bluuebunny/crossref_metadata_2025_split huggingface dataset:
Bacterial composition reflects fine-scale salinity changes while phylogenetic diversity exhibits a strong salt divide
Authors: Peralta Ariane L. , Muscarella Mario E. , Stucy Alexandra , Werba Jo A. , McCoy Michael W. 
Published: September 2021

ABSTRACTClimate change induced salinization events are predicted to intensify and lead to increased salt stress in freshwater aquatic ecosystems. As a consequence, formerly distinct abiotic conditions and associated biotic communities merge, and the emergence, loss, and persistence of microbial taxa modify the types and rates of ecosystem processes. This study examined how bacterial taxonomic and phylogenetic diversity and ecosystem function respond to acute salinization events where freshwater and estuarine communities and environments coalesce. We hypothesized that when the salinity change outpaces microbial adaptation or saline microbial populations are not yet established in formerly freshwater conditions, then these aquatic communities will exhibit diminished carbon cycling rates, decreased microbial diversity, and altered composition of microbial communities compared to historically freshwater communities. We used an experimental mesocosm approach to determine how salinity and the merging of distinct communities influenced resultant bacterial community structure and function. Each mesocosm represented different salinities (0, 5, 9, 13 psu). Two dispersal treatments, representing aquatic communities sourced from brackish 13 psu ponds and a mix of 13 psu and freshwater ponds, were added to all salinity levels and replicated four times. Results revealed that salinity, but not dispersal, decreased bacterial taxonomic and phylogenetic diversity. Carbon mineralization rates were highest in freshwater conditions and associated to bacterial taxa represented in low relative abundance. Acute salinity changes, such as localized flooding due to storm surge, will more negatively affect freshwater aquatic communities compared to chronic exposure to salinization where the communities have had time to adapt or turnover.IMPORTANCE STATEMENTClimate change induced salinization results in the mixing of formerly distinct environmental conditions and aquatic communities. This study examined the consequence of short-term, acute salinity stress on aquatic bacterial taxonomic and phylogenetic diversity and ecosystem function using an experimental approach. Results revealed that salinity, but not the source of aquatic communities, decreased bacterial taxonomic and phylogenetic diversity. Carbon mineralization rates, which represented ecosystem function, were highest in freshwater conditions and also associated with indicator bacterial taxa in low abundance relative to the total microbial community. Taken together, acute salinity changes will more negatively affect freshwater aquatic communities compared to chronic exposure to salinization where the communities have had time to adapt or turnover resulting in recovered biogeochemical functions.
3D Microenvironment-Specific Mechanosensing Regulates Neural Stem Cell Lineage Commitment
Authors: Baek Jieung , Lopez Paola A. , Lee Sangmin , Kim Taek-Soo , Kumar Sanjay , Schaffer David V. 
Published: September 2021

ABSTRACTWhile extracellular matrix (ECM) mechanics strongly regulate stem cell commitment, the field’s mechanistic understanding of this phenomenon largely derives from simplified two-dimensional (2D) culture substrates. Here we found a three-dimensional (3D) matrix-specific mechanoresponsive mechanism for neural stem cell (NSC) differentiation. NSC lineage commitment in 3D is maximally stiffness-sensitive in the range of 0.1-1.2 kPa, a narrower and more brain-mimetic range than we had previously identified in 2D (0.75 – 75 kPa). Transcriptomics revealed stiffness-dependent upregulation of early growth response 1 (Egr1) in 3D but not in 2D. Egr1 knockdown enhanced neurogenesis in stiff ECMs by driving β-catenin nuclear localization and activity in 3D, but not in 2D. Mechanical modeling and experimental studies under osmotic pressure indicate that stiff 3D ECMs are likely to stimulate Egr1 via increases in confining stress during cell volumetric growth. To our knowledge, Egr1 represents the first 3D-specific stem cell mechanoregulatory factor.
Evolution of degrees of carnivory and dietary specialization across Mammalia and their effects on speciation
Authors: Pollard Matthew D. , Puckett Emily E. 
Published: September 2021

AbstractConflation between omnivory and dietary generalism limits ecological and evolutionary analyses of diet, including estimating contributions to speciation and diversification. Additionally, categorizing species into qualitative dietary classes leads to information loss in these analyses. Here, we constructed two continuous variables – degree of carnivory (i.e., the position along the continuum from complete herbivory to complete carnivory) and degree of dietary specialization (i.e., the number and variety of food resources utilized) – to elucidate their histories across Mammalia, and to tease out their independent contributions to mammalian speciation. We observed that degree of carnivory significantly affected speciation rate across Mammalia, whereas dietary specialization did not. We further considered phylogenetic level in diet-dependent speciation and saw that degree of carnivory significantly affected speciation in ungulates, carnivorans, bats, eulipotyphlans, and marsupials, while the effect of dietary specialization was only significant in carnivorans. Across Mammalia, omnivores had the lowest speciation rates. Our analyses using two different categorical diet variables led to contrasting signals of diet-dependent diversification, and subsequently different conclusions regarding diet’s macroevolutionary role. We argue that treating variables such as diet as continuous instead of categorical reduces information loss and avoids the problem of contrasting macroevolutionary signals caused by differential discretization of biologically continuous traits.
Non-enzymatic assembly of active chimeric ribozymes from aminoacylated RNA oligonucleotides
Authors: Radakovic Aleksandar , DasGupta Saurja , Wright Tom H. , Aitken Harry R.M. , Szostak Jack W. 
Published: September 2021

AbstractAminoacylated tRNAs, which harbor a covalent linkage between amino acids and RNA, are a universally conserved feature of life. Because they are essential substrates for ribosomal translation, aminoacylated oligonucleotides must have been present in the RNA World prior to the evolution of the ribosome. One possibility we are exploring is that the aminoacyl ester linkage served another function before being recruited for ribosomal protein synthesis. The nonenzymatic assembly of ribozymes from short RNA oligomers under realistic conditions remains a key challenge in demonstrating a plausible pathway from prebiotic chemistry to the RNA World. Here, we show that aminoacylated RNAs can undergo template-directed assembly into chimeric amino acid-RNA polymers that are active ribozymes. We demonstrate that such chimeric polymers can retain the enzymatic function of their all-RNA counterparts by generating chimeric hammerhead, RNA ligase, and aminoacyl transferase ribozymes. Amino acids with diverse side chains form linkages that are well tolerated within the RNA backbone, potentially bringing novel functionalities to ribozyme catalysis. Our work suggests that aminoacylation chemistry may have played a role in primordial ribozyme assembly. Increasing the efficiency of this process provides an evolutionary rationale for the emergence of sequence and amino acid specific aminoacyl-RNA synthetase ribozymes, which could then have generated the substrates for ribosomal protein synthesis.Significance StatementThe emergence of the primordial ribosome from the RNA World would have required access to aminoacylated RNA substrates. The spontaneous generation of such substrates without enzymes is inefficient, and it remains unclear how they could be selected for in a prebiotic milieu. In our study we identify a role for aminoacylated RNA in ribozyme assembly, a longstanding problem in the origin of life research. We show that aminoacylated RNAs, but not unmodified RNAs, rapidly assemble into chimeric amino acid-bridged ribozymes that retain their native enzymatic activity. Our work therefore addresses two key challenges within the origin-of-life field: we demonstrate assembly of functional ribozymes and we identify a potential evolutionary benefit for RNA aminoacylation that is independent of coded peptide translation.
Intact reading ability in spite of a spatially distributed visual word form ‘area’ in an individual born without the left superior temporal lobe
Authors: Li Jin , Kean Hope , Fedorenko Evelina , Saygin Zeynep 
Published: September 2021

AbstractThe visual word form area (VWFA) is an experience-dependent region in the left ventral temporal cortex (VTC) of literate adults that responds selectively to visual words. Why does it emerge in this stereotyped location? Past research shows the VWFA is preferentially connected to the left-lateralized frontotemporal language network. However, it remains unclear whether the presence of a typical language network and its connections with VTC are critical for the VWFA’s emergence, and whether alternative functional architectures may support reading ability. We explored these questions in an individual (EG) born without the left superior temporal lobe but exhibiting normal reading ability. We recorded fMRI activation to visual words, objects, faces, and scrambled words in EG and neurotypical controls. We did not observe word selectivity either in EG’s right homotope of the VWFA (rVWFA)—the most expected location given that EG’s language network is right-lateralized—or in her spared left VWFA (lVWFA), despite typical face selectivity in both the right and left fusiform face area (rFFA, lFFA). We replicated these results across scanning sessions (5 years apart). Moreover, in contrast with the idea that the VWFA is simply part of the language network that responds to general linguistic information, no part of EG’s VTC showed selectivity to higher-level linguistic processing. Interestingly, multivariate pattern analyses revealed sets of voxels in EG’s rVWFA and lVWFA that showed 1) higher within- than between-category correlations for words (e.g., Words-Words>Words-Faces), and 2) higher within-category correlations for words than other categories (e.g., Words-Words>Faces-Faces). These results suggest that a typical left-hemisphere language network may be necessary for the emergence of focal word selectivity within the VTC, and that orthographic processing can be supported by a distributed neural code.
The copper resistome of group B Streptococcus reveals insight into the genetic basis of cellular survival during metal ion stress
Authors: Goh Kelvin G. K. , Sullivan Matthew J. , Ulett Glen C. 
Published: September 2021

AbstractIn bacteria, copper (Cu) can support metabolic processes as an enzymatic cofactor but can also cause cell damage if present in excess, leading to intoxication. In group B Streptococcus (GBS) a system for control of Cu efflux based on the canonical cop operon supports survival during Cu stress. In some other bacteria, genetic systems additional to the cop operon are engaged during Cu stress and also contribute to Cu management. Here, we examined genetic systems beyond the cop operon in GBS for regions that contribute to survival of GBS in Cu stress using a forward genetic screen and probe of the entire bacterial genome. A high-density mutant library, generated using pGh9-ISS1, was used to expose GBS to Cu stress and compared to non-exposed controls en masse. Nine genes were identified as essential for GBS survival in Cu stress, whereas five genes constrained GBS growth in Cu stress. The genes encode varied factors including enzymes for metabolism, cell wall synthesis, transporters and global transcriptional regulators. Targeted mutation of the genes validated their roles in GBS resistance to Cu stress. Notably, several genes, including stp1, yceG, plyB and rfaB were also essential for resistance to Zn stress. Excepting copA, the genes identified are new to the area of bacterial metal ion intoxication. We conclude that a discrete and limited suite of genes beyond the cop operon in GBS contribute to a repertoire of mechanisms used to survive Cu stress in vitro and achieve cellular homeostasis.Significance StatementGenetic systems for copper (Cu) homeostasis in bacteria, including Streptococci, are vital to survive metal ion stress. Genetic systems that underpin survival of GBS during Cu stress, beyond for the archetypal cop operon for Cu management, are undefined. We show that Streptococcus resists Cu intoxication by utilizing a discrete and limited suite of genes beyond the cop operon, including several genes that are new to the area of bacterial cell metal ion homeostasis. The Cu resistome of GBS defined here enhances our understanding of metal ion homeostasis in GBS.
Angiocrine IGFBP3 Spatially Coordinates IGF Signaling During Neonatal Cardiac Regeneration
Authors: Ali Shah R. , Elhelaly Waleed , Nguyen Ngoc Uyen Nhi , Li Shujuan , Menendez-Montes Ivan , Wang Zhaoning , Cui Miao , Elnwasany Abdallah , Xiao Feng , Thet Suwannee , Lam Nicholas T. , Cardoso Alisson , Pereira Ana Helena , Goodarzi Mohammad , Kinter Michael T. , Lemoff Andrew , Szweda Luke I. , Shelton John , Kimura Wataru , Sadek Hesham A. 
Published: September 2021

AbstractTo identify non-cell-autonomous effectors of cardiomyocyte mitosis, we analyzed a transcriptomic screen of regenerating and non-regenerating neonatal hearts for differentially-expressed secreted proteins – which we hypothesized could include candidate mitogens. We identified and validated IGFBP3, which has a Janus-like stabilizing and sequestering effect on IGF growth factors, as a neonatal injury-associated secreted protein. IGFBP3 is expressed by and secreted from vascular cells in the neonatal heart after cardiac injury, notably in the infarct border zone. We found that global deletion of IGFBP3 blunted neonatal regeneration, while gain-of-function experiments using recombinant IGFBP3 and a transgenic mouse model uncovered a pro-mitotic effect of IGFBP3 on cardiomyocytes in vitro and in the adult heart. We show that site-specific expression of an IGFBP3 protease (PAPP-A2) and its inhibitor (STC2) coordinate the spatial release of IGF2 in the infarct zone to regio-selectively activate the INSR-ERK-AKT cell growth pathways in cardiomyocytes. Collectively, our work highlights the spatiotemporal orchestration of endothelial-cardiomyocyte interactions that are required for neonatal cardiac regeneration.
Epicardial HDAC3 promotes myocardial growth through a novel microRNA pathway
Authors: Jang Jihyun , Song Guang , Li Qinshan , Song Xiaosu , Cai Chenleng , Kaushal Sunjay , Li Deqiang 
Published: September 2021

AbstractRationalEstablishment of the myocardial wall requires proper growth cues from nonmyocardial tissues. During heart development, the epicardium and epicardium-derived cells (EPDCs) instruct myocardial growth by secreting essential factors including fibroblast growth factor 9 (FGF9) and insulin-like growth factor 2 (IGF2). However, it is poorly understood how the epicardial secreted factors are regulated, in particular by chromatin modifications for myocardial formation.ObjectiveTo understand whether and how histone deacetylase 3 (HDAC3) in the developing epicardium regulates myocardial growth.Methods and ResultsWe deleted Hdac3 in the developing murine epicardium and mutant hearts showed ventricular myocardial wall hypoplasia with reduction of EPDCs. The cultured embryonic cardiomyocytes with supernatants from Hdac3 knockout (KO) mouse epicardial cells (MECs) also showed decreased proliferation. Genome-wide transcriptomic analysis revealed that Fgf9 and Igf2 were significantly down-regulated in Hdac3 KO MECs. We further found that Fgf9 and Igf2 expression is dependent on HDAC3 deacetylase activity. The supplementation of FGF9 or IGF2 can rescue the myocardial proliferation defects treated by Hdac3 KO supernatant. Mechanistically, we identified that microRNA (miR)-322 and miR-503 were upregulated in Hdac3 KO MECs and Hdac3 epicardial KO hearts. Overexpression of miR-322 or miR-503 repressed FGF9 and IGF2 expression, while knockdown of miR-322 or miR-503 restored FGF9 and IGF2 expression in Hdac3 KO MECs.ConclusionsOur findings reveal a critical signaling pathway in which epicardial HDAC3 promotes compact myocardial growth by stimulating FGF9 and IGF2 through repressing miR-322/miR-503, providing novel insights in elucidating etiology of congenital heart defects, and conceptual strategies to promote myocardial regeneration.
Mechanism of R-loop formation and conformational activation of Cas9
Authors: Pacesa Martin , Loeff Luuk , Querques Irma , Muckenfuss Lena M. , Sawicka Marta , Jinek Martin 
Published: September 2021

AbstractCas9 is a CRISPR-associated endonuclease capable of RNA-guided, site-specific DNA cleavage1–3. The programmable activity of Cas9 has been widely utilized for genome editing applications4–6, yet its precise mechanisms of target DNA binding and off-target discrimination remain incompletely understood. Here we report a series of cryo-EM structures of Streptococcus pyogenes Cas9 capturing the directional process of target DNA hybridization. In the early phase of R-loop formation, the Cas9 REC2 and REC3 domains form a positively charged cleft that accommodates the distal end of the target DNA duplex. Guide-target hybridization past the seed region induces rearrangements of the REC2/3 domains and relocation of the HNH nuclease domain to assume a catalytically incompetent checkpoint conformation. Completion of the guide-target heteroduplex triggers conformational activation of the HNH nuclease domain, enabled by distortion of the guide-target heteroduplex, and complementary REC2/3 domain rearrangements. Together, these results establish a structural framework for target DNA-dependent activation of Cas9 that sheds light on its conformational checkpoint mechanism and may facilitate the development of novel Cas9 variants and guide RNA designs with enhanced specificity and activity.
Proteomic Characterization of Isolated Arabidopsis Clathrin-Coated Vesicles Reveals Evolutionarily Conserved and Plant Specific Components
Authors: Dahhan Dana A. , Reynolds Gregory D. , Cárdenas Jessica J. , Eeckhout Dominique , Johnson Alexander , Yperman Klaas , Kaufmann Walter A. , Vang Nou , Yan Xu , Hwang Inhwan , Heese Antje , De Jaeger Geert , Friml Jiri , Van Damme Daniel , Pan Jianwei , Bednarek Sebastian Y. 
Published: September 2021

AbstractIn eukaryotes, clathrin-coated vesicles (CCVs) facilitate the internalization of material from the cell surface as well as the movement of cargo in post-Golgi trafficking pathways. This diversity of functions is partially provided by multiple monomeric and multimeric clathrin adaptor complexes that provide compartment and cargo selectivity. The adaptor- protein AP-1 complex operates as part of the secretory pathway at the trans-Golgi network, while the AP-2 complex and the TPLATE complex (TPC) jointly operate at the plasma membrane to execute clathrin-mediated endocytosis. Key to our further understanding of clathrin-mediated trafficking in plants will be the comprehensive identification and characterization of the network of evolutionarily conserved and plant- specific core and accessory machinery involved in the formation and targeting of CCVs. To facilitate these studies, we have analyzed the proteome of enriched trans-Golgi network/early endosome-derived and endocytic CCVs isolated from dividing and expanding suspension-cultured Arabidopsis cells. Tandem mass spectrometry analysis results were validated by differential chemical labeling experiments to identify proteins co-enriching with CCVs. Proteins enriched in CCVs included previously characterized CCV components and cargos such as the vacuolar sorting receptors in addition to conserved and plant-specific components whose function in clathrin-mediated trafficking has not been previously defined. Notably, in addition to AP-1 and AP-2, all subunits of the AP-4 complex, but not AP-3 or AP-5, were found to be in high abundance in the CCV proteome. The association of AP-4 with suspension-cultured Arabidopsis CCVs is further supported via additional biochemical data.
The beta-tubulin isotype TUBB6 controls microtubule and actin dynamics in osteoclasts
Authors: Maurin Justine , Morel Anne , Guérit David , Cau Julien , Urbach Serge , Blangy Anne , Bompard Guillaume 
Published: September 2021

ABSTRACTOsteoclasts are bone resorbing cells that participate in the maintenance of bone health. Pathological increase in osteoclast activity causes bone loss eventually resulting in osteoporosis. Actin cytoskeleton of osteoclasts organizes into a belt of podosomes, which sustains the bone resorption apparatus and is maintained by microtubules. Better understanding of the molecular mechanisms regulating osteoclast cytoskeleton is key to understand the mechanisms of bone resorption, in particular to propose new strategies against osteoporosis. We reported recently that β-tubulin isotype TUBB6 is key for cytoskeleton organization in osteoclasts and for bone resorption. Here, using an osteoclast model CRISPR/Cas9 KO for Tubb6, we show that TUBB6 controls both microtubule and actin dynamics in osteoclasts. Osteoclasts KO for Tubb6 have reduced microtubule growth speed with longer growth life time, higher levels of acetylation and smaller EB1-caps. On the other hand, lack of TUBB6 increases podosome life time while the belt of podosomes is destabilized. Finally, we performed proteomic analyses of osteoclast microtubule-associated protein enriched fractions. This highlighted ARHGAP10 as a new microtubule-associated protein, which binding to microtubules appears to be negatively regulated by TUBB6. ARHGAP10 is a negative regulator of CDC42 activity, which participates in actin organization in osteoclasts. Our results suggest that TUBB6 plays a key role in the control of microtubule and actin cytoskeleton dynamics in osteoclasts. Moreover, by controlling ARHGAP10 association with microtubules, TUBB6 may participate in the local control CDC42 activity to ensure efficient bone resorption.