An improved class of estimators for estimation of population distribution functions under stratified random sampling

The main objective of the current study is to suggest an enhanced family of log ratio-exponential type estimators for population distribution function (DF) using auxiliary information under stratified random sampling. Putting different choices in our suggested generalized class of estimators, we found some Specific estimators. The bias and MSE expressions of the estimators have been approximated up to the first order. By using the actual and simulated data sets, we measured the performance of estimators. Based on the results, the suggested estimators for DF show better performance as compared to the preliminary estimators considered here. The suggested estimators have a advanced efficiency than the other estimators examined with the estimators F ‾ ˆ l o g P R ( s t ) 2 , and F ‾ ˆ l o g P R ( s t ) 4 for both the actual and simulated data sets. The magnitude of the improvement in efficiency is noteworthy, indicating the superiority of the proposed estimators in terms of MSE.

Enhanced exponential ratio-cum-ratio estimator in ranked set sampling using transformed auxiliary information

Estimation of population mean is a determined subject issue in sampling surveys and many efforts have been paid by various researchers to enhance the precision of the estimates by utilizing the correlated auxiliary information. In connection with this, we suggest an improved exponential ratio-cum-ratio estimator using transformed auxiliary variables under ranked set sampling scheme. Theoretical comparison between estimators is made in terms of mean square errors (M S E s ), percentage relative efficiencies (P R E s ), and percentage relative root mean squared error (P R R M S E ). The numerical expression for the bias and M S E of the suggested estimator is derived up to first order of approximation. Based on the results of actual data sets and a simulation study, it is found that the suggested estimator perform well as compared to its existing counterparts.

The Post-Transcriptional Regulatory Element of Hepatitis B Virus: From Discovery to Therapy

The post-transcriptional regulatory element (PRE) is present in all HBV mRNAs and plays a major role in their stability, nuclear export, and enhancement of viral gene expression. Understanding PRE's structure, function, and mode of action is essential to leverage its potential as a therapeutic target. A wide range of PRE-based reagents and tools have been developed and assessed in preclinical and clinical settings for therapeutic and biotechnology applications. This manuscript aims to provide a systematic review of the characteristics and mechanism of action of PRE, as well as elucidating its current applications in basic and clinical research. Finally, we discuss the promising opportunities that PRE may provide to antiviral development, viral biology, and potentially beyond.

Improved estimation of population distribution function using twofold auxiliary information under simple random sampling

In this article, our main aim is to suggest enhanced families of estimators for estimating the population distribution function (DF) using twofold auxiliary evidence within the framework of simple random sampling. Numerical analysis is performed on four different actual data sets. The precision of the estimators is further investigated exhausting a simulation study. As equated with existing estimators, the suggested families of estimators have minimum mean square error (MSE) and higher percentage relative efficiency (PRE). The succeeding recommended family of estimators outperforms the first family of estimators across all data sets. These are positive indicators of its performance. The theoretical result shows that the recommended family of estimators performs better than the existing estimators. The extent of improvement in efficiency is noteworthy, indicating the superiority of the suggested estimators in terms of minimum MSE.

Polycomb protein binding and looping mediated by Polycomb Response Elements in the ON transcriptional state

Polycomb group proteins (PcG) mediate epigenetic silencing of important developmental genes and other targets. In Drosophila, canonical PcG-target genes contain Polycomb Response Elements (PREs) that recruit PcG protein complexes including PRC2 that trimethylates H3K27 forming large H3K27me3 domains. In the OFF transcriptional state, PREs loop with each other and this looping strengthens silencing. Here we address the question of what PcG proteins bind to PREs when canonical PcG target genes are expressed, and whether PREs loop when these genes are ON. Our data show that the answer to this question is PRE-specific but general conclusions can be made. First, within a PcG-target gene, some regulatory DNA can remain covered with H3K27me3 and PcG proteins remain bound to PREs in these regions. Second, when PREs are within H3K27ac domains, PcG-binding decreases, however, this depends on the protein and PRE. The DNA binding protein GAF, and the PcG protein Ph remain at PREs even when other PcG proteins are greatly depleted. In the ON state, PREs can still loop with each other, but also form loops with presumptive enhancers. These data support the model that, in addition to their role in PcG silencing, PREs can act as "promoter-tethering elements" mediating interactions between promoter proximal PREs and distant enhancers.

Estimation of finite population mean using double sampling under probability proportional to size sampling in the presence of extreme values

Values that are too large or small enough can be found in many data sets. Therefore, the estimator can yield ambiguous findings if several of the incredible deals are picked for the sample. When such extreme values occur, we propose improved estimators to determine the finite population means using double sampling based on probability proportional to size sampling (PPS). The properties of estimators are obtained up to the first order of approximations. When the size of the units varies widely, the PPS sampling technique may be employed. To determine the values of Pi when using PPS, we must be acquainted with the aggregate of the auxiliary variable X i . However the designs and estimation techniques we have looked at so far are unsuccessful and are less effective when this information is difficult to locate or when other information is missing. The two-phase approach is preferable and more feasible in these kinds of circumstances. To demonstrate how effectively the recommended estimators performed, we used three actual data sets. We show mathematically and theoretically that the suggested estimators outperform alternative estimators.

A new approach for estimating variance of a population employing information obtained from a stratified random sampling

In this article, we suggest an enhanced estimator for the estimation of finite population variance using twofold auxiliary variable under stratified random sampling. The numerical expressions for the bias and MSE are determined up to the first order of approximation. In order to effectively validate the theoretical findings, three actual data sets are included. Additionally, the application of the suggested estimators is demonstrated using a simulation study. Results of an empirical comparison among the suggested and existing estimators were investigated. To determine how good the suggested estimator, in comparison to the preliminary estimators, the MSE criterion is used. The suggested estimator has a smaller MSE and better PRE than existing estimators, according to numerical results utilizing actual data sets and a simulation analysis.

New generalized class of estimators for estimation of finite population mean based on probability proportional to size sampling using two auxiliary variables: A simulation study

This article aims to suggest a new generalized class of estimators based on probability proportional to size sampling using two auxiliary variables. The numerical expressions for the bias and mean squared error (MSE) are derived up to the first order of approximation. Four actual data sets are used to examine the performances of a new improved generalized class of estimators. From the results of real data sets, it is examined that the suggested estimator gives the minimum MSE and the percentage relative efficiency is higher than all existing estimators, which shows the importance of the new generalized class of estimators. To check the strength and generalizability of our proposed class of estimators, a simulation study is also accompanied. The consequence of the simulation study shows the worth of newly found proposed class estimators. Overall, we get to the conclusion that the proposed estimator outperforms as compared to all other estimators taken into account in this study.

Polycomb Recruiters Inside and Outside of the Repressed Domains

The establishment and stable inheritance of individual patterns of gene expression in different cell types are required for the development of multicellular organisms. The important epigenetic regulators are the Polycomb group (PcG) and Trithorax group (TrxG) proteins, which control the silenced and active states of genes, respectively. In Drosophila, the PcG/TrxG group proteins are recruited to the DNA regulatory sequences termed the Polycomb response elements (PREs). The PREs are composed of the binding sites for different DNA-binding proteins, the so-called PcG recruiters. Currently, the role of the PcG recruiters in the targeting of the PcG proteins to PREs is well documented. However, there are examples where the PcG recruiters are also implicated in the active transcription and in the TrxG function. In addition, there is increasing evidence that the genome-wide PcG recruiters interact with the chromatin outside of the PREs and overlap with the proteins of differing regulatory classes. Recent studies of the interactomes of the PcG recruiters significantly expanded our understanding that they have numerous interactors besides the PcG proteins and that their functions extend beyond the regulation of the PRE repressive activity. Here, we summarize current data about the functions of the PcG recruiters.

Stuxnet fine-tunes Notch dose during development with a functional Polycomb response element

Evolutionarily conserved Notch signaling is highly sensitive to changes in Notch receptor dose caused by intrinsic and environmental fluctuations. It is well known that epigenetic regulation responds dynamically to genetic, cellular, and environmental stresses. However, it is unclear whether the Notch receptor dose is directly regulated at the epigenetic level. Here, by studying the role of the upstream epigenetic regulator Stuxnet (Stx) in developmental signaling, we find that Stx promotes Notch receptor mRNA expression by counteracting the activity of Polycomb repressive complex 1 (PRC1). In addition, we provide evidence that Notch is a direct PRC1 target by identifying and validating in vivo the only bona fide Polycomb response element (PRE) among the seven Polycomb group (PcG)-binding sites revealed by DamID-seq and ChIP-seq analysis. Importantly, in situ deletion of this PRE results in increased Notch expression and phenotypes resembling Notch hyperactivation in cell fate specification. These results not only underscore the importance of epigenetic regulation in fine-tuning the Notch activity dose, but also the need to assess the physiological significance of omics-based PcG binding in development.

Lipid acyl chain protrusion induced by the influenza virus hemagglutinin fusion peptide detected by NMR paramagnetic relaxation enhancement

The glycoprotein spikes of membrane-enveloped viruses include a subunit that catalyzes fusion (joining) of the viral and target cell membranes. For influenza virus, this is subunit 2 of hemagglutinin which has a ∼ 20-residue N-terminal fusion peptide (Fp) region that binds target membrane. An outstanding question is whether there are associated membrane changes important for fusion. Several computational studies have found increased "protrusion" of lipid acyl chains near Fp, i.e. one or more chain carbons are closer to the aqueous region than the headgroup phosphorus. Protrusion may accelerate initial joining of outer leaflets of the two membranes into a stalk intermediate. In this study, higher protrusion probability in membrane with vs. without Fp is convincingly detected by larger Mn²⁺-associated increases in chain ¹³C NMR transverse relaxation rates (Γ₂'s). Data analysis provides a ratio Γ_2,neighbor/Γ_2,distant for lipids neighboring vs. more distant from the Fp. The calculated ratio depends on the number of Fp-neighboring lipids and the experimentally-derived range of 4 to 24 matches the range of increased protrusion probabilities from different simulations. For samples either with or without Fp, the Γ₂ values are well-fitted by an exponential decay as the ¹³C site moves closer to the chain terminus. The decays correlate with free-energy of protrusion proportional to the number of protruded -CH₂ groups, with free energy per -CH₂ of ∼0.25 k_BT. The NMR data support one major fusion role of the Fp to be much greater protrusion of lipid chains, with highest protrusion probability for chain regions closest to the headgroups.

NMR and Patch-Clamp Characterization of Yeast Mitochondrial Pyruvate Carrier Complexes

The mitochondrial pyruvate carrier (Mpc) plays an indispensable role in the transport of pyruvates across the mitochondrial inner membrane. Despite the two distinct homologous proteins, Mpc1 and Mpc2, were identified in 2012, there are still controversies on the basic functional units and oligomeric state of Mpc complexes. In this study, yeast Mpc1 and Mpc2 proteins were expressed in a prokaryotic heterologous system. Both homo- and hetero-dimers were successfully reconstituted in mixed detergents. Interactions among Mpc monomers were recorded utilizing paramagnetic relaxation enhancement (PRE) nuclear magnetic resonance (NMR) methods. By single-channel patch-clamp assays, we discovered that both the Mpc1-Mpc2 hetero-dimer and Mpc1 homo-dimer are able to transport K⁺ ions. Furthermore, the Mpc1-Mpc2 hetero-dimer demonstrated the ability to transport pyruvates, at a rate significantly higher than that of the Mpc1 homo-dimer, indicating that it could be the basic functional unit of Mpc complexes. Our findings provide valuable insights for further structural determination and the study of the transport mechanism of Mpc complexes.

Spatiotemporal trends of ultraviolet absorbents in oysters from the Pearl River Estuary, south China during 2015-2020

Ultraviolet absorbents (UVAs) are widely used in various industrial materials, pharmaceuticals, and personal care products, resulting in their frequent occurrences in sediment, water, and biota. However, our understanding of the spatiotemporal characteristics and long-term contamination status of UVAs is still limited. Here, a 6-year biomonitoring study with oysters during wet and dry seasons was conducted to examine the annual, seasonal, and spatial characteristics of UVAs in the Pearl River Estuary (PRE), China. The concentrations of Σ₆UVA ranged from 9.1 to 119 (geometric mean ± standard deviation: 31 ± 22) ng/g dry wt. and peaked in 2018. Significant spatiotemporal variations in UVA contamination were observed. The concentrations of UVAs in oysters during the wet season were higher than the dry season, and concentrations in the more industrialized eastern coast were higher than the western coast (p < 0.05). Environmental factors, including precipitation, temperature, and salinity in water significantly impacted the UVA bioaccumulation in the oysters. The present study highlights that long-term biomonitoring with oysters provided valuable insight in the magnitude and seasonal variation of UVAs in this highly dynamic estuary.

Identification and Characterization of PRE Genes in Moso Bamboo (Phyllostachys edulis)

Basic helix-loop-helix (bHLH)/HLH transcription factors are involved in various aspects of the growth and development of plants. Here, we identified four HLH genes, PePRE1-4, in moso bamboo plants that are homologous to Arabidopsis PRE genes. In bamboo seedlings, PePRE1/3 were found to be highly expressed in the internode and lamina joint by using quantitative RT-PCR analysis. In the elongating internode of bamboo shoots, PePRE genes are expressed at higher levels in the basal segment than in the mature top segment. Overexpression of PePREs (PePREs-OX) in Arabidopsis showed longer petioles and hypocotyls, as well as earlier flowering. PePRE1 overexpression restored the phenotype due to the deficiency of AtPRE genes caused by artificial micro-RNA. PePRE1-OX plants showed hypersensitivity to propiconazole treatment compared with the wild type. In addition, PePRE1/3 but not PePRE2/4 proteins accumulated as punctate structures in the cytosol, which was disrupted by the vesicle recycling inhibitor brefeldin A (BFA). PePRE genes have a positive function in the internode elongation of moso bamboo shoots, and overexpression of PePREs genes promotes flowering and growth in Arabidopsis. Our findings provided new insights about the fast-growing mechanism of bamboo shoots and the application of PRE genes from bamboo.

Improved family of estimators for the population mean using supplementary variables under PPS sampling

In this article, we suggest an enhanced family of estimators for estimation of population mean employing the supplementary variables under probability proportional to size sampling. Up to the first order of approximation, numerical formulations of the bias and mean square error of estimators are obtained. From our suggested improved family of estimators, we give sixteen different members. The recommended family of estimators has specifically been used to derive the characteristics of sixteen estimators based on the known population parameters of the study as well as auxiliary variables. The performances of the suggested estimators have been assessed using three actual data. Furthermore, a simulation investigation is also accompanied to evaluate the effectiveness of estimators. The proposed estimators have a smaller MSE and an advanced PRE when linked to existing estimators, which are based on actual data sets and simulation studies. Theoretically and empirically studies also reveal that the suggested estimators accomplish well than the usual estimators.

What are the optimum training parameters of progressive resistance exercise for changes in muscle function, activity and participation in people with cerebral palsy? A systematic review and meta-regression

OBJECTIVES

To explore the effect of progressive resistance exercise (PRE) on impairment, activity and participation of people with cerebral palsy (CP). Also, to determine which programme parameters provide the most beneficial effects.

DATA SOURCES

Electronic databases searched from the earliest available time.

ELIGIBILITY CRITERIA

Randomised controlled trials (RCTs) implementing PRE as an intervention in people with cerebral palsy were included.

STUDIES APPRAISAL & SYNTHESIS METHODS

Methodological quality of trials was assessed with the PEDro scale. Meta-analysis and meta-regression were completed.

RESULTS

We included 20 reports of 16 RCTs (n = 504 participants). Results demonstrated low certainty evidence that PRE improved muscle strength (pooled standardised mean difference (SMD)= 0.59 (95%CI: 0.16-1.01; I²=70%). This increase in muscle strength was maintained an average of 11 weeks after training stopped. Τhere was also moderate certainty evidence that it is inconclusive whether PRE has a small effect on gross motor function (SMD= 0.14 (95%CI: -0.09 to 0.36; I²=0%) or participation (SMD= 0.26 (95%CIs: -0.02 to 0.54; I²=0%). When PRE was compared with other therapy there were no between-group differences. Meta-regression demonstrated no effect of PRE intensity or training volume (frequency x total duration) on muscle strength (p > 0.5). No serious adverse events were reported. There is lack of evidence of the effectiveness of PRE in adults and non-ambulatory people with CP.

CONCLUSIONS

PRE is safe and increases muscle strength in young people with CP, which is maintained after training stops. The increase in muscle strength is unrelated to the PRE intensity or dose. CONTRIBUTION OF THE PAPER.

Identification of a polycomb responsive region in human HoxA cluster and its long-range interaction with polycomb enriched genomic regions

Polycomb and Trithorax group proteins (PcG, TrxG) epigenetically regulate developmental genes. These proteins bind with specific DNA elements, the Polycomb Response Element (PRE). Apart from mutations in polycomb/ trithorax proteins, altered cis-elements like PRE underlie the modified function and thus disease etiology. PREs are well studied in Drosophila, while only a few human PREs have been reported. We have identified a polycomb responsive DNA element, hPRE-HoxA3, in the intron of the HoxA3 gene. The hPRE-HoxA3 represses luciferase reporter activity in a PcG-dependent manner. The endogenous hPRE-HoxA3 element recruits PcG proteins and is enriched with repressive H3K27me3 marks, demonstrating that hPRE-HoxA3 is a part of the PcG-dependent gene regulatory network. Furthermore, it interacts with D11-12, the well-known PRE in the human Hox cluster. hPRE-Hox3 is a part of the 3-dimensional chromosomal domain organization as it is involved in the long-range interaction with other PcG enriched regions of Hox A, B, C, and D clusters.

Modified estimators of finite population distribution function based on dual use of auxiliary information under stratified random sampling

In survey sampling, information on auxiliary variables related to the main variable is often available in many practical problems. Since the mid-twentieth century, researchers have taken a keen interest in the use of auxiliary information due to its usefulness in estimation methods. The current study presents two new estimators for the distribution function of a finite population based on dual auxiliary variables. The new estimators can be used in situations where the researchers face some sort of complex data set. The mathematical equations for the bias and mean square error have been obtained for each proposed estimator. Besides, an empirical study simulation study has also been conducted to analyse the performance of estimators. It is found that the new suggested estimators of the distribution function of a finite population are more accurate than some of the existing estimators.

The Effect of ZnO, MgO, TiO2, and Na2O Modifiers on the Physical, Optical, and Radiation Shielding Properties of a TeTaNb Glass System

Novel glass samples with the composition 75TeO₂–5Ta₂O₅–15Nb₂O₅–5x (where x = ZnO, MgO, TiO₂, or Na₂O) in mole percent were prepared. The physical, optical, and gamma radiation shielding properties of the glass samples were studied over a wide energy spectrum ranging between 0.015 and 20 MeV. The glasses’ UV–vis spectra were utilized to evaluate the optical energy gap and refractive index. Glass samples had a refractive index ranging from 2.2005 to 2.0967. The results showed that the sample doped with zinc oxide (ZnO) recorded the highest density (ρ_glass), molar polarizability (α_m), molar refraction (Rm), refractive index (n), and third-order nonlinear optical susceptibility (χ³) and the lowest optical energy gap (E_opt) among the samples under investigation. When comparing the current glass system with various standard glass shielding materials, the prepared glass system showed superior shielding performance at energies ranging between 40 and 85 keV. These findings indicate that the prepared glass systems can be used in diagnostic X-rays, especially in dental applications.

Solid-State NMR Spectroscopy on Microbial Rhodopsins

Microbial rhodopsins represent the most abundant phototrophic systems known today. A similar molecular architecture with seven transmembrane helices and a retinal cofactor linked to a lysine in helix 7 enables a wide range of functions including ion pumping, light-controlled ion channel gating, or sensing. Deciphering their molecular mechanisms therefore requires a combined consideration of structural, functional, and spectroscopic data in order to identify key factors determining their function. Important insight can be gained by solid-state NMR spectroscopy by which the large homo-oligomeric rhodopsin complexes can be studied directly within lipid bilayers. This chapter describes the methodological background and the necessary sample preparation requirements for the study of photointermediates, for the analysis of protonation states, H-bonding and chromophore conformations, for 3D structure determination, and for probing oligomer interfaces of microbial rhodopsins. The use of data extracted from these NMR experiments is discussed in the context of complementary biophysical methods.

A Time-Kill Assay Study on the Synergistic Bactericidal Activity of Pomegranate Rind Extract and Zn (II) against Methicillin-Resistant Staphylococcus aureus (MRSA), Staphylococcus epidermidis,&nbsp;Escherichia coli, and Pseudomonas aeruginosa

There is a need for new antimicrobial systems due to increased global resistance to current antimicrobials. Pomegranate rind extract (PRE) and Zn (II) ions both possess a level of antimicrobial activity and work has previously shown that PRE/Zn (II) in combination possesses synergistic activity against Herpes simplex virus and Micrococcus luteus. Here, we determined whether such synergistic activity extended to other, more pathogenic, bacteria. Reference strains of methicillin-resistant Staphylococcus aureus (MRSA), Staphylococcus epidermidis, Escherichia coli, and Pseudomonas aeruginosa were cultured and subjected to challenge by PRE, Zn (II), or PRE + Zn (II), in time-kill assays. Data were obtained independently by two researchers using different PRE preparations. Statistically significant synergistic activity for PRE + Zn (II) was shown for all four bacterial strains tested compared to untreated controls, although the extent of efficacy and timescales varied. Zn (II) exerted activity and at 1 h, it was not possible to distinguish with PRE + Zn (II) combination treatment in all cases. PRE alone showed low activity against all four bacteria. Reproducible synergistic bactericidal activity involving PRE and Zn (II) has been confirmed. Potential mechanisms are discussed. The development of a therapeutic system that possesses demonstrable antimicrobial activity is supported which lends itself particularly to topical delivery applications, for example MRSA infections.

Ectopic expression of the atypical HLH FaPRE1 gene determines changes in cell size and morphology

PACLOBUTRAZOL RESISTANCE (PRE) genes code atypical HLH transcriptional regulators characterized by the absence of a DNA-binding domain but present an HLH dimerization domain. In vegetative tissues, the function of these HLH proteins has been related with cell elongation processes. In strawberry, three FaPRE genes are expressed, two of them (FaPRE2 and FaPRE3) in vegetative tissues while FaPRE1 is fruit receptacle-specific. Ubiquitous FaPRE1 accumulation produced elongated flower receptacles and plants due to the elongation of the main aerial vegetative organs, with the exception of leaves. Histological analysis clearly demonstrated that the observed phenotype was due to significant changes in the parenchymal cell's morphology. In addition, transcriptomic studies of the transgenic elongated flower receptacles allowed to identify a small group of differentially expressed genes that encode cell wall-modifying enzymes. Together, the data seem to indicate that, in the strawberry plant vegetative organs, FaPRE proteins could modulate the expression of genes related with the determination of the size and shape of the parenchymal cells.

Simultaneous measurement of 1HC/N-R2's for rapid acquisition of backbone and sidechain paramagnetic relaxation enhancements (PREs) in proteins

Paramagnetic relaxation enhancements (PREs) are routinely used to provide long-range distance restraints for the determination of protein structures, to resolve protein dynamics, ligand-protein binding sites, and lowly populated species, using Nuclear Magnetic Resonance Spectroscopy (NMR). Here, we propose a simultaneous ¹H-¹⁵ N, ¹H-¹³C SESAME based pulse scheme for the rapid acquisition of ¹H^C/N-R₂ relaxation rates for the determination of backbone and sidechain PREs of proteins. The ¹H^N-R₂ rates from the traditional and our approach on Ubiquitin (UBQ) are well correlated (R² = 0.99), revealing their potential to be used quantitatively. Comparison of the S57C UBQ calculated and experimental PREs provided backbone and side chain Q factors of 0.23 and 0.24, respectively, well-fitted to the UBQ NMR structure, showing that our approach can be used to acquire accurate PRE rates from the functionally important sites of proteins but in at least half the time as traditional methods.

Defining the Boundaries of Polycomb Domains in Drosophila

Polycomb group (PcG) proteins are an important group of transcriptional repressors that act by modifying chromatin. PcG target genes are covered by the repressive chromatin mark H3K27me3. Polycomb repressive complex 2 (PRC2) is a multiprotein complex that is responsible for generating H3K27me3. In Drosophila, PRC2 is recruited by Polycomb Response Elements (PREs) and then trimethylates flanking nucleosomes, spreading the H3K27me3 mark over large regions of the genome, the "Polycomb domains." What defines the boundary of a Polycomb domain? There is experimental evidence that insulators, PolII, and active transcription can all form the boundaries of Polycomb domains. Here we divide the boundaries of larval Polycomb domains into six different categories. In one category, genes are transcribed toward the Polycomb domain, where active transcription is thought to stop the spreading of H3K27me3. In agreement with this, we show that introducing a transcriptional terminator into such a transcription unit causes an extension of the Polycomb domain. Additional data suggest that active transcription of a boundary gene may restrict the range of enhancer activity of a Polycomb-regulated gene.

Capturing the Conformational Ensemble of the Mixed Folded Polyglutamine Protein Ataxin-3

Ataxin-3 is a deubiquitinase involved in protein quality control and other essential cellular functions. It preferentially interacts with polyubiquitin chains of four or more units attached to proteins delivered to the ubiquitin-proteasome system. Ataxin-3 is composed of an N-terminal Josephin domain and a flexible C terminus that contains two or three ubiquitin-interacting motifs (UIMs) and a polyglutamine tract, which, when expanded beyond a threshold, leads to protein aggregation and misfolding and causes spinocerebellar ataxia type 3. The high-resolution structure of the Josephin domain is available, but the structural and dynamical heterogeneity of ataxin-3 has so far hindered the structural description of the full-length protein. Here, we characterize non-expanded and expanded variants of ataxin-3 in terms of conformational ensembles adopted by the proteins in solution by jointly using experimental data from nuclear magnetic resonance and small-angle X-ray scattering with coarse-grained simulations. Our results pave the way to a molecular understanding of polyubiquitin recognition.

Polycomb and Trithorax Group Proteins: The Long Road from Mutations in Drosophila to Use in Medicine

Polycomb group (PcG) and Trithorax group (TrxG) proteins are evolutionarily conserved factors responsible for the repression and activation of the transcription of multiple genes in Drosophila and mammals. Disruption of the PcG/TrxG expression is associated with many pathological conditions, including cancer, which makes them suitable targets for diagnosis and therapy in medicine. In this review, we focus on the major PcG and TrxG complexes, the mechanisms of PcG/TrxG action, and their recruitment to chromatin. We discuss the alterations associated with the dysfunction of a number of factors of these groups in oncology and the current strategies used to develop drugs based on small-molecule inhibitors.

Lipid-nanodiscs formed by paramagnetic metal chelated polymer for fast NMR data acquisition

Lipid-nanodiscs have been shown to be an exciting innovation as a membrane-mimicking system for studies on membrane proteins by a variety of biophysical techniques, including NMR spectroscopy. Although NMR spectroscopy is unique in enabling the atomic-resolution investigation of dynamic structures of membrane-associated molecules, it, unfortunately, suffers from intrinsically low sensitivity. The long data acquisition often used to enhance the sensitivity is not desirable for sensitive membrane proteins. Instead, paramagnetic relaxation enhancement (PRE) has been used to reduce NMR data acquisition time or to reduce the amount of sample required to acquire an NMR spectra. However, the PRE approach involves the introduction of external paramagnetic probes in the system, which can induce undesired changes in the sample and on the observed NMR spectra. For example, the addition of paramagnetic ions, as frequently used, can denature the protein via direct interaction and also through sample heating. In this study, we show how the introduction of paramagnetic tags on the outer belt of polymer-nanodiscs can be used to speed-up data acquisition by significantly reducing the spin-lattice relaxation (T1) times with minimum-to-no alteration of the spectral quality. Our results also demonstrate the feasibility of using different types of paramagnetic ions (Eu3+, Gd3+, Dy3+, Er3+, Yb3+) for NMR studies on lipid-nanodiscs. Experimental results characterizing the formation of lipid-nanodiscs by the metal-chelated polymer, and their increased tolerance toward metal ions are also reported.

Pumilio response and AU-rich elements drive rapid decay of Pnrc2-regulated cyclic gene transcripts

Vertebrate segmentation is regulated by the segmentation clock, a biological oscillator that controls periodic formation of somites, or embryonic segments, which give rise to many mesodermal tissue types. This molecular oscillator generates cyclic gene expression with the same periodicity as somite formation in the presomitic mesoderm (PSM), an area of mesenchymal cells that give rise to mature somites. Molecular components of the clock include the Hes/her family of genes that encode transcriptional repressors, but additional genes cycle. Cyclic gene transcripts are cleared rapidly, and clearance depends upon the pnrc2 (proline-rich nuclear receptor co-activator 2) gene that encodes an mRNA decay adaptor. Previously, we showed that the her1 3'UTR confers instability to otherwise stable transcripts in a Pnrc2-dependent manner, however, the molecular mechanism(s) by which cyclic gene transcripts are cleared remained largely unknown. To identify features of the her1 3'UTR that are critical for Pnrc2-mediated decay, we developed an array of transgenic inducible reporter lines carrying different regions of the 3'UTR. We find that the terminal 179 nucleotides (nts) of the her1 3'UTR are necessary and sufficient to confer rapid instability. Additionally, we show that the 3'UTR of another cyclic gene, deltaC (dlc), also confers Pnrc2-dependent instability. Motif analysis reveals that both her1 and dlc 3'UTRs contain terminally-located Pumilio response elements (PREs) and AU-rich elements (AREs), and we show that the PRE and ARE in the last 179 ​nts of the her1 3'UTR drive rapid turnover of reporter mRNA. Finally, we show that mutation of Pnrc2 residues and domains that are known to facilitate interaction of human PNRC2 with decay factors DCP1A and UPF1 reduce the ability of Pnrc2 to restore normal cyclic gene expression in pnrc2 mutant embryos. Our findings suggest that Pnrc2 interacts with decay machinery components and cooperates with Pumilio (Pum) proteins and ARE-binding proteins to promote rapid turnover of cyclic gene transcripts during somitogenesis.

Paramagnetic-iterative relaxation matrix approach: extracting PRE-restraints from NOESY spectra for 3D structure elucidation of biomolecules

Paramagnetic relaxation enhancement (PRE) can be used to determine long-range distance restraints in biomolecules. The PREs are typically determined by analysis of intensity differences in HSQC experiments of paramagnetic and diamagnetic spin labels. However, this approach requires both isotope- and spin-labelling. Herein, we report a novel method to evaluate NOESY intensities in the presence of a paramagnetic moiety to determine PRE restraints. The advantage of our approach over HSQC-based approaches is the increased number of available signals without the need for isotope labelling. NOESY intensities affected by a paramagnetic center were evaluated during a structure calculation within the paramagnetic iterative relaxation matrix approach (P-IRMA). We applied P-IRMA to a 14-mer RNA with a known NMR solution structure, which allowed us to assess the quality of the PRE restraints. To this end, three different spin labels have been attached at different positions of the 14-mer to test the influence of flexibility on the structure calculation. Structural disturbances introduced by the spin label have been evaluated by chemical shift analysis. Furthermore, the impact of P-IRMA on the quality of the structure bundles were tested by intentionally leaving out available diamagnetic restraints. Our analyses show that P-IRMA is a powerful tool to refine RNA structures for systems that are insufficiently described by using only diamagnetic restraints.

PACLOBUTRAZOL-RESISTANCE Gene Family Regulates Floral Organ Growth with Unequal Genetic Redundancy in Arabidopsis thaliana

A PACLOBUTRAZOL-RESISTANCE (PRE) gene family, consisting of six genes in Arabidopsis thaliana, encodes a group of helix-loop-helix proteins that act in the growth-promoting transcriptional network. To delineate the specific role of each of the PRE genes in organ growth, we took a reverse genetic approach by constructing high order pre loss-of-function mutants of Arabidopsis thaliana. In addition to dwarf vegetative growth, some double or high order pre mutants exhibited defective floral development, resulting in reduced fertility. While pre2pre5 is normally fertile, both pre2pre6 and pre5pre6 showed reduced fertility. Further, the reduced fertility was exacerbated in the pre2pre5pre6 mutant, indicative of the redundant and critical roles of these PREs. Self-pollination assay and scanning electron microscopy analysis showed that the sterility of pre2pre5pre6 was mainly ascribed to the reduced cell elongation of anther filament, limiting access of pollens to stigma. We found that the expression of a subset of flower-development related genes including ARGOS, IAA19, ACS8, and MYB24 was downregulated in the pre2pre5pre6 flowers. Given these results, we propose that PREs, with unequal functional redundancy, take part in the coordinated growth of floral organs, contributing to successful autogamous reproduction in Arabidopsis thaliana.

Phylogenetic Analyses and GAGA-Motif Binding Studies of BBR/BPC Proteins Lend to Clues in GAGA-Motif Recognition and a Regulatory Role in Brassinosteroid Signaling

Plant GAGA-motif binding factors are encoded by the BARLEY B RECOMBINANT / BASIC PENTACYSTEINE (BBR/BPC) family, which fulfill indispensable functions in growth and development. BBR/BPC proteins control flower development, size of the stem cell niche and seed development through transcriptional regulation of homeotic transcription factor genes. They are responsible for the context dependent recruitment of Polycomb repressive complexes (PRC) or other repressive proteins to GAGA-motifs, which are contained in Polycomb repressive DNA-elements (PREs). Hallmark of the protein family is the highly conserved BPC domain, which is required for DNA binding. Here we study the evolution and diversification of the BBR/BPC family and its DNA-binding domain. Our analyses supports a further division of the family into four main groups (I-IV) and several subgroups, to resolve a strict monophyletic descent of the BPC domain. We prove a polyphyletic origin for group III proteins, which evolved from group I and II members through extensive loss of domains in the N-terminus. Conserved motif searches lend to the identification of a WAR/KHGTN consensus and a TIR/K motif at the very C-terminus of the BPC-domain. We could show by DPI-ELISA that this signature is required for DNA-binding in AtBPC1. Additional binding studies with AtBPC1, AtBPC6 and mutated oligonucleotides consolidated the binding to GAGA tetramers. To validate these findings, we used previously published ChIP-seq data from GFP-BPC6. We uncovered that many genes of the brassinosteroid signaling pathway are targeted by AtBPC6. Consistently, bpc6, bpc4 bpc6, and lhp1 bpc4 bpc4 mutants display brassinosteroid-dependent root growth phenotypes. Both, a function in brassinosteroid signaling and our phylogenetic data supports a link between BBR/BPC diversification in the land plant lineage and the complexity of flower and seed plant evolution.

Stable and rigid DTPA-like paramagnetic tags suitable for in vitro and in situ protein NMR analysis

Organic synthesis of a ligand with high binding affinities for paramagnetic lanthanide ions is an effective way of generating paramagnetic effects on proteins. These paramagnetic effects manifested in high-resolution NMR spectroscopy are valuable dynamic and structural restraints of proteins and protein-ligand complexes. A paramagnetic tag generally contains a metal chelating moiety and a reactive group for protein modification. Herein we report two new DTPA-like tags, 4PS-PyDTTA and 4PS-6M-PyDTTA that can be site-specifically attached to a protein with a stable thioether bond. Both protein-tag adducts form stable lanthanide complexes, of which the binding affinities and paramagnetic tensors are tunable with respect to the 6-methyl group in pyridine. Paramagnetic relaxation enhancement (PRE) effects of Gd(III) complex on protein-tag adducts were evaluated in comparison with pseudocontact shift (PCS), and the results indicated that both 4PS-PyDTTA and 4PS-6M-PyDTTA tags are rigid and present high-quality PREs that are crucially important in elucidation of the dynamics and interactions of proteins and protein-ligand complexes. We also show that these two tags are suitable for in-situ protein NMR analysis.

Cloning and functional characterization of human Pak1 promoter by steroid hormones

P21-activated kinase 1 (Pak1) is known to be involved in a plethora of functions including cell growth, survival and can lead to cell transformation and tumor progression especially in breast tissue. Multiple studies have shown Pak1 dysregulation as a change in DNA copy number as well as gene expression levels, suggesting many regulatory mechanisms at transcriptional and translational level. However, very little is known about the transcriptional regulation of the human Pak1 promoter. Here, we focus on Pak1 promoter regulation by steroid hormones along with their respective receptors that are also crucial players in breast tissue function and tumorigenesis. Our results show high Pak1 expression in breast cancer cell lines and in breast tumor tissue. It also suggests that Pak1 is hormone responsive, whose expression can be modulated by steroid hormones namely, estrogen in the form of 17β-estradiol (E2) and progesterone (P4). Sequence analysis of a 3.2kb Pak1 proximal promoter region shows the presence of PRE (progesterone response element) and ERE (estrogen response element) half sites, that were further cloned and characterized. Results from promoter analysis showed that Pak1 promoter activity is mediated by PR via its binding to PRE present on the Pak1 promoter that was further reaffirmed in vitro by electrophoretic mobility shift assay (EMSA) and chromatin immunoprecipitation assay (ChIP). Our results together suggest that it is the PR isoform B regulates Pak1 promoter. To our knowledge, this is the first study to report the detailed characterization and transcriptional regulation of the human Pak1 promoter by steroid hormones.

Human βB2-Crystallin Forms a Face-en-Face Dimer in Solution: An Integrated NMR and SAXS Study

βγ-Crystallins are long-lived eye lens proteins that are crucial for lens transparency and refractive power. Each βγ-crystallin comprises two homologous domains, which are connected by a short linker. γ-Crystallins are monomeric, while β-crystallins crystallize as dimers and multimers. In the crystal, human βB2-crystallin is a domain-swapped dimer while the N-terminally truncated βB1-crystallin forms a face-en-face dimer. Combining and integrating data from multi-angle light scattering, nuclear magnetic resonance, and small-angle X-ray scattering of full-length and terminally truncated human βB2-crystallin in solution, we show that both these βB2-crystallin proteins are dimeric, possess C2 symmetry, and are more compact than domain-swapped dimers. Importantly, no inter-molecular paramagnetic relaxation enhancement effects compatible with domain swapping were detected. Our collective experimental results unambiguously demonstrate that, in solution, human βB2-crystallin is not domain swapped and exhibits a face-en-face dimer structure similar to the crystal structure of truncated βB1-crystallin.

High resolution observed in 800 MHz DNP spectra of extremely rigid type III secretion needles

The cryogenic temperatures at which dynamic nuclear polarization (DNP) solid-state NMR experiments need to be carried out cause line-broadening, an effect that is especially detrimental for crowded protein spectra. By increasing the magnetic field strength from 600 to 800 MHz, the resolution of DNP spectra of type III secretion needles (T3SS) could be improved by 22 %, indicating that inhomogeneous broadening is not the dominant effect that limits the resolution of T3SS needles under DNP conditions. The outstanding spectral resolution of this system under DNP conditions can be attributed to its low overall flexibility.

Intermolecular Paramagnetic Relaxation Enhancement (PRE) Studies of Transient Complexes in Intrinsically Disordered Proteins

NMR interchain paramagnetic relaxation enhancement (PRE) techniques are a very powerful approach for detecting transient interchain interactions between intrinsically disordered proteins. These experiments, requiring a mixed sample containing a 1:1 ratio of isotope-labeled (15)N protein and natural abundance (14)N protein with a paramagnetic spin label, provide data that is limited to interchain interactions only. Application of these experiments to weakly associated transient species such as those that are present in the very early stages of self-assembly processes will aid our understanding of protein aggregation or fibril formation processes.

Hsp70 biases the folding pathways of client proteins

The 70-kDa heat shock protein (Hsp70) family of chaperones bind cognate substrates to perform a variety of different processes that are integral to cellular homeostasis. Although detailed structural information is available on the chaperone, the structural features of folding competent substrates in the bound form have not been well characterized. Here we use paramagnetic relaxation enhancement (PRE) NMR spectroscopy to probe the existence of long-range interactions in one such folding competent substrate, human telomere repeat binding factor (hTRF1), which is bound to DnaK in a globally unfolded conformation. We show that DnaK binding modifies the energy landscape of the substrate by removing long-range interactions that are otherwise present in the unbound, unfolded conformation of hTRF1. Because the unfolded state of hTRF1 is only marginally populated and transiently formed, it is inaccessible to standard NMR approaches. We therefore developed a (1)H-based CEST experiment that allows measurement of PREs in sparse states, reporting on transiently sampled conformations. Our results suggest that DnaK binding can significantly bias the folding pathway of client substrates such that secondary structure forms first, followed by the development of longer-range contacts between more distal parts of the protein.

Herbicide options for effective weed management in dry direct-seeded rice under scented rice-wheat rotation of western Indo-Gangetic Plains

Farmers' participatory field trials were conducted at Madhuban, and Taraori, the two participatory experimental sites/locations of the Cereal Systems Initiative for South Asia (CSISA), a collaborative project of IRRI and CIMMYT in Karnal district of Haryana, India, during Kharif (wet season) 2010 and 2011. This research aimed to evaluate preemergence (PRE) and postemergence (POST) herbicides for providing feasible and economically viable weed management options to farmers for predominant scented rice varieties. Treatments with pendimethalin PRE fb bispyribac-sodium + azimsulfuron POST had lower weed biomass at 45 days after sowing (DAS). At Madhuban, highest grain yield of scented basmati rice (3.43 t ha^-1) was recorded with the sequential application of pendimethalin PRE fb bispyribac-sodium + azimsulfuron POST. However, at Taraori, yields were similar with pendimethalin or oxadiargyl PRE fb bispyribac-sodium and/or azimsulfuron POST. Applying oxadiargyl by mixing with sand onto flooded field was less effective than spray applications in non-flooded field. The benefit-cost ratio of rice crop was higher with herbicide treatments at both sites as compared with the non-treated weed-free check except single PRE and POST applications and sequential application of oxadiargyl PRE fb oxadiargyl PRE. In a separate experiment conducted at Nagla and Taraori sites, scented rice cultivars' ('CSR 30' and 'Pusa 1121') tolerance to three rates of azimsulfuron (15, 25, and 35 g ai ha^-1) was evaluated over two years (2010 and 2011). CSR 30 (superfine, scented) was more sensitive to higher rates (35 g ai ha^-1) of azimsulfuron as compared to Pusa 1121 (fine, scented). Crop injuries were 8 and 28% in case of CSR 30; 5 and 15% in Pusa 1121 when applied with azimsulfuron 25 and 35 g ai ha^-1, respectively. Azimsulfuron applied at 35 g ai ha^-1 reduced yield in both cultivars but in CSR 30 yield reduction was twofold (11.5%) as that of Pusa 1121 (5.2%).

Role of Transcriptional Read-Through in PRE Activity in Drosophila melanogaster

Maintenance of the individual patterns of gene expression in different cell types is required for the differentiation and development of multicellular organisms. Expression of many genes is controlled by Polycomb (PcG) and Trithorax (TrxG) group proteins that act through association with chromatin. PcG/TrxG are assembled on the DNA sequences termed PREs (Polycomb Response Elements), the activity of which can be modulated and switched from repression to activation. In this study, we analyzed the influence of transcriptional read-through on PRE activity switch mediated by the yeast activator GAL4. We show that a transcription terminator inserted between the promoter and PRE doesn't prevent switching of PRE activity from repression to activation. We demonstrate that, independently of PRE orientation, high levels of transcription fail to dislodge PcG/TrxG proteins from PRE in the absence of a terminator. Thus, transcription is not the main factor required for PRE activity switch.

Toward optimal-resolution NMR of intrinsically disordered proteins

Proteins, which, in their native conditions, sample a multitude of distinct conformational states characterized by high spatiotemporal heterogeneity, most often termed as intrinsically disordered proteins (IDPs), have become a target of broad interest over the past 15years. With the growing evidence of their important roles in fundamental cellular processes, there is an urgent need to characterize the conformational behavior of IDPs at the highest possible level. The unique feature of NMR spectroscopy in the context of IDPs is its ability to supply details of their structural and temporal alterations at atomic-level resolution. Here, we briefly review recently proposed NMR-based strategies to characterize transient states populated by IDPs and summarize the latest achievements and future prospects in methodological development. Because low chemical shift dispersion represents the major obstacle encountered when studying IDPs by nuclear magnetic resonance, particular attention is paid to techniques allowing one to approach the physical limits of attainable resolution.

Sensitivity enhancement and contrasting information provided by free radicals in oriented-sample NMR of bicelle-reconstituted membrane proteins

Elucidating structure and topology of membrane proteins (MPs) is essential for unveiling functionality of these important biological constituents. Oriented-sample solid-state NMR (OS-NMR) is capable of providing such information on MPs under nearly physiological conditions. However, two dimensional OS-NMR experiments can take several days to complete due to long longitudinal relaxation times combined with the large number of scans to achieve sufficient signal sensitivity in biological samples. Here, free radicals 5-DOXYL stearic acid, TEMPOL, and CAT-1 were added to uniformly (15)N-labeled Pf1 coat protein reconstituted in DMPC/DHPC bicelles, and their effect on the longitudinal relaxation times (T1Z) was investigated. The dramatically shortened T1Z's allowed for the signal gain per unit time to be used for either: (i) up to a threefold reduction of the total experimental time at 99% magnetization recovery or (ii) obtaining up to 74% signal enhancement between the control and radical samples during constant experimental time at "optimal" relaxation delays. In addition, through OS-NMR and high-field EPR studies, free radicals were able to provide positional constraints in the bicelle system, which provide a description of the location of each residue in Pf1 coat protein within the bicellar membranes. This information can be useful in the determination of oligomerization states and immersion depths of larger membrane proteins.

Cyclic AMP enhances progesterone action in human myometrial cells

Cyclic AMP (cAMP) has been shown to promote progesterone and glucocorticoid action in a variety of cellular settings. In this study, we have used human myometrial cells to investigate whether cAMP potentiates the ability of progesterone to repress IL-1β-driven COX-2 expression. We found that forskolin enhanced progesterone-repression of IL-1β-driven COX-2 expression in association with delayed IL-1β-induced nuclear phospho-p65 entry and reduced NF-κB binding to the COX-2 promoter. Further, forskolin enhanced the progesterone-induced expression of FKBP5 and 11βHSD1, progesterone-driven activity of a progesterone response element (PRE) and progesterone receptor (PR)-B binding to a transfected PRE. In addition, forskolin treatment increased PR-B levels and reduced the PR-A:PR-B ratio while acutely decreasing the association between PR and nuclear receptor co-repressor (NCoR) and reducing NCoR levels after 6h. These findings are of importance in situations where enhancing progesterone activity is desirable, for example in the management of endometrial cancer, the promotion of endometrial receptivity or the maintenance of myometrial quiescence during pregnancy.

Isolation and expression analysis of proline metabolism-related genes in Chrysanthemum lavandulifolium

Proline plays a significant role in plant resistance to abiotic stresses, and its level is determined by a combination of synthesis, catabolism and transport. The primary proteins involved are Δ(1)-pyrroline-5-carboxylate synthetase (P5CS), proline dehydrogenase (PDH) and proline transporter (ProT). To utilise proline metabolism to improve the stress resistance of Chrysanthemum×morifolium, we isolated two P5CS-homologous genes (ClP5CS1 and ClP5CS2), one PDH gene (ClPDH) and four ProT-homologous genes (ClProT1-4) (GenBANK accession numbers: KF743136-KF743142) from Chrysanthemum lavandulifolium, which is closely related to chrysanthemums and exhibits strong resistance to stresses. Expression analysis of these genes in different organs and under various stresses indicated that ClP5CSs showed substantial constitutive expression, while ClPDH was only strongly expressed in the capitulum and was inhibited under most stresses. The expression patterns of four ClProT genes presented characteristics of organ specificity and disparity under stresses. Above all, the expression of ClProT2 was restricted to above-ground organs, especially strong in the capitulum and could be obviously induced by various stress conditions. Promoters of ClPDH and ClProTs contained many cis-acting regulatory elements involved in stress responses and plant growth and development. High levels of free proline were found in flower buds, the capitulum under the non-stress condition and later periods of stress conditions except cold treatment. Interestingly, organ specificity and disparity also exist in the level of free proline under different stress conditions. Our study indicates that ClProTs play significant roles in proline accumulation and stress responses, and that ClProT2 could be used to genetically modify the stress resistance of chrysanthemums. In addition, proline metabolism might be closely related to plant flowering and floral development.

Revisiting the roles of progesterone and allopregnanolone in the nervous system: resurgence of the progesterone receptors

Progesterone is commonly considered as a female reproductive hormone and is well-known for its role in pregnancy. It is less well appreciated that progesterone and its metabolite allopregnanolone are also male hormones, as they are produced in both sexes by the adrenal glands. In addition, they are synthesized within the nervous system. Progesterone and allopregnanolone are associated with adaptation to stress, and increased production of progesterone within the brain may be part of the response of neural cells to injury. Progesterone receptors (PR) are widely distributed throughout the brain, but their study has been mainly limited to the hypothalamus and reproductive functions, and the extra-hypothalamic receptors have been neglected. This lack of information about brain functions of PR is unexpected, as the protective and trophic effects of progesterone are much investigated, and as the therapeutic potential of progesterone as a neuroprotective and promyelinating agent is currently being assessed in clinical trials. The little attention devoted to the brain functions of PR may relate to the widely accepted assumption that non-reproductive actions of progesterone may be mainly mediated by allopregnanolone, which does not bind to PR, but acts as a potent positive modulator of γ-aminobutyric acid type A (GABA(A) receptors. The aim of this review is to critically discuss effects of progesterone on the nervous system via PR, and of allopregnanolone via its modulation of GABA(A) receptors, with main focus on the brain.

L-arginine does not improve biochemical and hormonal response in trained runners after 4 weeks of supplementation

It has been hypothesized that L-arginine improves exercise performance by increasing nitric oxide synthesis and levels of insulin and growth hormone (GH). Metabolic and hormonal responses to chronic L-arginine supplementation may clarify the mechanisms underlying its putative physiologic effects on physical performance. Therefore, the aim of this study was to investigate the effects that 4 weeks of supplementation with L-arginine would have on metabolic and hormonal parameters at rest and in response to exercise. Fifteen healthy runners were divided into treatment (ARG; 6 g L-arginine) and placebo (PLA; 6 g cornstarch) groups. On the first visit, blood samples were collected for baseline, and the supplement or placebo was provided. After 4 weeks of supplementation (second visit), blood samples were collected at the following intervals: at rest, immediately after the first 5-km time-trial running test (5km-TT), immediately after the second 5km-TT, and after 20 minutes of recovery (+20). In addition to exercise performance (total running time), plasma nitrate, nitrite, nitrate plus nitrite, cyclic guanosine monophosphate, lactate, ammonia and serum insulin, GH, insulin-like growth factor 1, and cortisol concentrations were evaluated. There were significant increases in plasma nitrite, cyclic guanosine monophosphate, lactate, ammonia and serum GH, and cortisol at the first 5km-TT, immediately after the second 5km-TT, and +20 in both ARG and PLA. Nitrate plus nitrite and nitrate increased only at +20. No significant change was observed in serum insulin and insulin-like growth factor 1 in any sample period. Total running time did not differ significantly between the 2 tests, in either ARG or PLA. Thus, according to our results, 4 weeks of L-arginine supplementation did not cause beneficial changes in metabolic and hormonal parameters, beyond those achieved with exercise alone.

Polypyrimidine tract binding protein (PTB) associates with intronic and exonic domains to squelch nuclear export of unspliced RNA

Retention of unspliced pre-messenger RNA (pre-mRNA) in the nucleus is essential for cell survival. Available nuclear factors must recognize and discern between diverse export signals present in pre-mRNA to establish an export inhibitory complex. We found that polypyrimidine domains present in both intron and exon were important for export inhibition of a minigene transcript based on hepatitis B virus pregenomic RNA. Overexpression of PTB drastically reduced export and presence of RRM4 domain seemed critical. This inhibitory network overrode stimulation from an exonic export-facilitating element. We posit that binding of PTB to multiple loci on pre-mRNA regulates nuclear retention.

The cytoplasmic domain of the T-cell receptor zeta subunit does not form disordered dimers

Intrinsically disordered regions in proteins play active roles in recognition, signaling and molecular sorting. They often undergo coupled folding and binding giving rise to largely ordered interfaces with their binding partners. The cytoplasmic region of the T-cell receptor zeta subunit (ζcyt) has been previously proposed to specifically dimerize in the absence of a disorder-to-order transition, suggesting an intriguing dimerization mechanism that may involve multiple transient interfaces. We show here using analytical ultracentrifugation, NMR, size-exclusion chromatography (SEC) and multi-angle light scattering that neither ζcyt nor the cytoplasmic region of CD3ε significantly populates a dimeric state but that they are mostly monomers in solution up to millimolar concentrations. They experience a salt- and concentration-dependent shift of their elution volume in SEC previously interpreted as dimerization. Our data show that ζcyt does not form a highly disordered protein complex and leaves open the question as to whether completely disordered dimers (or other oligomers) exist in nature.

Blockage of progesterone receptor effectively protects pancreatic islet beta cell viability

The progesterone receptor (PR), a member of nuclear receptor superfamily, is closely associated with gestational, type 1 and type 2 diabetes. However, the underlying mechanisms remain obscure. Here we found that PR activation increased the pro-inflammatory cytokines (PIC)-induced injury in Min6 cells, and PR blockage with siRNA interference protected the cells from damage. Moreover, the new discovered PR antagonist SC51089 effectively improved cell survival by reducing the PIC-stimulated cell apoptosis in Min6 cells. Immunoblotting assays indicated that either PR agonist progesterone (P4) or PR-B over-expression promoted the PIC-induced reinforces of extracellular-signal-regulated kinase 1/2 phosphorylation (p-Erk) and protein 53 (p53), and the attenuations of protein kinase B phosphorylation (p-AKT) and tumor necrosis factor receptor-associated factor 2 (TRAF2). SC51089 could reverse all the P4- or PR-B over-expression induced effects. In addition, PR siRNA inference based assay further supported that SC51089 protected pancreatic islet beta cells from the PR activation or PIC-induced injury by targeting PR and this protective action was mediated by AKT signaling pathway. To our knowledge, this current work might be the first report on the regulation of PR in pancreatic islet beta cell survival. It is expected that SC51089, as a non-steroid PR antagonist, might also find its potential in anti-diabetic research.

In vitro antioxidant and anti-inflammatory activities of extracts from Potentilla recta and its main ellagitannin, agrimoniin

ETHNOPHARMACOLOGICAL RELEVANCE

Potentilla recta is one of the numerous cinquefoil species growing in Poland. It is used in traditional medicine e.g. in the treatment of skin inflammation.

AIM OF THE STUDY

The purpose of the present study is to evaluate antioxidant and anti-inflammatory activities of extracts and subfractions of the P. recta herb (obtained by using solvents of different polarity) in in vitro systems as well as to examine their chemical composition.

MATERIALS AND METHODS

Antioxidant activities of the extracts, subfractions and agrimoniin were evaluated using DPPH and three other radicals (O2(-), H2O2, and HClO) generated in cell-free systems. Anti-hyaluronidase activity was measured by using the turbidimetric method. Inhibition of lipoxidase activity was measured spectrophotometrically, using linoleic acid as a substrate. The composition of the most active subfraction was determined using the HPLC-DAD-MS(n) method.

RESULTS

All tested samples showed scavenging activity against all the examined reactive species in a concentration-dependent manner. The highest scavenging activity against DPPH, H2O2 and HClO was observed in the ethyl acetate subfraction (PRE3) (SC50 ± SEM [μg/mL]: 25.39 ± 2.49, 1.79 ± 0.25 and 8.52 ± 1.16 respectively). It was only in the xanthine/xanthine oxidase system that the antioxidation potential of the diethyl ether subfraction (PRE2) (SC50 ± SEM [μg/mL]: 6.59 ± 1.33) was higher than that of the subfraction PRE3 (SC50 ± SEM [μg/mL]: 8.57 ± 1.37). Also, in the studies of lipoxidase and hyaluronidase inhibition activity the strongest effect was observed for PRE3, with IC50 [μg/mL] = 86.31 ± 5.46, and 12.99 ± 1.31, respectively. The chromatographic method (HPTLC-DPPH) revealed that the principal substance responsible for the activity, is a tannin like compound. Isolated agrimoniin showed significant reactive oxygen species scavenging activity and significant enzyme inhibition activity (including xanthine oxidase inhibition activity). Agrimoniin exerted the strongest scavenging activity against H2O2 (SC50 ± SEM [μM]: 0.20 ± 0.01). This compound also significantly inhibited the enzymatic activity of lipoxidase (IC50 [μM] = 36.47 ± 1.29), and, particularly, of hyaluronidase (IC50 [μM] = 2.65 ± 0.40).

CONCLUSIONS

The strong scavenging activity against H2O2, and the inhibition of the enzymatic activity of lipoxidase, and particularly, hyaluronidase observed for the tested subfractions and agrimoniin, partly explain the beneficial effects of P. recta in treatment of skin inflammation.