bluuebunny/crossref_metadata_2025_split huggingface dataset:
Plasma and wound fluids from trauma patients suppress neutrophil extracellular respiratory burst
Authors: Kim Hyo In , Park Jinbong , Konecna Barbora , Huang Wei , Riça Ingred , Gallo David , Otterbein Leo E. , Itagaki Kiyoshi , Hauser Carl J. 
Published: November 2021

BACKGROUND
Trauma increases susceptibility to secondary bacterial infections. The events suppressing antimicrobial immunity are unclear. Polymorphonuclear neutrophils (PMNs) migrate toward bacteria using chemotaxis, trap them in extracellular neutrophil extracellular traps, and kill them using respiratory burst (RB). We hypothesized that plasma and wound fluids from trauma patients alter PMN function.

METHODS
Volunteer PMNs were incubated in plasma or wound fluids from trauma patients (days 0 and 1, days 2 and 3), and their functions were compared with PMNs incubated in volunteer plasma. Chemotaxis was assessed in transwells. Luminometry assessed total and intracellular RB responses to receptor-dependent and independent stimulants. Neutrophil extracellular trap formation was assessed using elastase assays. The role of tissue necrosis in creating functionally suppressive systemic PMN environments was assessed using a novel pig model where PMNs were incubated in uninjured pig plasma or plasma from pigs undergoing intraperitoneal instillation of liver slurry.

RESULTS
Both plasma and wound fluids from trauma patients markedly suppress total PMN RB. Intracellular RB is unchanged, implicating suppression of extracellular RB. Wound fluids are more suppressive than plasma. Biofluids suppressed RB maximally early after injury and their effects decayed with time. Chemotaxis and neutrophil extracellular trap formation were suppressed by biofluids similarly. Lastly, plasma from pigs undergoing abdominal liver slurry instillation suppressed PMN RB, paralleling suppression by human trauma biofluids.

CONCLUSION
Trauma plasma and wound fluids suppress RB and other key PMNs antimicrobial functions. Circulating suppressive signals can be derived from injured or necrotic tissue at wound sites, suggesting a key mechanism by which tissue injuries can put the host at risk for infection.
Intercostal liposomal bupivacaine injection for rib fractures: A prospective randomized controlled trial
Authors: Wallen Taylor E. , Singer Kathleen E. , Makley Amy T. , Athota Krishna P. , Janowak Christopher F. , Hanseman Dennis , Salvator Ann , Droege Molly E. , Strilka Richard , Droege Christopher A. , Goodman Michael D. 
Published: November 2021

BACKGROUND
Blunt chest wall injury accounts for 15% of trauma admissions. Previous studies have shown that the number of rib fractures predicts inpatient opioid requirements, raising concerns for pharmacologic consequences, including hypotension, delirium, and opioid dependence. We hypothesized that intercostal injection of liposomal bupivacaine would reduce analgesia needs and improve spirometry metrics in trauma patients with rib fractures.

METHODS
A prospective, double-blinded, randomized placebo-control study was conducted at a Level I trauma center as a Food and Drug Administration investigational new drug study. Enrollment criteria included patients 18 years or older admitted to the intensive care unit with blunt chest wall trauma who could not achieve greater than 50% goal inspiratory capacity. Patients were randomized to liposomal bupivacaine or saline injections in up to six intercostal spaces. Primary outcome was to examine pain scores and breakthrough pain medications for 96-hour duration. The secondary endpoint was to evaluate the effects of analgesia on pulmonary physiology.

RESULTS
One hundred patients were enrolled, 50 per cohort, with similar demographics (Injury Severity Score, 17.9 bupivacaine 17.6 control) and comorbidities. Enrolled patients had a mean age of 60.5 years, and 47% were female. Rib fracture number, distribution, and targets for injection were similar between groups. While both groups displayed a decrease in opioid use over time, there was no change in mean daily pain scores. The bupivacaine group achieved higher incentive spirometry volumes over Days 1 and 2 (1095 mL, 1063 mL bupivacaine vs. 900 mL, 866 mL control). Hospital and intensive care unit lengths of stay were similar and there were no differences in postinjection pneumonia, use of epidural catheters or adverse events bet ween groups.

CONCLUSION
While intercostal liposomal bupivacaine injection is a safe method for rib fracture-related analgesia, it was not effective in reducing pain scores, opioid requirements, or hospital length of stay. Bupivacaine injection transiently improved incentive spirometry volumes, but without a reduction in the development of pneumonia.

LEVEL OF EVIDENCE
Therapeutic/care management, Level II.
On biological flow networks: Antagonism between hydrodynamic and metabolic stimuli as driver of topological transitions
Authors: Kramer Felix , Modes Carl D. 
Published: November 2021

AbstractA plethora of computational models have been developed in recent decades to account for the morphogenesis of complex biological fluid networks, such as capillary beds. Contemporary adaptation models are based on optimization schemes where networks react and adapt toward given flow patterns. Doing so, a system reduces dissipation and network volume, thereby altering its final form. Yet, recent numeric studies on network morphogenesis, incorporating uptake of metabolites by the embedding tissue, have indicated the conventional approach to be insufficient. Here, we systematically study a hybrid-model which combines the network adaptation schemes intended to generate space-filling perfusion as well as optimal filtration of metabolites. As a result, we find hydrodynamic stimuli (wall-shear stress) and filtration based stimuli (uptake of metabolites) to be antagonistic as hydrodynamically optimized systems have suboptimal uptake qualities and vice versa. We show that a switch between different optimization regimes is typically accompanied with a complex transition between topologically redundant meshes and spanning trees. Depending on the metabolite demand and uptake capabilities of the adaptating networks, we are further able to demonstrate the existence of nullity re-entrant behavior and the development of compromised phenotypes such as dangling non-perfused vessels and bottlenecks.Author summaryBiological flow networks, such as capillaries, do not grow fully developed and matured in their final and functional form. Instead they grow a rudimentary network which self-organizes bit by bit in the context of their surrounding tissue, perfusion and other stimuli. Interestingly, it has been repeatedly shown that this development is mechano-transductional in nature, coupling complex bio-chemical signaling to mechanical cues such as wall-shear stress. In accordance with previous studies we propose a minimal hybrid model that takes into account stimuli in the form of the actual metabolite uptake of the surrounding tissue and the conventional wall-shear stress approach, and incorporate these into the metabolic cost function scheme. We present a numeric evaluation of our model, displaying the antagonistic interplay of uptake and shear stress driven morphogenesis as well as the topological ramifications and frustrated network formations, i.e. dangling branches, bottlenecks and re-entrant behavior in terms of redundancy transitions.
Cell cycle-dependent chromatin dynamics at replication origins
Authors: Li Yulong , Hartemink Alexander J. , MacAlpine David M. 
Published: November 2021

ABSTRACTOrigins of DNA replication are specified by the ordered recruitment of replication factors in a cell cycle dependent manner. The assembly of the pre-replicative complex in G1 and the pre-initiation complex prior to activation in S-phase are well characterized; however, the interplay between the assembly of these complexes and the local chromatin environment is less well understood. To investigate the dynamic changes in chromatin organization at and surrounding replication origins, we used micrococcal nuclease (MNase) to generate genome-wide chromatin occupancy profiles of nucleosomes, transcription factors and replication proteins through consecutive cell cycles in Saccharomyces cerevisiae. During each G1 phase of two consecutive cell cycles, we observed the downstream repositioning of the origin-proximal +1 nucleosome and an increase in protected DNA fragments spanning the ARS consensus sequence (ACS) indicative of pre-RC assembly. We also found that the strongest correlation between the chromatin occupancy at the ACS and origin efficiency occurred in early S-phase consistent with the rate limiting formation of the Cdc45-Mcm2-7-GINS (CMG) complex being a determinant of origin activity. Finally, we observed nucleosome disruption and disorganization emanating from replication origins and traveling with the elongating replication forks across the genome in S-phase, likely reflecting the disassembly and assembly of chromatin ahead of and behind the replication fork, respectively. These results provide insights into cell cycle-regulated chromatin dynamics and how they relate to the regulation of origin activity.
Rapid nuclear deadenylation of mammalian messenger RNA
Authors: Alles Jonathan , Legnini Ivano , Pacelli Maddalena , Rajewsky Nikolaus 
Published: November 2021

AbstractPoly(A) tails protect RNAs from degradation and their deadenylation rates determine RNA stability. Although poly(A) tails are generated in the nucleus, deadenylation of tails has mostly been investigated within the cytoplasm. Here, we combined long-read sequencing with metabolic labeling, splicing inhibition, and cell fractionation experiments to quantify, separately, the genesis and trimming of nuclear and cytoplasmic tails in vitro and in vivo. We present evidence for genome-wide, nuclear synthesis of tails longer than 200 nt, which are rapidly shortened within minutes after transcription. Our data show that rapid deadenylation is a nuclear process, and that different classes of transcripts and even transcript isoforms have distinct nuclear tail lengths. For example, many long-noncoding RNAs escape rapid nuclear deadenylation. Modelling deadenylation dynamics predicts nuclear deadenylation about 10 times faster than cytoplasmic deadenylation. In summary, our data suggest that nuclear deadenylation is a key mechanism for regulating mRNA stability, abundance, and subcellular localization.
The Delta variant of SARS-CoV-2 maintains high sensitivity to interferons in human lung cells
Authors: Nchioua Rayhane , Schundner Annika , Klute Susanne , Noettger Sabrina , Zech Fabian , Koepke Lennart , Graf Alexander , Krebs Stefan , Blum Helmut , Kmiec Dorota , Frick Manfred , Kirchhoff Frank , Sparrer Konstantin M.J. 
Published: November 2021

AbstractInterferons are a major part of the anti-viral innate defense system. Successful pathogens, including the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), need to overcome these defenses to establish an infection. Early induction of interferons (IFNs) protects against severe coronavirus disease 2019 (COVID-19). In line with this, SARS-CoV-2 is inhibited by IFNs in vitro, and IFN-based therapies against COVID-19 are investigated in clinical trials. However, SARS-CoV-2 continues to adapt to the human population resulting in the emergence of variants characterized by increased transmission fitness and/or decreased sensitivity to preventive or therapeutic measures. It has been suggested that the efficient spread of these so-called “Variants of Concern” (VOCs) may also involve reduced sensitivity to IFNs. Here, we examined whether the four current VOCs (Alpha, Beta, Gamma and Delta) differ in replication efficiency or IFN sensitivity from an early isolate of SARS-CoV-2. All viruses replicated in a human lung cell line and in iPSC-derived alveolar type II cells (iAT2). The Delta variant showed accelerated replication kinetics and higher infectious virus production compared to the early 2020 isolate. Replication of all SARS-CoV-2 VOCs was reduced in the presence of exogenous type I, II and III IFNs. On average, the Alpha variant was the least susceptible to IFNs and the Alpha, Beta and Gamma variants show increased resistance against type III IFN. Although the Delta variant has outcompeted all other variants in humans it remained as sensitive to IFNs as an early 2020 SARS-CoV-2 isolate. This suggests that increased replication fitness rather than IFN resistance may be a reason for its dominance. Our results may help to understand changes in innate immune susceptibility of VOCs, and inform clinical trials exploring IFN-based COVID-19 therapies.
Persistence of Plasmodium cynomolgi hypnozoites in cynomolgus monkey iPS-derived hepatocytes
Authors: Pellisson Mélanie , Zeeman Anne-Marie , Doll Thierry , Kirchhofer-Allan Lucy , Schuierer Sven , Roma Guglielmo , Flannery Erika L. , Mikolajczak Sebastian A. , Kocken Clemens H. M. , Maeser Pascal , Rottmann Matthias , Mueller Matthias 
Published: November 2021

AbstractPlasmodium cynomolgi (Pc) is one of the few parasite species that forms quiescent liver stage parasites known as hypnozoites and is therefore a suitable model for Plasmodium vivax. Very little is known about liver stage dormancy, which hampers the search for compounds with anti-hypnozoite activity. Here, we present the development of a Pc in vitro infection model using stem cell-derived hepatocytes from Macaca fascicularis. IPS cells were established on feeder free condition and differentiated into hepatocytes via inducible overexpression of key transcription factors. The generated hepatocytes were infected with Pc sporozoites and hypnozoite formation as well as schizont development were confirmed by immunofluorescence. This system is a promising tool to study the mechanisms underlying liver stage dormancy and facilitate drug discovery against hypnozoites.
Global Mutational Sweep of SARS-CoV-2: from Chaos to Order
Authors: Wang Xin , Hu Mingda , Jin Yuan , Wang Boqian , Zhao Yunxiang , Liang Long , Yue Junjie , Ren Hongguang 
Published: November 2021

AbstractAnalysis of large-scale genome sequences demonstrates the mutation of SARS-CoV-2 has been undergoing significant sweeps. Driven by emerging variants, global sweeps are accelerated and purified over time. This may prolong the pandemic with repeating epidemics, presenting challenges to the control and prevention of SARS-CoV-2.
Mitogen-activated protein kinases associated sites of tobacco REPRESSION OF SHOOT GROWTH regulates its localization in plant cells
Authors: Wang Luyao , Gui Ying , Yang Bingye , Si Fangjie , Guo Jianhua , Jiang Chunhao 
Published: November 2021

AbstractPlant defense and growth rely on multiple transcriptional factors (TFs). REPRESSION OF SHOOT GROWTH (RSG) is known as one of the important TFs in tobacco (Nicotiana tabacum) with a basic leucine zipper domain. RSG was involved in plant gibberellin feedback regulation by inducing the expression of key genes. The tobacco calcium-dependent protein kinase, CDPK1 was reported to interact with RSG and manipulate its intracellular localization by phosphorylating Ser-114 of RSG. Here, we identified tobacco mitogen-activated protein kinase 3 (NtMPK3) as a RSG interacted protein kinase. Mutation of predicted MAPK-associated phosphorylation site of RSG (Thr-30, Ser-74 and Thr-135) significantly altered the intracellular localization of NtMPK3-RSG interaction complex. Nuclear transport of RSG and its amino acids mutants (T30A and S74A) were observed after treated with plant defense elicitor peptide flg22 in 5 min, while the two mutated RSG swiftly relocalized in tobacco cytoplasm in 30 min. Moreover, triple points mutation of RSG (T30A/S74A/T135A) mimics constant unphosphorylated status, and predominantly localized in tobacco cytoplasm. RSG (T30A/S74A/T135A) showed no relocalization effect under the treatments of either flg22, B. cereus AR156 or GA3, and was impaired in its role as TFs. Our results suggest that MAPK associated phosphorylation sites of RSG regulate its localization in tobacco and constant unphosphorylation of RSG in Thr-30, Ser-74 and Thr-135 keeps RSG predominantly localized in cytoplasm.
Esrra regulates Rplp1-mediated translation of lysosome proteins suppressed in non-alcoholic steatohepatitis and reversed by alternate day fasting
Authors: Tripathi Madhulika , Gauthier Karine , Sandireddy Reddemma , Zhou Jin , Gupta Priyanka , Sakthivel Suganya , Teo Wei Wen , Naing Yadanar Than , Arul Kabilesh , Tikno Keziah , Park Sung-Hee , Wu Yajun , Wang Lijin , Bay Boon-Huat , Sun Lei , Giguere Vincent , Chow Pierce K. H. , Ghosh Sujoy , McDonnell Donald P. , Yen Paul M. , Singh Brijesh K. 
Published: November 2021

AbstractBackgroundCurrently, little is known about the mechanism(s) regulating global and specific protein translation during non-alcoholic steatohepatitis (NASH).MethodsWe used puromycin-labelling, polysome profiling, ChIPseq and ChIP-qPCR, and gene manipulationin vitroand in dietary mouse models of NASH in this study.ResultsUsing unbiased label-free quantitative proteome, puromycin-labelling and polysome profiling, we observed a global decrease in protein translation during lipotoxicity in human primary hepatocytes, mouse hepatic AML12 cells, and livers from a dietary mouse model of NASH. Interestingly, proteomic analysis showed that Rplp1, which regulates ribosome and translation pathways, was one of the most downregulated proteins. Moreover, decreased Esrra expression and binding to the Rplp1 promoter, diminished Rplp1 gene expression during lipotoxicity. This, in turn, reduced global protein translation and Esrra/Rplp1-dependent translation of lysosome (Lamp2, Ctsd) and autophagy (sqstm1, Map1lc3b) proteins. Of note, Esrra did not increase its binding to these gene promoters or their gene transcription, confirming its regulation of their translation during lipotoxicity. Notably, hepatic Esrra-Rplp1-dependent translation of lysosomal and autophagy proteins also was impaired in NASH patients and liver-specificEsrraknockout mice.Remarkably, alternate day fasting induced Essra-Rplp1-dependent expression of lysosomal proteins, restored autophagy, and reduced lipotoxicity, inflammation, and fibrosis in hepatic cell culture andin vivomodels of NASH.ConclusionEsrra regulation of Rplp1-mediated translation of lysosome / autolysosome proteins was downregulated during NASH. Alternate day fasting activated this novel pathway and improved NASH, suggesting that Esrra and Rplp1 may serve as therapeutic targets for NASH. Our findings also provided the first example of a nuclear hormone receptor, Esrra, to not only regulate transcription but also protein translation, via induction of Rplp1.
Genome-wide identification of novel sRNAs in Streptococcus mutans
Authors: Krieger Madeline C , Merritt Justin , Raghavan Rahul 
Published: November 2021

ABSTRACTStreptococcus mutans is a major pathobiont involved in the development of dental caries. Its ability to utilize numerous sugars and to effectively respond to environmental stress promotes S. mutans proliferation in oral biofilms. Because of their quick action and low energetic cost, non-coding small RNAs (sRNAs) represent an ideal mode of gene regulation in stress response networks, yet their roles in oral pathogens have remained largely unexplored. We identified 15 novel sRNAs in S. mutans and show that they respond to four stress-inducing conditions commonly encountered by the pathogen in human mouth: sugar-phosphate stress, hydrogen peroxide exposure, high temperature, and low pH. To better understand the role of sRNAs in S. mutans, we further explored the function of the novel sRNA, SmsR4. Our data demonstrate that SmsR4 regulates the EIIA component of the sorbitol phosphotransferase system, which transports and phosphorylates the sugar alcohol sorbitol. The fine-tuning of EIIA availability by SmsR4 likely promotes S. mutans growth while using sorbitol as the main carbon source. Our work lays a foundation for understanding the role of sRNAs in regulating gene expression in stress response networks in S. mutans and highlights the importance of the underexplored phenomenon of posttranscriptional gene regulation in oral bacteria.IMPORTANCESmall RNAs (sRNAs) are important gene regulators in bacteria, but the identities and functions of sRNAs in Streptococcus mutans, the principal bacterium involved in the formation of dental caries, are unknown. In this study, we identified 15 putative sRNAs in S. mutans and show that they respond to four common stress-inducing conditions present in human mouth: sugar-phosphate stress, hydrogen peroxide exposure, high temperature, and low pH. We further show that the novel sRNA SmsR4 likely modulates sorbitol transport into the cell by regulating SMU_313 mRNA, which encodes the EIIA subunit of the sorbitol phosphotransferase system. Gaining a better understanding of sRNA-based gene regulation may provide new opportunities to develop specific inhibitors of S. mutans growth, thereby improving oral health.
Membrane adaptation in the hyperthermophilic archaeon Pyrococcus furiosus relies upon a novel strategy involving glycerol monoalkyl glycerol tetraether lipids
Authors: Tourte Maxime , Schaeffer Philippe , Grossi Vincent , Oger Philippe M. 
Published: November 2021

AbstractMicrobes preserve membrane functionality under fluctuating environmental conditions by modulating their membrane lipid composition. Although several studies have documented membrane adaptations in Archaea, the influence of most biotic and abiotic factors on archaeal lipid compositions remains underexplored. Here, we studied the influence of temperature, pH, salinity, the presence/absence of elemental sulfur, the carbon source, and the genetic background on the core lipid composition of the hyperthermophilic neutrophilic marine archaeon Pyrococcus furiosus. Every growth parameter tested affected the core lipid composition to some extent, the carbon source and the genetic background having the greatest influence. Surprisingly, P. furiosus appeared to only marginally rely on the two major responses implemented by Archaea, i.e., the regulation of the ratio of diether to tetraether lipids and that of the number of cyclopentane rings in tetraethers. Instead, this species increased the ratio of glycerol monoalkyl glycerol tetraethers (GMGT, aka. H-shaped tetraethers) to glycerol dialkyl glycerol tetrathers (GDGT) in response to decreasing temperature and pH and increasing salinity, thus providing for the first time evidence of adaptive functions for GMGT. Besides P. furiosus, numerous other species synthesize significant proportions of GMGT, which suggests that this unprecedented adaptive strategy might be common in Archaea.Significance statementWe describe here the membrane adaptive strategies the hyperthermophilic, neutrophilic, and marine model archaeon Pyrococcus furiosus implements in response to one of the largest sets of environmental stressors tested to date, including temperature, pH, salinity, presence/absence of elemental sulfur, carbon source, and genetic background. In contrast to the other archaea investigated so far, which response mainly involves the modulation of their diether/tetraether ratio and/or of their average number of cyclopentane rings, P. furiosus regulates its monoalkyl (so called H-shaped) to dialkyl tetraether ratio. Our study thus provides for the first time evidence of adaptive functions of archaeal monoalkyl tetraethers towards low temperature and pH and high salinity.