Bacterial sensor evolved by decreasing complexity.

Bacterial receptors feed into multiple signal transduction pathways that regulate a variety of cellular processes including gene expression, second messenger levels and motility. Receptors are typically activated by signal binding to ligand binding domains (LBD). Cache domains are omnipresent LBDs found in bacteria, archaea, and eukaryotes, including humans. They form the predominant family of extracytosolic bacterial LBDs and were identified in all major receptor types. Cache domains are composed of either a single (sCache) or a double (dCache) structural module. The functional relevance of bimodular LBDs remains poorly understood. Here, we identify the PacF chemoreceptor in the phytopathogen Pectobacterium atrosepticum that recognizes formate at the membrane distal module of its dCache domain, triggering chemoattraction. We further demonstrate that a family of formate-specific sCache domains has evolved from a dCache domain, exemplified by PacF, by losing the membrane proximal module. By solving high-resolution structures of two family members in complex with formate, we show that the molecular basis for formate binding at sCache and dCache domains is highly similar, despite their low sequence identity. The apparent loss of the membrane proximal module may be related to the observation that dCache domains bind ligands typically at the membrane distal module, whereas the membrane proximal module is not involved in signal sensing. This work advances our understanding of signal sensing in bacterial receptors and suggests that evolution by reducing complexity may be a common trend shaping their diversity. Significance: Many bacterial receptors contain multi-modular sensing domains indicative of complex sensory processes. The presence of more than one sensing module likely permits the integration of multiple signals, although, the molecular detail and functional relevance for these complex sensors remain poorly understood. Bimodular sensory domains are likely to have arisen from the fusion or duplication of monomodular domains. Evolution by increasing complexity is generally believed to be a dominant force. Here we reveal the opposite - how a monomodular sensing domain has evolved from a bimodular one. Our findings will thus motivate research to establish whether evolution by decreasing complexity is typical of other sensory domains.

A mini-resonant photoacoustic sensor based on a sphere-cylinder coupled acoustic resonator for high-sensitivity trace gas sensing.

This paper reports a mini-resonant photoacoustic sensor for high-sensitivity trace gas sensing. The sensor primarily contains a sphere-cylinder coupled acoustic resonator, a cylindrical buffer chamber, and a fiber-optic acoustic sensor. The acoustic field distributions of this mini-resonant photoacoustic sensor and the conventional T-type resonant photoacoustic sensor have been carefully evaluated, showing that the first-order resonance frequency of the present mini-resonant photoacoustic sensor is reduced by nearly a half compared to that of the T-type resonant photoacoustic sensor. The volume of the developed photoacoustic cavity is only about 0.8 cm3. Trace methane is selected as the target analytical gas and a detection limit of 101 parts-per-billion at 100-s integration time has been achieved, corresponding to a normalized noise equivalent absorption (NNEA) coefficient of 1.04 × 10-8 W·cm-1·Hz-1/2. The developed mini-resonant photoacoustic sensor provides potential for high-sensitivity trace gas sensing in narrow spaces.

Hippo/YAP1 promotes osteoporotic mice bone defect repair via the activating of Wnt signaling pathway.

BACKGROUND: This study is to investigate the role and mechanism of Hippo/YAP1 in the repair of osteoporotic bone defects in aged mice, both in vivo and in vitro. METHODS: We investigated the expression differences of the Hippo signaling in young and aged individuals both in vivo and in vitro. By manipulating the expression of Lats1/2 and Yap1, we investigated the role of Hippo/YAP1 in regulating osteogenic differentiation in aged BMSCs. In vivo, by intervening in the local and systemic expression of Lats1/2 and Yap1 respectively, we sought to demonstrate whether Hippo/YAP1 promotes the repair of bone defects in aged osteoporotic conditions. Finally, we delved into the underlying mechanisms of Hippo/YAP1 in regulating osteogenic differentiation. RESULTS: We observed differences in the expression of the Hippo signaling between young and aged individuals. After knocking out Lats1/2 in aged BMSCs, we observed that the upregulation of endogenous YAP1 promotes cellular osteogenic differentiation and proliferation capacity. Through interference with Yap1 expression, we provided strong evidence for the role of Hippo/YAP1 in promoting osteogenic differentiation in aged BMSCs. In vivo, we confirmed that Hippo/YAP1 promotes the repair of bone defects in aging osteoporosis. Moreover, we discovered an interaction relationship among YAP1, ß-catenin, and TEAD1. CONCLUSION: This study elucidates the role of Hippo/YAP1 in promoting the repair of osteoporotic bone defects in aged mice. Mechanistically, YAP1 functions by activating the Wnt/ß-catenin pathway, and this process is not independent of TEAD1.

LATS1/YAP1 Axis Controls Bone Regeneration on Distraction Osteogenesis by Activating Wnt/ß-Catenin.

The Hippo signaling pathway inhibits cell growth, and its components and functions are highly conserved in mammals. LATS1 is a core component of the Hippo signaling pathway associated with lymphatic invasion, astrogliosis, apoptosis, and autophagy. Nevertheless, the role of Hippo/LATS1 in osteogenesis remains unclear. In this study, we used ribonucleic acid (RNA) lentiviruses to inhibit the expression of Lats1 in bone marrow-derived stem cells (BMSCs) and distraction osteogenic regions in rats. Increased osteogenic, proliferative, and migratory abilities of BMSCs were observed in Lats1-inhibited BMSCs, while these phenotypes were partially reversed by YAP1 inhibition. In vivo, we found that the LATS1/YAP1 axis promoted osteogenesis during distraction osteogenesis (DO). ß-catenin was positively correlated with YAP1 expression in vivo and in vitro. When YAP1 was strongly positive in the nucleus, ß-catenin expression was upregulated; when YAP1 expression was inhibited by verteporfin, ß-catenin was not expressed in the nucleus. These findings suggest that the LATS1/YAP1 signaling axis promotes DO by activating the Wnt/ß-catenin signaling pathway. This study provides insights into the molecular mechanism of osteogenesis and a potential therapeutic strategy for bone regeneration in DO by associating with LATS1/YAP1-ß-catenin.

Highly sensitive trace gas detection based on a miniaturized 3D-printed Y-type resonant photoacoustic cell.

We report, what we believe to be, a novel miniaturized 3D-printed Y-type resonant photoacoustic cell (YRPAC) consisting of a frustum of cone-type buffer chamber and a cylindrical resonant chamber. The volume of the designed YRPAC is about 7.0 cm3, which is only about a half of the T-resonant photoacoustic cell (TRPAC). The finite element simulation of the sound field distribution of the TRPAC and YRPAC based on COMSOL shows that the photoacoustic signal is enhanced with the shape of the buffer chamber changing from the traditional cylinder to a frustum of cone. The photoacoustic spectroscopy (PAS) system, utilizing the YRPAC and TRPAC as the photoacoustic reaction units, a 1653.7 nm distributed feedback (DFB) laser as the excitation light source, a cantilever beam acoustic sensor as the acoustic sensing unit, and a high-speed spectrometer as the demodulation unit, has been successfully developed for high-sensitivity trace CH4 sensing. When the CH4 concentration is 1000 ppm, the 2f signal of YRPAC in the first-order resonance mode is 2.3 nm, which is 1.7 times higher than the 2f signal amplitude of TRPAC. The detection sensitivity and minimum detection limit for the PAS system are 2.29 pm/ppm and 52.8 parts per billion (ppb) at 100 s of averaging time. The reported YRPAC has higher sensitivity, smaller size, and faster response time compared to the conventional TRPAC, which can provide a new solution for PAS development.

Origin and functional diversification of PAS domain, a ubiquitous intracellular sensor.

Signal perception is a key function in regulating biological activities and adapting to changing environments. Per-Arnt-Sim (PAS) domains are ubiquitous sensors found in diverse receptors in bacteria, archaea, and eukaryotes, but their origins, distribution across the tree of life, and extent of their functional diversity are not fully characterized. Here, we show that using sequence conservation and structural information, it is possible to propose specific and potential functions for a large portion of nearly 3 million PAS domains. Our analysis suggests that PAS domains originated in bacteria and were horizontally transferred to archaea and eukaryotes. We reveal that gas sensing via a heme cofactor evolved independently in several lineages, whereas redox and light sensing via flavin adenine dinucleotide and flavin mononucleotide cofactors have the same origin. The close relatedness of human PAS domains to those in bacteria provides an opportunity for drug design by exploring potential natural ligands and cofactors for bacterial homologs.

Loop-mediated isothermal amplification (LAMP)/Cas12a assay for detection of Ralstonia solanacearum in tomato.

Introduction: Bacterial wilt (BW) caused by the aerobic, Gram-negative pathogenic species Ralstonia solanacearum (RS) is a major disease impacting commercial agriculture worldwide. Asian phylotype I of RS is the cause of tomato bacterial wilt, which has caused severe economic losses in southern China for many years. An urgent priority in control of bacterial wilt is development of rapid, sensitive, effective methods for detection of RS. Methods: We describe here a novel RS detection assay based on combination of loop-mediated isothermal amplification (LAMP) and CRISPR/Cas12a. crRNA1, with high trans-cleavage activity targeting hrpB gene, was selected out of four candidate crRNAs. Two visual detection techniques, involving naked-eye observation of fluorescence and lateral flow strips, were tested and displayed high sensitivity and strong specificity. Results and Discussion: The LAMP/Cas12a assay accurately detected RS phylotype Ⅰ in 14 test strains, and showed low detection limit (2.0 × 100 copies). RS in tomato stem tissue and soil samples from two field sites with suspected BW infection was identified accurately, suggesting potential application of LAMP/Cas12a assay as point-of-care test (POCT). The overall detection process took less than 2 h and did not require professional lab equipment. Our findings, taken together, indicate that LAMP/Cas12a assay can be developed as an effective, inexpensive technique for field detection and monitoring of RS.

Transmembrane Transcription Regulators Are Widespread in Bacteria and Archaea.

To adapt and proliferate, bacteria must sense and respond to the ever-changing environment. Transmembrane transcription regulators (TTRs) are a family of one-component transcription regulators that respond to extracellular information and influence gene expression from the cytoplasmic membrane. How TTRs function to modulate expression of their target genes while localized to the cytoplasmic membrane remains poorly understood. In part, this is due to a lack of knowledge regarding the prevalence of TTRs among prokaryotes. Here, we show that TTRs are highly diverse and prevalent throughout bacteria and archaea. Our work demonstrates that TTRs are more common than previously appreciated and are enriched within specific bacterial and archaeal phyla and that many TTRs have unique transmembrane region properties that can facilitate association with detergent-resistant membranes. IMPORTANCE One-component signal transduction systems are the major class of signal transduction systems among bacteria and are commonly cytoplasmic. TTRs are a group of unique one-component signal transduction systems that influence transcription from the cytoplasmic membrane. TTRs have been implicated in a wide array of biological pathways critical for both pathogens and human commensal organisms but were considered to be rare. Here, we demonstrate that TTRs are in fact highly diverse and broadly distributed in bacteria and archaea. Our findings suggest that transcription factors can access the chromosome and influence transcription from the membrane in both archaea and bacteria. This study challenges thus the commonly held notion that signal transduction systems require a cytoplasmic transcription factor and highlights the importance of the cytoplasmic membrane in directly influencing signal transduction.

Photoactive Yellow Protein Represents a Distinct, Evolutionarily Novel Family of PAS Domains.

Photoactive yellow protein (PYP) is a model photoreceptor. It binds a p-coumaric acid as a chromophore, thus enabling blue light sensing. The first discovered single-domain PYP from Halorhodospira halophila has been studied thoroughly in terms of its structural dynamics and photochemical properties. However, the evolutionary origins and biological role of PYP homologs are not well understood. Here, we show that PYP is an evolutionarily novel domain family of the ubiquitous PAS (Per-Arnt-Sim) superfamily. It likely originated from the phylum Myxococcota and was then horizontally transferred to representatives of a few other bacterial phyla. We show that PYP is associated with signal transduction either by domain fusion or by genome context. Key cellular functions modulated by PYP-initiated signal transduction pathways likely involve gene expression, motility, and biofilm formation. We identified three clades of the PYP family, one of which is poorly understood and potentially has novel functional properties. The Tyr42, Glu46, and Cys69 residues that are involved in p-coumaric acid binding in the model PYP from H. halophila are well conserved in the PYP family. However, we also identified cases where substitutions in these residues might have led to neofunctionalization, such as the proposed transition from light to redox sensing. Overall, this study provides definition, a newly built hidden Markov model, and the current genomic landscape of the PYP family and sets the stage for the future exploration of its signaling mechanisms and functional diversity. IMPORTANCE Photoactive yellow protein is a model bacterial photoreceptor. For many years, it was considered a prototypical model of the ubiquitous PAS domain superfamily. Here, we show that, in fact, the PYP family is evolutionarily novel, restricted to a few bacterial phyla and distinct from other PAS domains. We also reveal the diversity of PYP-containing signal transduction proteins and their potential mechanisms.

Mechanical, antibacterial, biocompatible and microleakage evaluation of glass ionomer cement modified by nanohydroxyapatite/polyhexamethylene biguanide.

This study aims to look for the best concentration of nanohydroxyapatite (NHA) and polyhexamethylene biguanide (PHMB) incorporated into glass ionomer cement (GIC) in accordance with ISO:9917-1 and evaluate its mechanical, antibacterial, biocompatible and microleakages properties. NHA was incorporated into Fuji Ⅱ GIC powder at 0-8.00 wt% concentration and specimens were prepared; the best concentration was sifted out according to ISO9917-1. Based on best NHA proportion, 0-0.80% PHMB was dispersed into powder and samples were respectively prepared. Mechanical properties include net setting time (ST), compressive strength (CS), microhardness (VNH), solubility and scanning electron microscopy (SEM) observation. Those met ISO standard were qualified to continue microleakage observation, antibacterial activity, and biocompatibility test. The results suggested that GIC/6%NHA/0.2% PHMB and GIC/6%NHA/0.4%PHMB showed great performances in mechanical, antibacterial, and microleakage improvements, and the cytotoxicity of modified GIC showed no statistical difference with pure GIC.

Effectiveness of virtual simulation and jaw model for undergraduate periodontal teaching.

BACKGROUND: The current study explored the effect of virtual simulation and jaw model on development of preclinical periodontal skills in undergraduate students. The study also sought to explore effectiveness of VR in periodontal preclinical training and determine adequate performance mode in basic periodontal education to improve future preclinical training strategies. METHODS: Sixty volunteer sophomores and juniors from the stomatology department in Lanzhou university were enrolled to the current study. Participants were randomly assigned into four groups (each group, n = 15) including the traditional jaw model group (Group J) which was the control group, virtual reality group (Group V), virtual-jaw group (Group V-J), and jaw-virtual group (Group J-V). Participants received training on uniform basic periodontal knowledge before completing the first theoretical assessment. Participants further underwent a total 8 h of operation training and completed a second theoretical assessment. Performance of participants was evaluated using the supragingival scaling processes, and clinical operation scores were graded by a blinded professional using an established standard scoring system. RESULTS: The findings showed no significant difference in the first theoretical outcomes between the four groups (P > 0.05). The scores of the second theoretical assessment were significantly improved for the V-J and J-V groups (60.00 ± 4.47, 58.33 ± 4.35) compared with the scores of the first theoretical exam (49.67 ± 4.81, 48.00 ± 4.93, P < 0.05). The operation process scores of students in Group V-J and J-V (72.00 ± 5.92; 70.00 ± 3.05) were significantly higher compared with the scores in the other two groups (V: 61.67 ± 7.85; J: 60.67 ± 2.58). The scaling process performance of students in Group V-J and J-V (53.00 ± 3.05; 63.40 ± 4.39) was improved compared with that of students in the other two groups (V: 41.90 ± 5.23; J: 47.40 ± 4.31). CONCLUSION: The findings show that combination of virtual reality and jaw model during periodontal preclinical training increases students' grades and improves acquiring of professional skills. Findings from the current study indicate that the jaw model should be applied prior to virtual reality to ensure high efficacy.

Satisfaction with life and depressive symptoms in living organ donors and non-donors: New insights from the National Living Donor Assistance Center.

BACKGROUND: Previous studies indicate there may be psychological consequences of being unable to serve as a living donor, but these have not been explored in a large national cohort of low-income individuals who initiated living donor evaluation in US transplant centers. METHODS: Using data from 6574 National Living Donor Assistance Center (NLDAC) participants (November 1, 2007-December 31, 2018), we utilized a cross-sectional study design to evaluate short-term depressive symptoms and satisfaction with life in living donors and non-donors (those who were declined or withdrew from evaluation) using the Satisfaction with Life Scale (SWLS) and the PHQ-8, with and without risk adjustment using linear regression. RESULTS: National Living Donor Assistance Center participants originated from 207 US transplant centers. 52% of NLDAC participants responded to the survey (n = 3423; donors = 2848 (58.6% of all donors), non-donors = 575 (33.5% of all non-donors); ncenters  = 201)). Respondents were significantly older, more likely to be female, white, non-Hispanic, married, more educated, more full-time employed, and more likely to be unrelated to the recipient vs non-respondents (all, P < .001). Among survey respondents, donors were significantly younger, more likely to be non-Hispanic, employed, and related to the recipient compared to non-donors (all, P < .05). Higher PHQ-8 scores were correlated with lower SWL scores (r = -.32, P < .001). Both groups displayed high SWLS (donors vs non-donors: 27.1 vs 26.3, P = .002). Both groups had low levels of depressive symptoms overall, but donors had more symptoms than non-donors (3.5 vs 2.4, P < .001). After risk adjustment, non-donors had significantly less depressive symptoms by PHQ-8 (28% lower, P < .001), but had lower life satisfaction (1.2 points lower, P < .001). CONCLUSIONS: Donors and non-donors have high global levels of overall life satisfaction and low levels of depressive symptoms at 8 weeks after donation or denial. While small effect sizes were observed between groups in these outcomes, being a non-donor was an independent risk factor for lower life satisfaction, which warrants further evaluation.

Best practices to optimize utilization of the National Living Donor Assistance Center for the financial assistance of living organ donors.

Living organ donors face direct costs when donating an organ, including transportation, lodging, meals, and lost wages. For those most in need, the National Living Donor Assistance Center (NLDAC) provides reimbursement to defray travel and subsistence costs associated with living donor evaluation, surgery, and follow-up. While this program currently supports 9% of all US living donors, there is tremendous variability in its utilization across US transplant centers, which may limit patient access to living donor transplantation. Based on feedback from the transplant community, NLDAC convened a Best Practices Workshop on August 2, 2018, in Arlington, VA, to identify strategies to optimize transplant program utilization of this valuable resource. Attendees included team members from transplant centers that are high NLDAC users; the NLDAC program team; and Advisory Group members. After a robust review of NLDAC data and engagement in group discussions, the workgroup identified concrete best practices for administrative and transplant center leadership involvement; for individuals filing NLDAC applications at transplant centers; and to improve patient education about potential financial barriers to living organ donation. Multiple opportunities were identified for intervention to increase transplant programs' NLDAC utilization and reduce financial burdens inhibiting expansion of living donor transplantation in the United States.

Return on investment for financial assistance for living kidney donors in the United States.

BACKGROUND: The National Living Donor Assistance Center (NLDAC) enables living donor kidney transplants through financial assistance of living donors, but its return on investment (ROI) through savings on dialysis costs remains unknown. METHODS: We retrospectively reviewed 2012-2015 data from NLDAC, the United States Renal Data System, and the Scientific Registry of Transplant Recipients to construct 1-, 3-, and 5-year ROI models based on NLDAC applications and national dialysis and transplant cost data. ROI was defined as state-specific federal dialysis cost minus (NLDAC program costs plus state-specific transplant cost), adjusted for median waiting time (WT). RESULTS: A total of 2425 NLDAC applications were approved, and NLDAC costs were USD $6.76 million. Median donor age was 41 years, 66.1% were female, and median income was $33 759; 43.6% were evaluated at centers with WT >72 months. Median dialysis cost/patient-year was $81 485 (IQR $74 489-$89 802). Median kidney transplant cost/patient-year was $30 101 (IQR $26 832-$33 916). Overall, ROI varied from 5.1-fold (1-year) to 28.2-fold (5-year), resulting in $256 million in savings. Higher ROI was significantly associated with high WT, larger dialysis and transplant costs differences, and more NLDAC applicants completing the donation process. CONCLUSIONS: Financial support for donor out-of-pocket expenses produces dramatic federal savings through incremental living donor kidney transplants.

Solid-phase extraction with the metal-organic framework MIL-101(Cr) combined with direct analysis in real time mass spectrometry for the fast analysis of triazine herbicides.

MIL-101(Cr) is an excellent metal-organic framework with high surface area and nanoscale cavities, making it promising in solid-phase extraction. Herein, we used MIL-101(Cr) as a solid-phase extraction packing material combined with fast detection of direct analysis in real time mass spectrometry (DART-MS) for the analysis of triazine herbicides. After systematic optimization of the operation parameters, including the gas temperature of DART, the moving speed of the 1D platform, solvent for desorption, amount of MIL-101(Cr) extraction time, eluent volume and salt concentration, this method can realize the simultaneous detection of five kinds of triazine herbicides. The limits of detection were 0.1∼0.2 ng/mL and the linear ranges covered more than two orders of magnitude with the quantitation limits of 0.5∼1 ng/mL. Moreover, the developed method has been applied for the analysis of lake water samples and the recoveries for spiked analytes were in the range of 85∼110%. These results showed that solid-phase extraction with metal-organic frameworks is an efficient sample preparation approach for DART-MS analysis and could find more applications in environmental analysis.

Membrane-based continuous remover of trifluoroacetic acid in mobile phase for LC-ESI-MS analysis of small molecules and proteins.

We developed a "continuous" trifluoroacetic acid (TFA) remover based on electrodialysis with bipolar membrane for online coupling of liquid chromatography (LC) and electrospray ionization mass spectrometry (ESI-MS) using TFA containing mobile phase. With the TFA remover as an interface, the TFA anion in the mobile phase was removed based on electrodialysis mechanism, and meanwhile, the anion exchange membrane was self-regenerated by the hydroxide ions produced by the bipolar membrane. So the remover could continuously work without any additional regeneration process. The established LC-TFA remover-MS system has been successfully applied for the qualitative and quantitative analysis of small molecules as well as proteins.