Testing prescribed burning to shift an agronomic grass community to a diverse native plant community.

Prescribed burning can be an effective land management tool. Here, we study changes in plant diversity and composition following experimental fire disturbance in microcosm units extracted from a twenty-five-year-old historically reclaimed grassland located at Highland Valley Copper mine in British Columbia (B.C.), Canada. Experimental microcosm units were dominated by agronomic grass species Elymus lanceolatus, Thinopyrum intermedium and Bromus inermis. The disturbance treatment was fire intensity, represented by three levels (light, moderate, and heavy), replicated six times per treatment. Fire intensity was controlled by modifying the weight of dried litter applied to each microcosm unit (50 g,150 g, 200g), along with the time each grass turf was burned (10 s, 15 s, 20 s). One day after the fire treatment was applied, microcosm units were seeded with a native species mix consisting of six grassland species common to southern B.C. to examine effectiveness of plant establishment postburn. Disturbance treatments resulted in higher overall alpha diversity, richness, evenness, and beta diversity. Plant community changes included colonization of seeded native forbs, grasses, and legumes in response to disturbance. Aboveground net primary productivity (ANPP) was net neutral within the light and moderate burning disturbance treatments but resulted in increased ANPP with heavy disturbance. Litter mass reduced plant diversity and ANPP, indicating that litter was a major factor in plant community dynamics. These results suggest disturbance by burning leads to short term positive plant community response towards increasing diversity of semi-arid grasslands, and aids in shifting plant communities to higher diversity composed of an increase in native plant species. Our results also suggest that without active management the gains observed in native species establishment might quickly be out shadowed and restricted by the previously dominant agronomic plant community.

Microbial composition and function in reclaimed mine sites along a reclamation chronosequence become increasingly similar to undisturbed reference sites.

Mine reclamation historically focuses on enhancing plant coverage to improve below and aboveground ecology. However, there is a great need to study the role of soil microorganisms in mine reclamation, particularly long-term studies that track the succession of microbial communities. Here, we investigate the trajectory of microbial communities of mining sites reclaimed between three and 26 years. We used high-throughput amplicon sequencing to characterize the bacterial and fungal communities. We quantified how similar the reclaimed sites were to unmined, undisturbed reference sites and explored the trajectory of microbial communities along the reclamation chronosequence. We also examined the ecological processes that shape the assembly of bacterial communities. Finally, we investigated the functional potential of the microbial communities through metagenomic sequencing. Our results reveal that the reclamation age significantly impacted the community compositions of bacterial and fungal communities. As the reclamation age increases, bacterial and fungal communities become similar to the unmined, undisturbed reference site, suggesting a favorable succession in microbial communities. The bacterial community assembly was also significantly impacted by reclamation age and was primarily driven by stochastic processes, indicating a lesser influence of environmental properties on the bacterial community. Furthermore, our read-based metagenomic analysis showed that the microbial communities' functional potential increasingly became similar to the reference sites. Additionally, we found that the plant richness increased with the reclamation age. Overall, our study shows that both above- and belowground ecological properties of reclaimed mine sites trend towards undisturbed sites with increasing reclamation age. Further, it demonstrates the importance of microbial genomics in tracking the trajectory of ecosystem reclamation.

Current reversal in polar flock at order-disorder interface.

We studied a system of polar self-propelled particles (SPPs) on a thin rectangular channel designed into three regions of order-disorder-order. The division of the three regions is made on the basis of the noise SPPs experience in the respective regions. The noise in the two wide regions is chosen lower than the critical noise of order-disorder transition and noise in the middle region or interface is higher than the critical noise. This makes the geometry of the system analogous to the Josephson junction (JJ) in solid-state physics. Keeping all other parameters fixed, we study the properties of the moving SPPs in the bulk as well as along the interface for different widths of the junction. On increasing interface width, the system shows an order-to-disorder transition from coherent moving SPPs in the whole system to the interrupted current for large interface width. Surprisingly, inside the interface, we observed the current reversal for intermediate widths of the interface. Such current reversal is due to the strong randomness present inside the interface, which makes the wall of the interface reflecting. Hence, our study gives new interesting collective properties of SPPs at the interface which can be useful to design switching devices using active agents.

Effective single component description of steady state structures of passive particles in an active bath.

We model a binary mixture of passive and active Brownian particles in two dimensions using the effective interaction between passive particles in the active bath. The activity of active particles and the size ratio of two types of particles are the two control parameters in the system. The effective interaction is calculated from the average force on two particles generated by the active particles. The effective interaction can be attractive or repulsive, depending on the system parameters. The passive particles form four distinct structural orders for different system parameters, viz., homogeneous structures, disordered cluster, ordered cluster, and crystalline structure. The change in structure is dictated by the change in nature of the effective interaction. We further confirm the four structures using a full microscopic simulation of active and passive mixture. Our study is useful to understand the different collective behavior in non-equilibrium systems.

Spotted knapweed (Centaurea stoebe) creates a soil legacy effect by modulating soil elemental composition in a semi-arid grassland ecosystem.

Invasive plants such as spotted knapweed (Centaurea stoebe) are particularly detrimental to fragile ecosystems like semi-arid grasslands in the interior British Columbia, impacting aboveground and belowground ecology. Physical removal of C. stoebe has been one of the most popular invasive species management strategies, but the impact of C. stoebe removal on soil has hardly been studied. Here, we examine the legacy effect of C. stoebe on soil elemental composition and ecosystem function following its removal in the Lac Du Bios Grasslands Protected Area, British Columbia. First, we selected 40 paired C. stoebe invaded and control (uninvaded) plots and removed all vegetation from these plots. We planted Festuca campestris seedlings in these plots and harvested and weighed the biomass after four months. Additionally, we quantified total carbon and nitrogen in soil. We observed that C. stoebe invaded plots had significantly lower F. campestris biomass. Moreover, the total carbon and nitrogen content, and carbon/nitrogen ratio were significantly lower in C. stoebe invaded plots. We further analyzed 12 common soil elements and found the elemental composition was significantly different in C. stoebe invaded plots compared to controls. We investigated the impact of elemental composition on soil ecosystem functions (such as total soil carbon, total soil nitrogen, and F. campestris productivity). Our analysis revealed significant relationships amongst the elemental composition and total soil carbon and nitrogen, and F. campestris productivity. The results indicate that C. stoebe exerts a legacy effect by altering the soil elemental composition that may subsequently impacts soil ecosystem functions such as plant productivity and total carbon and nitrogen content.

The steroid hormone estriol (E3) regulates epigenetic programming of fetal mouse brain and reproductive tract.

BACKGROUND: Estriol (E3) is a steroid hormone formed only during pregnancy in primates including humans. Although E3 is synthesized at large amounts through a complex pathway involving the fetus and placenta, it is not required for the maintenance of pregnancy and has classically been considered virtually inactive due to associated very weak canonical estrogen signaling. However, estrogen exposure during pregnancy may have an effect on organs both within and outside the reproductive system, and compounds with binding affinity for estrogen receptors weaker than E3 have been found to impact reproductive organs and the brain. Here, we explore potential effects of E3 on fetal development using mouse as a model system. RESULTS: We administered E3 to pregnant mice, exposing the fetus to E3. Adult females exposed to E3 in utero (E3-mice) had increased fertility and superior pregnancy outcomes. Female and male E3-mice showed decreased anxiety and increased exploratory behavior. The expression levels and DNA methylation patterns of multiple genes in the uteri and brains of E3-mice were distinct from controls. E3 promoted complexing of estrogen receptors with several DNA/histone modifiers and their binding to target genes. E3 functions by driving epigenetic change, mediated through epigenetic modifier interactions with estrogen receptors rather than through canonical nuclear transcriptional activation. CONCLUSIONS: We identify an unexpected functional role for E3 in fetal reproductive system and brain. We further identify a novel mechanism of estrogen action, through recruitment of epigenetic modifiers to estrogen receptors and their target genes, which is not correlated with the traditional view of estrogen potency.

Effect of polydispersity on the dynamics of active Brownian particles.

We numerically study the dynamics and the phases of self-propelled disk-shaped particles of different sizes with soft repulsive potential in two dimensions. Size diversity is introduced by the polydispersity index (PDI) ε, which is the width of the uniform distribution of the particle's radius. The self-propulsion speed of the particles controls the activity v. We observe enhanced dynamics for large size diversity among the particles. We calculate the effective diffusion coefficient D_{eff} in the steady state. The system exhibits four distinct phases, jammed phase with small D_{eff} for small activity and liquid phase with enhanced D_{eff} for large activity. The number fluctuation is larger and smaller than the equilibrium limit in the liquid and jammed phases, respectively. Further, the jammed phase is of two types: solid jammed and liquid jammed for small and large PDI. Whereas the liquid phase is called motility induced phase separation (MIPS) liquid for small PDI and for large PDI, we find enhanced diffusivity and call it the pure liquid phase. The system is studied for three packing densities ϕ, and the response of the system for polydispersity is the same for all ϕ's. Our study can help understand the behavior of cells of various sizes in a tissue, artificial self-driven granular particles, or living organisms of different sizes in a dense environment.

Only irrelevant angry, but not happy, expressions facilitate the response inhibition.

It has been debated that arousal rather than valence modulates the response-inhibition process. The processing of irrelevant information of happy and angry faces interacts with attention differently. In the present study, arousal-matched irrelevant happy and angry faces were used as stop-signals in the stop-signal paradigm. Participants were required to respond to go-signals (discriminate between X or O). Occasionally, a stop-signal was presented where participants were required to withhold their motor response. Results indicate a significant effect of emotion on response inhibition, which suggests that valence of a stop-signal modulates inhibitory control. More specifically, we found that only irrelevant angry, but not happy, expressions facilitate the response inhibition process. These results have theoretical implications for understanding the nature of emotions and its interaction with cognitive control functions.

Speed inhomogeneity accelerates information transfer in polar flock.

A collection of self-propelled particles (SPPs) shows coherent motion and exhibits a true long-range-ordered state in two dimensions. Various studies show that the presence of spatial inhomogeneities can destroy the usual long-range ordering in the system. However, the effects of inhomogeneity due to the intrinsic properties of the particles are barely addressed. In this paper we consider a collection of polar SPPs moving at inhomogeneous speed (IS) on a two-dimensional substrate, which can arise due to varying physical strengths of the individual particles. To our surprise, the IS not only preserves the usual long-range ordering present in homogeneous speed models but also induces faster ordering in the system. Furthermore, the response of the flock to an external perturbation is also faster, compared to the Vicsek-like model systems, due to the frequent update of neighbors of each SPP in the presence of the IS. Therefore, our study shows that an IS can promote information transfer in a moving flock.

O-GlcNAcase targets pyruvate kinase M2 to regulate tumor growth.

Cancer cells are known to adopt aerobic glycolysis in order to fuel tumor growth, but the molecular basis of this metabolic shift remains largely undefined. O-GlcNAcase (OGA) is an enzyme harboring O-linked ß-N-acetylglucosamine (O-GlcNAc) hydrolase and cryptic lysine acetyltransferase activities. Here, we report that OGA is upregulated in a wide range of human cancers and drives aerobic glycolysis and tumor growth by inhibiting pyruvate kinase M2 (PKM2). PKM2 is dynamically O-GlcNAcylated in response to changes in glucose availability. Under high glucose conditions, PKM2 is a target of OGA-associated acetyltransferase activity, which facilitates O-GlcNAcylation of PKM2 by O-GlcNAc transferase (OGT). O-GlcNAcylation inhibits PKM2 catalytic activity and thereby promotes aerobic glycolysis and tumor growth. These studies define a causative role for OGA in tumor progression and reveal PKM2 O-GlcNAcylation as a metabolic rheostat that mediates exquisite control of aerobic glycolysis.

Soil microbial response to metal contamination in a vegetated and urban brownfield.

The ubiquity of urban brownfields presents not only a challenge for environmental managers but also an opportunity to study the functional aspects of degraded ecosystems that are in close contact with human habitation. In this study, we investigate the soil microbial community response to heavy metal contamination at Liberty State Park (LSP), an urban brownfield in Jersey City, NJ, USA. Heavy metal contamination of the soils at LSP is heterogeneous, varying widely across site and among metals. We collected soils along a previously mapped gradient of metal contamination at LSP and sampled soil from a local and uncontaminated reference site (Hutcheson Memorial Forest (HMF)) for comparison. For all soils, we measured soil heavy metal concentrations, soil organic carbon content, bacterial density, and extracellular phosphatase activity as a proxy of ecosystem functioning. Additionally, we analyzed the microbial community composition using high-throughput sequencing. Data show that some sites within LSP have significantly higher phosphatase activity compared to HMF, indicating that some heavily contaminated LSP soils are highly functional. We also found that soil organic carbon and bacterial density have a significant and positive relationship with phosphatase activity. The microbial community analyses showed that the bacterial communities were sensitive to heavy metals and that the composition was significantly affected in particular by copper, zinc, and lead. The fungal communities, however, did not vary significantly with heavy metals. Our results shed important light on the composition and functioning of urban brownfield soils. A deeper understanding of these unique ecosystems is required for successful remediation, restoration and urban sustainability.

Abiotic factors determine functional outcomes of microbial inoculation of soils from a metal contaminated brownfield.

Whole community microbial inoculation can improve soil function in contaminated environments. Here we conducted a case study to investigate whether biotic factors (inoculum) or abiotic factors (soil base) have more impact on the extracellular enzymatic activities in a whole community microbial inoculation. To this end, we cross-inoculated microbial communities between two heavy metal-contaminated soils, with high and low extracellular enzyme activities, respectively. We measured extracellular phosphatase activity, a proxy for soil function, after self- and cross-inoculation of microbial communities into sterilized soils, and all activities were normalized to non-inoculated controls. We found that inoculation increased phosphatase activity in the soils. For soils treated with different inocula, we found significant differences in the microbial community compositions but no significant differences in the extracellular phosphatase activities normalized to their respective sterilized, non-inoculated controls (4.7 ±â€¯1.8 and 3.3 ±â€¯0.5 for soils inoculated with microbial communities from 146 to 43, respectively). On the other hand, normalized phosphatase activities between the two soil bases were significantly different (4.1 ±â€¯0.12 and 1.9 ±â€¯0.12 for soil bases 146 and 43, respectively) regardless of the source of the inoculum that did not vary between soil bases. The results indicate that the abiotic properties of the soils were a significant predictor for phosphatase activity but not for the end-point composition of the microbial community. The findings suggest that targeted microbial inocula from metal contaminated soils can increase phosphatase activity, and likely soil functioning in general, but the degree to which this happens depends on the abiotic environment, in this case, metal contamination.

Effect of language proficiency on proactive occulo-motor control among bilinguals.

We examined the effect of language proficiency on the status and dynamics of proactive inhibitory control in an occulo-motor cued go-no-go task. The first experiment was designed to demonstrate the effect of second language proficiency on proactive inhibitory cost and adjustments in control by evaluating previous trial effects. This was achieved by introducing uncertainty about the upcoming event (go or no-go stimulus). High- and low- proficiency Hindi-English bilingual adults participated in the study. Saccadic latencies and errors were taken as the measures of performance. The results demonstrate a significantly lower proactive inhibitory cost and better up-regulation of proactive control under uncertainty among high- proficiency bilinguals. An analysis based on previous trial effects suggests that high- proficiency bilinguals were found to be better at releasing inhibition and adjustments in control, in an ongoing response activity in the case of uncertainty. To further understand the dynamics of proactive inhibitory control as a function of proficiency, the second experiment was designed to test the default versus temporary state hypothesis of proactive inhibitory control. Certain manipulations were introduced in the cued go-no-go task in order to make the upcoming go or no-go trial difficult to predict, which increased the demands on the implementation and maintenance of proactive control. High- proficiency bilinguals were found to rely on a default state of proactive inhibitory control whereas low- proficiency bilinguals were found to rely on temporary/transient proactive inhibition. Language proficiency, as one of the measures of bilingualism, was found to influence proactive inhibitory control and appears to modulate the dynamics of proactive inhibitory control.

Transcriptional regulation of O-GlcNAc homeostasis is disrupted in pancreatic cancer.

Many intracellular proteins are reversibly modified by O-linked GlcNAc (O-GlcNAc), a post-translational modification that dynamically regulates fundamental cellular processes in response to diverse environmental cues. Accumulating evidence indicates that both excess and deficiency of protein O-GlcNAcylation can have deleterious effects on the cell, suggesting that maintenance of O-GlcNAc homeostasis is essential for proper cellular function. However, the mechanisms through which O-GlcNAc homeostasis is maintained in the physiologic state and altered in the disease state have not yet been investigated. Here, we demonstrate the existence of a homeostatic mechanism involving mutual regulation of the O-GlcNAc-cycling enzymes O-GlcNAc transferase (OGT) and O-GlcNAcase (OGA) at the transcriptional level. Specifically, we found that OGA promotes Ogt transcription through cooperation with the histone acetyltransferase p300 and transcription factor CCAAT/enhancer-binding protein ß (C/EBPß). To examine the role of mutual regulation of OGT and OGA in the disease state, we analyzed gene expression data from human cancer data sets, which revealed that OGT and OGA expression levels are highly correlated in numerous human cancers, particularly in pancreatic adenocarcinoma. Using a KrasG12D -driven primary mouse pancreatic ductal adenocarcinoma (PDAC) cell line, we found that inhibition of extracellular signal-regulated kinase (ERK) signaling decreases OGA glycosidase activity and reduces OGT mRNA and protein levels, suggesting that ERK signaling may alter O-GlcNAc homeostasis in PDAC by modulating OGA-mediated Ogt transcription. Our study elucidates a transcriptional mechanism that regulates cellular O-GlcNAc homeostasis, which may lay a foundation for exploring O-GlcNAc signaling as a therapeutic target for human disease.

O-GlcNAc signaling in cancer metabolism and epigenetics.

The covalent attachment of ß-D-N-acetylglucosamine monosaccharides (O-GlcNAc) to serine/threonine residues of nuclear and cytoplasmic proteins is a major regulatory mechanism in cell physiology. Aberrant O-GlcNAc modification of signaling proteins, metabolic enzymes, and transcriptional and epigenetic regulators has been implicated in cancer. Relentless growth of cancer cells requires metabolic reprogramming that is intertwined with changes in the epigenetic landscape. This review highlights the emerging role of protein O-GlcNAcylation at the interface of cancer metabolism and epigenetics.

O-GlcNAc transferase enables AgRP neurons to suppress browning of white fat.

Induction of beige cells causes the browning of white fat and improves energy metabolism. However, the central mechanism that controls adipose tissue browning and its physiological relevance are largely unknown. Here, we demonstrate that fasting and chemical-genetic activation of orexigenic AgRP neurons in the hypothalamus suppress the browning of white fat. O-linked ß-N-acetylglucosamine (O-GlcNAc) modification of cytoplasmic and nuclear proteins regulates fundamental cellular processes. The levels of O-GlcNAc transferase (OGT) and O-GlcNAc modification are enriched in AgRP neurons and are elevated by fasting. Genetic ablation of OGT in AgRP neurons inhibits neuronal excitability through the voltage-dependent potassium channel, promotes white adipose tissue browning, and protects mice against diet-induced obesity and insulin resistance. These data reveal adipose tissue browning as a highly dynamic physiological process under central control, in which O-GlcNAc signaling in AgRP neurons is essential for suppressing thermogenesis to conserve energy in response to fasting.

PfalDB: an integrated drug target and chemical database for Plasmodium falciparum.

Plasmodium falciparum is one of the deadliest protozoan parasite species among those that cause malaria. Uncontrolled use of antimalarial drugs has resulted in evolutionary selection pressure favoring high levels of resistance to antimalarials; currently P.falciparum shows resistance to all classes of antimalarials. Therefore it is essential to identify novel drug targets, and design selective anti-malarials which can overcome resistance. While many drug targets are freely available in various public domain resources, a single comprehensive source of data containing easily searchable and retrievable information is currently lacking. To facilitate the total integration and mining of data emerging from different drug consortia and also to prioritize drug targets for structure-based drug design, an open-access, inclusive comprehensive database for Plasmodium falciparum was established. Meta data of known/modeled structures along with binding site parameters of drug targets have been included in the database. Additionally, chemical compounds showing a positive inhibitory assay against Plasmodium falciparum or known drug targets have also been provided. The database is accessible at http://pfaldb.jnu.ac.in. The database provides diverse information regarding the structure, sequence, stage specific gene expression, pathway, action mechanism, essentiality and druggability for each drug target, and literature to assess the validation status of individual drug targets. It also includes information on individual anti-malarials with their activity and bioassay.

Cracking the O-GlcNAc code in metabolism.

Nuclear, cytoplasmic, and mitochondrial proteins are extensively modified by O-linked ß-N-acetylglucosamine (O-GlcNAc) moieties. This sugar modification regulates fundamental cellular processes in response to diverse nutritional and hormonal cues. The enzymes O-GlcNAc transferase (OGT) and O-linked ß-N-acetylglucosaminase (O-GlcNAcase) mediate the addition and removal of O-GlcNAc, respectively. Aberrant O-GlcNAcylation has been implicated in a plethora of human diseases, including diabetes, cancer, aging, cardiovascular disease, and neurodegenerative disease. Because metabolic dysregulation is a vital component of these diseases, unraveling the roles of O-GlcNAc in metabolism is of emerging importance. Here, we review the current understanding of the functions of O-GlcNAc in cell signaling and gene transcription involved in metabolism, and focus on its relevance to diabetes, cancer, circadian rhythm, and mitochondrial function.

O-GlcNAc transferase/host cell factor C1 complex regulates gluconeogenesis by modulating PGC-1α stability.

A major cause of hyperglycemia in diabetic patients is inappropriate hepatic gluconeogenesis. PGC-1α is a master regulator of gluconeogenesis, and its activity is controlled by various posttranslational modifications. A small portion of glucose metabolizes through the hexosamine biosynthetic pathway, which leads to O-linked ß-N-acetylglucosamine (O-GlcNAc) modification of cytoplasmic and nuclear proteins. Using a proteomic approach, we identified a broad variety of proteins associated with O-GlcNAc transferase (OGT), among which host cell factor C1 (HCF-1) is highly abundant. HCF-1 recruits OGT to O-GlcNAcylate PGC-1α, and O-GlcNAcylation facilitates the binding of the deubiquitinase BAP1, thus protecting PGC-1α from degradation and promoting gluconeogenesis. Glucose availability modulates gluconeogenesis through the regulation of PGC-1α O-GlcNAcylation and stability by the OGT/HCF-1 complex. Hepatic knockdown of OGT and HCF-1 improves glucose homeostasis in diabetic mice. These findings define the OGT/HCF-1 complex as a glucose sensor and key regulator of gluconeogenesis, shedding light on new strategies for treating diabetes.

Isolation, structure, and functional elucidation of a modified pentapeptide, cysteine protease inhibitor (CPI-2081) from Streptomyces species 2081 that exhibit inhibitory effect on cancer cell migration.

Cysteine proteases play an important role in cell migration and tumor metastasis. Therefore, their inhibitors are of colossal interest, having potential to be developed as effective antimetastatic drugs for tumor chemotherapy. Traditionally, secondary metabolites from streptomyces show a wide range of diversity with respect to their biological activity and chemical nature. In this article, we have described the characterization of small molecule cysteine protease inhibitor, CPI-2081 (compound 1), a mixture of two novel pentapeptides, compound 1a (736.71 Da), and compound 1b (842.78 Da), isolated from Streptomyces species NCIM2081, following solvent extraction and repeated HPLC based on C18 chemistry, and completely characterized using a variety of both 1D and 2D NMR spectroscopy. Further, it was found that nanomolar concentration of compound 1 is able to inhibit papain hydrolytic activity. Also, compound 1 significantly inhibits tumor cell migration at sub cytotoxic concentration, indicating its remarkable potential to be developed as antimetastatic drug, which will make chemotherapy more localized and specific, thereby minimizing the hazardous side effects on normal tissues.