Co-transcriptional folding of the glmS ribozyme enables a rapid response to metabolite.

The glmS ribozyme riboswitch, located in the 5' untranslated region of the Bacillus subtilis glmS messenger RNA (mRNA), regulates cell wall biosynthesis through ligand-induced self-cleavage and decay of the glmS mRNA. Although self-cleavage of the refolded glmS ribozyme has been studied extensively, it is not known how early the ribozyme folds and self-cleaves during transcription. Here, we combine single-molecule fluorescence with kinetic modeling to show that self-cleavage can occur during transcription before the ribozyme is fully synthesized. Moreover, co-transcriptional folding of the RNA at a physiological elongation rate allows the ribozyme catalytic core to react without the downstream peripheral stability domain. Dimethyl sulfate footprinting further revealed how slow sequential folding favors formation of the native core structure through fraying of misfolded helices and nucleation of a native pseudoknot. Ribozyme self-cleavage at an early stage of transcription may benefit glmS regulation in B. subtilis, as it exposes the mRNA to exoribonuclease before translation of the open reading frame can begin. Our results emphasize the importance of co-transcriptional folding of RNA tertiary structure for cis-regulation of mRNA stability.

Co-phase separation of Y14 and RNA in vitro and its implication for DNA repair.

The multifunctional RNA recognition motif-containing protein Y14/RBM8A participates in mRNA metabolism and is essential for the efficient repair of DNA double-strand breaks (DSBs). Y14 contains highly charged, low-complexity sequences in both the amino- and carboxy-terminal domains. The feature of charge segregation suggests that Y14 may undergo liquid-liquid phase separation (LLPS). Recombinant Y14 formed phase-separated droplets, which were sensitive to pH and salt concentration. Domain mapping suggested that LLPS of Y14 involves multivalent electrostatic interactions and is partly determined by the net charge of its low-complexity regions. Phospho-mimicry of the carboxy-terminal arginine-serine dipeptides of Y14 suppressed phase separation. Moreover, RNA could phase separate into Y14 droplets and modulate Y14 LLPS in a concentration-dependent manner. Finally, the capacity of Y14 in LLPS and coacervation with RNA in vitro correlated with its activity in DSB repair. These results reveal a molecular rule for LLPS of Y14 in vitro and an implication for its co-condensation with RNA in genome stability.

Structural basis of transcriptional activation by the OmpR/PhoB-family response regulator PmrA.

PmrA, an OmpR/PhoB-family response regulator, triggers gene transcription responsible for polymyxin resistance in bacteria by recognizing promoters where the canonical-35 element is replaced by the pmra-box, representing the PmrA recognition sequence. Here, we report a cryo-electron microscopy (cryo-EM) structure of a bacterial PmrA-dependent transcription activation complex (TAC) containing a PmrA dimer, an RNA polymerase σ70 holoenzyme (RNAPH) and the pbgP promoter DNA. Our structure reveals that the RNAPH mainly contacts the PmrA C-terminal DNA-binding domain (DBD) via electrostatic interactions and reorients the DBD three base pairs upstream of the pmra-box, resulting in a dynamic TAC conformation. In vivo assays show that the substitution of the DNA-recognition residue eliminated its transcriptional activity, while variants with altered RNAPH-interacting residues resulted in enhanced transcriptional activity. Our findings suggest that both PmrA recognition-induced DNA distortion and PmrA promoter escape play crucial roles in its transcriptional activation.

Novel kinase 1 regulates CD8+T cells as a potential therapeutic mechanism for idiopathic pulmonary fibrosis.

Idiopathic pulmonary fibrosis (IPF) is a rare, chronic and progressively worsening lung disease that poses a significant threat to patient prognosis, with a mortality rate exceeding that of some common malignancies. Effective methods for early diagnosis and treatment remain for this condition are elusive. In our study, we used the GEO database to access second-generation sequencing data and associated clinical information from IPF patients. By utilizing bioinformatics techniques, we identified crucial disease-related genes and their biological functions, and characterized their expression patterns. Furthermore, we mapped out the immune landscape of IPF, which revealed potential roles for novel kinase 1 and CD8+T cells in disease progression and outcome. These findings can aid the development of new strategies for the clinical diagnosis and treatment of IPF.

Granulomatous lobular mastitis co-existing with ductal carcinoma in situ: Report of three cases and review of the literature.

Granulomatous lobular mastitis (GLM) is a benign and infrequent chronic breast ailment. Although this lesion can be clinically and radiographically mistaken for early-onset breast cancer, it is a rare occurrence for the two to coexist. This report describes three such cases. In all three patients, the primary signs and symptoms were related to the formation of diffuse breast masses or abscesses. Breast ultrasound and MRI revealed glandular edema and dilated breast ducts. The biopsies of all lesions exhibited both granulomatous inflammation confined to the lobules of the breast, abundant interstitial inflammatory cell infiltrates, and apparently cancerous cells located in dilated ducts with intact basement membranes. The surgically excised specimens confirmed the diagnosis of GLM and ductal carcinoma in situ (DCIS) in all three patients who underwent breast mass resection. By clinical imaging and clinical manifestations, GLM may obscure a concurrent DCIS, as highlighted by the cases reported herein.

A West Nile virus nonlocal model with free boundaries and seasonal succession.

The paper deals with a West Nile virus (WNv) model, in which the nonlocal diffusion characterizes the long-range movement of birds and mosquitoes, the free boundaries describe their spreading fronts, and the seasonal succession accounts for the effect of the warm and cold seasons. The well-posedness of the mathematical model is established, and its long-term dynamical behaviours, which depend upon the generalized eigenvalues of the corresponding linearized differential operator, are investigated. For both spatially independent and nonlocal WNv models with seasonal successions, the generalized eigenvalues are studied and applied to determine whether the spreading or vanishing occurs. Our results extend those for the case with nonlocal diffusion but no free boundary and those for the case with free boundary but local diffusion, respectively. The generalized eigenvalues reveal that there exists positive correlation between the duration of the warm season and the risk of infection. Moreover, the initial infection length, the initial infection scale and the spreading ability to new areas all play important roles for the long time behaviors of the time dependent solutions.

Human mobility and disease prevalence.

We examine the effect of human mobility on disease prevalence by studying the dependence of the total infected population at endemic equilibria with respect to population diffusion rates of a diffusive epidemic model. For small diffusion rates, our results indicate that the total infected population size is strictly decreasing with respect to the ratio of the diffusion rate of the infected population over that of the susceptible population. Moreover, when the disease local reproductive function is spatially heterogeneous, we found that: (i) for large diffusion rate of the infected population, the total infected population size is strictly maximized at large diffusion rate of the susceptible population when the recovery rate is spatially homogeneous, while it is strictly maximized at intermediate diffusion rate of the susceptible population when the difference of the transmission and recovery rates are spatially homogeneous; (ii) for large diffusion rate of the susceptible population, the total infected population size is strictly maximized at intermediate diffusion rate of the infected population when the recovery rate is spatially homogeneous, while it is strictly minimized at large diffusion rate of the infected population when the difference of the transmission and recovery rates is spatially homogeneous. Numerical simulations are provided to complement the theoretical results. Our studies may provide some insight into the impact of human mobility on disease outbreaks and the severity of epidemics.

Directed movement changes coexistence outcomes in heterogeneous environments.

Understanding mechanisms of coexistence is a central topic in ecology. Mathematical analysis of models of competition between two identical species moving at different rates of symmetric diffusion in heterogeneous environments show that the slower mover excludes the faster one. The models have not been tested empirically and lack inclusions of a component of directed movement toward favourable areas. To address these gaps, we extended previous theory by explicitly including exploitable resource dynamics and directed movement. We tested the mathematical results experimentally using laboratory populations of the nematode worm, Caenorhabditis elegans. Our results not only support the previous theory that the species diffusing at a slower rate prevails in heterogeneous environments but also reveal that moderate levels of a directed movement component on top of the diffusive movement allow species to coexist. Our results broaden the theory of species coexistence in heterogeneous space and provide empirical confirmation of the mathematical predictions.

Total biomass of a single population in two-patch environments.

For the two-patch logistic model, we study the effect of dispersal intensity and dispersal asymmetry on the total population abundance and its distribution. Two complete classifications of the model parameter space are given: one concerning when dispersal causes smaller or larger total biomass than no dispersal, and the other addressing how the total biomass changes with dispersal intensity and dispersal asymmetry. The dependencies of the population abundance of each individual patch on dispersal intensity and dispersal asymmetry are also fully characterized. In addition, the maximal and minimal total population sizes induced by dispersal are determined for the logistic model with an arbitrary number of patches, and a weak order-preserving result correlated the local population abundances with and without dispersal is established.

Decreased Serum Wnt Antagonist Levels in Patients With Active Acromegaly.

OBJECTIVE: The Wnt signaling pathway is an important modulator of bone metabolism. This study aims to clarify the changes in Wnt antagonists in active and biochemically controlled acromegalic patients. METHODS: We recruited 77 patients recently diagnosed with acromegaly. Of those, 41 patients with complete follow-up data were included. Thirty healthy patients matched for age, sex, and body mass index served as controls. At baseline and posttreatment, Wnt antagonists (sclerostin [SOST], dickkopf-related protein 1 [DKK-1], and Wnt inhibitory factor 1 [WIF-1]), bone turnover markers (osteocalcin, procollagen type 1 N-terminal propeptide [P1NP], and C-terminal telopeptide of type 1 collagen [CTX]) and the bone remodeling index were investigated. RESULTS: Acromegalic patients had higher serum osteocalcin, P1NP, and CTX and a higher bone remodeling index than controls (P < .01). Serum SOST, DKK-1, and WIF-1 levels were significantly decreased in patients compared to controls (all P < .01). Serum SOST and WIF-1 levels were negatively correlated with growth hormone levels; SOST levels were positively correlated with WIF-1. After treatment, serum bone turnover markers and the bone remodeling index decreased, while SOST and WIF-1 significantly increased (P < .05). DKK-1 levels did not change compared to baseline (P > .05). In biochemically controlled patients, SOST and WIF-1 levels and bone turnover markers were restored and did not differ from those of the control participants (all P > .05). CONCLUSION: Patients with active acromegaly exhibited significantly decreased Wnt antagonist levels. The reduction in Wnt antagonists is a compensatory mechanism to counteract increased bone fragility in active acromegaly.

Global dynamics of a generalist predator-prey model in open advective environments.

This paper deals with a system of reaction-diffusion-advection equations for a generalist predator-prey model in open advective environments, subject to an unidirectional flow. In contrast to the specialist predator-prey model, the dynamics of this system is more complex. It turns out that there exist some critical advection rates and predation rates, which classify the global dynamics of the generalist predator-prey system into three or four scenarios: (1) coexistence; (2) persistence of prey only; (3) persistence of predators only; and (4) extinction of both species. Moreover, the results reveal significant differences between the specialist predator-prey system and the generalist predator-prey system, including the evolution of the critical predation rates with respect to the ratio of the flow speeds; the take-over of the generalist predator; and the reduction in parameter range for the persistence of prey species alone. These findings may have important biological implications on the invasion of generalist predators in open advective environments.

Structural basis for promoter DNA recognition by the response regulator OmpR.

OmpR, a response regulator of the EnvZ/OmpR two-component system (TCS), controls the reciprocal regulation of two porin proteins, OmpF and OmpC, in bacteria. During signal transduction, OmpR (OmpR-FL) undergoes phosphorylation at its conserved Asp residue in the N-terminal receiver domain (OmpRn) and recognizes the promoter DNA from its C-terminal DNA-binding domain (OmpRc) to elicit an adaptive response. Apart from that, OmpR regulates many genes in Escherichia coli and is important for virulence in several pathogens. However, the molecular mechanism of the regulation and the structural basis of OmpR-DNA binding is still not fully clear. In this study, we presented the crystal structure of OmpRc in complex with the F1 region of the ompF promoter DNA from E. coli. Our structural analysis suggested that OmpRc binds to its cognate DNA as a homodimer, only in a head-to-tail orientation. Also, the OmpRc apo-form showed a unique domain-swapped crystal structure under different crystallization conditions. Biophysical experimental data, such as NMR, fluorescent polarization and thermal stability, showed that inactive OmpR-FL (unphosphorylated) could bind to promoter DNA with a weaker binding affinity as compared with active OmpR-FL (phosphorylated) or OmpRc, and also confirmed that phosphorylation may only enhance DNA binding. Furthermore, the dimerization interfaces in the OmpRc-DNA complex structure identified in this study provide an opportunity to understand the regulatory role of OmpR and explore the potential for this "druggable" target.

Control Strategies for a Multi-strain Epidemic Model.

This article studies a multi-strain epidemic model with diffusion and environmental heterogeneity. We address the question of a control strategy for multiple strains of the infectious disease by investigating how the local distributions of the transmission and recovery rates affect the dynamics of the disease. Our study covers both full model (in which case the diffusion rates for all subgroups of the population are positive) and the ODE-PDE case (in which case we require a total lock-down of the susceptible subgroup and allow the infected subgroups to have positive diffusion rates). In each case, a basic reproduction number of the epidemic model is defined and it is shown that if this reproduction number is less than one then the disease will be eradicated in the long run. On the other hand, if the reproduction number is greater than one, then the disease will become permanent. Moreover, we show that when the disease is permanent, creating a common safety area against all strains and lowering the diffusion rate of the susceptible subgroup will result in reducing the number of infected populations. Numerical simulations are presented to support our theoretical findings.

Three-patch Models for the Evolution of Dispersal in Advective Environments: Varying Drift and Network Topology.

We study the evolution of dispersal in advective three-patch models with distinct network topologies. Organisms can move between connected patches freely and they are also subject to the passive, directed drift. The carrying capacity is assumed to be the same in all patches, while the drift rates could vary. We first show that if all drift rates are the same, the faster dispersal rate is selected for all three models. For general drift rates, we show that the infinite diffusion rate is a local Convergence Stable Strategy (CvSS) for all three models. However, there are notable differences for three models: For Model I, the faster dispersal is always favored, irrespective of the drift rates, and thus the infinity dispersal rate is a global CvSS. In contrast, for Models II and III a singular strategy will exist for some ranges of drift rates and bi-stability phenomenon happens, i.e., both infinity and zero diffusion rates are local CvSSs. Furthermore, for both Models II and III, it is possible for two competing populations to coexist by varying drift and diffusion rates. Some predictions on the dynamics of n-patch models in advective environments are given along with some numerical evidence.

Maximizing the total population with logistic growth in a patchy environment.

This paper is concerned with a nonlinear optimization problem that naturally arises in population biology. We consider the population of a single species with logistic growth residing in a patchy environment and study the effects of dispersal and spatial heterogeneity of patches on the total population at equilibrium. Our objective is to maximize the total population by redistributing the resources among the patches under the constraint that the total amount of resources is limited. It is shown that the global maximizer can be characterized for any number of patches when the diffusion rate is either sufficiently small or large. To show this, we compute the first variation of the total population with respect to resources in the two patches case. In the case of three or more patches, we compute the asymptotic expansion of all patches by using the Taylor expansion with respect to the diffusion rate. To characterize the shape of the global maximizer, we use a recurrence relation to determine all coefficients of all patches.

Evolution of anisotropic diffusion in two-dimensional heterogeneous environments.

We consider a system of two competing populations in two-dimensional heterogeneous environments. The populations are assumed to move horizontally and vertically with different probabilities, but are otherwise identical. We regard these probabilities as dispersal strategies. We show that the evolutionarily stable strategies are to move in one direction only. Our results predict that it is more beneficial for the species to choose the direction with smaller variation in the resource distribution. This finding seems to be in agreement with the classical results of Hastings (1983) and Dockery et al. (1998) for the evolution of slow dispersal, i.e. random diffusion is selected against in spatially heterogeneous environments. These conclusions also suggest that broader dispersal strategies should be considered regarding the movement in heterogeneous habitats.

Structural basis for -35 element recognition by σ4 chimera proteins and their interactions with PmrA response regulator.

In class II transcription activation, the transcription factor normally binds to the promoter near the -35 position and contacts the domain 4 of σ factors (σ4 ) to activate transcription. However, σ4 of σ70 appears to be poorly folded on its own. Here, by fusing σ4 with the RNA polymerase ß-flap-tip-helix, we constructed two σ4 chimera proteins, one from σ70σ470c and another from σSσ4Sc of Klebsiella pneumoniae. The two chimera proteins well folded into a monomeric form with strong binding affinities for -35 element DNA. Determining the crystal structure of σ4Sc in complex with -35 element DNA revealed that σ4Sc adopts a similar structure as σ4 in the Escherichia coli RNA polymerase σS holoenzyme and recognizes -35 element DNA specifically by several conserved residues from the helix-turn-helix motif. By using nuclear magnetic resonance (NMR), σ470c was demonstrated to recognize -35 element DNA similar to σ4Sc . Carr-Purcell-Meiboom-Gill relaxation dispersion analyses showed that the N-terminal helix and the ß-flap-tip-helix of σ470c have a concurrent transient α-helical structure and DNA binding reduced the slow dynamics on σ470c . Finally, only σ470c was shown to interact with the response regulator PmrA and its promoter DNA. The chimera proteins are capable of -35 element DNA recognition and can be used for study with transcription factors or other factors that interact with domain 4 of σ factors.

Analysis of Differentially Expressed Long Noncoding RNA in Renal Ischemia-Reperfusion Injury.

BACKGROUND: Renal ischemia-reperfusion (IR) injury is one of the major causes of acute renal failure which seriously endangers the health and life of patients. Currently, there is still lack of comprehensive knowledge of the molecular mechanism of renal IR injury, and the regulatory role of long noncoding RNA (lncRNA) in renal IR damage remains poorly understood. AIM: The aim of this study was to analyze the expression spectrum of lncRNA in renal IR damage in mice and to explore specific lncRNA that may be involved in regulating the development of human renal IR injury. METHODS: RNA-Seq was used to investigate the lncRNA profile of renal IR injury in a mouse model, and conservation analysis was performed on mouse lncRNAs with differential expression (fragments per kilobase of transcript per million mapped reads ≥2) by BLASTN. The potential functions and associated pathways of the differentially expressed lncRNA were explored by bioinformatics analysis. The cell hypoxia model was used to detect the expression of the candidate lncRNA. RESULTS: Of the 45,923 lncRNA transcripts detected in the samples, and 5,868 lncRNAs were found to be significantly differentially expressed (p < 0.05 and fold change ≥ 2) in 24-h IR kidney tissue compared to the expression in the control group. It was found that 56 differently expressed mouse lncRNA transcripts have human homology by analyzing the conserved sequences. We also found that lncRNA-NONHSAT183385.1 expression significantly increased in HK2 cells after 24 h of hypoxia and increased further 6 h after reoxygenation, and after 24 h of reoxygenation it was dramatically downregulated, indicating that NONHSAT183385.1 may be involved in the pathophysiological process of renal tubular epithelial cells in response to ischemia in human renal IR. CONCLUSION: Our study revealed differentially expressed lncRNAs in renal IR damage in mice and identified a set of conserved lncRNAs, which would help to explore lncRNAs that may play important regulatory roles in human renal IR injury.

Are Two-Patch Models Sufficient? The Evolution of Dispersal and Topology of River Network Modules.

We study the dynamics of two competing species in three-patch models and illustrate how the topology of directed river network modules may affect the evolution of dispersal. Each model assumes that patch 1 is at the upstream end, patch 3 is at the downstream end, but patch 2 could be upstream, or middle stream, or downstream, depending on the specific topology of the modules. We posit that individuals are subject to both unbiased dispersal between patches and passive drift from one patch to another, depending upon the connectivity of patches. When the drift rate is small, we show that for all models, the mutant species can invade when rare if and only if it is the slower disperser. However, when the drift rate is large, most models predict that the faster disperser wins, while some predict that there exists one evolutionarily singular strategy. The intermediate range of drift is much more complex: most models predict the existence of one singular strategy, but it may or may not be evolutionarily stable, again depending upon the topology of modules, while one model even predicts that for some intermediate drift rate, singular strategy does not exist and the faster disperser wins the competition.

Evolution of dispersal in spatial population models with multiple timescales.

We study the evolutionary stability of dispersal strategies, including but not limited to those that can produce ideal free population distributions (that is, distributions where all individuals have equal fitness and there is no net movement of individuals at equilibrium). The environment is assumed to be variable in space but constant in time. We assume that there is a separation of times scales, so that dispersal occurs on a fast timescale, evolution occurs on a slow timescale, and population dynamics and interactions occur on an intermediate timescale. Starting with advection-diffusion models for dispersal without population dynamics, we use the large time limits of profiles for population distributions together with the distribution of resources in the environment to calculate growth and interaction coefficients in logistic and Lotka-Volterra ordinary differential equations describing population dynamics. We then use a pairwise invasibility analysis approach motivated by adaptive dynamics to study the evolutionary and/or convergence stability of strategies determined by various assumptions about the advection and diffusion terms in the original advection-diffusion dispersal models. Among other results we find that those strategies which can produce an ideal free distribution are evolutionarily stable.