Are proposed early genetic codes capable of encoding viable proteins?

Proteins are elaborate biopolymers balancing between contradicting intrinsic propensities to fold, aggregate or remain disordered. Assessing their primary structural preferences observable without evolutionary optimization has been reinforced by the recent identification of de novo proteins that have emerged from previously non-coding sequences. In this paper we investigate structural preferences of hypothetical proteins translated from random DNA segments using the standard genetic code and three of its proposed evolutionarily predecessor models encoding 10, 6 and 4 amino acids, respectively. Our only main assumption is that the disorder, aggregation and transmembrane helix predictions used are able to reflect the differences in the trends of the protein sets investigated. We found that the 10-residue code encodes proteins that resemble modern proteins in their predicted structural properties. All of the investigated early genetic codes give rise to proteins with enhanced disorder and diminished aggregation propensities. Our results suggest that an ancestral genetic code similar to the proposed 10-residue one is capable of encoding functionally diverse proteins but these might have existed under conditions different from today's common physiological ones. The existence of a protein functional repertoire for the investigated earlier stages which is quite distinct as it is today can be deduced from the presented results

CoNSEnsX: an ensemble view of protein structures and NMR-derived experimental data

<p>Abstract</p> <p>Background</p> <p>In conjunction with the recognition of the functional role of internal dynamics of proteins at various timescales, there is an emerging use of dynamic structural ensembles instead of individual conformers. These ensembles are usually substantially more diverse than conventional NMR ensembles and eliminate the expectation that a single conformer should fulfill all NMR parameters originating from 10¹⁶- 10¹⁷molecules in the sample tube. Thus, the accuracy of dynamic conformational ensembles should be evaluated differently to that of single conformers.</p> <p>Results</p> <p>We constructed the web application CoNSEnsX (Consistency of NMR-derived Structural Ensembles with eXperimental data) allowing fast, simple and convenient assessment of the correspondence of the ensemble as a whole with diverse independent NMR parameters available. We have chosen different ensembles of three proteins, human ubiquitin, a small protease inhibitor and a disordered subunit of cGMP phosphodiesterase 5/6 for detailed evaluation and demonstration of the capabilities of the CoNSEnsX approach.</p> <p>Conclusions</p> <p>Our results present a new conceptual method for the evaluation of dynamic conformational ensembles resulting from NMR structure determination. The designed CoNSEnsX approach gives a complete evaluation of these ensembles and is freely available as a web service at <url>http://consensx.chem.elte.hu</url>.</p

The role of landscape history in determining allelic richness of European ground squirrels (Spermophilus citellus) in Central Europe

Genetic diversity is of paramount importance for individual fitness and evolutionary potential of populations. For conservation planning it is crucial to know how genetically diverse a species is and what factors may explain variation of genetic diversity among populations. Our aim was to evaluate the effects of landscape history, ecological isolation, and local population size on allelic richness of local populations in European ground squirrels (Spermophiluscitellus). We genotyped 144 individuals from nine local populations collected in two neighbouring regions with decades of different landscape history. We assessed allelic richness, ecological isolation and local population size by eleven polymorphic microsatellites, the isolation index of Rodríguez and Delibes,and standardised counts of burrows openings, respectively. Statistical models indicated a strong effect of landscape history on allelic richness of local populations. Ecological isolation of local populations apparently played only a marginal role, and local population size was an unimportant factor. Our modelling results highlight the dominant role of landscape history for the genetic diversity of S. citellus. The strong landscape history effect encountered presently includes a different region-specific socio-economic development due to distinct agricultural systems in the two regions, especially after World War II. Levels of ecological isolation of local populations have diverged in an extent too small to explain variation of local allelic richness. The lack of significant effect of local population size suggests that census sizes of the populations studied are all not critically low. Moreover,census and estimated effective population sizes were not closely related. Establishing corridors or translocating S. citellus in the species’ historical range should be encouraged to promote gene flow between local populations and counteract the loss of genetic diversity by drift, provided that no conflicting factors (ecological, epidemiological, etc.) exist

Survival of Myocardial Infarction Patients with Diabetes Mellitus at the Invasive Era (Results from the Városmajor Myocardial Infarction Registry)

Introduction. Due to the lifelong nature of diabetes mellitus (DM), it has been demonstrated to have significant effects on patients’ morbidity and mortality. The present study aimed to assess the effects of DM on the clinical outcome and survival in patients who underwent percutaneous coronary intervention (PCI) due to myocardial infarction (MI) and to examine the relationship of DM to the type of the MI and to left ventricular (LV) and renal functions. Methods. A total of 12,270 patients with ST-elevation MI (STEMI) or non-ST-elevation MI (NSTEMI) were revascularized at our Institution between 2005 and 2013. In this pool of patients, 4388 subjects had DM, while 7018 cases had no DM. Results. In both STEMI and NSTEMI, the 30-day and 1-year survival were worse in diabetic patients as compared to non-diabetic cases. In the patients with DM, NSTEMI showed worse prognosis within 1-year than STEMI similarly to non-diabetic subjects. Regarding survival, the presence of DM seemed to be more important than the type of MI. Regardless of the presence of DM, reduced LV function was a maleficent prognostic sign and DM significantly reduced the prognosis both in case of reduced and normal LV function. Survival is primarily affected by LV function, rather than DM. Worse renal function is associated with worse 30-day and 1-year survival in both cases with and without DM. Considering different renal functions, the presence of DM worsens both short- and long-term survival. Survival is primarily affected by renal function, rather than DM. Conclusions. The results from a high-volume PCI center confirm significant the negative prognostic impact of DM on survival in MI patients. DM is a more important prognostic factor than the type of the MI. However, survival is primarily affected by LV and renal functions, rather than DM. These results could highlight our attention on the importance of recent DM treatment with new drugs including SGLT-2 inhibitors and GLP-1 antagonists with beneficial effects on survival

Is youth unemployment really the major worry? (AOM)

Youth unemployment is neither the only nor the basic problem of the European labour market. The comparative analysis of unemployment data demonstrates that the unemployment of older people is even more serious. The article proves that the weight of young people in total unemployment has as a tendency been declining in the “inner periphery” of the EU, among them in Central and Eastern European member states (CEECs). The trend is just the opposite in the developed or “core” countries of the Union where youngsters took a higher share in total unemployment in 2012 than 10-12 years ago. In Europe there are millions of young people beyond the active unemployed who do not want to work or think they cannot find a job that fulfils their expectations and refuse to take part in any kind of education or training (NEETs-“Not in Employment, Education or Training”). By estimating the rate of NEETs in the adult population the article claims that the NEETs-phenomenon is not the differentia specifica of the youth. At the end the article details two suggestions for the mitigation of the problem. It concludes that the joblessness in Europe is an old and tendencially worsening problem that cannot be solved by particular policies

The Absence of N-Acetyl-D-glucosamine Causes Attenuation of Virulence of Candida albicans upon Interaction with Vaginal Epithelial Cells In Vitro.

To better understand the molecular events underlying vulvovaginal candidiasis, we established an in vitro system. Immortalized vaginal epithelial cells were infected with live, yeast form C. albicans and C. albicans cultured in the same medium without vaginal epithelial cells were used as control. In both cases a yeast to hyphae transition was robustly induced. Whole transcriptome sequencing was used to identify specific gene expression changes in C. albicans. Numerous genes leading to a yeast to hyphae transition and hyphae specific genes were upregulated in the control hyphae and the hyphae in response to vaginal epithelial cells. Strikingly, the GlcNAc pathway was exclusively triggered by vaginal epithelial cells. Functional analysis in our in vitro system revealed that the GlcNAc biosynthesis is involved in the adherence to, and the ability to kill, vaginal epithelial cells in vitro, thus indicating the key role for this pathway in the virulence of C. albicans upon vulvovaginal candidiasis

Cyano-and ketone-containing selenoesters as multi-target compounds against resistant cancers

Fifteen selenocompounds, comprising of eight ketone-containing selenoesters (K1–K8, also known as oxoselenoesters) and seven cyano-containing selenoesters (N1–N7, known also as cyanoselenoesters), have been designed, synthesized, and evaluated as novel anticancer agents. These compounds are derivatives of previously reported active selenoesters and were prepared following a three-step one-pot synthetic route. The following evaluations were performed in their biological assessment: cytotoxicity determination, selectivity towards cancer cells in respect to non-cancer cells, checkerboard combination assay, ABCB1 inhibition and inhibition of ABCB1 ATPase activity, apoptosis induction, and wound healing assay. As key results, all the compounds showed cytotoxicity against cancer cells at low micromolar concentrations, with cyanoselenoesters being strongly selective. All of the oxoselenoesters, except K4, were potent ABCB1 inhibitors, and two of them, namely K5 and K6, enhanced the activity of doxorubicin in a synergistic manner. The majority of these ketone derivatives modulated the ATPase activity, showed wound healing activity, and induced apoptosis, with K3 being the most potent, with a potency close to that of the reference compound. To summarize, these novel derivatives have promising multi-target activity, and are worthy to be studied more in-depth in future works to gain a greater understanding of their potential applications against cancer.The study was supported by the projects SZTE ÁOK-KKA 2018/270-62-2 of the University of Szeged, Faculty of Medicine and GINOP-2.3.2-15-2016-00038 (Hungary); and Consejo Superior de Investigaciones Científicas (CSIC, Spain, project LINKA20285). This research was funded by VISEGRAD FUND, grant number 22010090; and by the mobility project from the Czech Ministry of Education, Youth and Sports INTER-COST, grant number LTC19007. This article is based upon work from COST Action 17104 , supported by COST (European Cooperation in Science and Technology), (http://www.cost.eu, accessed on 17 September 2021). The study was supported also by two cultural associations: “Trevinca” and “Iniciativas Ropelanas”

Role of Right Ventricular Global Longitudinal Strain in Predicting Early and Long-Term Mortality in Cardiac Resynchronization Therapy Patients.

BACKGROUND: Right ventricular (RV) dysfunction has been associated with poor prognosis in chronic heart failure (HF). However, less data is available about the role of RV dysfunction in patients with cardiac resynchronization therapy (CRT). We aimed to investigate if RV dysfunction would predict outcome in CRT. DESIGN: We enrolled prospectively ninety-three consecutive HF patients in this single center observational study. All patients underwent clinical evaluation and echocardiography before CRT and 6 months after implantation. We assessed RV geometry and function by using speckle tracking imaging and calculated strain parameters. We performed multivariable Cox regression models to test mortality at 6 months and at 24 months. RESULTS: RV dysfunction, characterized by decreased RVGLS (RV global longitudinal strain) [10.2 (7.0-12.8) vs. 19.5 (15.0-23.9) %, p<0.0001] and RVFWS (RV free wall strain) [15.6 (10.0-19.3) vs. 17.4 (10.5-22.2) %, p = 0.04], improved 6 months after CRT implantation. Increasing baseline RVGLS and RVFWS predicted survival independent of other parameters at 6 months [hazard ratio (HR) = 0.37 (0.15-0.90), p = 0.02 and HR = 0.42 (0.19-0.89), p = 0.02; per 1 standard deviation increase, respectively]. RVGLS proved to be a significant independent predictor of mortality at 24 months [HR = 0.53 (0.32-0.86), p = 0.01], and RVFWS showed a strong tendency [HR = 0.64 (0.40-1.00), p = 0.05]. The 24-month survival was significantly impaired in patients with RVGLS below 10.04% before CRT implantation [area under the curve = 0.72 (0.60-0.84), p = 0.002, log-rank p = 0.0008; HR = 5.23 (1.76-15.48), p = 0.003]. CONCLUSIONS: Our findings indicate that baseline RV dysfunction is associated with poor short-term and long-term prognosis after CRT implantation

Quantification of the relative contribution of the different right ventricular wall motion components to right ventricular ejection fraction

Abstract Three major mechanisms contribute to right ventricular (RV) pump function: (i) shortening of the longitudinal axis with traction of the tricuspid annulus towards the apex; (ii) inward movement of the RV free wall; (iii) bulging of the interventricular septum into the RV and stretching the free wall over the septum. The relative contribution of the aforementioned mechanisms to RV pump function may change in different pathological conditions. Our aim was to develop a custom method to separately assess the extent of longitudinal, radial and anteroposterior displacement of the RV walls and to quantify their relative contribution to global RV ejection fraction using 3D data sets obtained by echocardiography. Accordingly, we decomposed the movement of the exported RV beutel wall in a vertex based manner. The volumes of the beutels accounting for the RV wall motion in only one direction (either longitudinal, radial, or anteroposterior) were calculated at each time frame using the signed tetrahedron method. Then, the relative contribution of the RV wall motion along the three different directions to global RV ejection fraction was calculated either as the ratio of the given direction’s ejection fraction to global ejection fraction and as the frame-by-frame RV volume change (∆V/∆t) along the three motion directions. The ReVISION (Right VentrIcular Separate wall motIon quantificatiON) method may contribute to a better understanding of the pathophysiology of RV mechanical adaptations to different loading conditions and diseases