bluuebunny/crossref_metadata_2025_split huggingface dataset:
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

AbstractPrecise 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

SummaryHuman 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.HighlightsDDX4 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

AbstractThe 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

ABSTRACTGlobal 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

AbstractHigh-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 summaryWe 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

AbstractAnimals 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

AbstractBackgroundDuring 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.ResultsTo 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.ConclusionsOur 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

AbstractThe 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 StatementIn 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

AbstractTransmembrane 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

AbstractHistone 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

AbstractAdult 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.