bluuebunny/crossref_metadata_2025_split huggingface dataset:
Transmembrane helices mediate the formation of a stable ternary complex of cyt b5 reductase, cyt b5, and SCD1
Authors: Shen Jiemin , Wu Gang , Tsai Ah-Lim , Zhou Ming 
Published: November 2021

AbstractMammalian cytochrome b5 (cyt b5) and cytochrome b5 reductase (b5R) are electron carrier proteins required for many membrane-embedded oxidoreductases. Both cyt b5 and b5R have a cytosolic domain anchored to the membrane by a single transmembrane helix (TM). It is not clear if b5R, cyt b5 and their partner oxidoreductases assemble as binary or ternary complexes. Here we show that b5R and cyt b5 form a stable binary complex, and that b5R, cyt b5 and a membrane-embedded oxidoreductase, stearoyl-CoA desaturase 1 (SCD1) form a stable ternary complex. The formation of the complexes significantly enhances electron transfer rates, and that the single TM of cyt b5 and b5R mediated assembly of the complexes. These results reveal a novel functional role of TMs in cyt b5 and b5R and suggest that an electron transport chain composed of a stable ternary complex may be a general feature in oxidoreductases that require the participation of cyt b5 and b5R.
Causation without correlation: parasite-mediated frequency-dependent selection and infection prevalence
Authors: Lively Curtis M. , Xu Julie , Ben-Ami Frida 
Published: November 2021

Parasite-mediated selection is thought to maintain host genetic diversity for resistance. We might thus expect to find a strong positive correlation between host genetic diversity and infection prevalence across natural populations. Here we used computer simulations to examine host-parasite coevolution in 20 simi-isolated clonal populations across a broad range of values for both parasite virulence and parasite fecundity. We found that the correlation between host genetic diversity and infection prevalence can be significantly positive for intermediate values of parasite virulence and fecundity. But the correlation can also be weak and statistically non-significant, even when parasite-mediated frequency-dependent selection is the sole force maintaining host diversity. Hence correlational analyses of field populations, while useful, might underestimate the role of parasites in maintaining host diversity.Subject Area. Evolution
Microfluidic system-based time-course tracking of physical proximity between cells and its effect on gene expression for elucidating live single cancer-immune cell interactions
Authors: Flores Bianca C. T. , Chawla Smriti , Ma Ning , Sanada Chad , Kujur Praveen Kumar , Chinen Ludmilla T. D. , Hukari Kyle , Lynch Mark , Ramalingam Naveen , Sengupta Debarka , Jeffrey Stefanie S. 
Published: November 2021

SummaryCell-cell communication and physical interactions play a vital role in cancer initiation, homeostasis, progression, and immune response. Here, we report a system that combines live capture of different cell types, co-incubation, time-lapse imaging, and gene expression profiling of doublets using a microfluidic integrated fluidic circuit (IFC) that enables measurement of physical distances between cells and the associated transcriptional profiles due to cell-cell interactions. The temporal variations in natural killer (NK) - triple-negative breast cancer (TNBC) cell distances were tracked and compared with terminally profiled cellular transcriptomes. The results showed the time-bound activities of regulatory modules and alluded to the existence of transcriptional memory. Our experimental and bioinformatic approaches serve as a proof of concept for interrogating live cell interactions at doublet resolution, which can be applied across different cancers and cell types.
Investigating Increased CO2 concentration on the pH of various plant species
Authors: Schafer Joshua , Puga Troy , Harris Pearce , Strasser Nora , Branum Gary , Agbedanu Prince N 
Published: November 2021

AbstractThe concept of bioremediation is quickly becoming the norm in the resolution of environmental issues. The steady increase in carbon dioxide (CO2) levels, as documented by NASA, inspired scientists to engineer plants to absorb excess CO2 from the atmosphere. Here, we have explored the consequences of the uptake of excess CO2 by select plants. Carbon dioxide dissolves in H2O to produce H2CO3, which dissociates to yield H+ ions. We hypothesized that increased CO2 absorption results in decrease in pH of plant sap. Three plants (Byophyllum pinnatum, Romaine Lettuce and Nevada Lettuce), exposed to increased CO2 concentrations (15%), demonstrated a consistent increase in pH towards alkalinity compared to control plants. Based on the outcome being opposite of what we have hypothesized, our results suggest Byophyllum pinnatum, Romaine lettuce and Nevada lettuce, all have a unique homeostatic system to prevent over-absorption of CO2 in a CO2-rich environment.
Single-sample proteome enrichment enables missing protein recovery and phenotype association
Authors: Wong Bertrand Jern Han , Kong Weijia , Goh Wilson Wen Bin 
Published: November 2021

AbstractProteomic studies characterize the protein composition of complex biological samples. Despite recent developments in mass spectrometry instrumentation and computational tools, low proteome coverage remains a challenge. To address this, we present Proteome Support Vector Enrichment (PROSE), a fast, scalable, and effective pipeline for scoring protein identifications based on gene co-expression matrices. Using a simple set of observed proteins as input, PROSE gauges the relative importance of proteins in the phenotype. The resultant enrichment scores are interpretable and stable, corresponding well to the source phenotype, thus enabling reproducible recovery of missing proteins. We further demonstrate its utility via reanalysis of the Cancer Cell Line Encyclopedia (CCLE) proteomic data, with prediction of oncogenic dependencies and identification of well-defined regulatory modules. PROSE is available as a user-friendly Python module from https://github.com/bwbio/PROSE.
Defining Innate Immune Responses to the Human Gut Microbiota from Phylum to Strain
Authors: Spindler Matthew P. , Siu Sophia S. , Mogno Ilaria , Li Zhihua , Yang Chao , Mehandru Saurabh , Britton Graham J. , Faith Jeremiah J. 
Published: November 2021

SUMMARYThe functional potential of the gut microbiota remains largely uncharacterized. Efforts to understand how the immune system responds to commensal organisms have been hindered by the large number of strains that comprise the human gut microbiota. We develop a screening platform to measure innate immune responses towards 277 bacterial strains isolated from the human gut microbiota. We find that innate immune responses to gut derived bacteria are as strong as responses towards pathogenic bacteria, and vary from phylum to strain. Myeloid cells differentially rely upon TLR2 or TLR4 to sense particular taxa, an observation that predicts in vivo function. These innate immune responses can be modeled using combinations of up to 8 TLR agonists. Furthermore, the immunogenicity of strains is stable over time and following transplantation into new humans. Collectively, we demonstrate a powerful high-throughput approach to determine how commensal microorganisms shape innate immune phenotypes.
Contribution of infection and vaccination to seroprevalence through two COVID waves in Tamil Nadu, India
Authors: Selvavinayagam T.S. , Somasundaram A. , Selvam Jerard Maria , Ramachandran Sabareesh , Sampath P. , Vijayalakshmi V. , Ajith Brabhu Kumar C. , Subramaniam Sudharshini , Parthipan K. , Raju S. , Avudaiselvi R. , Prakash V. , Yogananth N. , Subramanian Gurunathan , Roshini A. , Dhiliban D.N. , Imad Sofia , Tandel Vaidehi , Parasa Rajeswari , Sachdeva Stuti , Malani Anup 
Published: November 2021

AbstractFour rounds of serological surveys were conducted, spanning two COVID waves (October 2020 and April-May 2021), in Tamil Nadu (population 72 million) state in India. Each round included representative populations in each district of the state, totaling ≥20,000 persons per round. State-level seroprevalence was 31.5% in round 1 (October-November 2020), after India’s first COVID wave. Seroprevalence fell to 22.9% in 2 (April 2021), consistent with waning of antibodies from natural infection. Seroprevalence rose to 67.1% by round 3 (June-July 2021), reflecting infections from the Delta-variant induced second COVID wave. Seroprevalence rose to 93.1% by round 4 (December 2021-January 2022), reflecting higher vaccination rates. Antibodies also appear to wane after vaccination. Seroprevalence in urban areas was higher than in rural areas, but the gap shrunk over time (35.7 v. 25.7% in round 1, 89.8% v. 91.4% in round 4) as the epidemic spread even in low-density rural areas.Article Summary LineAntibodies waned after India’s first COVID wave and both vaccination and infection contributed its roughly 90% seroprevalence after its second wave.
Determination of nuclear position by the arrangement of actin filaments using deep generative networks
Authors: Vasudevan Jyothsna , Zheng Chuanxia , Wan James G. , Cham Tat-Jen , Teck Lim Chwee , Fernandez Javier G. 
Published: November 2021

AbstractThe cell nucleus is a dynamic structure that changes locales during cellular processes such as proliferation, differentiation, or migration1, and its mispositioning is a hallmark of several disorders2,3. As with most mechanobiological activities of adherent cells, the repositioning and anchoring of the nucleus are presumed to be associated with the organization of the cytoskeleton, the network of protein filaments providing structural integrity to the cells4. However, this correlation between cytoskeleton organization and nuclear position has not, to date, been demonstrated, as it would require the parameterization of the extraordinarily intricate cytoskeletal fiber arrangements. Here, we show that this parameterization and demonstration can be achieved outside the limits of human conceptualization, using generative network and raw microscope images, relying on machine-driven interpretation and selection of parameterizable features. The developed transformer-based architecture was able to generate high-quality, completed images of more than 8,000 cells, using only information on actin filaments, predicting the presence of a nucleus and its exact localization in more than 70 per cent of instances. Our results demonstrate one of the most basic principles of mechanobiology with a remarkable level of significance. They also highlight the role of deep learning as a powerful tool in biology beyond data augmentation and analysis, capable of interpreting—unconstrained by the principles of human reasoning—complex biological systems from qualitative data.
Liver ductal organoids reconstruct intrahepatic biliary trees in decellularized liver grafts
Authors: Tomofuji Katsuhiro , Fukumitsu Ken , Kondo Jumpei , Horie Hiroshi , Makino Kenta , Wakama Satoshi , Ito Takashi , Oshima Yu , Ogiso Satoshi , Ishii Takamichi , Inoue Masahiro , Hatano Etsuro 
Published: November 2021

AbstractThree-dimensional scaffolds decellularized from native organs are a promising technique to establish engineered liver grafts and overcome the current shortage of donor organs. However, limited sources of bile duct cells and inappropriate cell distribution in bioengineered liver grafts have hindered their practical application. Organoid technology is anticipated to be an excellent tool for the advancement of regenerative medicine. In the present study, we reconstructed intrahepatic bile ducts in a rat decellularized liver graft by recellularization with liver ductal organoids. Using an ex vivo perfusion culture system, we demonstrated the biliary characteristics of repopulated mouse liver organoids, which maintained bile duct markers and reconstructed biliary tree-like networks with luminal structures. We also established a method for the co-recellularization with engineered bile ducts and primary hepatocytes, revealing the appropriate cell distribution to mimic the native liver. We then utilized this model in human organoids to demonstrate the reconstructed bile ducts. Our results show that liver ductal organoids are a potential cell source for bile ducts from bioengineered liver grafts using three-dimensional scaffolds.
Global landscape of replicative DNA polymerase usage in the human genome
Authors: Koyanagi Eri , Kakimoto Yoko , Yoshifuji Fumiya , Natsume Toyoaki , Higashitani Atsushi , Ogi Tomoo , Carr Antony M. , Kanemaki Masato T. , Daigaku Yasukazu 
Published: November 2021

AbstractThe division of labour among DNA polymerase underlies the accuracy and efficiency of replication. However, the roles of replicative polymerases have not been directly established in human cells. We developed polymerase usage sequence (Pu-seq) in HCT116 cells and mapped Polε and Polα usage genome wide. The polymerase usage profiles show Polε synthesises the leading strand and Polα contributes mainly to lagging strand synthesis. Combining the Polε and Polα profiles, we accurately predict the genome-wide pattern of fork directionality plus zones of replication initiation and termination. We confirm that transcriptional activity contributes to the pattern of initiation and termination and, by separately analysing the effect of transcription on both co-directional and converging forks, demonstrate that coupled DNA synthesis of leading and lagging strands in both co- directional and convergent forks is compromised by transcription. Polymerase uncoupling is particularly evident in the vicinity of large genes, including the two most unstable common fragile sites, FRA3B and FRA3D, thus linking transcription-induced polymerase uncoupling to chromosomal instability.
Tomographic Volumetric Bioprinting of Heterocellular Bone-like Tissues in Seconds
Authors: Gehlen Jenny , Qiu Wanwan , Schädli Gian Nutal , Müller Ralph , Qin Xiao-Hua 
Published: November 2021

AbstractTomographic volumetric bioprinting (VBP) has recently emerged as a powerful tool for rapid solidification of cell-laden hydrogel constructs within seconds. However, its practical applications in tissue engineering requires a detailed understanding of how different printing parameters (concentration of resins, laser dose) affect cell activity and tissue formation. Herein, we explore a new application of VBP in bone tissue engineering by merging a soft gelatin methacryloyl (GelMA) bioresin (<5 kPa) with 3D endothelial co-culture to generate heterocellular bone-like constructs with enhanced functionality. To this, a series of bioresins with varying concentrations of GelMA and lithium Phenyl(2,4,6-trimethylbenzoyl)phosphinate (LAP) photoinitiator were formulated and characterized in terms of photo-reactivity, printability and cell-compatibility. A bioresin with 5% GelMA and 0.05% LAP was identified as the optimal formulation for VBP of complex perfusable constructs within 30 s at high cell viability (>90%). The fidelity was validated by micro-computed tomography and confocal microscopy. Compared to 10% GelMA, this bioresin provided a softer and more permissive environment for osteogenic differentiation of human mesenchymal stem cells (hMSCs). The expression of osteoblastic markers (collagen-I, ALP, osteocalcin) and osteocytic markers (podoplanin, Dmp1) was monitored for 42 days. After 21 days, early osteocytic markers were significantly increased in 3D co-cultures with human umbilical vein endothelial cells (HUVECs). Additionally, we demonstrate VBP of a perfusable, pre-vascularized model where HUVECs self-organized into an endothelium-lined channel. Altogether, this work leverages the benefits of VBP and 3D co-culture, offering a promising platform for fast scaled biofabrication of 3D bone-like tissues with unprecedented functionality.Graphical abstractStatement of significanceThis study explores new strategies for ultrafast bio-manufacturing of bone tissue models by leveraging the advantages of tomographic volumetric bioprinting (VBP) and endothelial co-culture. After screening the properties of a series of photocurable gelatin methacryloyl (GelMA) bioresins, a formulation with 5% GelMA was identified with optimal printability and permissiveness for osteogenic differentiation of human mesenchymal stem cells (hMSC). We then established 3D endothelial co-cultures to test if the heterocellular interactions may enhance the osteogenic differentiation in the printed environments. This hypothesis was evidenced by increased gene expression of early osteocytic markers in 3D co-cultures after 21 days. Finally, VBP of a perfusable cell-laden tissue construct is demonstrated for future applications in vascularized tissue engineering.
Detection, not mortality, constrains the evolution of virulence
Authors: Kennedy David A. 
Published: November 2021

AbstractWhy would a pathogen evolve to kill its hosts when killing a host ends a pathogen’s own opportunity for transmission? A vast body of scientific literature has attempted to answer this question using “trade-off theory,” which posits that host mortality persists due to its cost being balanced by benefits of other traits that correlate with host mortality. The most commonly invoked trade-off is the mortality-transmission trade-off, where increasingly harmful pathogens are assumed to transmit at higher rates from hosts while the hosts are alive, but the pathogens truncate their infectious period by killing their hosts. Here I show that costs of mortality are too small to plausibly constrain the evolution of disease severity except in systems where survival is rare. I alternatively propose that disease severity can be much more readily constrained by a cost of behavioral change due to the detection of infection, whereby increasingly harmful pathogens have increasing likelihood of detection and behavioral change following detection, thereby limiting opportunities for transmission. Using a mathematical model, I show the conditions under which detection can limit disease severity. Ultimately, this argument may explain why empirical support for trade-off theory has been limited and mixed.
Mechanism of glycogen synthase inactivation and interaction with glycogenin
Authors: Marr Laura , Biswas Dipsikha , Daly Leonard A. , Browning Christopher , Vial Sarah , Maskell Daniel P. , Hudson Catherine , Pollard John , Bertrand Jay , Ranson Neil A. , Khatter Heena , Eyers Claire E. , Sakamoto Kei , Zeqiraj Elton 
Published: November 2021

AbstractGlycogen is the major glucose reserve in eukaryotes, and defects in glycogen metabolism and structure lead to disease. Glycogenesis involves interaction of glycogenin (GN) with glycogen synthase (GS), where GS is activated by glucose-6-phosphate (G6P) and inactivated by phosphorylation. We describe the 2.6 Å resolution cryo-EM structure of phosphorylated human GS revealing an autoinhibited GS tetramer flanked by two GN dimers. Phosphorylated N- and C-termini from two GS protomers converge near the G6P-binding pocket and buttress against GS regulatory helices. This keeps GS in an inactive conformation mediated by phospho-Ser641 interactions with a composite “arginine cradle”. Structure-guided mutagenesis perturbing interactions with phosphorylated tails led to increased basal/unstimulated GS activity. We propose that multivalent phosphorylation supports GS autoinhibition through interactions from a dynamic “spike” region, allowing a tuneable rheostat for regulating GS activity. This work therefore provides new insights into glycogen synthesis regulation and facilitates studies of glycogen-related diseases.
Correlational selection and genetic architecture promote the leaf economics spectrum in a perennial grass
Authors: Heckman Robert W. , Bonnette Jason E. , Campitelli Brandon E. , Fay Philip A. , Juenger Thomas E. 
Published: November 2021

AbstractThe leaf economics spectrum (LES) is hypothesized to result from a trade-off between resource acquisition and conservation. Yet few studies have examined the evolutionary mechanisms behind the LES, perhaps because most species exhibit relatively specialized leaf economics strategies. In a genetic mapping population of the phenotypically diverse grassPanicum virgatum, we evaluate two interacting mechanisms that may drive LES evolution: 1) genetic architecture, where multiple traits are coded by the same gene (pleiotropy) or by genes in close physical proximity (linkage), and 2) correlational selection, where selection acts non-additively on combinations of multiple traits. We found evidence suggesting that shared genetic architecture (pleiotropy) controls covariation between two pairs of leaf economics traits. Additionally, at five common gardens spanning 17 degrees of latitude, correlational selection favored particular combinations of leaf economics traits. Together, these results demonstrate how the LES can evolve within species.
Deep Learning-based Automated Rare Sperm Identification from Testes Biopsies
Authors: Lee Ryan , Witherspoon Luke , Robinson Meghan , Lee Jeong Hyun , Duffy Simon P. , Flannigan Ryan , Ma Hongshen 
Published: November 2021

ABSTRACTNon-obstructive azoospermia (NOA), the most severe form of male infertility, is currently treated using microsurgical sperm extraction (microTESE) to retrieve sperm cells for in vitro fertilization via intracytoplasmic sperm injection (IVF-ICSI). The success rate of this procedure for NOA patients is currently limited by the ability of andrologists to identify a few rare sperm cells among millions of background testis cells. To improve this success rate, we developed a convolution neural network (CNN) to detect rare sperm from low-resolution microscopy images of microTESE samples. Our CNN uses the U-Net architecture to perform pixel-based classification on image patches from brightfield microscopy, which is followed by morphological analysis to detect individual sperm instances. This CNN is trained using microscopy images of fluorescently labeled sperm, which is fixed to eliminate their motility, and doped into testis biopsies obtained from NOA patients. We initially tested this algorithm using purified sperm samples at different imaging magnifications in order to determine the upper bounds of performance. We then tested this algorithm by doping rare sperm cells into testis biopsy samples from NOA patients and found a sperm detection F1 score of 85.2%. These results demonstrate the potential to use automated microscopy to dramatically increase the amount of testis biopsy tissue that could be comprehensively examined, which greatly increases the chance of finding rare viable sperm, and thereby increases the success rates of IVF-ICSI for couples with NOA.