Variability in the Essential‐Oil Composition of Sideritis scardica Griseb. from Native Bulgarian Populations

The essential‐oil composition of six native populations of Sideritis scardica from Bulgaria was studied by GC‐FID and GC/MS analyses. Altogether, 37 components, representing 73.1 to 79.2% of the total oil content were identified. Among them, α‐pinene (4.4–25.1%), β‐pinene (2.8–18.0%), oct‐1‐en‐3‐ol (2.3–8.0%), phenylacetaldehyde (0.5–9.5%), β‐bisabolene (1.3–11.0%), benzyl benzoate (1.1–14.3%), and m‐camphorene ( 1 ; 0.3–12.4%) were the main compounds. All samples were characterized by low contents of oxygenated mono‐ and sesquiterpenes (≤1.6 and 2.3%, resp.). Principal component analysis (PCA) and cluster analysis (CA) showed a significant variability in the chemical composition of the studied samples as well as a correlation between the oil profiles and the ecological conditions of the natural habitats of S. scardica.     

Variability of the Needle Essential Oils of Juniperus deltoides R.P.Adams from Different Populations in Serbia and Croatia

The essential‐oil compositions of one Croatian and three Serbian populations of Juniperus deltoides R.P.Adams have been determined by GC/MS analysis. In total, 147 compounds were identified, representing 97.3–98.3% of the oil composition. The oils were dominated by monoterpenes, which are characteristic components for the species of the section Juniperus. Two monoterpenes, α‐pinene and limonene, were the dominant constituents, with a summed‐up average content of 49.45%. Statistical methods were used to determine the diversity of the terpene classes and the common terpenes between the newly described J. deltoides populations from Serbia and Croatia. Only reports on several specimens from this species have been reported so far, and there are no studies that treat population diversity. Cluster analysis of the oil contents of 21 terpenes showed high correlation with the geographical distribution of the populations, separating the Croatian from the Serbian populations. The comparison of the essential‐oil compositions obtained in the present study with literature data, showed the separation of J. deltoides and J. oxycedrus ssp. oxycedrus from the western Mediterranean region.     

Endangered Pinzgauer cattle subtype Jochberger Hummel are genetically distinct

Autochthonous cattle breeds are an important part of cultural heritage and reservoir of genetic diversity. Usually, such breeds have been selected over centuries and reflect adaptation to a specific local environment and human demands. However, owing to low effective population size in conjunction with increased inbreeding and genetic drift, many of these lineages are threatened with extinction. The Jochberger Hummel (‘Jochberger Bumblebee’) is such an endangered subtype of the Pinzgauer cattle originating from a single polled female calf. To evaluate the suspected uniqueness of this subtype and to assess whether it should be kept separate or managed together with the Pinzgauer cattle as one population, I examined the genetic diversity in a set of 844 cattle (Angus, Charolais, Holstein, Jochberger Hummel, Pinzgauer, Uckermaerker and Tux-Zillertaler) using principal component and biogeographical ancestry analysis. The analysis showed that the Jochberger Hummel is still a distinct subtype of Pinzgauer cattle with less than 5% admixture and a low inbreeding coefficient.     

甘肃盐池湾斑头雁巢址选择

2019年4至6月,采用定点观察法和样方法研究甘肃盐池湾国家级自然保护区斑头雁(Anser indicus)巢址选择。研究期间共发现斑头雁巢332个,斑头雁在繁殖期有3种营巢生境,即浅水沼泽、湖心小岛以及山崖,其巢址类型有草垛巢、地面巢和山崖裸岩巢3种。浅水沼泽、湖心小岛以及山崖3种营巢生境中窝卵数分别为(4.7±2.7)枚(n=204)、(4.2±1.9)枚(n=108)及(3.1±0.6)枚(n=20),孵化成功率分别为48.65%(n=199)、45.27%(n=148)及24.00%(n=25),繁殖成功率分别为66.67%(n=42)、74.28%(n=35)及36.36%(n=11)。主成分分析显示,影响浅水沼泽生境中斑头雁巢址选择的主要环境因素依次为水源因素、隐蔽因素、干扰因素和食物因素;影响湖心小岛生境中斑头雁巢址选择的主要环境因素依次为隐蔽因素、食物因素、干扰因素;影响山崖生境中斑头雁巢址选择的主要环境因素依次为地形因素、食物及水源因素、干扰因素。本研究表明,斑头雁在不同营巢生境中,巢址选择的最主要环境因素并不相同,主要依赖生境特征及周围环境因素特征。     

Binding mechanism of spinosine and venenatine molecules with p300 HAT enzyme: Molecular screening,molecular dynamics and free-energy analysis

The chromatin modification is regulated by the histone acetyltransferase (HAT) and histone deacetyltransferase (HDAC) enzymes; abnormal function of these enzymes leads to several malignant diseases. The inhibition of these enzymes using natural ligand molecules is an emerging technique to cure these diseases. The in vitro analysis of natural molecules, venenatine, spinosine, palmatine and taxodione are giving the best inhibition rate against p300 HAT enzyme. However, the detailed understanding of binding and the stability of these molecules with p300 HAT is not yet known. The aim of the present study is focused to determine the binding strength of the molecules from molecular dynamics simulation analysis. The docking analysis confirms that, the venenatine (−6.97 kcal/mol - conformer 8), spinosine (−6.52 kcal/mol conformer −10), palmatine (−5.72 kcal/mol conformer-3) and taxodione (−4.99 kcal/mol conformer-4) molecules form strong hydrogen bonding interactions with the key amino acid residues (Arg1410, Thr1411 and Trp1466) present in the active site of p300. In the molecular dynamics (MD) simulation, the spinosine retain these key interactions with the active site amino acid residues (Arg1410, Thr1411, and Trp1466) than venenatine and are stable throughout the simulation. The RMSD value of spinosine (0.5 to 1.3 Å) and venenatine (0.3 to 1.3 Å) are almost equal during the MD simulation. However, during the MD simulation, the intermolecular interaction between venenatine and the active site amino acid residues (Arg1410, Thr1411, and Trp1466) decreased on comparing with the spinosine-p300 interaction. The binding free energy of the spinosine (−15.30 kcal/mol) is relatively higher than the venenatine (−11.8 kcal/mol); this increment is attributed to the strong hydrogen bonding interactions of spinosine molecule with the active site amino acid residues of p300.     

Multivariate palaeoecological analysis of a late quaternary small mammal succession from North Bulgaria

The basic assumption of the analysis is that the stratigraphical change of relative abundance of the small mammal species is a phenomenon due to a certain number of environmental factors. In order to reveal these factors and to make some palaeoclimatic reconstructions the following approaches have been used: 1. Analysis of intrinsic structure of the initial data by using principal component analysis (PCA)—delimitation of recurrent groups of species and ordination of assemblages; 2. Extension backward in time of known ecological preference of taxa, forming a particular recurrent group; 3. Comparison of the results with the analysis of assemblages from “known”; (Holocene) environment. On the basis of ecological appearance of particular recurrent groups it is assumed that the main factors are temperatures and effective moisture. The reconstructed values for these environmental factors obtained on the basis of the Holocene recurrent groups of small mammals shows similarity to the recent climate in the area.     

Using principal component analysis and support vector machine to predict protein structural class for low-similarity sequences via PSSM

The accurate identification of protein structure class solely using extracted information from protein sequence is a complicated task in the current computational biology. Prediction of protein structural class for low-similarity sequences remains a challenging problem. In this study, the new computational method has been developed to predict protein structural class by fusing the sequence information and evolution information to represent a protein sample. To evaluate the performance of the proposed method, jackknife cross-validation tests are performed on two widely used benchmark data-sets, 1189 and 25PDB with sequence similarity lower than 40 and 25%, respectively. Comparison of our results with other methods shows that the proposed method by us is very promising and may provide a cost-effective alternative to predict protein structural class in particular for low-similarity data-sets.     

Studying the collective motions of the adenosine A2A receptor as a result of ligand binding using principal component analysis

Abstract

Adenosine receptors (ARs) belong to family A of GPCRs that are involved in many diseases, including cerebral and cardiac ischemic diseases, immune and inflammatory disorders, etc. Thus, they represent important therapeutic targets to treat these conditions. Computational techniques such as molecular dynamics (MD) simulations permit researchers to obtain structural information about these proteins, and principal component analysis (PCA) allows for the identification of collective motions. There are available structures for the active form (3QAK) and the inactive form (3EML) of A2AR which permit us to gain insight about their activation/inactivation mechanism. In this work, we have proposed an inverse strategy using MD simulations where the active form was coupled to the antagonist caffeine and the inactive form was coupled to adenosine agonist. Moreover, we have included four reported thermostabilizing mutations in the inactive form to study A2AR structural differences under different conditions. Some observations stand out from the PCA studies. For instance, the apo structures showed remarkable similarities, and the principal components (PCs) were rearranged in a ligand-dependent manner. Additionally, the active conformation was less stable compared to the inactive one. Some PCs inverted their direction in the presence of a ligand, and comparison of the PCs between 3EML and 3EML_ADN showed that adenosine induced major changes in the structure of A2AR. Rearrangement of PCs precedes and drives conformational changes that occur after ligand binding. Knowledge about these conformational changes provides important insights about the activity of A2AR.