Plant Diversity Patterns Along Altitudinal Gradient in Understory Communities of Darkesh Region, Bojnord, Iran

The ecotone region of Darkesh with an area of 22,500 hectares is located in the Irano-Turanian xeric-continental bioclimatic zone of Khorassan-Kopet Dagh. To investigate the plant diversity patterns of understory communities along three elevation classes of 1100-1600, 1600-2100, and 2100-2600 m, 187 plots were sampled randomly and abundance and cover of species were recorded using 4-m2 plots. Beta diversity and Hill indices were calculated by using R and PAST software. A total of 252 species were recorded including 31 perennial grasses. The most abundant grasses were Poa nemoralis, Poa bulbosa, Bromus sterilis, Brachypodium sylvaticum, and Dactylis glomerata subsp. glomerata. Poa nemoralis was an important dominant grass under Quercus community. From the standpoint of species richness, Hill indices were highest under woods stories along the elevation of 1100-1600 m. Understories of oak forest and alpine communities had almost the same indices and were in the second rank compared to woods communities. Based on the β diversity index, the wood understory had the highest indices followed by Quercus and alpine communities. By increasing the elevations, the diversity of understory communities also decreased

Geometrically Reduced Number of Protein Ground State Candidates

Geometrical properties of protein ground states are studied using an algebraic approach. It is shown that independent from inter-monomer interactions, the collection of ground state candidates for any folded protein is unexpectedly small: For the case of a two-parameter Hydrophobic-Polar lattice model for $L$-mers, the number of these candidates grows only as $L^2$. Moreover, the space of the interaction parameters of the model breaks up into well-defined domains, each corresponding to one ground state candidate, which are separated by sharp boundaries. In addition, by exact enumeration, we show there are some sequences which have one absolute unique native state. These absolute ground states have perfect stability against change of inter-monomer interaction potential.Comment: 9 page, 4 ps figures are include

Species diversity and ecological studies of phytoplankton in the Bazangan Lake

Bazangan, the Khorasan largest natural lake, is located in Northeast. 120km from Mashhad with the area of 690000m2. The purpose of this study was to characterize ecological aspects and to compare seasonal variations in species diversity of phytoplanktons in the surface water of littoral zone in the Bazangan lake. Samples were collected from eleven stations in each season during the year 2002. Some ecological factors such as pH. EC, salinity, hardness of water, nutrients and water temperature were measured. Four macroalgae and 33 phytoplankton species belonging to 5 algae groups viz. Chrysophyta (21 species). Chlorophyta (7 species), Cyanophyta (4 species) and Pyrrophyta (1 species) were identified. Diatoma tennis. Fragillaria crotonensis, Lilothrix subtilissinia and Merisinopodia punctata had the most species abundance. Comparing to other groups, Chrysophyta was abundant in all seasons mostly in the spring and summer. Different numerical indices of diversity such as species richness, evenness and diversity as well as parametric families of diversity were obtained in different seasons based on the abundance data of phytoplanktons. The results showed that the highest species diversity of the phytoplanktons could be seen in the summer and autumn. The Bazangan is classified as an oligothroph and a subsaline lake

The Origin of the Designability of Protein Structures

We examined what determines the designability of 2-letter codes (H and P) lattice proteins from three points of view. First, whether the native structure is searched within all possible structures or within maximally compact structures. Second, whether the structure of the used lattice is bipartite or not. Third, the effect of the length of the chain, namely, the number of monomers on the chain. We found that the bipartiteness of the lattice structure is not a main factor which determines the designability. Our results suggest that highly designable structures will be found when the length of the chain is sufficiently long to make the hydrophobic core consisting of enough number of monomers.Comment: 17 pages, 2 figure

Statistical properties of contact vectors

We study the statistical properties of contact vectors, a construct to characterize a protein's structure. The contact vector of an N-residue protein is a list of N integers n_i, representing the number of residues in contact with residue i. We study analytically (at mean-field level) and numerically the amount of structural information contained in a contact vector. Analytical calculations reveal that a large variance in the contact numbers reduces the degeneracy of the mapping between contact vectors and structures. Exact enumeration for lengths up to N=16 on the three dimensional cubic lattice indicates that the growth rate of number of contact vectors as a function of N is only 3% less than that for contact maps. In particular, for compact structures we present numerical evidence that, practically, each contact vector corresponds to only a handful of structures. We discuss how this information can be used for better structure prediction.Comment: 20 pages, 6 figure

Highly Designable Protein Structures and Inter Monomer Interactions

By exact computer enumeration and combinatorial methods, we have calculated the designability of proteins in a simple lattice H-P model for the protein folding problem. We show that if the strength of the non-additive part of the interaction potential becomes larger than a critical value, the degree of designability of structures will depend on the parameters of potential. We also show that the existence of a unique ground state is highly sensitive to mutation in certain sites.Comment: 14 pages, Latex file, 3 latex and 6 eps figures are include

Geometric and Statistical Properties of the Mean-Field HP Model, the LS Model and Real Protein Sequences

Lattice models, for their coarse-grained nature, are best suited for the study of the ``designability problem'', the phenomenon in which most of the about 16,000 proteins of known structure have their native conformations concentrated in a relatively small number of about 500 topological classes of conformations. Here it is shown that on a lattice the most highly designable simulated protein structures are those that have the largest number of surface-core switchbacks. A combination of physical, mathematical and biological reasons that causes the phenomenon is given. By comparing the most foldable model peptides with protein sequences in the Protein Data Bank, it is shown that whereas different models may yield similar designabilities, predicted foldable peptides will simulate natural proteins only when the model incorporates the correct physics and biology, in this case if the main folding force arises from the differing hydrophobicity of the residues, but does not originate, say, from the steric hindrance effect caused by the differing sizes of the residues.Comment: 12 pages, 10 figure

Endoscopic mucosal resection: still a reliable therapeutic option for gastrointestinal neuroendocrine tumors

Background: Neuroendocrine tumors (NETs), as a rare and heterogeneous category of solid tumors, feature various morphologies and behaviors. In recent years, the incidence of NETs has continued to increase. Endoscopic mucosal resection (EMR) is one of the therapeutic modalities for the treatment of gastric and rectal NETs. Methods: We evaluated patients with well-differentiated NETs of the stomach, duodenum, or rectum between 2011 and 2018. In this study, all cases with tumors confined to the mucosal or submucosal layers and smaller than 20 mm were resected using the EMR technique. We used EUS, CT scan, or MRI to exclude patients with advanced disease. All patients were actively monitored for recurrence according to the recommended protocols. Results: A total of 36 patients with NETs entered the study; 17 (47.2) were female and the remaining 19 (52.8) were male, with a total age range of 20�74 years (mean: 52.47 ± 13.47 years). Among the tumors, 31 cases (86.1) were G1 and the remaining 5 (13.9) were G2. Based on the pathology reports, 22 tumors (61.1) were smaller than 1 cm, while the remaining 14 (38.9) were between 1�2 cm. Twenty-two patients (61.1) had a margin of specimen involved with the tumor. No recurrence was observed during the mean follow-up time of 63.5 ± 19.8 months (range: 39�103 months). All 36 cases survived during the study period. Conclusion: Conventional EMR procedure provides low chance of R0 (complete resection) achievement in gastrointestinal NETs smaller than 20 mm and limited to the mucosa or sub mucosa. However, it could be an option if patients are closely followed. Postoperative marginal involvement is not a reliable predictor of disease recurrence, which may be explained by the deleterious effect of heat coagulation and cauterization applied during tumor removal. © 2021, The Author(s)

Mean-Field HP Model, Designability and Alpha-Helices in Protein Structures

Analysis of the geometric properties of a mean-field HP model on a square lattice for protein structure shows that structures with large number of switch backs between surface and core sites are chosen favorably by peptides as unique ground states. Global comparison of model (binary) peptide sequences with concatenated (binary) protein sequences listed in the Protein Data Bank and the Dali Domain Dictionary indicates that the highest correlation occurs between model peptides choosing the favored structures and those portions of protein sequences containing alpha-helices.Comment: 4 pages, 2 figure