bluuebunny/crossref_metadata_2025 huggingface dataset:
Neonatal Transfusion Practice
Authors: Orsi Kelly Cristina Sbampato Calado , Kita Vanessa Yukie , de Souza Adja Havreluk Paiva , Tsunemi Miriam Harumi , Avelar Ariane Ferreira Machado
Published: November 2021

The objective of this study was to verify the influence of the gravitational infusion method or syringe infusion pump on changes in hemolysis markers of irradiated and nonirradiated packed red blood cells (PRBCs) in vitro administered in a neonate peripheral intravenous catheter. An experimental study was conducted in a laboratory under controlled environmental conditions. Irradiated and nonirradiated PRBCs were administered in triplicate by the gravitational method and 10-mL/hour syringe infusion pump, in peripheral intravenous catheter, Vialon, 24-G caliber. Aliquots were collected directly from the PRBC bag, after manual filling of the infusion system and after infusion by the catheters. The following hemolytic markers were analyzed: degree of hemolysis (%), hematocrit (Ht, %), free hemoglobin (fHb, g/dL), potassium (K, mmol/L), and lactate dehydrogenase (LDH, U/L). Mann-Whitney and Student's t tests were used, P ≤ .05. The gravitational method significantly influenced increasing fHb (P = .007), Ht (P = .002), K (P = .002), and LDH (P = .003) values after PRBC irradiated infusion. The infusion of irradiated and non-irradiated PRBCs interferes with changes in hemolytic markers with the gravitational method. Syringe infusion pump proved to be a beneficial and safe alternative to irradiated and nonirradiated PRBC transfusion in newborns.
An Introduction to Neonatal EEG
Authors: Ryan Mary Anne , Mathieson Sean , Dempsey Eugene , Boylan Geraldine
Published: November 2021

Newborn care has witnessed significant improvements in survival, but ongoing concerns persist about neurodevelopmental outcome. Protecting the newborn brain is the focus of neurocritical care in the intensive care unit. Brain-focused care places emphasis on clinical practices supporting neurodevelopment in conjunction with early detection, diagnosis, and treatment of brain injury. Technology now facilitates continuous cot-side monitoring of brain function. Neuromonitoring techniques in neonatal intensive care units include the use of electroencephalography (EEG) or amplitude-integrated EEG (aEEG) and near-infrared spectroscopy. This article aims to provide an introduction to EEG, which is appropriate for neonatal healthcare professionals.
A Systematic Review on Outcomes of Preterm Small for Gestational Infants Born to Women With Hypertensive Disorders in Pregnancy
Authors: Avorgbedor Forgive , Gondwe Kaboni W. , Zou Baiming , Conklin Jamie L. , Yeo Seonae
Published: November 2021

There is a lack of knowledge on the intersection between prematurity, small for gestational age, and hypertensive disorders of pregnancy (HDP). Therefore, the aim of this systematic review was to examine the outcomes of preterm infants who were small for gestational age born to women with HDP. Searches were conducted with no date restriction through the final search date of May 13, 2020, in the following databases: PubMed, Web of Science Core Collection, Cumulative Index of Nursing and Allied Health Literature Plus with Full Text (EBSCOhost), and Embase (Elsevier). A total of 6 studies were eligible for this review. The adjusted odds of mortality and necrotizing enterocolitis were significantly lower in the pregnancy-induced hypertension (PIH)/HDP group than in the non-PIH/HDP group. There was no significant difference in the odds of respiratory distress syndrome, bronchopulmonary dysplasia, and intraventricular hemorrhage between PIH/HDP and non-PIH/HDP groups. There was no significant difference between PIH/HDP and non-PIH/HDP groups in cystic periventricular leukomalacia, retinopathy of prematurity, late-onset sepsis, patent ductus arteriosus, length of hospital stays, duration of supplemental oxygen use, duration of mechanical ventilation, and continuous airway pressure. The studies included in this systematic review demonstrated that PIH/HDP is associated with lower infant mortality and necrotizing enterocolitis.
IRAK1 and IRAK4 as emerging therapeutic targets in hematologic malignancies
Authors: Bennett Joshua , Starczynowski Daniel T.
Published: November 2021

Purpose of review

Cell intrinsic and extrinsic perturbations to inflammatory signaling pathways are a hallmark of development and progression of hematologic malignancies. The interleukin 1 receptor-associated kinases (IRAKs) are a family of related signaling intermediates (IRAK1, IRAK2, IRAK3, IRAK4) that operate at the nexus of multiple inflammatory pathways implicated in the hematologic malignancies. In this review, we explicate the oncogenic role of these kinases and review recent therapeutic advances in the dawning era of IRAK-targeted therapy.

Recent findings

Emerging evidence places IRAK signaling at the confluence of adaptive resistance and oncogenesis in the hematologic malignancies and solid tissue tumors. Preclinical investigations nominate the IRAK kinases as targetable molecular dependencies in diverse cancers.

IRAK-targeted therapies that have matriculated to early phase trials are yielding promising preliminary results. However, studies of IRAK kinase signaling continue to defy conventional signaling models and raise questions as to the design of optimal treatment strategies. Efforts to refine IRAK signaling mechanisms in the malignant context will inspire deliberate IRAK-targeted drug development and informed combination therapy.
Effects of sling exercise therapy on post-stroke walking impairment: a systematic review and meta-analysis
Authors: Long Junzi , Zhang Yasu , Liu Xiaomin , Jin Xiaoqin
Published: November 2021

Walking impairment is a common consequence of stroke, resulting in long-term disability. Trunk muscle strength has been proven to be associated with post-stroke walking performance. As a type of trunk training, sling exercise therapy (SET) has been widely used to improve the trunk function in stroke patients. The purpose of this systematic review was to investigate the efficacy of SET on post-stroke walking impairment. Seven databases were systematically searched for eligible studies from their inception to 1 August 2021. Review Manager 5.3 software was used for this meta-analysis. The overall quality of included studies was evaluated by the physiotherapy evidence database scale. Twenty-five randomized controlled trials involving 1504 patients were included (23 in China and two in South Korea). In summary, SET more effectively improved the walking ability of post-stroke patients than conventional physical therapy or trunk training. The pooled analysis demonstrated that SET had positive effects on the 10 m maximum walking speed, integrated electromyography value of rectus femoris, biceps femoris and gastrocnemius, functional ambulation category, timed up and go test, and step length. At least in East Asia, our findings support SET to manage the post-stroke walking impairment.
Modelling the impact of age-stratified public health measures on SARS-CoV-2 transmission in Canada
Authors: Gabriele-Rivet Vanessa , Spence Kelsey L. , Ogden Nicholas H. , Fazil Aamir , Turgeon Patricia , Otten Ainsley , Waddell Lisa A. , Ng Victoria
Published: November 2021

Public health measures applied exclusively within vulnerable populations have been suggested as an alternative to community-wide interventions to mitigate SARS-CoV-2 transmission. With the population demography and healthcare capacity of Canada as an example, a stochastic age-stratified agent-based model was used to explore the progression of the COVID-19 epidemic under three intervention scenarios (infection-preventing vaccination, illness-preventing vaccination and shielding) in individuals above three age thresholds (greater than or equal to 45, 55 and 65 years) while lifting shutdowns and physical distancing in the community. Compared with a scenario with sustained community-wide measures, all age-stratified intervention scenarios resulted in a substantial epidemic resurgence, with hospital and ICU bed usage exceeding healthcare capacities even at the lowest age threshold. Individuals under the age threshold were severely impacted by the implementation of all age-stratified interventions, with large numbers of avoidable deaths. Among all explored scenarios, shielding older individuals led to the most detrimental outcomes (hospitalizations, ICU admissions and mortality) for all ages, including the targeted population. This study suggests that, in the absence of community-wide measures, implementing interventions exclusively within vulnerable age groups could result in unmanageable levels of infections, with serious outcomes within the population. Caution is therefore warranted regarding early relaxation of community-wide restrictions.
Diversity within the Dickeya zeae complex, identification of Dickeya zeae and Dickeya oryzae members, proposal of the novel species Dickeya parazeae sp. nov.
Authors: Hugouvieux-Cotte-Pattat Nicole , Van Gijsegem Frédérique
Published: November 2021

The genus

Dickeya

comprises plant pathogens that cause diseases in a large range of economically important crops and ornamentals. Strains previously assigned to the species

Dickeya zeae

are major pathogens attacking vital crops such as maize and rice. They are also frequently isolated from surface water. The newly described species

Dickeya oryzae

is closely related to

D. zeae

members, so that the limit between the two species can be difficult to define. In order to clearly distinguish the two species, globally described by the term ‘

D. zeae

complex’, we sequenced the genome of four new water isolates and compared them to 14 genomes available in databases. Calculation of average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) values confirmed the phylogenomic classification into the two species

D. zeae

and

D. oryzae

. It also allowed us to propose a new species, Dickeya parazeae sp. nov., to characterize a clade distinct from those containing the

D. zeae

type strain NCPPB2538T. Strain S31T (CFBP 8716T=LMG 32070T) isolated from water in France is proposed as the type strain of the new species. Phenotypic analysis of eight publically available strains revealed traits common to the five tested

D. oryzae

members but apparently not shared by the

D. oryzae

type strain. Genomic analyses indicated that a simple distinction between the species

D. zeae

, D. parazeae and

D. oryzae

can be obtained on the basis of the recA sequence.

D. oryzae

can be distinguished from the two other species by growth on l-tartaric acid. Based on the recA marker, several strains previously identified as

D. zeae

were re-assigned to the species D. parazeae or

D. oryzae

. This study also highlighted the broad host range diversity of these three species.
Vescimonas gen. nov., Vescimonas coprocola sp. nov., Vescimonas fastidiosa sp. nov., Pusillimonas gen. nov. and Pusillimonas faecalis sp. nov. isolated from human faeces
Authors: Kitahara Maki , Shigeno Yuko , Shime Mari , Matsumoto Yuki , Nakamura Shota , Motooka Daisuke , Fukuoka Shota , Nishikawa Hiroyoshi , Benno Yoshimi
Published: November 2021

Six strains of Gram-stain-negative, obligately anaerobic, non-spore-forming, non-motile rods were isolated from human faeces. Based on phylogenetic characteristics, the six isolates were included in the family

Ruminococcaceae

, and divided into three groups. The six isolates showed 16S rRNA gene sequence similarity values lower than 96.2 % to the closely related species,

Oscillibacter ruminantium

GH1T,

Oscillibacter valericigenes

Sjm18-20T and Dysosmobacter welbiomis J115T. Coherently with the 16S rRNA gene sequence results, the in silico DNA–DNA hybridization and average nucleotide identity values clearly indicated that strains MM35T, MM50T and MM59T belong to different species from the closely related three species. Based on phenotypic features and phylogenetic positions, three novel species, Vescimonas coprocola gen. nov., sp. nov., Vescimonas fastidiosa gen. nov., sp. nov. and Pusillimonas faecalis gen. nov., sp. nov. are proposed. The type strain of V. coprocola is strain MM50T (=JCM 34012T=DSM 111893T). The type strain of V. fastidiosa is strain MM35T (=JCM 34016T=DSM 111899T). The type strain of P. faecalis is strain MM59T (=JCM 34011T=DSM 111669T). The DNA G+C contents estimated according to the whole genomes of strains MM35T, MM50T and MM59T were 56.4, 58.2 and 55.2 mol%, respectively.
Novel circular DNA virus identified in Opuntia discolor (Cactaceae) that codes for proteins with similarity to those of geminiviruses
Authors: Fontenele Rafaela S. , Köhler Matias , Majure Lucas C. , Avalos-Calleros Jesús A. , Argüello-Astorga Gerardo R. , Font Fabián , Vidal Andreza H. , Roumagnac Philippe , Kraberger Simona , Martin Darren P. , Lefeuvre Pierre , Varsani Arvind
Published: November 2021

Viral metagenomic studies have enabled the discovery of many unknown viruses and revealed that viral communities are much more diverse and ubiquitous than previously thought. Some viruses have multiple genome components that are encapsidated either in separate virions (multipartite viruses) or in the same virion (segmented viruses). In this study, we identify what is possibly a novel bipartite plant-associated circular single-stranded DNA virus in a wild prickly pear cactus, Opuntia discolor, that is endemic to the Chaco ecoregion in South America. Two ~1.8 kb virus-like circular DNA components were recovered, one encoding a replication-associated protein (Rep) and the other a capsid protein (CP). Both of the inferred protein sequences of the Rep and CP are homologous to those encoded by members of the family Geminiviridae. These two putatively cognate components each have a nonanucleotide sequence within a likely hairpin structure that is homologous to the origins of rolling-circle replication (RCR), found in diverse circular single-stranded DNA viruses. In addition, the two components share similar putative replication-associated iterative sequences (iterons), which in circular single-stranded DNA viruses are important for Rep binding during the initiation of RCR. Such molecular features provide support for the possible bipartite nature of this virus, which we named utkilio virus (common name of the Opuntia discolor in South America) components A and B. In the infectivity assays conducted in Nicotiana benthamiana plants, only the A component of utkilio virus, which encodes the Rep protein, was found to move and replicate systemically in N. benthamiana. This was not true for component B, for which we did not detect replication, which may have been due to this being a defective molecule or because of the model plants (N. benthamiana) used for the infection assays. Future experiments need to be conducted with other plants, including O. discolor, to understand more about the biology of these viral components.
Lack of evidence for a role of anthrax toxin receptors as surface receptors for collagen VI and for its cleaved off C5 domain (endotrophin)
Authors: Przyklenk Matthias , Heumüller Stefanie Elisabeth , Lütke Steffen , Sengle Gerhard , Koch Manuel , Paulsson Mats , Schiavinato Alvise , Wagener Raimund
Published: November 2021

The widely expressed microfibril-forming collagen VI is subject to proteolytic cleavage and it has been proposed that the cleaved off C-terminal Kunitz domain (C5) of the α3 chain is an adipokine important for tumor progression and fibrosis. Under the name “endotrophin” the C5 fragment has also been shown to be a potent biomarker for fibro-inflammatory diseases. However, the biochemical mechanisms behind endotrophin activity have not been investigated. In earlier studies, the anthrax toxin receptor 1 was found to bind to C5, but this potential interaction has not been further studied. Given the proposed physiological role of endotrophin we aimed to determine how the endotrophin signal is transmitted to the recipient cells. Surprisingly, we could not detect any interaction between endotrophin and anthrax toxin receptor 1 or its close relative, anthrax toxin receptor 2. Moreover, we could not detect binding of fully assembled collagen VI to either anthrax toxin receptor. We also performed similar experiments with the collagen VI surface receptor NG2 (CSPG4). We could confirm that NG2 is a collagen VI receptor that binds to assembled collagen VI, but not to the cleaved C5/endotrophin. A cellular receptor for C5/endotrophin therefore still remains elusive.
Comparative genomics and characterization of SARS-CoV-2 P.1 (Gamma) Variant of Concern (VOC) from Amazonas, Brazil
Authors: Zimerman Ricardo Ariel , Gröhs Ferrareze Patrícia Aline , Cadegiani Flávio Adsuara , Wambier Carlos Gustavo , Fonseca Daniel do Nascimento , de Souza Andrea Roberto , Goren Andy , Rotta Liane Nanci , Ren Zhihua , Thompson Claudia Elizabeth
Published: November 2021

Background

P.1 lineage (Gamma) was first described in the State of Amazonas, northern Brazil, in the end of 2020, and has emerged as a very important variant of concern (VOC) of SARS-CoV-2 worldwide. P.1 has been linked to increased infectivity, higher mortality and immune evasion, leading to reinfections and potentially reduced efficacy of vaccines and neutralizing antibodies.

Methods

The samples of 276 patients from the State of Amazonas were sent to a central referral laboratory for sequencing by gold standard techniques, through Illumina MiSeq platform. Both global and regional phylogenetic analyses of the successfully sequenced genomes were conducted through maximum likelihood method. Multiple alignments were obtained including previously obtained unique human SARS-CoV-2 sequences. The evolutionary histories of spike and non-structural proteins from ORF1a of northern genomes were described and their molecular evolution was analyzed for detection of positive (FUBAR, FEL, and MEME) and negative (FEL and SLAC) selective pressures. To further evaluate the possible pathways of evolution leading to the emergence of P.1, we performed specific analysis for copy-choice recombination events. A global phylogenomic analysis with subsampled P.1 and B.1.1.28 genomes was applied to evaluate the relationship among samples.

Results

Forty-four samples from the State of Amazonas were successfully sequenced and confirmed as P.1 (Gamma) lineage. In addition to previously described P.1 characteristic mutations, we find evidence of continuous diversification of SARS-CoV-2, as rare and previously unseen P.1 mutations were detected in spike and non-structural protein from ORF1a. No evidence of recombination was found. Several sites were demonstrated to be under positive and negative selection, with various mutations identified mostly in P.1 lineage. According to the Pango assignment, phylogenomic analyses indicate all samples as belonging to the P.1 lineage.

Conclusion

P.1 has shown continuous evolution after its emergence. The lack of clear evidence for recombination and the positive selection demonstrated for several sites suggest that this lineage emergence resulted mainly from strong evolutionary forces and progressive accumulation of a favorable signature set of mutations.
Mitonuclear interactions affect locomotor activity and sleep in Drosophila melanogaster
Authors: Anderson Lucy , Camus M. Florencia , Monteith Katy M. , Salminen Tiina S. , Vale Pedro F.
Published: November 2021

Mitochondria are organelles that produce cellular energy in the form of ATP through oxidative phosphorylation, and this primary function is conserved between many taxa. Locomotion is a trait that is highly reliant on metabolic function and expected to be greatly affected by disruptions to mitochondrial performance. To this end, we aimed to examine how activity and sleep vary between Drosophila melanogaster strains with different geographic origins, how these patterns are affected by mitochondrial DNA (mtDNA) variation, and how breaking up co-evolved mito-nuclear gene combinations affect the studied activity traits. The results demonstrate that Drosophila strains from different locations differ in sleep and activity, and the extent of variation differs between sexes, females in general being more active. By comparing activity and sleep of mtDNA variants introgressed onto a common nuclear background in cytoplasmic hybrid (cybrid) strains, we establish that mtDNA variation affects both traits, sex specifically. Furthermore, by using previously published mtDNA copy number data, we detected a positive correlation between mtDNA copy number and the activity levels of the cybrid flies. Altogether, our study shows that both mtDNA variation and mitonuclear interactions affect activity and sleep patterns, highlighting the important role that both genomes play on life-history trait evolution.
Multi-area recordings and optogenetics in the awake, behaving marmoset
Authors: Jendritza Patrick , Klein Frederike J. , Fries Pascal
Published: November 2021

The common marmoset has emerged as a key primate model in neuroscience. Marmosets are small in size, show great potential as transgenic models and exhibit complex behaviors. These advantages place the marmoset model in the critical gap between rodents and larger primates. Thus, it is necessary to develop technology that enables monitoring and manipulation of the neural circuits underlying the behavior of the marmoset. Here, we present a novel approach to record and optogenetically manipulate neural activity in the awake, behaving marmoset. Our design utilizes a light-weight, 3D printed titanium chamber that can house several high-density silicon probes for semi-chronic recordings, while enabling simultaneous optogenetic stimulation. Surgical procedures are streamlined via custom 3D printed guides and implantation holders. We demonstrate the application of our method by recording multi- and single-unit data from areas V1 and V6 with 192 channels simultaneously, and show for the first time that optogenetic activation of excitatory neurons in area V6 can influence behavior in a detection task. Together, the work presented here will support future studies investigating the neural basis of perception and behavior in the marmoset.
Silencing neuronal activity is required for developmental circuit remodeling
Authors: Mayseless Oded , Rachad El Yazid , Shapira Gal , Fiala André , Schuldiner Oren
Published: November 2021

Postnatal refinement of neuronal connectivity shapes the mature nervous system. Pruning of exuberant connections involves both cell autonomous and non-cell autonomous mechanisms, such as neuronal activity. While the role of neuronal activity in the plasticity of excitatory synapses has been extensively studied, the involvement of inhibition is less clear. Furthermore, the role of activity during stereotypic developmental remodeling, where competition is not as apparent, is not well understood.

Here we use the Drosophila mushroom body as a model to show that regulated silencing of neuronal activity is required for developmental axon pruning of the γ-Kenyon cells. We demonstrate that silencing neuronal activity is mechanistically achieved by cell autonomous expression of the inward rectifying potassium channel (irk1) combined with inhibition by the GABAergic APL neuron. These results support the Hebbian-like rule ‘use it or lose it’, where inhibition can destabilize connectivity and promote pruning while excitability stabilizes existing connections.
Examining the Unit Costs of COVID-19 Vaccine Delivery in Kenya
Authors: Orangi Stacey , Kairu Angela , Ngatia Anthony , Ojal John , Barasa Edwine
Published: November 2021

Introduction

Vaccines are considered the path out of the COVID-19 pandemic. The government of Kenya is implementing a phased strategy to vaccinate the Kenyan population, initially targeting populations at high risk of severe disease and infection. We estimated the financial and economic unit costs of procuring and delivering the COVID-19 vaccine in Kenya across various vaccination strategies.

Methods

We used an activity-based costing approach to estimate the incremental costs of COVID-19 vaccine delivery, from a health systems perspective. Document reviews and key informant interviews (n=12) were done to inform the activities, assumptions and the resources required. Unit prices were derived from document reviews or from market prices. Both financial and economic vaccine procurement costs per person vaccinated with 2-doses, and the vaccine delivery costs per person vaccinated with 2-doses were estimated and reported in 2021USD.

Results

The financial costs of vaccine procurement per person vaccinated with 2-doses ranged from $2.89-$13.09 in the 30% and 100% coverage levels respectively, however, the economic cost was $17.34 across all strategies. Financial vaccine delivery costs per person vaccinated with 2-doses, ranged from $4.28-$3.29 in the 30% and 100% coverage strategies: While the economic delivery costs were two to three times higher than the financial costs. The total procurement and delivery costs per person vaccinated with 2-doses ranged from $7.34-$16.47 for the financial costs and $29.7-$24.68 for the economic costs for the 30% and 100% coverage respectively. With the exception of procurement costs, the main cost driver of financial and economic delivery costs was supply chain costs (47-59%) and advocacy, communication and social mobilization (29-35%) respectively.

Conclusion

This analysis presents cost estimates that can be used to inform local policy and may further inform parameters used in cost-effectiveness models. The results could potentially be adapted and adjusted to country-specific assumptions to enhance applicability in similar low-and middle-income settings.
Interferon pathway lupus risk alleles modulate risk of death from acute COVID-19
Authors: Nln Ilona , Fernandez-Ruiz Ruth , Wampler Muskardin Theresa L. , Paredes Jacqueline L. , Blazer Ashira D. , Tuminello Stephanie , Attur Mukundan , Iturrate Eduardo , Petrilli Christopher M. , Abramson Steven B. , Chakravarti Aravinda , Niewold Timothy B.
Published: November 2021

Type I interferon (IFN) is critical in our defense against viral infections. Increased type I IFN pathway activation is a genetic risk factor for systemic lupus erythematosus (SLE), and a number of common risk alleles contribute to the high IFN trait. We hypothesized that these common gain-of-function IFN pathway alleles may be associated with protection from mortality in acute COVID-19. We studied patients admitted with acute COVID-19 (756 European-American and 398 African-American ancestry). Ancestral backgrounds were analyzed separately, and mortality after acute COVID-19 was the primary outcome. In European-American ancestry, we found that a haplotype of interferon regulatory factor 5 (IRF5) and alleles of protein kinase cGMP-dependent 1 (PRKG1) were associated with mortality from COVID-19. Interestingly, these were much stronger risk factors in younger patients (OR=29.2 for PRKG1 in ages 45-54). Variants in the IRF7 and IRF8 genes were associated with mortality from COVID-19 in African-American subjects, and these genetic effects were more pronounced in older subjects. Combining genetic information with blood biomarker data such as C-reactive protein, troponin, and D-dimer resulted in significantly improved predictive capacity, and in both ancestral backgrounds the risk genotypes were most relevant in those with positive biomarkers (OR for death between 14 and 111 in high risk genetic/biomarker groups). This study confirms the critical role of the IFN pathway in defense against COVID-19 and viral infections, and supports the idea that some common SLE risk alleles exert protective effects in anti-viral immunity.

Background

We find that a number of IFN pathway lupus risk alleles significantly impact mortality following COVID-19 infection. These data support the idea that type I IFN pathway risk alleles for autoimmune disease may persist in high frequency in modern human populations due to a benefit in our defense against viral infections.

Translational Significance

We develop multivariate prediction models which combine genetics and known biomarkers of severity to result in greatly improved prediction of mortality in acute COVID-19. The specific associated alleles provide some clues about key points in our defense against COVID-19.
Polyamines and eIF5A hypusination facilitate SREBP2 translation and cholesterol synthesis to enhance enterovirus attachment and infection
Authors: Firpo Mason R. , Petite Marine J. , LoMascolo Natalie J. , Shah Priya S. , Mounce Bryan C.
Published: November 2021

Metabolism is key to cellular processes that underlie the ability of a virus to productively infect. Polyamines are small metabolites vital for many host cell processes including proliferation, transcription, and translation. Polyamine depletion also inhibits virus infection via diverse mechanisms, including inhibiting polymerase activity and viral translation. We showed that Coxsackievirus B3 (CVB3) attachment requires polyamines; however, the mechanism was unknown. Here, we report polyamines’ involvement in translation, through a process called hypusination, promotes expression of cholesterol synthesis genes by supporting SREBP2 translation, the master transcriptional regulator of cholesterol synthesis genes. Measuring bulk transcription, we found polyamines support expression of cholesterol synthesis genes, regulated by SREBP2. Polyamine depletion inhibits CVB3 by depleting cellular cholesterol. Exogenous cholesterol rescues CVB3 attachment, and mutant CVB3 resistant to polyamine depletion exhibits resistance to cholesterol perturbation. This study provides a novel link between polyamine and cholesterol homeostasis, a mechanism through which polyamines impact CVB3 infection.
MutationalPatterns: The one stop shop for the analysis of mutational processes
Authors: Manders Freek , Brandsma Arianne M. , de Kanter Jurrian , Verheul Mark , Oka Rurika , van Roosmalen Markus J. , van der Roest Bastiaan , van Hoeck Arne , Cuppen Edwin , van Boxtel Ruben
Published: November 2021

Background

The collective of somatic mutations in a genome represents a record of mutational processes that have been operative in a cell. These processes can be investigated by extracting relevant mutational patterns from sequencing data.

Results

Here, we present the next version of MutationalPatterns, an R/Bioconductor package, which allows in-depth mutational analysis of catalogues of single and double base substitutions as well as small insertions and deletions. Major features of the package include the possibility to perform regional mutation spectra analyses and the possibility to detect strand asymmetry phenomena, such as lesion segregation. On top of this, the package also contains functions to determine how likely it is that a signature can cause damaging mutations (i.e., mutations that affect protein function). This updated package supports stricter signature refitting on known signatures in order to prevent overfitting. Using simulated mutation matrices containing varied signature contributions, we showed that reliable refitting can be achieved even when only 50 mutations are present per signature. Additionally, we incorporated bootstrapped signature refitting to assess the robustness of the signature analyses. Finally, we applied the package on genome mutation data of cell lines in which we deleted specific DNA repair processes and on large cancer datasets, to show how the package can be used to generate novel biological insights.

Conclusions

This novel version of MutationalPatterns allows for more comprehensive analyses and visualization of mutational patterns in order to study the underlying processes. Ultimately, in-depth mutational analyses may contribute to improved biological insights in mechanisms of mutation accumulation as well as aid cancer diagnostics. MutationalPatterns is freely available at http://bioconductor.org/packages/MutationalPatterns.
Bacterial growth in multicellular aggregates leads to the emergence of complex lifecycles
Authors: Schwartzman Julia A , Ebrahimi Ali , Chadwick Grayson , Sato Yuya , Orphan Victoria , Cordero Otto X
Published: November 2021

In response to environmental stresses such as starvation, many bacteria facultatively aggregate into multicellular structures that can attain new metabolic functions and behaviors. Despite the ubiquity and relevance of this form of collective behavior, we lack an understanding of how the spatiotemporal dynamics of aggregate development emerge from cellular physiology. Here, we show that the coupling between growth and spatial gradient formation leads to the emergence of a complex lifecycle, akin to those known for multicellular bacteria. Under otherwise carbon-limited growth conditions, the marine bacterium Vibrio splendidus 12B01 forms multicellular groups to collectively harvest carbon from the brown-algal polysaccharide alginate. This is achieved during growth on dissolved alginate polymer through formation of spherical, clonal clusters of cells that grow up to 40 µm in radius. Clusters develop striking spatial patterning as they grow due to phenotypic differentiation of sub-populations into a ‘shell’ of static cells surrounding a motile ‘core’. Combining in situ measurements of cell physiology with transcriptomics, we show that shell cells express adhesive type IV pili, while motile core cells express carbon storage granules. The emergence of shell and core phenotypes is cued by opposing gradients of carbon and nitrogen that form within cell clusters due to local metabolic activity. Eventually, the shell ruptures, releasing the carbon-storing core, and we show that carbon-storing cells more readily propagate on alginate than non-carbon storing cells. We propose that phenotypic differentiation promotes the resilience of 12B01 groups by enabling clonal groups to grow larger and propagate more effectively. Phenotypic differentiation may be a widespread, but overlooked, strategy among bacteria to enhance resilience in the context of resource limitation.
Reactivation of Epstein Barr Virus from Latency Involves Increased RNA Polymerase Activity at CTCF Binding Sites on The Viral Genome
Authors: Dunn Laura E. M. , Lu Fang , Su Chenhe , Lieberman Paul M. , Baines Joel D.
Published: November 2021

The ability of Epstein-Barr Virus (EBV) to switch between latent and lytic infection is key to its long-term persistence, yet the molecular mechanisms behind this switch remain unclear. To investigate transcriptional events during the latent to lytic switch we utilized Precision nuclear Run On followed by deep Sequencing (PRO-Seq) to map cellular RNA polymerase (Pol) activity to single-nucleotide resolution on the host and EBV genome in three different models of EBV latency and reactivation. In latently infected Mutu I Burkitt Lymphoma (BL) cells, Pol activity was enriched at the Qp promoter, the EBER region and the BHLF1/LF3 transcripts. Upon reactivation with phorbol ester and sodium butyrate, early phase Pol activity occurred bidirectionally at CTCF sites within the LMP-2A, EBER-1 and RPMS1 loci. PRO-Seq analysis of Akata cells reactivated from latency with anti-IgG and a lymphoblastoid cell-line (LCL) reactivated with small molecule C60 showed a similar pattern of early bidirectional transcription initiating around CTCF binding sites, although the specific CTCF sites and viral genes were different for each latency model. The functional importance of CTCF binding, transcription and reactivation was confirmed using an EBV mutant lacking the LMP-2A CTCF binding site. This virus was unable to reactivate and had disrupted Pol activity at multiple CTCF binding sites relative to WT virus. Overall, these data suggest that CTCF regulates the viral early transcripts during reactivation from latency. These activities likely help maintain the accessibility of the viral genome to initiate productive replication.

Author summary

The ability of EBV to switch between latent and lytic infection is key to its long-term persistence in memory B-cells and its ability to persist in proliferating cells is strongly linked to oncogenesis. During latency, most viral genes are epigenetically silenced, and the virus must overcome this repression to reactivate lytic replication. Reactivation occurs once the immediate early (IE) EBV lytic genes are expressed. However, the molecular mechanisms behind the switch from the latent transcriptional program to begin transcription of the IE genes remain unknown. In this study, we mapped RNA polymerase (Pol) positioning and activity during latency and reactivation. Unexpectedly, Pol activity was not enriched at the IE genes immediately after reactivation but accumulated at distinct regions characteristic of transcription initiation on the EBV genome previously shown to be associated with CTCF. We propose that CTCF binding at these regions retains Pol to maintain a stable latent chromosome conformation and a rapid response to various reactivation signals.
Quorum sensing signal autoinducer-2 inhibits sporulation ofBacillusby interacting with RapC and functions across species
Authors: Xiong Qin , Zhang Huihui , Shu Xia , Sun Xiting , Feng Haichao , Xu Zhihui , Kovács Ákos T. , Liu Yunpeng , Zhang Ruifu
Published: November 2021

Collective behavior of bacteria is regulated by quorum sensing (QS). Bacterial cells sense the density of the population and induce corresponding traits and developmental processes. Autoinducer-2 (AI-2) is a common QS signal that regulates behavior of both Gram-positive and Gram-negative bacteria. In spite of the plethora of processes described to be influenced by AI-2 in diverse Gram-negative bacteria, the AI-2-regulated processes inBacilliare relatively unexplored. Previously, we demonstrated that AI-2 regulates root colonization ofBacillus velezensisSQR9, a well-studied plant beneficial rhizobacterium. Here, we describe a novel function for AI-2 inB. velezensisSQR9 related to development of dormant spores. AI-2 inhibited the initiation of spore development throught the phosphatase RapC and the DNA binding regulator ComA. Using mutant strains and protein-protein interaction studies, we demonstrate that AI-2 interacts with RapC to stimulate its binding to ComA and therefore inactive ComA. We further demonstrate that ComA is essential for Spo0A-regulated sporulation inB. velezensisSQR9. Finally, the AI-2 molecule could be shared cross species for inhibitingBacillussporulation. Our study revealed a novel function and regulation mechanism of AI-2 in sporulation inhibition ofBacillithat overall suggests sporulation to be a population-level decision process inBacillirather than just a individual cell behavior.

Author summary

Quorum sensing (QS) regulates many bacterial social behavior. Bacteria cells could moniter and respond cell density by sensing the self produced QS signals. While most QS signals are unique for either Gram-positive or Gram-negative bacteria, autoinducer-2 (AI-2) is a QS signal that could produced by both bacteria groups. However, knowledge of the mechanism of AI-2 affecting bacterial behavior is poorly understood. Here, we found AI-2 inhibiteBacillus velezensisSQR9 sporulation, a generally known bacterial individual behavior. We further revealed the mechanism of AI-2 influencing sporulation ofB. velezensisSQR9 was dependent on RapC and ComA. AI-2 interacts with RapC to stimulate its binding to ComA and therefore inactive ComA, and then inhibited the Spo0A-regulated sporulation. Interestingly, we showB. velezensisSQR9 could also sense the AI-2 produced by other bacteria and reduce their own sporulation. Taken together we discovered the novel function of AI-2 in sporulation, which will expand the significance of QS signal that they regulate not only social behavior but also individual behavior of bacteria.
Cholesterol and sphingomyelin are critical for Fcγ receptor-mediated phagocytosis of Cryptococcus neoformans by macrophages
Authors: Bryan Arielle M. , You Jeehyun Karen , Li Guangtao , Kim JiHyun , Singh Ashutosh , Morstein Johannes , Trauner Dirk , Pereira de Sá Nívea , Normile Tyler G. , Farnoud Amir M. , London Erwin , Del Poeta Maurizio
Published: November 2021

Cryptococcus neoformans is a fungal pathogen that causes life-threatening meningoencephalitis in lymphopenic patients. Pulmonary macrophages comprise the first line of host defense upon inhalation of fungal spores, whereby macrophages either aid in clearance or serve as a niche for its dissemination. Given that macrophages play a key role in the outcome of a cryptococcal infection, it is crucial to understand factors that mediate phagocytosis of C. neoformans. Since lipid rafts (high order plasma membrane domains enriched in cholesterol and sphingomyelin) have been implicated in facilitating phagocytosis, we evaluated whether these ordered domains govern macrophages’ ability to phagocytose C. neoformans. We found that cholesterol or sphingomyelin depletion resulted in significantly deficient IgG-mediated phagocytosis of the fungus. Moreover, repletion of macrophage cells with a raft-promoting sterol (7-dehydrocholesterol) rescued this phagocytic deficiency while a raft-inhibiting sterol (coprostanol) significantly decreased IgG-mediated phagocytosis of C. neoformans. Using a photoswitchable sphingomyelin (AzoSM), we observed that the raft-promoting conformation (trans-AzoSM) resulted in efficient phagocytosis whereas raft-inhibiting conformation (cis-AzoSM) significantly blunted phagocytosis in a reversible manner. We observed that the effect on phagocytosis may be mediated by facilitating Fcγ receptor (FcγR) function, whereby IgG immune complexes cross-link to FcγRIII, resulting in tyrosine phosphorylation of FcR γ-subunit (FcRγ), an important accessory protein in the FcγR signaling cascade. Correspondingly, cholesterol or sphingomyelin depletion resulted in decreased FcRγ phosphorylation. Repletion with 7-dehydrocholesterol restored phosphorylation, whereas repletion with coprostanol showed FcRγ phosphorylation comparable to unstimulated cells. Together, these data suggest that lipid rafts are critical for facilitating FcγRIII-mediated phagocytosis of C. neoformans.
A Hidden Structural Variation in a Known IRD Gene: A Cautionary Tale of Two New Disease Candidate Genes
Authors: Scott Hilary A , Larson Anna , Rong Shi Song , Mehrotra Sudeep , Butcher Rossano , Chao Katherine R , Wiggs Janey , Place Emily M. , Pierce Eric A , Bujakowska Kinga M
Published: November 2021

Rod cone dystrophy (RCD), also known as retinitis pigmentosa, is an inherited condition leading to vision loss, affecting 1/3500 people. Over 270 genes are known to be implicated in the inherited retinal degenerations (IRDs), yet genetic diagnosis for ~30% IRD of patients remains elusive despite advances in sequencing technologies. The goal of this study was to determine the genetic causality in a family with Rod-cone dystrophy (RCD). Family members were given a full ophthalmic exam at the Retinal Service at MEE and consented to genetic testing. Whole exome sequencing (WES) was performed and variants of interest were Sanger validated. Functional assays were conducted in zebrafish along with splicing assays in relevant cell lines to determine the impact on retinal function.
WES identified variants in two potential candidate genes that segregated with disease: GNL3 (G Protein Nucleolar 3) c.1187+3A>C and c.1568-8C>A; and PDE4DIP (Phosphodiester 4D Interacting Protein) c.3868G>A (p.Glu1290Lys) and c.4603G>A (p.Ala1535Thr). Both genes were promising candidates based on their retinal involvement (development and interactions with IRD-associated proteins), however the functional assays did not validate either gene. Subsequent WES reanalysis with an updated bioinformatics pipeline and widened search parameters led to the detection of a 94bp duplication in PRPF31 (pre-mRNA Processing Factor 31) c.73_266dup (p.Asp56GlyfsTer33) as the causal variant.
Our study demonstrates the importance of thorough functional characterization of new disease candidate genes, and the value of reanalyzing NGS sequence data, which in our case led to identification of a hidden pathogenic variant in a known IRD gene.
Neutron diffraction investigation of copper tellurite glasses with high real-space resolution
Authors: Kaur Navjot , Khanna Atul , Hannon Alex C.
Published: November 2021

High real-space resolution neutron diffraction measurements up to 34 Å−1 were performed on a series of xCuO–(100 − x)TeO2 (x = 30, 40 and 50 mol%) glasses that were synthesized by the melt-quenching technique. The Fourier transformation of neutron diffraction structure factors was used to generate the pair distribution functions, with the first peak at 1.90 Å due to the overlapping Te–O and Cu–O atomic pairs. Reverse Monte Carlo (RMC) simulations were performed on the structure factors and the six partial atomic pair distributions of Cu–Cu, Cu–Te, Cu–O, Te–Te, Te–O and O–O were calculated. The Te–O and Cu–O distributions are very similar and asymmetrical, which revealed that there is a significant short-range disorder in the tellurite network due to the existence of a wide range of Te—O and Cu—O bond lengths. A high-Q (magnitude of momentum transfer function) neutron diffraction study revealed that the average Te–O coordination number decreases steadily from 3.45 to 3.18 with an increase in CuO concentration from 30 to 50 mol% in the glass network. Similar coordination number modifications were earlier found by the RMC analysis of neutron diffraction data sets of copper tellurite glasses that were performed up to lower Q maximum values of 9.5 Å−1. The comparison of high-Q and low-Q neutron diffraction studies reveals that RMC is a powerful and possibly the only technique that is available to elucidate the glass short-range and medium-range structural properties when diffraction data are available up to low Q values of, say, 9.5 Å−1, and when cation–oxygen bond lengths are strongly overlapping and cannot be resolved by Fourier transformation. In situ high-temperature (473 K) neutron diffraction studies of 50CuO–50TeO2 glass revealed that significant distortion of the tellurite network occurs with heating.