bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification, characterisation and recombinant expression of flavonoid 3’,5’-hydroxylases and cytochrome P450 reductases fromVacciniumspecies
Authors: Kukk Kaia 
Published: January 2023

ABSTRACTFlavonoid 3’,5’-hydroxylases (F3′5′Hs) play a key role in biosynthesis of blue coloured anthocyanin complexes in plants. Thus these proteins have potential application in the development of a natural blue coloured food dye using microbial cell factories. However, F3′5′Hs are membrane proteins that require a redox partner, NADPH-cytochrome P450 reductase (CPR). The aim of the research was to identify F3′5′H sequences fromVacciniumspecies plants and express the respective proteins in yeast to test their potential in biotechnological production of precursors of anthocyanins. In this study, novel coding DNA sequences of F3′5′Hs fromVaccinium myrtillusandVaccinium uliginosum, and two CPRs fromV. myrtilluswere identified and characterised. The newly obtained proteins and F3′5′H fromVaccinium corymbosumand CPR fromHelianthus annuuswere expressed inPichia pastoris. Addition of DMSO into the culture medium increased production of F3′5′Hs and CPRs. A truncated form ofV. corymbosumF3′5′H, that lacked the predicted first N-terminal alpha helix, expressed at higher level compared to the full-length protein.VacciniumF3′5′Hs were combined with different CPRs and substrates to identify which CPR acts as a redox partner for F3′5′Hs and which substrates are preferred. Unfortunately, only substrates but not the products could be detected, indicating that the recombinant F3′5′Hs were inactive. Therefore, despite progress in protein expression,P. pastoriswas not a suitable host for producingVacciniumF3′5′Hs.
An expert-based global assessment of threats and conservation measures for subterranean ecosystems
Authors: Nanni Veronica , Piano Elena , Cardoso Pedro , Isaia Marco , Mammola Stefano 
Published: January 2023

ABSTRACTSubterranean ecosystems host unique biodiversity and deliver important services to humans. Yet, available data for subterranean ecosystems are limited in space and/or taxonomic scope and global monitoring programs are absent, preventing practitioners to develop effective conservation and management strategies. Expert opinion may help overcome some of these knowledge gaps. We designed a global survey to quantify the importance of anthropogenic impacts and conservation measures for subterranean ecosystems. We obtained 279 responses from 155 experts in different subterranean habitats, taxa, and regions. Experts perceived surface habitat change, direct habitat destruction (e.g., pollution, damming, mining), and climate change as the most relevant threats impacting subterranean ecosystems. Legislation, land protection, and education were scored as the most effective conservation measures, whereas species-level conservation was deemed less relevant. Whenever lacking hard data, expert opinion may be an effective, largely available, yet often overlooked source of information to implement timely conservation interventions for subterranean ecosystems.
Identification of druggable host dependency factors shared by multiple SARS-CoV-2 variants of concern
Authors: Frasson Ilaria , Diamante Linda , Zangrossi Manuela , Carbognin Elena , Pietà Anna Dalla , Penna Alessandro , Rosato Antonio , Verin Ranieri , Torrigiani Filippo , Salata Cristiano , Vaccaro Lorenzo , Cacchiarelli Davide , Richter Sara N. , Montagner Marco , Martello Graziano 
Published: January 2023

AbstractThe high mutation rate of SARS-CoV-2 leads to emergence of several variants, some of which are resistant to vaccines and drugs targeting viral elements. Targeting host dependency factors – cell proteins required for viral replication - would help avoid resistance. However, whether different SARS-CoV-2 variants induce conserved cell responses and exploit the same core host factors is still unclear.We compared three variants of concern and observed that the host transcriptional response was conserved, differing only in kinetics and magnitude. By CRISPR screening we identified the host genes required for infection by each variant: most of the identified genes were shared by multiple variants, both in lung and colon cells. We validated our hits with small molecules and repurposed FDA-approved drugs. All drugs were highly effective against all tested variants, including delta and omicron, new variants that emerged during the study. Mechanistically, we identified ROS production as a pivotal step in early virus propagation. Antioxidant drugs, such as N-acetyl cysteine (NAC), were effective against all variants both in human lung cells, and in a humanised mouse model. Our study supports the use of available antioxidant drugs, such as NAC, as a general and effective anti-COVID-19 approach.
YAP-dependent autophagy is controlled by AMPK, SIRT1 and flow intensity in kidney epithelial cells
Authors: Claude-Taupin Aurore , Roccio Federica , Garfa-Traoré Meriem , Regnier Alice , Burtin Martine , Morel Etienne , Terzi Fabiola , Codogno Patrice , Dupont Nicolas 
Published: January 2023

AbstractShear stress generated by the urinary fluid flow is an important regulator of renal function. Its dysregulation is observed in various chronic and acute kidney diseases. Previously, we demonstrated that primary cilium-dependent autophagy allows kidney epithelial cells to adapt their metabolism in response to fluid flow. Here, we show that nuclear YAP/TAZ negatively regulates autophagy machinery in kidney epithelial cells subjected to fluid flow. This crosstalk is supported by a primary cilium-dependent activation of AMPK and SIRT1, independently of the Hippo pathway. We confirmed the relevance of the YAP/TAZ-autophagy molecular dialogin vivousing a zebrafish model of kidney development and a unilateral ureteral obstruction mouse model. In addition, anin vitroassay simulating the pathological flow observed at early stages of chronic kidney disease (CKD) activated YAP, leading to a primary cilium-dependent inhibition of autophagy. Our findings demonstrate the importance of YAP/TAZ and autophagy in the translation of fluid flow into cellular and physiological responses. Dysregulation of this pathway is associated with the early onset of CKD.
Brain-localized CD4 and CD8 T cells perform correlated random walks and not Levy walks
Authors: Patel Dhruv , Lin Raymond , Majumder Barun , Ganusov Vitaly V. 
Published: January 2023

AbstractFor survival of the organism T cells must efficiently control pathogens invading different peripheral tissues but whether such control (and lack of thereof) is achieved by utilizing different movement strategies remains poorly understood. Liver-localized CD8 T cells perform correlated random walks — a type of a Brownian walk – in liver sinusoids but in some condition these T cells may also perform Levy flights – rapid and large displacements by floating with the blood flow. CD8 T cells in lymph nodes or skin also undergo Brownian walks. A recent study suggested that brain-localized CD8 T cells, specific toToxoplasma gondii, perform generalized Levy walks – a walk type in which T cells alternate pausing and displacing long distances — which may indicate that brain is a unique organ where T cells exhibit movement strategies different from other tissues. We quantified movement patterns of brain-localizedPlasmodium berghei-specific CD4 and CD8 T cells by using well-established statistical and computational methods. Interestingly, we found that T cells change their movement pattern with time since infection and that CD4 T cells move faster and turn less than CD8 T cells. Importantly, both CD4 and CD8 T cells move in the brain by correlated random walks without long displacements challenging previous observations. We have also re-analyzed the movement data of brain-localized CD8 T cells inT. gondii-infected mice and found no evidence of Levy walks. We hypothesize that the previous conclusion of Levy walks ofT. gondii-specific CD8 T cells in the brain was reached due to missing time-frames in the data that create an impression of large displacements between assumed-to-be-sequential movements. Taken together, our results suggests that movement strategies of CD8 T cells are largely similar between LNs, liver, and the brain and consistent with correlated random walks and not Levy walks.
A shift in the mechanisms controlling hippocampal engram formation during brain maturation
Authors: Ramsaran Adam I. , Wang Ying , Golbabaei Ali , Yeung Bi-ru Amy , de Snoo Mitchell L. , Rashid Asim J. , Awasthi Ankit , Lau Jocelyn , Tran Lina M. , Ko Sangyoon Y. , Abegg Andrin , Duan Lana Chunan , McKenzie Cory , Gallucci Julia , Ahmed Moriam , Kaushik Rahul , Dityatev Alexander , Josselyn Sheena A. , Frankland Paul W. 
Published: January 2023

The ability to form precise, episodic memories develops with age, with young children only able to form gist-like memories that lack precision. The cellular and molecular events in the developing hippocampus that underlie the emergence of precise, episodic-like memory formation are unclear. In mice, the absence of a competitive neuronal engram allocation process in the immature hippocampus precluded the formation of sparse engrams and precise memories until the fourth postnatal week, when inhibitory circuits in the hippocampus mature. This age-dependent shift in precision of episodic-like memories involved the functional maturation of parvalbumin-expressing interneurons in subfield CA1 by extracellular perineuronal nets which is necessary and sufficient for the onset of competitive neuronal allocation, sparse engram formation, and memory precision.One-Sentence SummaryEpisodic-like memory precision requires maturation of hippocampal inhibitory interneurons by the extracellular matrix.
Ecological and life history drivers of avian skull evolution
Authors: Hunt Eloise S. E. , Felice Ryan N. , Tobias Joseph A. , Goswami Anjali 
Published: January 2023

AbstractOne of the most famous examples of adaptive radiation is that of the Galápagos finches, where skull morphology, particularly the beak, varies with feeding ecology. Yet increasingly studies are questioning the strength of this correlation between feeding ecology and morphology in relation to the entire neornithine radiation, suggesting that other factors also significantly affect skull evolution. Here, we broaden this debate to assess the influence of a range of ecological and life history factors, specifically habitat density, migration, and developmental mode, in shaping avian skull evolution. Using 3D geometric morphometric data to robustly quantify skull shape for 354 extant species spanning avian diversity, we fitted flexible phylogenetic regressions and estimated evolutionary rates for each of these factors across the full dataset. The results support a highly significant relationship between skull shape and both habitat density and migration, but not developmental mode. We further found heterogenous rates of evolution between different character states within habitat density, migration, and developmental mode, with rapid skull evolution in species which occupy dense habitats, are migratory, or are precocial. These patterns demonstrate that diverse factors impact the tempo and mode of avian phenotypic evolution, and that skull evolution in birds is not simply a reflection of feeding ecology.Impact summaryAlmost 200 years ago, Darwin found that the beaks of Galápagos finches were different shapes in birds with different diets. Nowadays, it is well established that phylogeny, allometry, and ecology can also be key factors in shaping skulls. Yet, the influence of specific aspects of ecology, as well as life history, on morphological evolution remain poorly constrained. Here, we examined whether three novel factors also influence the shape of bird skulls and rates of evolution: habitat density, migration, or developmental mode. To do so, we combine high resolution 3D quantification of skull shape with dense taxonomic sampling across living birds. Our analyses revealed that skull shape varies in birds based on the density of vegetation in their habitats and on the extent to which they migrate. However, how independent birds are when they are born does not appear to influence overall skull shape. Despite these differences in how much they influence the shape of the skull, habitat density, migration and life history all influence the rate at which bird skulls evolve. Birds evolved fastest if they live in densely vegetated habitats, migrate long distances, or are precocial. These results add to the growing body of evidence that skull evolution in birds is impacted by a diverse range of factors, and suggests that habitat density, migration and life history should be considered in future analyses on drivers of phenotypic evolution.
Spin-Coupled Electron Densities of Iron-Sulfur Cluster Imaged byIn SituSerial Laue Diffraction
Authors: Ren Zhong , Zhang Fan , Kang Weijia , Wang Cong , Shin Heewhan , Zeng Xiaoli , Gunawardana Semini , Bowatte Kalinga , Krauß Norbert , Lamparter Tilman , Yang Xiaojing 
Published: January 2023

AbstractIron-sulfur clusters are inorganic cofactors found in many proteins involved in fundamental biological processes including DNA processing. The prokaryotic DNA repair enzyme PhrB, a member of the protein family of cryptochromes and photolyases, carries a four-iron-four-sulfur cluster [4Fe4S] in addition to the catalytic cofactor flavin adenine dinucleotide (FAD) and a second pigment 6,7-dimethyl-8-ribityllumazine (DMRL). The light-induced redox reactions of this multi-cofactor protein complex were recently shown as two interdependent photoreductions of FAD and DMRL mediated by the [4Fe4S] cluster functioning as an electron cache to hold a fine balance of electrons. Here, we apply the more traditional temperature-scan cryo-trapping technique in protein crystallography and the newly developed technology ofin situserial Laue diffraction at room temperature. These diffraction methods in dynamic crystallography enable us to capture strong signals of electron density changes in the [4Fe4S] cluster that depict quantized electronic movements. The mixed valence layers of the [4Fe4S] cluster due to spin coupling and their dynamic responses to light illumination are observed directly in our difference maps between its redox states. These direct observations of the quantum effects in a protein bound iron-sulfur cluster have thus opened a window into the mechanistic understanding of metal clusters in biological systems.
Dynamical modelling of proliferative-invasive plasticity and IFNγ signaling in melanoma reveals mechanisms of PD-L1 expression heterogeneity
Authors: Subhadarshini Seemadri , Sahoo Sarthak , Debnath Shibjyoti , Somarelli Jason A. , Jolly Mohit Kumar 
Published: January 2023

ABSTRACTPhenotypic heterogeneity of melanoma cells contributes to drug tolerance, increased metastasis, and immune evasion in patients with progressive disease. Diverse mechanisms have been individually reported to shape extensive intra- and inter-tumoral phenotypic heterogeneity, such as IFNγ signaling and proliferative to invasive transition, but how their crosstalk impacts tumor progression remains largely elusive. Here, we integrate dynamical systems modeling with transcriptomic data analysis at bulk and single-cell levels to investigate underlying mechanisms behind phenotypic heterogeneity in melanoma and its impact on adaptation to targeted therapy and immune checkpoint inhibitors. We construct a minimal core regulatory network involving transcription factors implicated in this process and identify the multiple “attractors” in the phenotypic landscape enabled by this network. Our model predictions about synergistic control of PD-L1 by IFNγ signaling and proliferative to invasive transition were validated experimentally in three melanoma cell lines – MALME3, SK-MEL-5 and A375. We demonstrate that the emergent dynamics of our regulatory network comprising MITF, SOX10, SOX9, JUN and ZEB1 can recapitulate experimental observations about the co-existence of diverse phenotypes (proliferative, neural crest-like, invasive) and reversible cell-state transitions among them, including in response to targeted therapy and immune checkpoint inhibitors. These phenotypes have varied levels of PD-L1, driving heterogeneity in immune-suppression. This heterogeneity in PD-L1 can be aggravated by combinatorial dynamics of these regulators with IFNγ signaling. Our model predictions about changes in proliferative to invasive transition and PD-L1 levels as melanoma cells evade targeted therapy and immune checkpoint inhibitors were validated in multiple data sets fromin vitroandin vivoexperiments. Our calibrated dynamical model offers a platform to test combinatorial therapies and provide rational avenues for the treatment of metastatic melanoma. This improved understanding of crosstalk among PD-L1 expression, proliferative to invasive transition and IFNγ signaling can be leveraged to improve the clinical management of therapy-resistant and metastatic melanoma.
BRDriver: Breast Cancer Driver Gene Predictor
Authors: Perera Rajitha , Perera Roshan 
Published: January 2023

AbstractThe breast cancer mortality rate is high in developing countries as the early detection of cancer is deficient in patients. The identification of the genes that drive cancer is one of the major approaches in the early detection of breast cancer. Several computational tools have been developed to predict the cancer driver genes. However, there is no gold-standard method for identifying breast cancer driver genes. Therefore, this study aims to develop a model to predict high-confidence breast cancer diver genes using already-developed computational tools and already-produced breast cancer data. Primary breast cancer data were retrieved from the Cancer Genome Atlas Program (TCGA). Here we use twenty-seven different gene prediction tools that calculate each gene’s effect and variant in the primary gene dataset. The primary dataset feeds as the input for each tool. The results retrieved from each tool are recorded as the secondary dataset. The latest breast cancer driver gene set was retrieved from DriverDBv3 and included as the target attribute. Training and testing subsets were selected using k-fold cross-validation from the secondary dataset. Attributes from the secondary dataset were ranked according to their correlation with breast cancer driver genes. The ranked data were trained using different supervised machine-learning algorithms. The attributes and the learning algorithm which produced the highest classification accuracy were selected to build the new model, BReast cancer Driver (BRDriver). The new model BRDriver achieved 0.999 area under the curve and 0.999 classification accuracy on breast invasive carcinoma data. TP53 was the most predicted breast cancer drive gene (n=246) predicted by BRDriver. Interestingly, our BRDriver model predicted CDKN2A and NFE2L2 genes as new breast cancer driver genes. Furtherin vivoandin vitrostudies are required to determine whether these genes are indeed cancer-driver genes. Many computational tools developed to identify the cancer driver genes and variants. A few methodologies were developed to combine these tools and increase efficiency for detecting breast cancer driver genes. Our BRDriver overcomes the difficulties and produces high-confidence breast cancer driver genes.
LZTR1 polymerization provokes cardiac pathology in recessive Noonan syndrome
Authors: Busley Alexandra Viktoria , Gutiérrez-Gutiérrez Óscar , Hammer Elke , Koitka Fabian , Mirzaiebadizi Amin , Steinegger Martin , Pape Constantin , Böhmer Linda , Schroeder Henning , Kleinsorge Mandy , Engler Melanie , Cirstea Ion Cristian , Gremer Lothar , Willbold Dieter , Altmüller Janine , Marbach Felix , Hasenfuss Gerd , Zimmermann Wolfram-Hubertus , Ahmadian Mohammad Reza , Wollnik Bernd , Cyganek Lukas 
Published: January 2023

AbstractNoonan syndrome patients harboring causative variants inLZTR1are particularly at risk to develop severe and early-onset hypertrophic cardiomyopathy. However, the underling disease mechanisms ofLZTR1missense variants driving the cardiac pathology are poorly understood. Hence, therapeutic options for Noonan syndrome patients are limited. In this study, we investigated the mechanistic consequences of a novel homozygous causative variantLZTR1L580Pby using patient-specific and CRISPR/Cas9-corrected iPSC-cardiomyocytes. Molecular, cellular, and functional phenotyping in combination within silicoprediction of protein complexes uncovered a uniqueLZTR1L580P-specific disease mechanism provoking the cardiac hypertrophy. The homozygous variant was predicted to alter the binding affinity of the dimerization domains facilitating the formation of linear LZTR1 polymer chains. The altered polymerization resulted in dysfunction of the LZTR1-cullin 3 ubiquitin ligase complexes and subsequently, in accumulation of RAS GTPases, thereby provoking global pathological changes of the proteomic landscape ultimately leading to cellular hypertrophy. Furthermore, our data showed that cardiomyocyte-specific MRAS degradation is mediated by LZTR1 via the autophagosome, whereas RIT1 degradation is mediated by both LZTR1-dependent and LZTR1-independent proteasomal pathways. Importantly, uni-or biallelic genetic correction of theLZTR1L580Pmissense variant rescued the molecular and cellular disease-associated phenotype, providing proof-of-concept for CRISPR-based gene therapies.
The potato resistance protein Rx1 multimerizes upon activation by the Coat Protein of PVX
Authors: Knip Marijn , Latul Emy , Takken Frank LW 
Published: January 2023

AbstractNucleotide-binding Leucine Rich repeat-type immune receptors (NLRs) are intracellular proteins that sense the presence of pathogen-derived elicitors and subsequently trigger an immune response. NLR proteins have to be strictly regulated as immune responses typically result in death of affected host cells. Regulation mechanisms of NLR activation are well studied, however steps immediately following NLR activation are largely unexplained. Multimerization of NLRs is thought to be involved, although currently no unambiguous paradigm regarding the dynamics of this process exists. Some NLRs form high-molecular weight complexes before activation, others exclusively after activation, or, like Rx1, none could be detected. We investigated NLR complex formation in transgenicN. benthamianastably expressing the potato Rx1 protein from its native promoter. Activation of the Rx1-resistance response was synchronized by dexamethasone-controlled expression of its elicitor; the Potato Virus X Coat Protein. Rx1 self-associates upon activation: Rx1 homomers are absent before dexamethasone application, a complex could be detected 1 hour after application, but surprisingly is again absent after 2 hours or later. These results show that self-association of NLR proteins upon activation can be transient, explaining the difficulties of detecting them during the normal, non-synchronized infection process as this typically involves few affected cells at any time.