bluuebunny/crossref_metadata_2025_split huggingface dataset:
Control of Biofilm Formation by anAgrobacterium tumefaciensPterin-Binding Periplasmic Protein Conserved Among Pathogenic Bacteria
Authors: Greenwich Jennifer L. , Eagan Justin L. , Feirer Nathan , Boswinkle Kaleb , Minasov George , Shuvalova Ludmilla , Inniss Nicole L. , Raghavaiah Jakka , Ghosh Arun K. , Satchell Karla J.F. , Allen Kylie D. , Fuqua Clay 
Published: November 2023

ABSTRACTBiofilm formation and surface attachment in multiple Alphaproteobacteria is driven by unipolar polysaccharide (UPP) adhesins. The pathogenAgrobacterium tumefaciensproduces a UPP adhesin, which is regulated by the intracellular second messenger cyclic diguanylate monophosphate (cdGMP). Prior studies revealed that DcpA, a diguanylate cyclase-phosphodiesterase (DGC-PDE), is crucial in control of UPP production and surface attachment. DcpA is regulated by PruR, a protein with distant similarity to enzymatic domains known to coordinate the molybdopterin cofactor (MoCo). Pterins are bicyclic nitrogen-rich compounds, several of which are formed via a non-essential branch of the folate biosynthesis pathway, distinct from MoCo. The pterin-binding protein PruR controls DcpA activity, fostering cdGMP breakdown and dampening its synthesis. Pterins are excreted and we report here that PruR associates with these metabolites in the periplasm, promoting interaction with the DcpA periplasmic domain. The pteridine reductase PruA, which reduces specific dihydro-pterin molecules to their tetrahydro forms, imparts control over DcpA activity through PruR. Tetrahydromonapterin preferentially associates with PruR relative to other related pterins, and the PruR-DcpA interaction is decreased in apruAmutant. PruR and DcpA are encoded in an operon that is conserved amongst multiple Proteobacteria including mammalian pathogens. Crystal structures reveal that PruR and several orthologs adopt a conserved fold, with a pterin-specific binding cleft that coordinates the bicyclic pterin ring. These findings define a new pterin-responsive regulatory mechanism that controls biofilm formation and related cdGMP-dependent phenotypes inA. tumefaciensand is found in multiple additional bacterial pathogens.SIGNIFICANCEBiofilms are bacterial communities attached to surfaces, physiologically distinct from free-living cells, and a common cause of persistent infections. Here we define the mechanism of a novel biofilm regulatory system based on excreted metabolites called pterins, that is conserved within a wide range of Gram-negative bacteria, including multiple pathogens of animals and plants. The molecular mechanism of pterin-dependent regulation is reported including structural determination of several members of a new family of pterin-binding proteins. Pterins are produced across all domains of life and mechanistic insights into this regulatory circuit could lead to new advances in antibiofilm treatments.
Lymphatic muscle cells are unique cells that undergo aging induced changes
Authors: Lei Pin-Ji , Ruscic Katarina J. , Roh Kangsan , Rajotte Johanna J. , O’Melia Meghan J. , Bouta Echoe M. , Marquez Marla , Pereira Ethel R. , Kumar Ashwin S. , Arroyo-Ataz Guillermo , Razavi Mohammad S. , Zhou Hengbo , Menzel Lutz , Kumra Heena , Duquette Mark , Huang Peigen , Baish James W. , Munn Lance L. , Ubellacker Jessalyn M. , Jones Dennis , Padera Timothy P. 
Published: November 2023

AbstractLymphatic muscle cells (LMCs) within the wall of collecting lymphatic vessels exhibit tonic and autonomous phasic contractions, which drive active lymph transport to maintain tissue-fluid homeostasis and support immune surveillance. Damage to LMCs disrupts lymphatic function and is related to various diseases. Despite their importance, knowledge of the transcriptional signatures in LMCs and how they relate to lymphatic function in normal and disease contexts is largely missing. We have generated a comprehensive transcriptional single-cell atlas—including LMCs—of collecting lymphatic vessels in mouse dermis at various ages. We identified genes that distinguish LMCs from other types of muscle cells, characterized the phenotypical and transcriptomic changes in LMCs in aged vessels, and uncovered a pro-inflammatory microenvironment that suppresses the contractile apparatus in advanced-aged LMCs. Our findings provide a valuable resource to accelerate future research for the identification of potential drug targets on LMCs to preserve lymphatic vessel function as well as supporting studies to identify genetic causes of primary lymphedema currently with unknown molecular explanation.
Evolution is All You Need in Promoter Design and Optimization
Authors: Ren Ruohan , Yu Hongyu , Teng Jiahao , Mao Sihui , Bian Zixuan , Tao Yangtianze , Yau Stephen S.-T. 
Published: November 2023

AbstractPredicting the strength of promoters and guiding their directed evolution is a crucial task in synthetic biology. This approach significantly reduces the experimental costs in conventional promoter engineering. Previous studies employing machine learning or deep learning methods have shown some success in this task, but their outcomes were not satisfactory enough, primarily due to the neglect of evolutionary information. In this paper, we introduce the Chaos-Attention net for Promoter Evolution (CAPE) to address the limitations of existing methods. We comprehensively extract evolutionary information within promoters using chaos game representation and process the overall information with DenseNet and Transformer. Our model achieves state-of-the-art results on two kinds of distinct tasks. The incorporation of evolutionary information enhances the model’s accuracy, with transfer learning further extending its adaptability. Furthermore, experimental results confirm CAPE’s efficacy in simulating in silico directed evolution of promoters, marking a significant advancement in predictive modeling for prokaryotic promoter strength. Our paper also presents a user-friendly website for the practical implementation of in silico directed evolution on promoters.
Design and Mathematical Analysis of Synthetic Inhibitory Circuits that Program Self-Organizing Multicellular Structures
Authors: Lam Calvin 
Published: November 2023

ABSTRACTBottom-up approaches are becoming increasingly popular for studying multicellular self-organization and development. In contrast to the classic top-down approach, where parts of the organization/developmental process are broken to understand the process, the goal is to build the process to understand it. For example, synthetic circuits have been built to understand how cell-cell communication and differential adhesion can drive multicellular development. The majority of current bottom-up efforts focus on using activatory circuits to engineer and understand development, but efforts with inhibitory circuits have been minimal. Yet, inhibitory circuits are ubiquitous and vital to native developmental processes. Thus, inhibitory circuits are a crucial yet poorly studied facet of bottom-up multicellular development. To demonstrate the potential of inhibitory circuits for building and developing multicellular structures, I designed several synthetic inhibitory circuits that combine engineered cell-cell communication and differential adhesion. Using a previously validatedin silicoframework, I examine the capability of these circuits for synthetic development. I show that the designed inhibitory circuits can build a variety of patterned, self-organized structures and even morphological oscillations. These results support that inhibitory circuits can be powerful tools for building, studying, and understanding developmental processes.Graphical Abstract
Microwave assisted acidification for green hydrogen and organic acids production
Authors: Barth Maximilian , Werner Magdalena , Otto Pascal , Richwien Benjamin , Bahramsari Samira , Krause Maximilian , Schwan Benjamin , Abendroth Christian 
Published: November 2023

AbstractBackgroundThe integration of anaerobic digestion into bio-based industries can create synergies, which help to make anaerobic digestion self-sustaining. Two-stage digesters with separate acidification stages allow to produce green hydrogen and short-chain fatty acids, which are promising industrial products. Heat shocks can be used to foster the production of these products. However, the practical applicability is oft not addressed sufficiently. The here presented work aims to close this gap.MethodsBatch experiments were conducted in 5 litre double-walled tank reactors incubated at 37 °C. Short microwave heat shocks of 25 min duration and exposure times of 5 - 10 min at 80 °C were performed and compared to oven heat shocks. Pairwise experimental group differences for gas production and chemical parameters were determined using ANOVA and post-hoc tests. High-throughput 16S rRNA gene amplicon sequencing was performed to analyse taxonomic profiles.ResultsHeat shocking the entire seed sludge, the highest hydrogen productivity was observed at a substrate load of 50 g/l with 1.09 mol H2/mol hexose. With 1.01 mol H2/mol hexose, microwave assisted treatment was not significantly different from oven-based treatments. The study emphasised the better repeatability of heat shocks with microwave-assisted experiments, showing low variation coefficients averaging 29 %. Microwave pre-treatment indicates a high predictability and a stronger microbiome shift to Clostridia than the oven. The pre-treatment of heat shocks supported the formation of butyric acid up to 10.8 g/l in average and a peak of 24.01 g/l at a butyric/acetic acid ratio of 2.0.ConclusionResults show the suitability to heat shock the entire seed sludge rather than just a small inoculum, which makes the process more relevant for industrial application. A microwave-based treatment has proven to be a promising alternative to oven-based treatments, which ultimately might facilitate the implementation into industrial systems. The approach becomes economically sustainable with high-temperature heat pumps with a coefficient of performance (COP) of 4.3.
Droplet bioprinting of acellular and cell-laden structures at high-resolutions
Authors: Kunwar Puskal , Aryal Ujjwal , Poudel Arun , Fougnier Daniel , Geffert Zachary J , Xie Rui , Li Zhen , Soman Pranav 
Published: November 2023

AbstractAdvances in Digital Light Processing (DLP) based (bio) printers have made printing of intricate structures at high resolution possible using a wide range of photosensitive bioinks. A typical setup of a DLP bioprinter includes a vat or reservoir filled with liquid bioink, which presents challenges in terms of cost associated with bioink synthesis, high waste, and gravity-induced cell settling, contaminations, or variation in bioink viscosity during the printing process. Here, we report a vat-free, low-volume, waste-free droplet bioprinting method capable of rapidly printing 3D soft structures at high resolution using model bioinks. A multiphase many-body dissipative particle dynamics (mDPD) model was developed to simulate the dynamic process of droplet-based DLP printing and elucidate the roles of surface wettability and bioink viscosity. Process variables such as light intensity, photo-initiator concentration, and bioink formulations were optimized to print 3D soft structures (∼0.4 to 3 kPa) with an XY resolution of 38 ± 1.5 μm and Z resolution of 237±5.4 μm. To demonstrate its versatility, droplet bioprinting was used to print a range of acellular 3D structures such as a lattice cube, a Mayan pyramid, a heart-shaped structure, and a microfluidic chip with endothelialized channels. Droplet bioprinting, performed using model C3H/10T1/2 cells, exhibited high viability (90%) and cell spreading. Additionally, microfluidic devices with internal channel network lined with endothelial cells showed robust monolayer formation while osteoblast-laden constructs showed mineral deposition upon osteogenic induction. Overall, droplet bioprinting could be a low-cost, no-waste, easy-to-use, method to make customized bioprinted constructs for a range of biomedical applications.
Semaphorin 6A in Retinal Ganglion Cells Regulates Functional Specialization of the Inner Retina
Authors: James Rebecca E. , Hamilton Natalie R. , Huffman Lola Nicole , Pasterkamp Jeroen , Goff Loyal A. , Kolodkin Alex L. 
Published: November 2023

ABSTRACTTo form functional circuits, neurons must settle in their appropriate cellular locations and then project and elaborate neurites to contact their target synaptic neuropils. Laminar organization within the vertebrate retinal inner plexiform layer (IPL) facilitates pre- and postsynaptic neurite targeting, yet, the precise mechanisms underlying establishment of functional IPL subdomains are not well understood. Here we explore mechanisms defining the compartmentalization of OFF and ON neurites generally, and OFF and ON direction-selective neurites specifically, within the developing IPL. We show that semaphorin 6A (Sema6A), a repulsive axon guidance cue, is required for delineation of OFF versus ON circuits within the IPL: in theSema6anull IPL, the boundary between OFF and ON domains is blurred. Furthermore, Sema6A expressed by retinal ganglion cells (RGCs) directs laminar segregation of OFF and ON starburst amacrine cell (SAC) dendritic scaffolds, which themselves serve as a substrate upon which other retinal neurites elaborate. These results demonstrate for the first time that RGCs, the first neuron-type born within the retina, play an active role in functional specialization of the IPL.Retinal ganglion cell-dependent regulation of OFF and ON starburst amacrine cell dendritic scaffold segregation prevents blurring of OFF versus ON functional domains in the murine inner plexiform layer.
Diffusion in a quantized vector space generates non-idealized protein structures and predicts conformational distributions
Authors: Liu Yufeng , Chen Linghui , Liu Haiyan 
Published: November 2023

AbstractThe power of diffusion probabilistic models (DDPMs) in protein design was recently demonstrated by methods that performs three-dimensional protein backbone denoising. However, these DDPMs tend to generate protein backbones of idealized secondary structures and short loops, lacking diverse, non-idealized local structural elements which are essential for the rich conformational dynamics of natural proteins. Moreover, the sampling power of DDPMs have not yet been utilized for predicting the conformational distributions of natural proteins of dynamic structures. Aiming at these two needs, we developed a model named PVQD (protein vector quantization and diffusion), which used an auto-encoder with vector quantization and a generative diffusion model in the latent space to jointly performing the challenging task of modeling complicated protein structures within an end-to-end framework. Our study demonstrated that in design PVQD generated designable protein structures containing non-idealized elements, while in single sequence-based structure prediction PVQD reproduced experimentally observed conformational variations for a set of natural proteins of dynamic structures.
Chromosome-level scaffolding of haplotype-resolved assemblies using Hi-C data without reference genomes
Authors: Zeng Xiaofei , Yi Zili , Zhang Xingtan , Du Yuhui , Li Yu , Zhou Zhiqing , Chen Sijie , Zhao Huijie , Yang Sai , Wang Yibin , Chen Guoan 
Published: November 2023

AbstractScaffolding is crucial for constructing most chromosome-level genomes. The high-throughput chromatin conformation capture (Hi-C) technology has become the primary scaffolding strategy due to its convenience and cost-effectiveness. As sequencing technologies and assembly algorithms advance, constructing haplotype-resolved genomes is increasingly preferred because haplotypes can provide additional genetic information on allelic and non-allelic variations. ALLHiC is a widely used allele-aware scaffolding tool designed for this purpose. However, its dependence on chromosome-level reference genomes and a higher chromosome misassignment rate still impede the unraveling of haplotype-resolved genomes. In this paper, we present HapHiC, a reference-independent allele-aware scaffolding tool with superior performance on chromosome assignment as well as contig ordering and orientation. Additionally, we provide new insights into the challenges in allele-aware scaffolding by conducting comprehensive analyses on various adverse factors. Finally, with the help of HapHiC, we constructed the haplotype-resolved allotriploid genome forMiscanthus×giganteus, an important lignocellulosic bioenergy crop. HapHiC is available athttps://github.com/zengxiaofei/HapHiC.
An integrated method for single cell proteomics with simultaneous measurements of intracellular drug concentration implicates new mechanisms for adaptation to KRASG12Dinhibitors
Authors: Orsburn Benjamin C. 
Published: November 2023

AbstractIt is well established that a population of single human cells will often respond to the same drug treatment in a heterogeneous manner. In the context of chemotherapeutics, these diverse responses may lead to individual adaptation mechanisms and ultimately multiple distinct methods of resistance. The obvious question from a pharmacology perspective is how intracellular concentrations of active drug varies between individual cells, and what role does that variation play in drug response heterogeneity? To date, no integrated methods for rapidly measuring intracellular drug levels while simultaneously measuring drug responses have been described. This study describes a method for single cell preparation that allows proteins to be extracted and digested from single cells while maintaining conditions for small molecules to be simultaneously measured. The method as described allows up to 40 cells to be analyzed per instrument per day. When applied to a KRASG12Dsmall molecule inhibitor I observe a wide degree of intracellular levels of the drug, and that proteomic responses largely stratify based on the concentration of drug within each single cell. Further work is in progress to develop and standardize this method and – more importantly – to normalize drug measurements against direct measurements of cell volume. However, these preliminary results appear promising for the identification of single cells with unique drug response mechanisms. All data described in this study has been made publicly available through the ProteomeXchange consortium under accession PXD046002.Abstract graphic
Comparative cytogenetics of kenaf (Hibiscus cannabinusL.) breeding lines reveal chromosomal variability and instability
Authors: Ankrah Nii-Ayi , El-nagish Abdullah , Breitenbach Sarah , Tetteh Antonia , Heitkam Tony 
Published: November 2023

ABSTRACTKenaf (Hibiscus cannabinus), a native warm-seasonal crop in Africa, is being considered for genetic improvement for local bast fiber production. To expedite its genetic improvement through breeding, kenaf genotypes from Ghana were assessed for genomic diversity regarding their chromosomal composition and ploidy levels. To gain insight into the repetitive DNA fractions in kenaf, the organization of 5S and 35S rRNA genes, as well as telomeric signal patterns were studied by a molecular cytogenetic approach.Using multi-color fluorescentin situhybridization, distinct rDNA loci andArabidopsis-type telomeres were revealed. The 5S rRNA genes were conserved in kenaf and localized in interstitial regions of two chromosomes across all accessions. The 35S rRNA genes were variable across the kenaf accessions and localized at sub-terminal ends and rarely interstitially in eight or six chromosome arms. Telomeric signals were observed at terminal ends of all chromosomes, with smaller signals also interstitially. The chromosome configuration of Ghana kenaf accessions was confirmed to be 2n=2x=36, each. We discuss the chromosomal variability and the likely genomic instability in the kenaf breeding lines from Ghana.To our knowledge, this is the first report on molecular cytogenetics on kenaf and thus, provides valuable insights into the genome of kenaf that will be useful for breeding. Additionally, this study provides a basis for further studies to analyze the repetitive DNA sequences and develop reference karyotypes to reveal genetic and evolutionary relationships between cultivated and wildHibiscusspecies.
Structure of a Rhs effector clade domain identifies new mechanistic insights into type VI secretion system toxin delivery
Authors: Hayes Brooke K. , Harper Marina , Venugopal Hariprasad , Lewis Jessica M. , Wright Amy , Steele Joel R. , Steer David L. , Schittenhelm Ralf B. , Boyce John D. , McGowan Sheena 
Published: November 2023

AbstractThe type VI secretion system (T6SS) is a molecular machine utilised by many Gram-negative bacteria to deliver antibacterial toxins directly into adjacent bacteria, often providing a competitive advantage. Rearrangement hotspot (Rhs) effectors are known T6SS cargo effectors, but the precise delivery and activation of these toxins is poorly defined. We present the structure of a novel T6SS Rhs effector (Tse15) from the multidrug resistant nosocomial pathogenAcinetobacter baumannii. Tse15 forms a triple layered ý-cocoon Rhs domain with an N-terminal α-helical clade domain and an unfolded C-terminal toxin domain located entirely inside the Rhs cage. We identify that Tse15 is cleaved into three domains, through two independent auto-cleavage events involving aspartyl protease activity for toxin self-cleavage and a nucleophilic glutamic acid for the cleavage of the N-terminal clade domain. Proteomic analyses showed that the N-terminal clade and toxin domains, but not the ý-strand rich Rhs cage, are delivered outside of the cell, suggesting a novel mechanism for Rhs toxin delivery and activation. Our findings suggest that this delivery mechanism requires an interaction between the N-terminal clade and toxin domains, with the clade domain acting as the internal chaperone to mediate tethering of the toxin to the T6SS machinery. Conservation of the clade domain in other Gram-negative bacteria suggest this may be a common mechanism for T6SS toxin delivery.
An engineered glioblastoma model yields novel macrophage-secreted drivers of invasion
Authors: Akins Erin A. , Wilkins Dana , Aghi Manish K. , Kumar Sanjay 
Published: November 2023

AbstractGlioblastomas (GBMs) are highly invasive brain tumors replete with brain- and blood-derived macrophages, collectively known as tumor-associated macrophages (TAMs). Targeting TAMs has been proposed as a therapeutic strategy but has thus far yielded limited clinical success in slowing GBM progression, due in part to an incomplete understanding of TAM function in GBM. Here, by using an engineered hyaluronic acid-based 3D invasion platform, patient-derived GBM cells, and multi-omics analysis of GBM tumor microenvironments, we show that M2-polarized macrophages stimulate GBM stem cell (GSC) mesenchymal transition and invasion. We identify TAM-derived transforming growth factor beta induced (TGFβI/BIGH3) as a pro-tumorigenic factor in the GBM microenvironment. In GBM patients, BIGH3 mRNA expression correlates with poor patient prognosis and is highest in the most aggressive GBM molecular subtype. Inhibiting TAM-derived BIGH3 signaling with a blocking antibody or small molecule inhibitor suppresses GSC invasion. Our work highlights the utility of 3Din vitrotumor microenvironment platforms to investigate TAM-cancer cell crosstalk and offers new insights into TAM function to guide novel TAM-targeting therapies.