Mar1, a high mobility group box protein, regulates n-alkane adsorption and cell morphology of the dimorphic yeast Yarrowia lipolytica.

The dimorphic yeast Yarrowia lipolytica possesses an excellent ability to utilize n-alkane as a sole carbon and energy source. Although there are detailed studies on the enzymes that catalyze the reactions in the metabolic processes of n-alkane in Y. lipolytica, the molecular mechanism underlying the incorporation of n-alkane into the cells remains to be elucidated. Because Y. lipolytica adsorbs n-alkane, we postulated that Y. lipolytica incorporates n-alkane through direct interaction with it. We isolated and characterized mutants defective in adsorption to n-hexadecane. One of the mutants harbored a nonsense mutation in MAR1 (Morphology and n-alkane Adsorption Regulator 1) encoding a protein containing a high mobility group box. The deletion mutant of MAR1 exhibited defects in adsorption to n-hexadecane and filamentous growth on solid media, whereas the strain that overexpressed MAR1 exhibited hyperfilamentous growth. Fluorescence microscopic observations suggested that Mar1 localizes in the nucleus. RNA-sequencing analysis revealed the alteration of the transcript levels of several genes, including those encoding transcription factors and cell surface proteins, by the deletion of MAR1. These findings suggest that MAR1 is involved in the transcriptional regulation of the genes required for n-alkane adsorption and cell morphology transition.IMPORTANCEYarrowia lipolytica, a dimorphic yeast capable of assimilating n-alkane as a carbon and energy source, has been extensively studied as a promising host for bioconversion of n-alkane into useful chemicals and bioremediation of soil and water contaminated by petroleum. While the metabolic pathway of n-alkane in this yeast and the enzymes involved in this pathway have been well characterized, the molecular mechanism to incorporate n-alkane into the cells is yet to be fully understood. Due to the ability of Y. lipolytica to adsorb n-alkane, it has been hypothesized that Y. lipolytica incorporates n-alkane through direct interaction with it. In this study, we identified a gene, MAR1, which plays a crucial role in the transcriptional regulation of the genes necessary for the adsorption to n-alkane and the transition of the cell morphology in Y. lipolytica. Our findings provide valuable insights that could lead to advanced applications of Y. lipolytica in n-alkane bioconversion and bioremediation.

A Case of Multiple Brain Tuberculomas in the Subarachnoid Cisterns: Recognition of Radiological Characteristics Regarding the Development of Paradoxical Response during Antituberculosis Treatment.

Brain tuberculoma and its occurrence within the subarachnoid cisterns is rare in Japan. Serological and cerebrospinal fluid (CSF) examinations and imaging findings lack specificity; thus, preoperative diagnosis is often challenging. This report presents the case of a 70-year-old woman admitted to our hospital with a one-month history of low-grade fever and altered mental status. Based on the CSF analysis and her history of latent tuberculosis infection seven years ago, she was strongly suspected of suffering from tuberculous meningitis (TBM). Consequently, the patient was enrolled in a clinical trial for antituberculosis treatment (ATT). CSF soluble interleukin-2 receptor level decreased from 2,926 U/mL on day 1 to 225 U/mL 42 days after initiating ATT. Her condition improved after five weeks; however, contrast-enhanced T1-weighted magnetic resonance imaging (MRI) revealed multiple enhanced lesions within the basal subarachnoid cisterns 25 days after admission. As the number and size of these lesions increased, a biopsy confirmed brain tuberculoma diagnosis, and the treatment was continued. In conclusion, when intracisternal scattered mass lesions are identified during TBM treatment, we should consider the possibility of tuberculoma developments arising from a paradoxical response (PR) during the treatment. Serial MRIs are crucial in monitoring PR development in cisternal tuberculomas, an extension of severe TBM. Finally, a PR can be effectively managed by continuing ATT with adjunctive corticosteroids.

SARS-CoV-2 evolution in the Omicron era.

Since SARS-CoV-2 BA.5 (Omicron) emerged and spread in 2022, Omicron lineages have markedly diversified. Here we review the evolutionary trajectories and processes that underpin the emergence of these lineages, and identify the most prevalent sublineages. We discuss the potential origins of second-generation BA.2 lineages. Simple and complex recombination, antigenic drift and convergent evolution have enabled SARS-CoV-2 to accumulate mutations that alter its antigenicity. We also discuss the potential evolutionary trajectories of SARS-CoV-2 in the future.

Emergence and antibody evasion of BQ, BA.2.75 and SARS-CoV-2 recombinant sub-lineages in the face of maturing antibody breadth at the population level.

BACKGROUND: The Omicron era of the COVID-19 pandemic commenced at the beginning of 2022 and whilst it started with primarily BA.1, it was latter dominated by BA.2 and the related sub-lineage BA.5. Following resolution of the global BA.5 wave, a diverse grouping of Omicron sub-lineages emerged derived from BA.2, BA.5 and recombinants thereof. Whilst emerging from distinct lineages, all shared similar changes in the Spike glycoprotein affording them an outgrowth advantage through evasion of neutralising antibodies. METHODS: Over the course of 2022, we monitored the potency and breadth of antibody neutralization responses to many emerging variants in the Australian community at three levels: (i) we tracked over 420,000 U.S. plasma donors over time through various vaccine booster roll outs and Omicron waves using sequentially collected IgG pools; (ii) we mapped the antibody response in individuals using blood from stringently curated vaccine and convalescent cohorts. (iii) finally we determine the in vitro efficacy of clinically approved therapies Evusheld and Sotrovimab. FINDINGS: In pooled IgG samples, we observed the maturation of neutralization breadth to Omicron variants over time through continuing vaccine and infection waves. Importantly, in many cases, we observed increased antibody breadth to variants that were yet to be in circulation. Determination of viral neutralization at the cohort level supported equivalent coverage across prior and emerging variants with isolates BQ.1.1, XBB.1, BR.2.1 and XBF the most evasive. Further, these emerging variants were resistant to Evusheld, whilst increasing neutralization resistance to Sotrovimab was restricted to BQ.1.1 and XBF. We conclude at this current point in time that dominant variants can evade antibodies at levels equivalent to their most evasive lineage counterparts but sustain an entry phenotype that continues to promote an additional outgrowth advantage. In Australia, BR.2.1 and XBF share this phenotype and, in contrast to global variants, are uniquely dominant in this region in the later months of 2022. INTERPRETATION: Whilst the appearance of a diverse range of omicron lineages has led to primary or partial resistance to clinically approved monoclonal antibodies, the maturation of the antibody response across both cohorts and a large donor pools importantly observes increasing breadth in the antibody neutralisation responses over time with a trajectory that covers both current and known emerging variants. FUNDING: This work was primarily supported by Australian Medical Foundation research grants MRF2005760 (SGT, GM & WDR), Medical Research Future Fund Antiviral Development Call grant (WDR), the New South Wales Health COVID-19 Research Grants Round 2 (SGT & FB) and the NSW Vaccine Infection and Immunology Collaborative (VIIM) (ALC). Variant modeling was supported by funding from SciLifeLab's Pandemic Laboratory Preparedness program to B.M. (VC-2022-0028) and by the European Union's Horizon 2020 research and innovation programme under grant agreement no. 101003653 (CoroNAb) to B.M.

Extended-spectrum antibiotics for community-acquired pneumonia with a low risk for drug-resistant pathogens.

OBJECTIVES: The potential hazards of extended-spectrum antibiotic therapy for patients with community-acquired pneumonia (CAP) with low risk for drug-resistant pathogens (DRPs) remain unclear; however, risk assessment for DRPs is essential to determine the initial antibiotics to be administered. The study objective was to assess the effect of unnecessary extended-spectrum therapy on the mortality of such patients. METHODS: A post hoc analysis was conducted after a prospective multicenter observational study for CAP. Multivariable logistic regression analysis was performed to assess the effect of extended-spectrum therapy on 30-day mortality. Three sensitivity analyses, including propensity score analysis to confirm the robustness of findings, were also performed. RESULTS: Among 750 patients with CAP, 416 with CAP with a low risk for DRPs were analyzed; of these, 257 underwent standard therapy and 159 underwent extended-spectrum therapy. The 30-day mortality was 3.9% and 13.8% in the standard and extended-spectrum therapy groups, respectively. Primary analysis revealed that extended-spectrum therapy was associated with increased 30-day mortality compared with standard therapy (adjusted odds ratio 2.82; 95% confidence interval 1.20-6.66). The results of the sensitivity analyses were consistent with those of the primary analysis. CONCLUSION: Physicians should assess the risk for DRPs when determining the empirical antibiotic therapy and should refrain from administering unnecessary extended-spectrum antibiotics for patients with CAP with a low risk for DRPs.

Controlled introduction of defects into single-walled carbon nanotubes via a fluorination-defluorination strategy using xenon difluoride and their alkaline oxygen reduction reaction catalytic activity.

The defect edges in carbon nanomaterials have attracted attention as catalytic active sites for the oxygen reduction reaction (ORR) of the cathode in electrolyte fuel cells, and the defect control in carbon nanomaterials is becoming increasingly important. This study evaluates a fluorination-defluorination strategy for the controlled introduction of defects into single-walled carbon nanotubes (SWCNTs) involving the fluorination of SWCNTs using xenon difluoride (XeF2) and their subsequent defluorination through thermal annealing. We synthesized fluorinated SWCNTs with different fluorine contents using gaseous XeF2 and annealed the fluorinated SWCNTs at 1000 °C for 3 h under nitrogen gas flow. Structural analyses revealed that SWCNTs derived from fluorinated SWCNTs with low fluorine contents primarily had single point defects. In contrast, SWCNTs derived from fluorinated SWCNTs with high fluorine contents had vacancy defects with edges. According to the ORR catalyst evaluation in alkaline aqueous solution, SWCNTs with edge defects, rather than point defects, can improve the efficiency of ORR catalytic activity. The proposed fluorination-defluorination strategy using gaseous XeF2 is expected to enable the controlled introduction of defects in different types of carbon materials.

Large magnetocapacitance beyond 420% in epitaxial magnetic tunnel junctions with an MgAl2O4 barrier.

Magnetocapacitance (MC) effect has been observed in systems where both symmetries of time-reversal and space-inversion are broken, for examples, in multiferroic materials and spintronic devices. The effect has received increasing attention due to its interesting physics and the prospect of applications. Recently, a large tunnel magnetocapacitance (TMC) of 332% at room temperature was reported using MgO-based (001)-textured magnetic tunnel junctions (MTJs). Here, we report further enhancement in TMC beyond 420% at room temperature using epitaxial MTJs with an MgAl2O4(001) barrier with a cation-disordered spinel structure. This large TMC is partially caused by the high effective tunneling spin polarization, resulted from the excellent lattice matching between the Fe electrodes and the MgAl2O4 barrier. The epitaxial nature of this MTJ system sports an enhanced spin-dependent coherent tunneling effect. Among other factors leading to the large TMC are the appearance of the spin capacitance, the large barrier height, and the suppression of spin flipping through the MgAl2O4 barrier. We explain the observed TMC by the Debye-Fröhlich modelled calculation incorporating Zhang-sigmoid formula, parabolic barrier approximation, and spin-dependent drift diffusion model. Furthermore, we predict a 1000% TMC in MTJs with a spin polarization of 0.8. These experimental and theoretical findings provide a deeper understanding on the intrinsic mechanism of the TMC effect. New applications based on large TMC may become possible in spintronics, such as multi-value memories, spin logic devices, magnetic sensors, and neuromorphic computing.

Treadmill Training for Common Marmoset to Strengthen Corticospinal Connections After Thoracic Contusion Spinal Cord Injury.

Spinal cord injury (SCI) leads to locomotor dysfunction. Locomotor rehabilitation promotes the recovery of stepping ability in lower mammals, but it has limited efficacy in humans with a severe SCI. To explain this discrepancy between different species, a nonhuman primate rehabilitation model with a severe SCI would be useful. In this study, we developed a rehabilitation model of paraplegia caused by a severe traumatic SCI in a nonhuman primate, common marmoset (Callithrix jacchus). The locomotor rating scale for marmosets was developed to accurately assess the recovery of locomotor functions in marmosets. All animals showed flaccid paralysis of the hindlimb after a thoracic contusive SCI, but the trained group showed significant locomotor recovery. Kinematic analysis revealed significantly improved hindlimb stepping patterns in trained marmosets. Furthermore, intracortical microstimulation (ICMS) of the motor cortex evoked the hindlimb muscles in the trained group, suggesting the reconnection between supraspinal input and the lumbosacral network. Because rehabilitation may be combined with regenerative interventions such as medicine or cell therapy, this primate model can be used as a preclinical test of therapies that can be used in human clinical trials.

Chronic pain-induced neuronal plasticity in the bed nucleus of the stria terminalis causes maladaptive anxiety.

The comorbidity of chronic pain and mental dysfunctions such as depression and anxiety disorders has long been recognized, but the underlying mechanisms remain poorly understood. Here, using a mouse model of neuropathic pain, we demonstrated neuronal plasticity in the bed nucleus of the stria terminalis (BNST), which plays a critical role in chronic pain-induced maladaptive anxiety. Electrophysiology demonstrated that chronic pain increased inhibitory inputs to lateral hypothalamus (LH)-projecting BNST neurons. Chemogenetic manipulation revealed that sustained suppression of LH-projecting BNST neurons played a crucial role in chronic pain-induced anxiety. Furthermore, using a molecular genetic approach, we demonstrated that chronic pain elevated the excitability of a specific subpopulation of BNST neurons, which express cocaine- and amphetamine-regulated transcript (CART). The elevated excitability of CART-positive neurons caused the increased inhibitory inputs to LH-projecting BNST neurons, thereby inducing anxiety-like behavior. These findings shed light on how chronic pain induces psychiatric disorders, characterized by maladaptive anxiety.

Preserved intersegmental coordination during locomotion after cervical spinal cord injury in common marmosets.

It is known that primates including human regain some locomotor function after a partial spinal cord injury, but the locomotor pattern is different from before the injury. Although these observations have many implications for improving rehabilitative strategies, these mechanisms are not well understood. In this study, we used a common marmoset hemisection SCI model to examine temporal changes in locomotor pattern, in particular, intersegmental coordination of left hindlimb. Marmoset showed loss of detectable function in the left forelimb and hindlimb after left unilateral hemisection of cervical spinal cord. At two weeks after injury, weight-bearing of the left forelimb during locomotion was limited, but the left hindlimb was able to plantar step. Then marmosets showed gradual recovery in walking ability, but kinematics analysis showed differences in the endpoint trajectory and joint angle movement. Furthermore, intersegmental coordination in left hindlimb represented by planar covariation was preserved over time after the injury. Previous studies have reported that planar covariance is disrupted in patients with stroke or SCI, and that improvement in planarity correlates with recovery in walking ability after rehabilitation. In this study, quadrupedal marmosets were able to walk without loss of balance even after SCI; the different balance needs of bipedal and quadrupedal walkers may lead to differences in planar covariation. Our results show that planar covariation was preserved at all time points after the cervical unilateral hemisection.

Vinyl bag cover method to avoid droplet-containing aerosol escape from endoscopic forceps channel caps during COVID-19 pandemic (with Video 1 and Video 2).

Endoscopists are at high risk of allowing transmission of coronavirus disease 2019 (COVID-19) during gastrointestinal endoscopy (GIE) procedures under pandemic conditions. The main avenues of droplet-containing aerosol generated during GIE are the mouth, anus, and endoscopic forceps channel. Although the usefulness of personal protective equipment for preventing COVID-19 dissemination has been well reported, measures to address infected aerosol escaping during endoscopic forceps use have been neglected. Pathogen-contaminated aerosol from the endoscopic forceps channel, leading into the gastrointestinal lumen, has been confirmed and is a highly problematic source of infection. We developed a technique that entails covering the forceps entry/exit hole with a vinyl bag, thereby preventing contamination of the endoscopy room by the infected aerosol that escapes from this hole. The technique can be used in daily clinical endoscopic practice. Furthermore, this shielding technique is useful for all patients who undergo GIE, regardless of the purpose of the procedure such as for making a diagnosis, administering therapy, or in an urgent situation. In this letter, we introduce our novel, easily performed, inexpensive method of infection prevention by disallowing infected aerosol to escape from a COVID-19-infected patient into the air during a procedure that requires the use of endoscopic forceps.

[Analysis of the Distribution of Community Pharmacies and Pharmacists in Miyagi Prefecture].

In Japan, the aging of the population is serious problem. The Ministry of Health, Labour and Welfare is constructing a new support system for elderly people called "Community-based integrated care system". In this system, community pharmacists are expected to play an important role as healthcare professionals for the whole community, including elderly people. Since pharmacists will be needed to manage community health in addition to their daily tasks, it is required to reassess the distribution of community pharmacies and pharmacists. In this study, we surveyed their distribution in Miyagi prefecture by using statistical data from public institutions and reevaluated the distribution to raise problems. Based on the numbers of community pharmacies and pharmacists per 1000 population in the whole Miyagi prefecture, each area was ranked to 2 categories and analyzed regarding population, aging rate and inhabitable land area. It was disclosed that the higher aging rate areas had the higher rate of category below the average of whole Miyagi prefecture, especially in the number of pharmacists. When the numbers of pharmacies and pharmacists per the inhabitable land area were used, the uneven distribution became clearer than when those per population were used. These findings suggested that it was important to characterize the areas by not only the ratios of community pharmacies and pharmacists to population numbers but also by the aging rates and inhabitable land area, which were related to the work efficiency of pharmacists and accessibility for resident to pharmacies.

Circularly Polarized Luminescence of a Stereogenic Curved Paraphenylene Anchoring a Chiral Binaphthyl in Solution and Solid State.

Invited for the cover of this issue are Masashi Hasegawa, Yoshitane Imai, Yasuhiro Mazaki and co-workers at Kitasato University, Kindai University and Osaka University. The image depicts a stereogenic twisted cycloparaphenylene that exhibits circularly polarized luminescence in a polymethyl methacrylate thin film. Read the full text of the article at 10.1002/chem.202004283.

Circularly Polarized Luminescence of a Stereogenic Curved Paraphenylene Anchoring a Chiral Binaphthyl in Solution and Solid State.

A curved stereogenic [6]paraphenylene ([6]PP), anchoring a chiral binaphthyl scaffold at 7,7'-positions, was prepared and investigated for its properties as a solid-state circularly polarized luminescence (CPL) dye. X-ray analysis revealed a helically twisted structure of PP units induced by axial chirality of binaphthyl framework. The curved [6]PP exhibits fluorescence in powder and polymethyl methacrylate (PMMA) film as well as solution. A significant increase in quantum yield was observed for a non-fluid PMMA film owing the suppression of the molecular motion. The gCPL values of the dye in solution and as PMMA film were almost the same (4.3-4.4×10-3 ) and lager than that in powder. TD-DFT calculations in the excited state suggest that the exciton can be delocalized into a twisted PP unit to produce a larger magnetic transition dipole moment.

Silver Nanoparticles Induce DNA Hypomethylation through Proteasome-Mediated Degradation of DNA Methyltransferase 1.

Nanoparticles are used in many fields and in everyday products. Silver nanoparticles are the most frequently used nanoparticles; for example, in food-related products, owing to their antibacterial activity. However, it has been pointed out that they might have unexpected biological effects, and evaluation of their effects is underway. Although there is a growing body of evidence that nanoparticles can also induce epigenetic changes, there is still little information on the underlying mechanisms. Here, we evaluated changes in DNA methylation induced by silver nanoparticles and attempted to elucidate the induction mechanism. Immunofluorescence staining analysis revealed that silver nanoparticles with a diameter of 10, 50, or 100 nm (nAg10, nAg50, and nAg100, respectively) decreased the content of methylated DNA in A549 alveolar epithelial cells. The level of DNA methyltransferase 1 (Dnmt1) protein, which is involved in maintaining methylation during DNA replication, was significantly decreased, whereas that of Dnmt3b, which is responsible for de novo DNA methylation, was significantly increased by nAg10 treatment. Co-treatment with nAg10 and cycloheximide, which inhibits translation by inhibiting the translocation step of protein synthesis, decreased the level of Dnmt1 in comparison with nAg10-treated A549 cells, indicating a post-translational effect of nAg10. Furthermore, pretreatment with the proteasome inhibitor lactacystin restored the levels of Dnmt1 protein and DNA methylation in nAg10-treated cells. Collectively, these results suggest that nAg10 induced DNA hypomethylation through a proteasome-mediated degradation of Dnmt1.

Benchmarking principal component analysis for large-scale single-cell RNA-sequencing.

BACKGROUND: Principal component analysis (PCA) is an essential method for analyzing single-cell RNA-seq (scRNA-seq) datasets, but for large-scale scRNA-seq datasets, computation time is long and consumes large amounts of memory. RESULTS: In this work, we review the existing fast and memory-efficient PCA algorithms and implementations and evaluate their practical application to large-scale scRNA-seq datasets. Our benchmark shows that some PCA algorithms based on Krylov subspace and randomized singular value decomposition are fast, memory-efficient, and more accurate than the other algorithms. CONCLUSION: We develop a guideline to select an appropriate PCA implementation based on the differences in the computational environment of users and developers.

PUB4, a CERK1-Interacting Ubiquitin Ligase, Positively Regulates MAMP-Triggered Immunity in Arabidopsis.

Lysin motif (LysM) receptor-like kinase CERK1 is a co-receptor essential for plant immune responses against carbohydrate microbe-associated molecular patterns (MAMPs). Concerning the immediate downstream signaling components of CERK1, receptor-like cytoplasmic kinases such as PBL27 and other RLCK VII members have been reported to regulate immune responses positively. In this study, we report that a novel CERK1-interacting E3 ubiquitin ligase, PUB4, is also involved in the regulation of MAMP-triggered immune responses. Knockout of PUB4 resulted in the alteration of chitin-induced defense responses, indicating that PUB4 positively regulates reactive oxygen species generation and callose deposition but negatively regulates MAPK activation and defense gene expression. On the other hand, detailed analyses of a double knockout mutant of pub4 and sid2, a mutant of salicylic acid (SA) synthesis pathway, showed that the contradictory phenotype of the pub4 mutant was actually caused by abnormal accumulation of SA in this mutant and that PUB4 is a positive regulator of immune responses. The present and recent findings on the role of PUB4 indicate that PUB4 is a unique E3 ubiquitin ligase involved in the regulation of both plant immunity and growth/development.

Social vital signs for improving awareness about social determinants of health.

We, Team SAIL, have held sessions introducing social vital signs (SVS). SVS is a useful tool for evaluating patient's social determinants of health (SDH).