bluuebunny/crossref_metadata_2025_split huggingface dataset:
Analysis of tandem mass spectrometry data with CONGA: Combining Open and Narrow searches with Group-wise Analysis
Authors: Freestone Jack , Noble William S. , Keich Uri 
Published: May 2023

AbstractSearching tandem mass spectrometry proteomics data against a database is a well-established method for assigning peptide sequences to observed spectra but typically cannot identify peptides harboring unexpected post-translational modifications (PTMs). Open modification searching aims to address this problem by allowing a spectrum to match a peptide even if the spectrum’s precursor mass differs from the peptide mass. However, expanding the search space in this way can lead to a loss in statistical power to detect peptides. We therefore developed a method, called CONGA, that takes into account results from both types of searches—a traditional “narrow window” search and an open modification search—while carrying out rigorous false discovery rate (FDR) control. The result is an algorithm that provides the best of both worlds: the ability to detect unexpected PTMs without a concomitant loss of power to detect unmodified peptides.
Climatic niches provide insights into the evolutionary origins and ecological significance of the succulent CAM syndrome around the world
Authors: Hernández-Hernández Tania , Vásquez-Cruz Marilyn , Loera Israel , DelAngel Melina , Nakamura Miguel 
Published: May 2023

AbstractAlthough distributed globally, plants possessing the succulent syndrome are thought to have evolved to adapt to arid climates, because they possess modifications that increase their water use efficiency. Here we study the evolution and the ecological nature of the succulent CAM syndrome at a global scale by analyzing the climatic niches of succulents within the Caryophyllales, testing the hypothesis of a climatic niche specialization by comparing them with their non-succulent, non-arid adapted relatives. We assembled and carefully curated a worldwide dataset of 5447 species in 28 families, and analyzed the current and evolutionary trajectories of climatic niches with an array of statistical methods including ecological niche modeling, phylogenetic regression and divergence dates estimation. Our results confirm the Core Caryophyllales tend to inhabit drylands probably since their origin in the Early Cretaceous. However, the succulent syndrome appeared later with some lineages diversifying profusely afterwards. The climatic niche of succulents is not differentiated from their non-succulent relatives, but narrower, and contained within the non-succulents’, showing no relationship with extreme conditions such as high aridity or temperatures. Our results support alternative interpretations of the origin of the CAM syndrome and the ecological significance of succulence, as well as the prolific radiation of richest lineages.HighlightsThe climatic niche occupied by succulent CAM plants is not different from their non-succulent relatives. Estimated dates and character reconstruction suggest CO2 scarcity as the evolutionary pressure under these plants originated.
The soluble guanylyl cyclase pathway is inhibited to evade androgen deprivation-induced senescence and enable progression to castration resistance
Authors: Zhang Ling , Troccoli Clara I. , Mateo-Victoriano Beatriz , Lincheta Laura Misiara , Jackson Erin , Shu Ping , Plastini Trisha , Tao Wensi , Kwon Deukwoo , Chen Xi , Sharma Janaki , Jorda Merce , Gulley James L. , Bilusic Marijo , Lockhart Albert Craig , Beuve Annie , Rai Priyamvada 
Published: May 2023

AbstractCastration-resistant prostate cancer (CRPC) is fatal and therapeutically under-served. We describe a novel CRPC-restraining role for the vasodilatory soluble guanylyl cyclase (sGC) pathway. We discovered that sGC subunits are dysregulated during CRPC progression and its catalytic product, cyclic GMP (cGMP), is lowered in CRPC patients. Abrogating sGC heterodimer formation in castration-sensitive prostate cancer (CSPC) cells inhibited androgen deprivation (AD)-induced senescence, and promoted castration-resistant tumor growth. We found sGC is oxidatively inactivated in CRPC. Paradoxically, AD restored sGC activity in CRPC cells through redox-protective responses evoked to protect against AD-induced oxidative stress. sGC stimulation via its FDA-approved agonist, riociguat, inhibited castration-resistant growth, and the anti-tumor response correlated with elevated cGMP, indicating on-target sGC activity. Consistent with known sGC function, riociguat improved tumor oxygenation, decreasing the PC stem cell marker, CD44, and enhancing radiation-induced tumor suppression. Our studies thus provide the first evidence for therapeutically targeting sGC via riociguat to treat CRPC.Statement of significanceProstate cancer is the second highest cancer-related cause of death for American men. Once patients progress to castration-resistant prostate cancer, the incurable and fatal stage, there are few viable treatment options available. Here we identify and characterize a new and clinically actionable target, the soluble guanylyl cyclase complex, in castration-resistant prostate cancer. Notably we find that repurposing the FDA-approved and safely tolerated sGC agonist, riociguat, decreases castration-resistant tumor growth and re-sensitizes these tumors to radiation therapy. Thus our study provides both new biology regarding the origins of castration resistance as well as a new and viable treatment option.
Beyond Blast: Enabling Microbiologists to Better Extract Literature, Taxonomic Distributions and Gene Neighborhood Information for Protein Families
Authors: Reed Colbie J. , Denise Rémi , Hourihan Jacob , Babor Jill , Jaroch Marshall , Martinelli Maria , Hutinet Geoffrey , de Crécy-Lagard Valérie 
Published: May 2023

AbstractCapturing the published corpus of information on all members of a given protein family should be an essential step in any study focusing on specific members of that said family. Using a previously gathered dataset of more than 280 references mentioning a member of the DUF34 (NIF3/Ngg1-interacting Factor 3), we evaluated the efficiency of different databases and search tools, and devised a workflow that experimentalists can use to capture the most published information on members of a protein family in the least amount of time. To complement this workflow, web-based platforms allowing for the exploration of protein family members across sequenced genomes or for the analysis of gene neighborhood information were reviewed for their versatility and ease of use. Recommendations that can be used for experimentalist users, as well as educators, are provided and integrated within a customized, publicly accessible Wiki.Data summaryThe authors confirm all supporting data, code, and protocols have been provided within the article or through supplementary data files. Complete set of supplementary data sheets may be accessed via FigShare.
An elastic proteinaceous envelope encapsulates the earlyArabidopsisembryo
Authors: Harnvanichvech Yosapol , Borassi Cecilia , Daghma Diaa Eldin S. , van der Kooij Hanne M. , Sprakel Joris , Weijers Dolf 
Published: May 2023

AbstractPlant external surfaces are often covered by barriers that control the exchange of molecules, protect from pathogens, and offer mechanical integrity. A key question is when and how such surface barriers are generated. Post-embryonic surfaces have well-studied barriers, including the cuticle, and late Arabidopsis embryo was shown to be protected by an endosperm-derived sheath deposited onto a primordial cuticle. Here we show that both cuticle and sheath are preceded by another structure during the earliest stages of embryogenesis. This structure, which we named the embryonic envelope, is tightly wrapped around the embryonic surface but can be physically detached by cell wall digestion. We show that this structure is composed primarily of Extensin and ArabinogalactanO-glycoproteins and lipids, which appear to form a dense and elastic crosslinked embryonic envelope. The envelope forms in cuticle-deficient mutants and in a mutant that lacks endosperm. This embryo-derived envelope is therefore distinct from previously described cuticle and sheath structures. We propose that it acts as an expandable diffusion barrier, as well as a means to mechanically confine the embryo to maintain its tensegrity during early embryogenesis.Summary statementThe early Arabidopsis embryo is surrounded by a proteinaceous envelope that is distinct from the cuticle or embryo sheath
Structural basis of the T4 bacteriophage primosome assembly and primer synthesis
Authors: Feng Xiang , Spiering Michelle M. , de Luna Almeida Santos Ruda , Benkovic Stephen J. , Li Huilin 
Published: May 2023

ABSTRACTThe T4 bacteriophage gp41 helicase and gp61 primase assemble into a primosome complex to couple DNA unwinding with RNA primer synthesis for DNA replication. How a primosome is assembled and how the length of the RNA primer is defined in the T4 bacteriophage, or in any model system, are unclear. Here we report a series of cryo-EM structures of T4 primosome assembly intermediates at resolutions up to 2.7 Å. We show that the gp41 helicase is an open spiral in the absence of ssDNA, and ssDNA binding triggers a large-scale scissor-like conformational change that drives the open spiral to a closed ring that activates the helicase. We found that the activation of the gp41 helicase exposes a cryptic hydrophobic primase-binding surface allowing for the recruitment of the gp61 primase. The primase binds the gp41 helicase in a bipartite mode in which the N-terminal Zn-binding domain (ZBD) and the C-terminal RNA polymerase domain (RPD) each contain a helicase-interacting motif (HIM1 and HIM2, respectively) that bind to separate gp41 N-terminal hairpin dimers, leading to the assembly of one primase on the helicase hexamer. Based on two observed primosome conformations – one in a DNA-scanning mode and the other in a post RNA primer-synthesis mode – we suggest that the linker loop between the gp61 ZBD and RPD contributes to the T4 pentaribonucleotide primer. Our study reveals T4 primosome assembly process and sheds light on RNA primer synthesis mechanism.
Fitness and transcriptomic analysis of pathogenicVibrio parahaemolyticusin seawater at different shellfish harvesting temperatures
Authors: Liu Zhuosheng , Liao Chao , Wang Luxin 
Published: May 2023

ABSTRACTTo better characterize the population dynamics ofVibrio parahaemolyticus(Vp) containing different virulence genes, twoVpstrains were inoculated into seawater separately and incubated at temperatures (30 and 10 °C) mimicking summer and winter pre-harvest shellfish rearing seasons. The cellular responses of these two strains, one containing the thermostable direct hemolysin (tdh+) gene and the other one containingtdh-related hemolysin (trh+) gene, were studied at the transcriptomic level. Results showed that, at 30 °C,tdh+ andtrh+ strains reached 6.77 ± 0.20 and 6.14 ± 0.07 Log CFU/ml respectively after 5 days. During this time, higher growth rate was observed in thetdh+ strain than thetrh+ strain. When being kept at 10 °C, bothVpstrains persisted at ca. 3.0 Log CFU/ml in seawater with no difference observed between them. Growth and persistence predictive models were then established based on the Baranyi equation. The goodness of fit scores ranged from 0.674 to 0.950. RNA sequencing results showed that downregulated central energy metabolism and weakened degradation of branched chain amino acid were observed only intrh+ strain not intdh+ strain at 30 °C. This might be one reason for the lower growth rates of thetrh+ strain at 30 °C. Histidine metabolism and biofilm formation pathways were significantly downregulated in both strains at 10 °C. No significant difference was observed for virulence-associated gene expression between 10 and 30 °C, regardless of the strains.SIGINIFICANCEGiven the involvement ofVpin a wide range of seafood outbreaks, a systematical characterization ofVpfitness and transcriptomic changes at temperatures of critical importance for seafood production and storage is needed. In this study, predictive models describing the behavior ofVpstrains containing different virulence factors are established. While no difference was observed at the lower temperature (10 C),tdh+ strain had faster growth rate than thetrh+ strain. Transcriptomic analysis showed that significantly higher number of genes were upregulated at 30 °C than 10 °C. Majority of differentially expressed genes ofVpat 30 °C were annotated to functional categories supporting cellular growth. At the lower temperature, the down regulation of the biofilm formation pathway and histidine metabolism indicates that the current practice of storing seafood at lower temperatures not only protect the seafood quality but also ensure the seafood safety.
The lncRNANeat1is associated with astrocyte reactivity and memory deficits in a mouse model of Alzheimer’s disease
Authors: Irwin Ashleigh B , Martina Verdion , Sint Jago Silvienne C , Bahabry Rudhab , Schreiber Anna Maria , Lubin Farah D. 
Published: May 2023

AbstractDysregulation of long non-coding RNAs (lncRNAs) have been associated with Alzheimer’s disease (AD). However, the functional role of lncRNAs in AD remains unclear. Here, we report a crucial role for the lncRNANeat1in astrocyte dysfunction and memory deficits associated with AD. Transcriptomics analysis show abnormally high expression levels ofNEAT1in the brains of AD patients relative to aged-matched healthy controls, with the most significantly elevated levels in glial cells. In a human transgenic APP-J20 (J20) mouse model of AD, RNA-fluorescentin situhybridization characterization ofNeat1expression in hippocampal astrocyte versus non-astrocyte cell populations revealed a significant increase inNeat1expression in astrocytes of male, but not female, mice. This corresponded with increased seizure susceptibility in J20 male mice. Interestingly,Neat1deficiency in the dCA1 in J20 male mice did not alter seizure threshold. Mechanistically,Neat1deficiency in the dorsal area CA1 of the hippocampus (dCA1) J20 male mice significantly improved hippocampus-dependent memory.Neat1deficiency also remarkably reduced astrocyte reactivity markers suggesting thatNeat1overexpression is associated with astrocyte dysfunction induced by hAPP/Aβ in the J20 mice. Together, these findings indicate that abnormalNeat1overexpression may contribute to memory deficits in the J20 AD model not through altered neuronal activity, but through astrocyte dysfunction.
Identifying candidatede novogenes expressed in the somatic female reproductive tract ofDrosophila melanogaster
Authors: Lombardo Kaelina D. , Sheehy Hayley K. , Cridland Julie M. , Begun David J. 
Published: May 2023

ABSTRACTMost eukaryotic genes have been vertically transmitted to the present from distant ancestors. However, variable gene number across species indicates that gene gain and loss also occurs. While new genes typically originate as products of duplications and rearrangements of pre-existing genes, putativede novogenes - genes born out of previously non-genic sequence - have been identified. Previous studies ofde novogenes inDrosophilahave provided evidence that expression in male reproductive tissues is common. However, no studies have focused on female reproductive tissues. Here we begin addressing this gap in the literature by analyzing the transcriptomes of three female reproductive tract organs (spermatheca, seminal receptacle, and parovaria) in three species - our focal species,D. melanogaster- and two closely related species,D. simulansandD. yakuba, with the goal of identifying putativeD. melanogaster-specificde novogenes expressed in these tissues. We discovered several candidate genes, which, consistent with the literature, tend to be short, simple, and lowly expressed. We also find evidence that some of these genes are expressed in otherD. melanogastertissues and both sexes. The relatively small number of candidate genes discovered here is similar to that observed in the accessory gland, but substantially fewer than that observed in the testis.
Structure of the N-terminal didomain d1_d2 of the Thrombospondin type-1 domain-containing 7A
Authors: Bochel Alice , Mortensen Simon A. , Seifert Larissa , Hengel Felicitas E. , Jeffries Cy M. , Chojnowski Grzegorz , Kretz Oliver , Huber Tobias B. , Tomas Nicola M. , Wilmanns Matthias 
Published: May 2023

AbstractThrombospondin type-1 domain-containing 7A (THSD7A) is a large extracellular protein that is found in podocyte foot processes of the kidney glomerulus. It has been established as a causative autoantigen in membranous nephropathy. Amongst the predicted 21 thrombospondin repeat domains of its extracellular segment, the highest frequency of autoimmune response has been associated with the two N-terminal domains. Here, we show that antibodies against this THSD7A segment in mice induce typical clinical and morphological signs of membranous nephropathy. The high-resolution structure of these two domains reveals a non-canonical thrombospondin repeat fold that is distinct from the established type 1 thrombospondin repeat. As it shares a conserved disulfide pattern with the canonical fold, we refer to these domains d1 and d2 as type 1A thrombospondin repeats. Both domains comprise a seven layered CC-W-PP-R-W-QQ-CC pattern, which is only partly shared by other THSD7A thrombospondin repeat domains. The two domains form a well-defined V-shaped tandem arrangement. Our findings provide crucial insight into specific structural features of these two domains that are distinct from other regions of THSD7A and hence could cause the high level of antigenicity found for these two domains.
In silicoevolution of protein binders with deep learning models for structure prediction and sequence design
Authors: Goudy Odessa J , Nallathambi Amrita , Kinjo Tomoaki , Randolph Nicholas , Kuhlman Brian 
Published: May 2023

AbstractThere has been considerable progress in the development of computational methods for designing protein-protein interactions, but engineering high-affinity binders without extensive screening and maturation remains challenging. Here, we test a protein design pipeline that uses iterative rounds of deep learning (DL)-based structure prediction (AlphaFold2) and sequence optimization (ProteinMPNN) to design autoinhibitory domains (AiDs) for a PD-L1 antagonist. Inspired by recent advances in therapeutic design, we sought to create autoinhibited (or masked) forms of the antagonist that can be conditionally activated by proteases. Twenty-threede novodesigned AiDs, varying in length and topology, were fused to the antagonist with a protease sensitive linker, and binding to PD-L1 was tested with and without protease treatment. Nine of the fusion proteins demonstrated conditional binding to PD-L1 and the top performing AiDs were selected for further characterization as single domain proteins. Without any experimental affinity maturation, four of the AiDs bind to the PD-L1 antagonist with equilibrium dissociation constants (KDs) below 150 nM, with the lowest KDequal to 0.9 nM. Our study demonstrates that DL-based protein modeling can be used to rapidly generate high affinity protein binders.Significance statementProtein-protein interactions are critical to most processes in biology, and improved methods for designing protein binders will enable the creation of new research reagents, diagnostics, and therapeutics. In this study, we show that a deep learning-based method for protein design can create high-affinity protein binders without the need for extensive screening or affinity maturation.
The D84G mutation in STIM1 causes nuclear envelope dysfunction and myopathy in mice
Authors: Bryson Victoria , Wang Chaojian , Zhou Zirui , Singh Kavisha , Volin Noah , Yildirim Eda , Rosenberg Paul 
Published: May 2023

AbstractStromal interaction molecule 1 (STIM1) is a Ca2+sensor located in the sarcoplasmic reticulum (SR) of skeletal muscle where it is best known for its role in store operated Ca2+entry (SOCE). Genetic syndromes resulting from STIM1 mutations are recognized as a cause of muscle weakness and atrophy. Here, we focus on a gain of function mutation that occurs in humans and mice (STIM1+/D84Gmice) where muscles exhibit constitutive SOCE. Unexpectedly, this constitutive SOCE did not affect global Ca2+transients, SR Ca2+content or excitation contraction coupling (ECC) and was therefore unlikely to underlie the reduced muscle mass and weakness observed in these mice. Instead, we demonstrate that the presence of D84G STIM1 in the nuclear envelope of STIM1+/D84Gmuscle disrupts nuclear-cytosolic coupling causing severe derangement in nuclear architecture, DNA damage, and altered lamina A associated gene expression. Functionally, we found D84G STIM1 reduced the transfer of Ca2+from the cytosol to the nucleus in myoblasts resulting in a reduction of [Ca2+]N. Taken together, we propose a novel role for STIM1 in the nuclear envelope that links Ca2+signaling to nuclear stability in skeletal muscle.
STIM1 interacts with HCN4 channels to coordinate diastolic depolarization in the mouse Sinoatrial node
Authors: Zhang Hengtao , Graham Victoria , Nepliouev Igor , Stiber Jonathan A. , Rosenberg Paul 
Published: May 2023

AbstractCardiomyocytes in the sinoatrial node (SAN) are specialized to undergo spontaneous diastolic depolarization (DD) to create action potentials (AP) that serve as the origin of the heartbeat. Two cellular clocks govern DD: the membrane clock where ion channels contribute ionic conductance to create DD and the Ca2+clock where rhythmic Ca2+release from sarcoplasmic reticulum (SR) during diastole contributes pacemaking. How the membrane and Ca2+clocks interact to synchronize and drive DD is not well understood. Here, we identified stromal interaction molecule 1 (STIM1), the activator of store operated Ca2+entry (SOCE), in the P-cell cardiomyocytes of the SAN. Functional studies from STIM1 KO mice reveal dramatic changes in properties of AP and DD. Mechanistically, we show that STIM1 regulates the funny currents and HCN4 channels that are required to initiate DD and maintain sinus rhythm in mice. Taken together, our studies suggest that STIM1 acts as a sensor for both the Ca2+and membrane clocks for mouse SAN for cardiac pacemaking.