bluuebunny/crossref_metadata_2025_split huggingface dataset:
Type I IFN promotes pathogenic inflammatory monocyte maturation during H5N1 infection
Authors: Fourati Slim , Jimenez-Morales David , Hultquist Judd , Chang Max W. , Benner Christopher , Krogan Nevan , Pache Lars , Chanda Sumit , Sekaly Rafick-Pierre , García-Sastre Adolfo , Uccellini Melissa B. 
Published: January 2022

AbstractLy6Chi inflammatory monocytes show high IFN responses, and contribute to both protective and pathogenic functions following influenza virus infection. In order to understand the significance of IFN responses in this subset, we examined monocytes during infection with a lethal H5N1 virus that induces high levels of IFN and a low-pathogenicity H1N1 virus that induces low levels of IFN. We show that H5N1 infection results in early recruitment of high numbers of Ly6Chi monocytes and induction of chemokines and Ifnb1. Using unbiased transcriptomic and proteomic approaches, we also find that monocytes are significantly enriched during H5N1 infection and are associated with chemokine and IFN signatures in mice, and with severity of symptoms after influenza virus infection in humans. Recruited Ly6Chi monocytes subsequently become infected in the lung, produce IFN-β, and mature into FasL+ monocyte-derived cells (FasL+MCs) expressing dendritic cell markers. Both Ccr2-/- and Faslgld mice are protected from lethal infection, indicating that monocytes contribute to pathogenesis. Global loss of type I and type III IFN signaling in Stat2-/- mice results in loss of monocyte recruitment, likely reflecting a requirement for IFN-dependent chemokine induction. Here we show that IFN is not directly required for monocyte recruitment on an IFN-sufficient background, but is required for maturation to FasL+MCs. Loss of IFN signaling skews to a Ly6Clo phenotype associated with tissue repair, suggesting that IFN signaling in monocytes is a critical determinant of influenza virus pathogenesis.
COVID-19 policies in practice and their direct and indirect impacts in Northern California jails
Authors: Liu Yiran E. , LeBoa Christopher , Rodriguez Marcela , Sherif Beruk , Trinidad Chrisele , Rosario Michael del , Allen Sophie , Clifford Christine , Redding Jennifer , Chen Wei-ting , Rosas Lisa G. , Morales Carlos , Chyorny Alexander , Andrews Jason R. 
Published: January 2022

ABSTRACTBackgroundAlthough the increased risk of COVID-19 in carceral facilities is well documented, little is known about the practical barriers to infection control and indirect impacts of pandemic policies in these settings. Evidence in jails is especially scarce.MethodsBetween July 8, 2020 and April 30, 2021 we performed SARS-CoV-2 serology testing and administered a questionnaire among residents and staff in four Northern California jails. We analyzed seroprevalence in conjunction with demographic factors and survey responses of self-perceived COVID-19 risk, recent illness, COVID-19 test results, and symptom reporting behaviors. We additionally assessed COVID-19 policies in practice and evaluated their impacts on court dates, mental health, and routine health care. We engaged stakeholder representatives, including incarcerated individuals and their advocates, to guide study design, conduct, and interpretation.ResultsWe enrolled 788 incarcerated individuals and 380 staff across four county jails. Most seropositive individuals had not previously tested positive for COVID-19, despite many suspecting prior infection. Among incarcerated participants, we identified deficient access to face masks and prevalent symptom underreporting associated with fears of isolation and perceptions of medical neglect in jail. Incarcerated participants also reported substantial hindrances to court cases and reductions in routine health care due to COVID-19. Incarcerated individuals and staff both cited worsened mental health due to COVID-19, which for incarcerated individuals was largely attributable to further isolation from loved ones and other pandemic restrictions on recreation and programming.ConclusionPerceptions of inadequate protection from COVID-19 were pervasive among incarcerated individuals. Simultaneously, restrictive measures compounded poor mental health and fostered fears of isolation that undermined effective infection control. Custody officials should work to systematically improve provision of masks, understand and mitigate fears and mistrust, and take proactive steps to minimize the detrimental impacts of restrictive policies on residents’ mental health and well-being.
Immunologic response, Efficacy, and Safety of Vaccines Against COVID-19 Infection in Children and Adolescents Aged 2 – 21 years old: A Systematic Review
Authors: Sadeghi Sara , Kalantari Yasamin , Shokri Sima , Fallahpour Morteza , Nafisi Nahid , Goodarzi Azadeh 
Published: January 2022

AbstractBackgroundsChildren and adolescents form a large proportion of societies and play an important role in the transmission of COVID-19. On the other hand, their education, mental and physical wellness, and safety are compromised which makes vaccination a crucial step to return to normal life.Aims and objectivesTo collect and summarize all data about the immune response, effectiveness, and safety of available COVID-19 vaccines for people aged 2 – 21 years old.MethodsA thorough systematic review was performed on available publications in English language regarding immunogenicity, efficacy, and safety of COVID-19 vaccines in individuals aged 2 – 21 years old. Types of selected studies were clinical trials, observational studies, and cohort. Searched databases comprised Ovid Medline, Cochrane Library, Embase, Scopus, Web of Sciences, Google Scholar, andClinicalTrials.govwebsite. Data extraction and analysis were performed in Microsoft Word software, version 16.56.ResultsThe COVID-19 vaccination was evaluated in a total of 50,148 children and adolescents in 22 published studies and 5,279 participants in two ongoing clinical trials. Data were collected about multiple vaccines including BNT162b2 (Pfizer), mRNA-1273 (Moderna), JNJ-78436735 (Johnson and Johnson), CoronaVac (Sinovac), BBIBP-CorV (Sinopharm), adenovirus type-5-vectored vaccine, ZyCov-D, and BBV152 (COVAXIN). The immune response and efficacy of such vaccines were 96% – 100% in healthy children and adolescents and were also acceptable in those with underlying diseases and suppressed immune systems. The current systematic review revealed favorable safety profiles of employed vaccines in children and adolescents; however, adverse reactions such as myocarditis and myopericarditis were reported which were transient and resolved entirely.ConclusionVaccinating children and adolescents aged 2 – 21 years old is beneficial to abort the COVID-19 pandemic. Moreover, the risk-benefit assessments revealed favorable results for vaccinating children and adolescents, especially those with underlying disease, alongside adults to prevent transmission, severe infection, negative outcomes, and new variants formation.
Precise DNA Cloning via PAMless CRISPR-SpRYgests
Authors: Christie Kathleen A. , Guo Jimmy A. , Silverstein Rachel A. , Doll Roman M. , Mabuchi Megumu , Stutzman Hannah E. , Ma Linyuan , Robb G. Brett , Kleinstiver Benjamin P. 
Published: January 2022

AbstractWhile restriction enzymes (REs) remain the gold-standard for manipulating DNA in vitro, they have notable drawbacks including a dependence on short binding motifs that constrain their ability to cleave DNA substrates. Here we overcome limitations of REs by developing an optimized molecular workflow that leverages the PAMless nature of a CRISPR-Cas enzyme named SpRY to cleave DNA at practically any sequence. Using SpRY for DNA digests (SpRYgests), we establish a method that permits the efficient cleavage of DNA substrates at any base pair. We demonstrate the effectiveness of SpRYgests using more than 130 gRNAs, illustrating the versatility of this approach to improve the precision of and simplify several cloning workflows, including those not possible with REs. We also optimize a rapid and simple one-pot gRNA synthesis protocol, which reduces cost and makes the overall SpRYgest workflow comparable to that of RE digests. Together, SpRYgests are straightforward to implement and can be utilized to improve a variety of DNA engineering applications.
Optimized cell culture conditions promote ex-vivo manipulation and expansion of primitive hematopoietic stem cells for therapeutic gene editing
Authors: Rai Rajeev , Vetharoy Winston , Naseem Asma , Steinberg Zohar , Thrasher Adrian J , Santilli Giorgia , Cavazza Alessia 
Published: January 2022

AbstractDuring the last few years, gene editing has emerged as a powerful tool for the therapeutic correction of monogenic diseases. CRISPR/Cas9 applied to hematopoietic stem and progenitor cells (HSPCs) has shown great promise in proof-of-principle preclinical studies to treat haematological disorders, and clinical trials using these tools are now underway. Nonetheless, there remain important challenges that need to be addressed, such as the efficiency of targeting primitive, long-term repopulating HSPCs and expand them in vitro for clinical purposes. Here we have tested the effect exerted by different culture media compositions on the ability of HSPCs to proliferate and undergo homology directed repair-mediated knock-in of a reporter gene, while preserving their stemness features during ex-vivo culture. We tested different combinations of compounds and demonstrated that by supplementing the culture media with inhibitors of histone deacetylases, and/or by fine-tuning its cytokine composition it is possible to achieve high levels of gene targeting in long-term repopulating HSPCs both in vitro and in vivo, with a beneficial balance between preservation of stemness and cell expansion, thus allowing to obtain a significant amount of edited, primitive HSPCs compared to established, state-of-the-art culture conditions. Overall, the implantation of this optimized ex vivo HSPC culture protocol will improve the efficacy, feasibility and applicability of gene editing and will likely provide one step further to unlock the full therapeutic potential of such powerful technology.
Identification of Salivary Gland Escape Barriers to Western Equine Encephalitis Virus in the Natural Vector, Culex tarsalis
Authors: Stauft Charles B. , Phillips Aaron T. , Wang Tony T. , Olson Kenneth E. 
Published: January 2022

AbstractHerein we describe a previously uninvestigated salivary gland escape barrier (SEB) in Culex tarsalis mosquitoes infected with two different strains of Western equine encephalitis virus (WEEV). The WEEV strains were originally isolated either from mosquitoes (IMP181) or a human patient (McMillan). Both IMP181 and McMillan viruses were fully able to infect the salivary glands of Culex tarsalis after intrathoracic injection as determined by expression of mCherry fluorescent protein. IMP181, however, was better adapted to transmission as measured by virus titer in saliva as well as transmission rates in infected mosquitoes. We used chimeric recombinant WEEV strains to show that inclusion of IMP181-derived structural genes partially circumvents the SEB.Author StatementDuring the first half of the previous century, WEEV was responsible for large outbreaks throughout the northern United States and Canada that caused severe disease in horses and people. Over the past 60 years, cases of WEEV have mysteriously faded and the pathogen is rarely encountered in the clinic today. Salivary gland escape barriers (SEB) are a relatively neglected field of study in arbovirology, and this study provides a valuable contribution to the field by describing a SEB found in otherwise vector competent Culex tarsalis mosquitoes. Although midgut barriers are well studied, less is known about barriers to transmission in the salivary glands. Although salivary gland infection occurs at a high rate following direct injection of virus into the hemocoel, we noticed that only ∼20-30% of infected mosquitoes transmit detectable infectious virus in their saliva. Additionally, although the more pathogenic patient-derived McMillan strain of WEEV infected salivary glands at a similar rate, its transmission was more severely restricted than the mosquito-derived but less pathogenic Imperial 181 strain. We were able to trace determinants of viral transmission to the 6K/E1 region of the gene encoding the viral structural polyprotein. WEEV is a valuable research model for the closely related Eastern equine encephalitis virus and Venezuelan equine encephalitis virus we believe that our findings are applicable to other members of Togaviridae.
Forward masking in a bottlenose dolphin Tursiops truncatus: Dependence on azimuthal positions of the masker and test sources
Authors: Popov Vladimir V. , Nechaev Dmitry I. , Supin Alexander Ya. , Sysueva Evgeniya V. 
Published: January 2022

AbstractForward masking was investigated by the auditory evoked potentials (AEP) method in a bottlenose dolphin Tursiops truncatus using stimulation by two successive acoustic pulses (the masker and test) projected from spatially separated sources. The positions of the two sound sources either coincided with or were symmetrical relative to the head axis at azimuths from 0 to ±90°. AEPs were recorded either from the vertex or from the lateral head surface next to the auditory meatus. In the last case, the test source was ipsilateral to the recording side, whereas the masker source was either ipsi- or contralateral. For lateral recording, AEP release from masking (recovery) was slower for the ipsi-than for the contralateral masker source position. For vertex recording, AEP recovery was equal both for the coinciding positions of the masker and test sources and for their symmetrical positions relative to the head axis. The data indicate that at higher levels of the auditory system of the-dolphin, binaural convergence makes the forward masking nearly equal for ipsi- and contralateral positions of the masker and test.
Structural basis of ion – substrate coupling in the Na+-dependent dicarboxylate transporter VcINDY
Authors: Sauer David B. , Marden Jennifer J. , Sudar Joseph C. , Song Jinmei , Mulligan Christopher , Wang Da-Neng 
Published: January 2022

AbstractThe Na+-dependent dicarboxylate transporter from Vibrio cholerae (VcINDY) is a prototype for the divalent anion sodium symporter (DASS) family. While the utilization of an electrochemical Na+ gradient to power substrate transport is well established for VcINDY, the structural basis of this coupling between sodium and substrate binding is not currently understood. Here, using a combination of cryo-EM structure determination, succinate binding and site-directed cysteine alkylation assays, we demonstrate that the VcINDY protein couples sodium- and substrate-binding via a previously unseen induced-fit mechanism. In the absence of sodium, substrate binding is abolished, with the succinate binding regions exhibiting increased flexibility, including HPinb, TM10b and the substrate clamshell motifs. Upon sodium binding, these regions become structurally ordered and create a proper binding site for the substrate. Taken together, these results provide strong evidence that VcINDY’s induced-fit mechanism is a result of the sodium-dependent formation of the substrate binding site.
EnteroBase: Hierarchical clustering of 100,000s of bacterial genomes into species/sub-species and populations
Authors: Achtman Mark , Zhou Zhemin , Charlesworth Jane , Baxter Laura 
Published: January 2022

AbstractThe definition of bacterial species is traditionally a taxonomic issue while bacterial populations are identified by population genetics. These assignments are species specific, and depend on the practitioner. Legacy multilocus sequence typing is commonly used to identify sequence types (STs) and clusters (ST Complexes). However, these approaches are not adequate for the millions of genomic sequences from bacterial pathogens that have been generated since 2012. EnteroBase (http://enterobase.warwick.ac.uk) automatically clusters core genome MLST allelic profiles into hierarchical clusters (HierCC) after assembling annotated draft genomes from short read sequences. HierCC clusters span core sequence diversity from the species level down to individual transmission chains. Here we evaluate HierCC’s ability to correctly assign 100,000s of genomes to the species/subspecies and population levels for Salmonella, Escherichia, Clostridoides, Yersinia, Vibrio and Streptococcus. HierCC assignments were more consistent with maximum-likelihood super-trees of core SNPs or presence/absence of accessory genes than classical taxonomic assignments or 95% ANI. However, neither HierCC nor ANI were uniformly consistent with classical taxonomy of Streptococcus. HierCC was also consistent with legacy eBGs/ST Complexes in Salmonella or Escherichia and with O serogroups in Salmonella. Thus, EnteroBase HierCC supports the automated identification of and assignment to species/subspecies and populations for multiple genera.
Dendritic branch structure compartmentalizes voltage-dependent calcium influx in cortical layer 2/3 pyramidal cells
Authors: Landau Andrew T. , Park Pojeong , Wong-Campos J. David , Tian He , Cohen Adam E. , Sabatini Bernardo L. 
Published: January 2022

AbstractBack-propagating action potentials (bAPs) regulate synaptic plasticity by evoking voltage-dependent calcium influx throughout dendrites. Attenuation of bAP amplitude in distal dendritic compartments alters plasticity in a location-specific manner by reducing bAP-dependent calcium influx. However, it is not known if neurons exhibit branch-specific variability in bAP-dependent calcium signals, independent of distance-dependent attenuation. Here, we reveal that bAPs fail to evoke calcium influx through voltage-gated calcium channels (VGCCs) in a specific population of dendritic branches in cortical layer 2/3 pyramidal cells, despite evoking substantial VGCC-mediated calcium influx in sister branches. These branches contain VGCCs and successfully propagate bAPs in the absence of synaptic input; nevertheless, they fail to exhibit bAP-evoked calcium influx due to a branch-specific reduction in bAP amplitude. We demonstrate that these branches have more elaborate branch structure compared to sister branches, which causes a local reduction in electrotonic impedance and bAP amplitude. Finally, we show that bAPs still amplify synaptically-mediated calcium influx in these branches because of differences in the voltage-dependence and kinetics of VGCCs and NMDA-type glutamate receptors. Branch-specific compartmentalization of bAP-dependent calcium signals may provide a mechanism for neurons to diversify synaptic tuning across the dendritic tree.
H2A.Z deposition by SWR1C involves multiple ATP-dependent steps
Authors: Fan Jiayi , Moreno Andrew T. , Baier Alexander S. , Loparo Joseph J. , Peterson Craig L. 
Published: January 2022

SummaryThe histone variant H2A.Z is a conserved feature of nucleosomes flanking protein-coding genes. Deposition of H2A.Z requires ATP-dependent replacement of nucleosomal H2A by a chromatin remodeler related to the multi-subunit enzyme, yeast SWR1C. How these enzymes use ATP to promote this nucleosome editing reaction remains unclear. Here we use single-molecule and ensemble methodologies to identify three ATP-dependent phases in the H2A.Z deposition reaction. Real-time analysis of single nucleosome remodeling events reveals an initial, priming step that occurs after ATP addition that likely involves transient DNA unwrapping from the nucleosome. Priming is followed by rapid loss of histone H2A, which is subsequently released from the H2A.Z nucleosomal product. Surprisingly, the rates of both priming and the release of the H2A/H2B dimer are sensitive to ATP concentration. This complex reaction pathway provides multiple opportunities to regulate the timely and accurate deposition of H2A.Z at key genomic locations.
Functional interplay between arginyl-tRNA synthetases and arginyltransferase
Authors: Avcilar-Kucukgoze Irem , Kashina Anna 
Published: January 2022

AbstractProtein arginylation, mediated by arginyltransferase ATE1, is a posttranslational modification of emerging biological importance that consists of transfer of the amino acid Arg to protein and peptide substrates. ATE1 utilizes charged tRNAArg as the donor of the arginyl group, which depends on the activity of Arg-tRNA synthetases (RARS) and is also utilized in translation. The mechanisms that regulate the functional balance between ATE1, RARS and translation are unknown. Here we addressed the functional interplay between these mechanisms using intracellular arginylation sensor in cell lines with overexpression or deletion of ATE1 and RARS isoforms. We find that arginylation levels depend on the physiological state of the cells but are not directly affected by translation activity or availability of RARS isoforms. However, displacement of RARS from the multi-synthetase complex leads to an increase in intracellular arginylation independently of RARS enzymatic activity. This effect is accompanied by ATE1’s redistribution into the cytosol. Our results provide the first comprehensive analysis of the interdependence between translation, arginyl-tRNA synthesis, and arginylation.Key PointsIntracellular arginylation depends on the physiological state of the cell, but does not compete with the translation machineryA fraction of ATE1 binds directly to both long and short Arg-tRNA synthetases (RARS)Displacement of long RARS from the multi-tRNA synthetase complex increases cytosolic fraction and activity of ATE1
Oleic acid-related anti-inflammatory effects in force-stressed PdL fibroblasts are mediated by H3 lysine acetylation associated with altered IL10 expression
Authors: Schuldt Lisa , von Brandenstein Katrin , Jacobs Collin , Symmank Judit 
Published: January 2022

AbstractThe initiation of a spatially and temporally limited inflammation is essential for tissue and bone remodeling by the periodontal ligament (PdL) located between teeth and alveolar bone. Obesity-associated hyperlipidemic changes may impair PdL fibroblast (PdLF) functions, disturbing their inflammatory response to mechanical stress such as those occurring during orthodontic tooth movement (OTM). Recently, we reported an attenuated pro-inflammatory response of human PdLF (HPdLF) to compressive forces when stimulated with monounsaturated oleic acid (OA). Fatty acids, including OA, could serve as alternative source of acetyl-CoA, thereby affecting epigenetic histone marks such as histone 3 lysine acetylation (H3Kac) in a lipid metabolism-dependent manner. In this study, we therefore aimed to investigate the extent to which OA exerts its anti -inflammatory effect via changes in H3Kac. Six-hour compressed HPdLF showed increased H3Kac when cultured with OA. Inhibition of histone deacetylases resulted in a comparable IL10 increase as observed in compressed OA cultures. In contrast, inhibition of histone acetyltransferases, particularly p300/CBP, in compressed HPdLF exposed to OA led to an inflammatory response comparable to compressed control cells. OA-dependent increased association of H3Kac to IL10 promoter regions in force-stressed HPdLF further strengthened the assumption that OA exhibits its anti-inflammatory properties via modulation of this epigenetic mark. In conclusion, our study strongly suggests that obesity-related hyperlipidemia affect the functions of PdL cells via alterations in their epigenetic code. Since epigenetic inhibitors are already widely used clinically, they may hold promise for novel approaches to limit obesity-related risks during OTM.