Over the past decade, quasicrystalline order has been observed in many soft-matter systems: in dendritic micelles, in star and tetrablock terpolymer melts and in diblock copolymer and surfactant ...micelles. The formation of quasicrystals from such a broad range of 'soft' macromolecular micelles suggests that they assemble by a generic mechanism rather than being dependent on the specific chemistry of each system. Indeed, micellar softness has been postulated and shown to lead to quasicrystalline order. Here we theoretically explore this link by studying two-dimensional hard disks decorated with step-like square-shoulder repulsion that mimics, for example, the soft alkyl shell around the aromatic core in dendritic micelles. We find a family of quasicrystals with 10-, 12-, 18- and 24-fold bond orientational order which originate from mosaics of equilateral and isosceles triangles formed by particles arranged core-to-core and shoulder-to-shoulder. The pair interaction responsible for these phases highlights the role of local packing geometry in generating quasicrystallinity in soft matter, complementing the principles that lead to quasicrystal formation in hard tetrahedra. Based on simple interparticle potentials, quasicrystalline mosaics may well find use in diverse applications ranging from improved image reproduction to advanced photonic materials.
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DOBA, IJS, IZUM, KILJ, KISLJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Understanding the mechanical properties and porosity of reproductive tissues is vital for regenerative medicine and tissue engineering. This study investigated the changes in Young's modulus (YM), ...storage modulus (E'), loss modulus (E"), and porosity of native and decellularized bovine reproductive tissues during the estrous cycle. Testis tunica albuginea had significantly higher YM, E', and E" than the inner testis, indicating greater stiffness and viscoelasticity. Endometrium showed no distinct differences in YM, E', or E" across the estrous cycle or between horns. Ovaries exhibited significant variations in YM, E', E", and porosity, with higher YM and E' in the ipsilateral cortex and medulla during the luteal phase. Decellularized ovarian tissues displayed increased porosity. The oviduct displayed no significant differences in YM or E' in the isthmus, but the contralateral ampulla had reduced YM and E' in the luteal phase. These findings offer valuable insights into the dynamic mechanical properties and porosity of reproductive tissues, facilitating the development of biomimetic scaffolds for tissue engineering applications.
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IZUM, KILJ, NUK, PILJ, PNG, SAZU, UL, UM, UPUK
The COVID-19 pandemic presents unique requirements for accessible, reliable testing, and many testing platforms and sampling techniques have been developed over the course of the pandemic. Not all ...test methods have been systematically compared to each other or a common gold standard, and the performance of tests developed in the early epidemic have not been consistently re-evaluated in the context of new variants. We conducted a repeated measures study with adult healthcare workers presenting for SARS-CoV-2 testing. Participants were tested using seven testing modalities. Test sensitivity was compared using any positive PCR test as the gold standard. A total of 325 individuals participated in the study. PCR tests were the most sensitive (saliva PCR 0.957 ± 0.048, nasopharyngeal PCR 0.877 ± 0.075, oropharyngeal PCR 0.849 ± 0.082). Standard nasal rapid antigen tests were less sensitive but roughly equivalent (BinaxNOW 0.613 ± 0.110, iHealth 0.627 ± 0.109). Oropharyngeal rapid antigen tests were the least sensitive (BinaxNOW 0.400 ± 0.111, iHealth brands 0.311 ± 0.105). PCR remains the most sensitive testing modality for the diagnosis of COVID-19 and saliva PCR is significantly more sensitive than oropharyngeal PCR and equivalent to nasopharyngeal PCR. Nasal AgRDTs are less sensitive than PCR but have benefits in convenience and accessibility. Saliva-based PCR testing is a viable alternative to traditional swab-based PCR testing for the diagnosis of COVID-19.
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IZUM, KILJ, NUK, PILJ, PNG, SAZU, UL, UM, UPUK
The bacterium
is capable of two kinds of flagellum-mediated motility: swimming, which occurs in liquid, and swarming, which occurs on a surface. Swarming is distinct from swimming in that it requires ...secretion of a surfactant, an increase in flagellar density, and perhaps additional factors. Here we report a new gene,
, located within the 32 gene
operon dedicated to flagellar biosynthesis and chemotaxis, which when mutated abolished swarming motility. SwrD was not required for surfactant production, flagellar gene expression, or an increase in flagellar number. Instead, SwrD was required to increase flagellar power. Mutation of
reduced swimming speed and torque of tethered flagella, and all
-related phenotypes were restored when the stator subunits MotA and MotB were overexpressed either by spontaneous suppressor mutations or by artificial induction. We conclude that swarming motility requires flagellar power in excess of that which is needed to swim.
Bacteria swim in liquid and swarm over surfaces by rotating flagella, but the difference between swimming and swarming is poorly understood. Here we report that SwrD of
is necessary for swarming because it increases flagellar torque and cells mutated for
swim with reduced speed. How flagellar motors generate power is primarily studied in
, and SwrD likely increases power in other organisms, like the
,
,
, and the
.
NusA and NusG are transcription factors that stimulate RNA polymerase pausing in
. While NusA was known to function as an intrinsic termination factor in
, the role of NusG in this process was ...unknown. To examine the individual and combinatorial roles that NusA and NusG play in intrinsic termination, Term-seq was conducted in wild type, NusA depletion, Δ
, and NusA depletion Δ
strains. We determined that NusG functions as an intrinsic termination factor that works alone and cooperatively with NusA to facilitate termination at 88% of the 1400 identified intrinsic terminators. Our results indicate that NusG stimulates a sequence-specific pause that assists in the completion of suboptimal terminator hairpins with weak terminal A-U and G-U base pairs at the bottom of the stem. Loss of NusA and NusG leads to global misregulation of gene expression and loss of NusG results in flagella and swimming motility defects.
Summary
Multicellular development requires the careful orchestration of gene expression to correctly create and position specialized cells. In the filamentous cyanobacterium Anabaena sp. strain PCC ...7120, nitrogen‐fixing heterocysts are differentiated from vegetative cells in a reproducibly periodic and physiologically relevant pattern. While many genetic factors required for heterocyst development have been identified, the role of HetZ has remained unclear. Here, we present evidence to clarify the requirement of hetZ for heterocyst production and support a model where HetZ functions in the patterning stage of differentiation. We show that a clean, nonpolar deletion of hetZ fails to express the developmental genes hetR, patS, hetP and hetZ correctly and fails to produce heterocysts. Complementation and overexpression of hetZ in a hetP mutant revealed that hetZ was incapable of bypassing hetP, suggesting that it acts upstream of hetP. Complementation and overexpression of hetZ in a hetR mutant, however, demonstrated bypass of hetR, suggesting that it acts downstream of hetR and is capable of bypassing the need for hetR for differentiation irrespective of nitrogen status. Finally, protein–protein interactions were observed between HetZ and HetR, Alr2902 and HetZ itself. Collectively, this work suggests a regulatory role for HetZ in the patterning phase of cellular differentiation in Anabaena.
Anabaena sp. strain PCC 7120 differentiates nitrogen‐fixing heterocysts from vegetative cells in a reproducibly periodic and physiologically relevant pattern. HetZ is known to impact heterocyst development. In this study, we clarify the placement of HetZ in the genetic program controlling development and find that it acts downstream of HetR, the master regulator of differentiation and upstream of HetP, a factor involved in the commitment to a differentiated cell fate, at the transition between patterning and commitment.
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BFBNIB, FZAB, GIS, IJS, KILJ, NLZOH, NUK, OILJ, SAZU, SBCE, SBMB, UL, UM, UPUK
Flagellin (Hag) is one of the most abundant proteins in
Here we show that each flagellar filament is assembled from ∼12,000 Hag monomers and that there is a cytoplasmic pool of Hag that is restricted ...to 5% of the total. Hag is thought to be restricted at the level of translation by a partner-switching mechanism involving FliW and the homodimeric RNA-binding protein CsrA (CsrA
). We further show that the mechanism of translation inhibition is hypersensitive due to a 1:1 ratio of Hag to FliW, a 1:1 inhibitory ratio of FliW to CsrA
, and a nearly 1:1 ratio of CsrA
to
transcripts. Equimolarity of all components couples single-molecule detection of Hag export to compensatory translation and causes cytoplasmic Hag concentrations to oscillate around the level of FliW. We found that stoichiometry is ensured by genetic architecture, translational coupling, and the ability of CsrA
to restrict
transcript accumulation. We further show that homeostasis prevents Hag hyperaccumulation that would otherwise cause severe defects in intracellular architecture, perhaps due to increased molecular crowding. We note that FliW-CsrA-mediated structural homeostasis has similarities to that seen with some toxin-antitoxin systems.
The intracellular concentration of flagellar filament protein Hag is restricted by the Hag-FliW-CsrA system in
Here we show that the Hag-FliW-CsrA
system functions at nearly 1:1:1 stoichiometry and that the system is both robust with respect to perturbation and hypersensitive to the Hag intracellular concentration. Moreover, restriction of cytoplasmic Hag levels is important for maintaining proper intracellular architecture, as artificial Hag hyperaccumulation led to generalized spatial defects and a high frequency of minicell production. The Hag-FliW-CsrA system is conserved in the deeper branches of bacterial phylogeny, and we note that the Hag-FliW-CsrA "homeostasis module" resembles a toxin-antitoxin system where, by analogy, CsrA is the "toxin," FliW is the "antitoxin," and Hag is the target.
Abstract Background The purpose of this study was to evaluate the diagnostic value of dual-energy computed tomography (DECT) in detecting lymph node (LN) metastasis in patients with colorectal ...cancer. Methods Data from 81 LNs from 28 patients with colorectal adenocarcinoma were retrospectively analyzed. All patients received DECT before surgery without any neoadjuvant therapy. The diagnostic value was assessed using the iodine concentration (IC). Results In the pathological findings, 35 (43.2%) LNs from 13 patients were metastatic and 46 (56.8%) LNs from 17 patients were non-metastatic. The mean IC of metastatic LNs in the portal venous phase (PP) was 1.60 mg/ml, which was significantly lower compared with non-metastatic LNs (3.25 mg/ml, p < 0.001). Receiver operating characteristic (ROC) analysis revealed that the IC in PP had the highest ability to discriminate LN metastasis (area under the ROC curve AUC 0.932). The sensitivity, specificity, positive predictive value, negative predictive value, and accuracy of IC in PP (cutoff 2.1 mg/ml) were 87.0%, 88.6%, 85.3%, 90.0%, and 87.9%, respectively. When clinically obvious metastatic LNs in conventional CT findings were excluded, 50 LNs remained (5 metastatic and 45 non-metastatic LNs). In this subgroup analysis, the IC in PP remained the most powerful predictor of metastatic LNs (cutoff: 2.1 mg/ml, AUC 0.933). Conclusions The evaluation of IC in DECT may improve the diagnostic capabilities of discriminating metastatic LNs. This method may be particularly useful when conventional CT findings lead to equivocal results.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UL, UM, UPCLJ, UPUK
SUMMARY We previously revealed that Japanese encephalitis virus (JEV) seroprevalence was 4.5% in pigs on Ishigaki Island from 2005 to 2007. However, a partial E gene sequence (151 bp) of the JEV ...genome (JEV/sw/Ishigaki/1/2005) was detected in one pig. Phylogenetic analysis showed that JEV/sw/Ishigaki/1/2005 belonged to genotype III and to the same lineages isolated in Taiwan from 2006 to 2008. Serum samples were collected from 128 pigs on Ishigaki from 2009 to 2010, 24 wild boars on Ishigaki from 2008 to 2010, and 117 wild boars on Iriomote Island from 2008 to 2010. Four (3.1%) pigs on Ishigaki were positive for JEV antibody, but all wild boars on the island were negative. Fifty-two (44.4%) wild boars on Iriomote were positive for JEV antibody, in contrast to a seroprevalence of 3.7% in 2000 and 2004. JEV on Iriomote and/or in Taiwan might be related to transmission on Ishigaki.
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BFBNIB, NMLJ, NUK, PNG, SAZU, UL, UM, UPUK
This paper outlines the methods and results for monitoring forest change and resulting carbon emissions for the 1990–2000 and 200–2005 periods carried out over tropical Central and South America. To ...produce our forest change estimates we used a systematic sample of medium resolution satellite data processed to forest change maps covering 1230 sites of 20 km by 20 km, each located at the degree confluence. Biomass data were spatially associated to each individual sample site so that annual carbon emissions could be estimated. For our study area we estimate that forest cover in the study area had fallen from 763 Mha (s.e. 10 Mha) in 1990 to 715 Mha (s.e. 10 Mha) in 2005. During the same period other wooded land (i.e., non-forest woody vegetation) had fallen from 191 Mha (s.e. 5.5 Mha) to 184 Mha (s.e. 5.5 Mha). This equates to an annual gross loss of 3.74 Mha∙y−1 of forests (0.50% annually) between 1990 and 2000, rising to 4.40 Mha∙y−1 in the early 2000s (0.61% annually), with Brazil accounting for 69% of the total losses. The annual carbon emissions from the combined loss of forests and other wooded land were calculated to be 482 MtC∙y−1 (s.e. 29 MtC∙y−1) for the 1990s, and 583 MtC∙y−1 (s.e. 48 MtC∙y−1) for the 2000 to 2005 period. Our maximum estimate of sinks from forest regrowth in tropical South America is 92 MtC∙y−1. These estimates of gross emissions correspond well with the national estimates reported by Brazil, however, they are less than half of those reported in a recent study based on the FAO country statistics, highlighting the need for continued research in this area.
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