproducible, and flexible protocol for the characterization of complex cancer phosphoproteomes in real-time, highlighting the potential for phosphoproteomics to aid in the improvement of clinical treatment strategies.
Hi-LASSO: High-performance python and apache spark packages for feature selection with high-dimensional data
Authors: Jo Jongkwon , Jung Seungha , Park Joongyang , Kim Youngsoon , Kang Mingon
Published: May 2022

High-dimensional LASSO (Hi-LASSO) is a powerful feature selection tool for high-dimensional data. Our previous study showed that Hi-LASSO outperformed the other state-of-the-art LASSO methods. However, the substantial cost of bootstrapping and the lack of experiments for a parametric statistical test for feature selection have impeded to apply Hi-LASSO for practical application. In this paper, the Python package and its Spark library are efficiently implemented in a parallel manner for practice with real-world problems, as well as providing the capability of the parametric statistical tests for feature selection on high-dimensional data. We demonstrate Hi-LASSO’s outperformance with various intensive experiments in a practical manner. Hi-LASSO will be efficiently and easily performed by using the packages for feature selection. Hi-LASSO packages are publicly available at https://github.com/datax-lab/Hi-LASSO under the MIT license. The packages can be easily installed by Python PIP, and additional documentation is available at https://pypi.org/project/hi-lasso and https://pypi.org/project/Hi-LASSO-spark.

Author summary

We provide the brief presentation in the literature of Hi-LASSO comparing to Random LASSO. Then, we describe Hi-LASSO’s open-source packages in Python and Apache Spark, specifying parameters. The open-source packages improves efficiency and scalability of Hi-LASSO, so that the time-consuming bootstrapping-based parametric statistical test can be practically applied for high-dimensional data. We conducted intensive experiments to assess the performance of the packages with the parametric statistical test using simulation data, semi-real datasets, and TCGA cancer dataset. The Hi-LASSO packages showed outstanding and robust performance in feature selection. The packages are available through PyPI and can be easily installed using Python PIP.
Protein preference and elevated plasma FGF21 induced by dietary protein restriction is similar in both male and female mice
Authors: Volcko K.L. , McCutcheon J.E.
Published: May 2022

Animals that are moderately protein restricted respond to this dietary stress by increasing consumption of protein-containing foods. This is true in many species, including rodents. Rodent models of protein restriction have typically relied on only male subjects, and there are plausible reasons why female rodents may respond differently to dietary protein restriction. To address this gap in knowledge, the current experiments examined protein preference after two weeks on a 5% protein diet or 20% protein control diet, in male and female mice. We found that female mice, like male mice, increase consumption of 4% casein (protein) relative to 4% maltodextrin (carbohydrate) when presented with both simultaneously. Interestingly, this increased consumption was due to more bursts in females and more licks per burst in males, indicating possible differences in mechanism by which increased intake is achieved. Stage of the estrous cycle did not affect female responses. Moreover, we measured plasma FGF21 – a hormone induced by protein restriction and necessary for protein preference – in male and female mice. Here, we found no statistical differences between protein-restricted males, females in diestrus, or females in proestrus. In non-restricted mice FGF21 levels were low, but significantly higher in females in proestrus than females in diestrus or males. Overall, these experiments highlight the importance of including female subjects in studies of food choice and macronutrient restriction.

Highlights

- Protein-restricted male and female mice exhibit protein preference

- Estrous cycle stage does not influence protein preference

- Estrous cycle stage does not affect plasma FGF21 during protein restriction

- Non-restricted females in proestrus have higher FGF21 than those in diestrus or males
A transcriptional program shared across lineages underlies cell differentiation during metazoan development
Authors: Ruiz-Romero Marina , Klein Cecilia C. , Pérez-Lluch Sílvia , Abad Amaya , Breschi Alessandra , Guigó Roderic
Published: May 2022

Background

During development, most cells undergo striking changes in order to develop into functional tissues. All along this process, the identity of each tissue arises from the particular combination of regulatory transcription factors that specifically control the expression of relevant genes for growth, pattern formation and differentiation. In this scenario, regulation of gene expression turns out to be essential to determine cell fate and tissue specificity.

Results

To characterize the dynamic transcriptional profiles during cellular differentiation, we tracked down the transcriptome of committed cells in different Drosophila melanogaster tissues and compartments at a number of developmental stages. We found that during fly development, temporal transcriptional changes shared across lineages are much larger than spatial lineage-specific transcriptional changes, and that cellular differentiation is dominated by a transcriptional program, common to multiple lineages, that governs the transition from undifferentiated to fully differentiated cells independently from the differentiation end point. The program is under weak epigenetic regulation, and it is characterized by downregulation of genes associated with cell cycle, and concomitant activation of genes involved in oxidative metabolism. Largely orthogonal to this program, tissue specific transcriptional programs, defined by a comparatively small number of genes are responsible for lineage specification. Transcriptome comparisons with worm, mouse and human, reveal that this transcriptional differentiation program is broadly conserved within metazoans.

Conclusions

Our data provides a novel perspective to metazoan development, and strongly suggest a model, in which the main transcriptional drive during cell type and tissue differentiation is the transition from precursor undifferentiated to terminally differentiated cells, irrespective of cell type.
Chemogenetic disconnection between the orbitofrontal cortex and the rostromedial caudate nucleus disrupts motivational control of goal-directed action
Authors: Oyama Kei , Hori Yukiko , Mimura Koki , Nagai Yuji , Eldridge Mark A G , Saunders Richard C , Miyakawa Naohisa , Hirabayashi Toshiyuki , Hori Yuki , Inoue Ken-ichi , Suhara Tetsuya , Takada Masahiko , Higuchi Makoto , Richmond Barry J , Minamimoto Takafumi
Published: May 2022

The orbitofrontal cortex (OFC) and its major downstream target within the basal ganglia—the rostromedial caudate nucleus (rmCD)—are involved in reward-value processing and goal-directed behavior. However, a causal contribution of the pathway linking these two structures to goal-directed behavior has not been established. Using the chemogenetic technology of Designer Receptors Exclusively Activated by Designer Drugs with a crossed inactivation design, we functionally and reversibly disrupted interactions between the OFC and rmCD in two male macaque monkeys. We injected an adeno-associated virus vector expressing an inhibitory designer receptor (hM4Di) into the OFC and contralateral rmCD, the expression of which was visualized in vivo by positron emission tomography (PET) and confirmed by post-mortem immunohistochemistry. Functional disconnection of the OFC and rmCD resulted in a significant and reproducible loss of sensitivity to the cued reward value for goal-directed action. This decreased sensitivity was most prominent when monkeys had accumulated a certain amount of reward. These results provide causal evidence that the interaction between the OFC and the rmCD is needed for motivational control of action on the basis of the relative reward value and internal drive. This finding extends current understanding of the physiological basis of psychiatric disorders in which goal-directed behavior is affected, such as obsessive-compulsive disorder.

Significance Statement

In daily life, we routinely adjust the speed and accuracy of our actions on the basis of the value of expected reward. Abnormalities in these kinds of motivational adjustments might be related to behaviors seen in psychiatric disorders such as obsessive-compulsive disorder. In the current study, we show that the connection from the orbitofrontal cortex to the rostromedial caudate nucleus is essential formotivational control of action in monkeys. This finding expands our knowledge about how the primate brain controls motivation and behavior and provides a particular insight into disorders like obsessive-compulsive disorder, in which altered connectivity between the orbitofrontal cortex and the striatum has been implicated.
Evolutionary history of metazoan TMEM16 family
Authors: Yuan Xuye , Zhu Yu , Kadowaki Tatsuhiko
Published: May 2022

Transmembrane protein 16 (TMEM16) functions as either a Ca2+-activated Cl- channel (CaCC) or phospholipid scramblase (CaPLSase) and plays diverse physiological roles. It is well conserved in eukaryotes; however, the origin and evolution of different subfamilies in Metazoa are not yet understood. To uncover the evolutionary history of the TMEM16 family, we analyzed 412 proteins from 74 invertebrate species using evolutionary genomics. We found that the TMEM16C–F and J subfamilies are vertebrate-specific, but the TMEM16A/B, G, H, and K subfamilies are ancient and present in many, but not all metazoan species. The most ancient subfamilies in Metazoa, TMEM16L and M, are only maintained in limited species. TMEM16N and O are Cnidaria- and Ecdysozoa-specific subfamilies, respectively, and Ctenophora, Xenacoelomorpha, and Rotifera contain species-specific proteins. We also identified TMEM16 genes that are closely linked together in the genome, suggesting that they have been generated via recent gene duplication. The anoctamin domain structures of invertebrate-specific TMEM16 proteins predicted by AlphaFold2 contain conserved Ca2+-binding motifs and permeation pathways with either narrow or wide inner gates. The inner gate distance of TMEM16 protein may have frequently switched during metazoan evolution, and thus determined the function of the protein as either CaCC or CaPLSase. These results demonstrate that TMEM16 family has evolved by gene gain and loss in metazoans, and the genes have been generally under purifying selection to maintain protein structures and physiological functions.
Inactivation of histone chaperone HIRA unmasks a link between normal embryonic development of melanoblasts and maintenance of adult melanocyte stem cells
Authors: Jaber-Hijazi Farah , Swaminathan Karthic , Gilroy Kathryn , Wenzel Alexander T. , Lagnado Anthony , Kirschner Kristina , Robertson Neil , Reid Claire , Fullarton Neil , Pawlikowski Jeff , Blyth Karen , Mesirov Jill P. , Rai Taranjit Singh , Passos João F. , Machesky Laura M. , Adams Peter D.
Published: May 2022

Histone chaperone HIRA is thought to play a role in both early development and aging, but little is known about connections between the two processes. Here, we explore this relationship using a lineage-specific knockout mouse model, TyrCre::Hirafl/fl, in which HIRA is deficient in the pigmentary system consisting of embryonic melanoblasts, postnatal melanocytes and melanocyte stem cells (McSCs). Hira knockout leads to reduced melanoblast numbers during embryogenesis, but wild type numbers of melanocytes at birth, normally functioning juvenile and young adult McSCs, and only a very mildly hypopigmented first hair coat. However, on closer analysis, Hira knockout melanocytic cells of newborn mice exhibit molecular markers characteristic of cell aging and proliferative deficits. As they age, TyrCre::Hirafl/fl mice display marked defects in McSC maintenance and premature hair graying. Importantly, these defects are only observed when HIRA is inactivated during embryogenesis, not post-natally. This genetic model illustrates how normal embryonic development lays the foundation for maintenance of adult tissue specific stem cells and so suppression of degenerative phenotypes of aging.
Evolutionary conservation and divergence of the transcriptional regulation of bivalve shell secretion across life history stages
Authors: Cavallo Alessandro , Clark Melody S. , Peck Lloyd S. , Harper Elizabeth M. , Sleight Victoria A.
Published: May 2022

Adult molluscs produce shells with diverse morphologies and ornamentations, different colour patterns and microstructures. The larval shell however, is a phenotypically more conserved structure. How do developmental and evolutionary processes generate varying diversity at different life history stages? Using live-imaging, histology, scanning electron microscopy and transcriptomic profiling, we have described shell development in a heteroconchian bivalve the Antarctic clam,Laternula ellipticaand compared it to adult shell secretion processes in the same species. Adult downstream shell genes, such as those encoding extracellular matrix proteins and biomineralisation enzymes, were largely not expressed during shell development, and instead, a development-specific downstream gene repertoire was expressed. Upstream regulatory genes such as transcription factors and signalling molecules were conserved between developmental and adult shell secretion. Comparing heteroconchian transcriptomic data with recently reported pteriomorphian larval shell proteome data suggests that, despite being phenotypically more conserved, the downstream effectors constituting the larval shell “tool-kit” may be as diverse as that of adults. Overall, our new data suggests that a larval shell formed using development-specific downstream effector genes is a conserved and ancestral feature of the bivalve lineage, and possibly more broadly across the molluscs.
Interspecific allometric scaling in eDNA production in fishes reflects physiological and surface area allometry
Authors: Yates M.C , Wilcox T. W. , Stoeckle M.Y. , Heath D.D.
Published: May 2022

Relating environmental DNA (eDNA) signal strength to organism abundance requires a fundamental understanding of eDNA production. A number of studies have demonstrated that eDNA production may scale allometrically – that is, larger organisms tend to exhibit lower mass-specific eDNA production rates, likely due to allometric scaling in key processes related to eDNA production (e.g. surface area, excretion/egestion). While most previous studies have examined intra-specific allometry, physiological rates and organism surface area also scale allometrically across species. We therefore hypothesize that eDNA production will similarly exhibit inter-specific allometric scaling. To evaluate this hypothesis, we reanalyzed previously published eDNA data from Stoeckle et al. (2021) which compared metabarcoding read count to organism count and biomass data obtained from trawl surveys. Using a Bayesian model we empirically estimated the value of the allometric scaling coefficient (‘b’) for bony fishes to be 0.67 (credible interval = 0.58 – 0.77), although our model failed to converge for chondrichthyan species. We found that integrating allometry significantly improved correlations between organism abundance and metabarcoding read count relative to traditional metrics of abundance (density and biomass) for bony fishes. Although substantial unexplained variation remains in the relationship between read count and organism abundance, our study provides evidence that eDNA production tends to scale allometrically across species. Future studies investigating the relationship between eDNA signal strength and metrics of fish abundance could potentially be improved by accounting for allometry – a scaling coefficient value of ∼2/3 appears to be both theoretically and empirically justified.
Circulating U13 small nucleolar RNA as a candidate biomarker for Huntington’s disease
Authors: Romano Silvia , Romano Carmela , Peconi Martina , Fiore Alessia , Bellucci Gianmarco , Morena Emanuele , Troili Fernanda , Cipollini Virginia , Annibali Viviana , Giglio Simona , Mechelli Rosella , Ferraldeschi Michela , Veneziano Liana , Mantuano Elide , Sani Gabriele , Vecchione Andrea , Umeton Renato , Giubilei Franco , Salvetti Marco , Corbo Rosa Maria , Scarabino Daniela , Ristori Giovanni
Published: May 2022

Background and Objectives

Fluid biomarkers are a recent field of interest in Huntington disease (HD). We focused on small circulating RNAs from plasma of subjects with prodromal (pre-HD) and overt disease by a two-stage approach: an unbiased investigation by an array method and a validation study to quantify a significant small nucleolar RNA.

Methods

Through Affymetrix Gene-Chip-miRNA-Array we performed an exploratory study on 9 HD patients, 8 healthy subjects (HS) and 5 psychiatric patients (PP; who share drugs with HD patients, to control for iatrogenic effects). Through real time PCR we validated the results in an independent population of 24 HD patients, 15 pre-HD, 24 PP, 28 Alzheimer’s disease (AD) patients (added to control the disease-specificity of our finding) and 23 HS. A bioinformatic analysis was also performed to interpret our finding.

Results

The microarray results showed a significant signal for U13 small nucleolar RNA (SNORD13) that was increased in plasma of HD patients compared to controls (fold change, 1.54, p =0.003 HD vs. HS, and fold change 1.44 p = 0.0026 HD vs. PP). In the validation population the significant increase in HD patients was evident compared to both pre-HD and the three control groups (p<0.00001). The plasma levels of SNORD13 correlated with the status of mutant huntingtin carrier and the disease duration (respectively R=0.69; p<0.000001; R=0.49; p=0.015). Through receiver operating characteristic (ROC) curve analysis, we showed high accuracy of plasmatic SNORD13 in discriminating HD patients from pre-HD and control groups (AUC=0.963), outperforming values reported in another study for intrathecal or plasmatic mutant huntingtin and neurofilament light chain as biomarkers of overt HD. The bioinformatic analysis on SNORD13 interactome and pathway analysis showed enrichments for factors involved in nuclear functions beyond the ribosome biogenesis.

Discussion

We report the unprecedented finding of a potential role of small nucleolar RNAs in HD. Circulating SNORD13 seems a good biomarker for clinical purposes. It seems to be specific for HD and to peripherally report a plausible ‘tipping point’ in the pathogenic cascade at neuronal level, possibly paving the way for new therapeutic targets.
Ventral Hippocampal Infusions of C20:0 Ceramide Stimulate Microglia and Induce Anhedonia-like Behavior in Female and Male Rats
Authors: Sambolín Lubriel , Feliciano Adariana , Tirado Lizmarie , Suárez Cristina , Pacheco Dariangelly , Fonseca Wilfred , Hernández Anixa , Colón Maria , Porter James
Published: May 2022

Increased long-chain C20:0 ceramides have been found in the serum of patients with depression. Moreover, ceramides are linked with increased microglia reactivity and inflammatory cytokine production, which are associated with depression. Since ceramides can readily cross the blood brain barrier, peripheral C20:0 ceramides could enter the brain, activate microglia, and induce depressive-like behavior. In this study, we determined whether localized infusion of C20:0 ceramides into the ventral hippocampus (VH) of rats is sufficient to activate microglia and induce depressive-like behaviors. Adult male and female rats received infusions of C20:0 ceramides or vehicle solution every other day for 2 weeks. After the third infusion, C20:0-infused animals showed reduced sucrose preference suggesting anhedonia-like behavior. However, 4-6 days after the last infusion, animals infused with C20:0 ceramides did not show anhedonia-like or despair-like behavior suggesting the behavioral effect was reversible. After the final behavioral test, C20:0-infused animals had more Iba-1+ microglia in the VH. Despite the increased number of VH microglia, the expression of inflammatory genes was not increased. In conclusion, our data suggest that localized increases in C20:0 ceramides in the VH are sufficient to induce microglia activation and reversible anhedonia-like behavior.
Multiple modes of substrate hydrolysis-induced covalent modification of strigolactone receptors
Authors: Chen Jiming , Shukla Diwakar
Published: May 2022

The strigolactone signaling pathway in plants is unconventional among plant hormone signaling pathways in that the receptor also acts as an enzyme that hydrolyzes the strigolactone substrate. While the canonical view of strigolactone hydrolysis is that it occurs via a nucleophilic attack on the butenolide ring of strigolactone, an alternative Michael addition mechanism in which hydrolysis occurs via a nucleophilic attack on the enol-ether bridge has been proposed. Furthermore, while it is known that a hydrolysis-induced covalent modification to the receptor promotes strigolactone receptor activation, the nature of this covalent modification has been disputed. Here, we employ QM/MM string method simulations to determine the favored pathway of strigolactone hydrolysis and the nature of the covalent modification that acts as a promoter of strigolactone receptor activation. Our simulations show that strigolactone hydrolysis occurs via an acyl substitution pathway beginning with nucleophilic attack on the butenolide ring, which is well corroborated by previous experimental literature. Additionally, we show that multiple possible modes of covalent modifications to the catalytic residues by the butenolide ring are able to form and interconvert, reconciling several seemingly conflicting views on the hydrolysis-induced covalent modification to strigolactone receptors.