Unravelling the architecture of membrane proteins with conditional random fields

In this thesis we use Conditional Random Fields (CRFs) as a sequential classifier to predict the location of transmembrane helical regions in membrane proteins. CRFs allow for a seamless and principled integration of biological domain knowledge into the model and are known to have several advantages over other approaches. We have used this flexibility in order to incorporate several biologically inspired features into the model. We compared our approach with twenty eight other methods and received the highest score in the percentage of residues predicted correctly. We have also carried out experiments comparing CRFs against Maximum Entropy Models (MEMMs). Our results confirm that CRFs overcome the label bias problem, which are known to afflict MEMMs. Furthermore, we have used CRFs to analyze the architecture of the protein complex, Cytochrome c oxidase, and have recreated the results obtained from physical experiments

Yield of Early Maturing Sunflower Varieties, Different-Aged Crops as a Secondary Crop in the Zarafshan and Surkhandarya Oases of Uzbekistan

In Uzbekistan, oilseed sunflowers are grown mainly as a secondary crop on fertile land free from cereals. Every summer, 1.1-1.3 million hectares of irrigated land in the country are cleared of cereals. Due to the hot climate in the southern oasis (Surkhandarya region), grain is harvested in the first 10 days of June, and in the Zarafshan oasis (Samarkand region) in the third 10 days of June, winter wheat is harvested.. Due to the different weather conditions in Surkhandarya and Samarkand regions, the sowing period of sunflower as a secondary crop differs significantly.  Yields will also vary. Yields of early maturing sunflower SAI 20-80 and Dilbar varieties planted between June 20, June 30, July 10 and July 20 were analyzed as a repeat crop to determine the optimal planting time of sunflowers in both oasis soil climatic conditions

Unravelling the architecture of membrane proteins with conditional random fields

In this thesis we use Conditional Random Fields (CRFs) as a sequential classifier to predict the location of transmembrane helical regions in membrane proteins. CRFs allow for a seamless and principled integration of biological domain knowledge into the model and are known to have several advantages over other approaches. We have used this flexibility in order to incorporate several biologically inspired features into the model. We compared our approach with twenty eight other methods and received the highest score in the percentage of residues predicted correctly. We have also carried out experiments comparing CRFs against Maximum Entropy Models (MEMMs). Our results confirm that CRFs overcome the label bias problem, which are known to afflict MEMMs. Furthermore, we have used CRFs to analyze the architecture of the protein complex, Cytochrome c oxidase, and have recreated the results obtained from physical experiments

Productivity of Barley Varieties and Samples in Non-Irrigated Conditions

This article provides information on the role of barley in the creation of the fodder base of livestock, drought tolerance, the order of cultivation in arable lands, varieties with high productivity, samples

OIL CROPS WITH ANCHORAGE IN IRRIGATED LANDS

When the seeds of representatives of rapeseed oil crops like rapeseed, mustard seed, oil radish, bryukva, and tifon are sown in the fall and wintered directly in the field, as described in this article's conditions of the irrigated lands of our country (cotton-grain complex), only 3.5– 10.0% of the lawns are affected by frost, and the lawns from early spring baravj develop. This makes it possible to harvest 2.5–3.0 tons of sara seeds on average per hectare in the early summer; the germination rate is 92–95 percent, and the yield is 15–17 million per hectare

Intraoperative sentinel lymph node mapping in laparoscopic operations for colorectal cancer

INTRODUCTION: Laparoscopic resections in colorectal cancer gain an increasing popularity. Sentinel lymph node mapping in colorectal cancer and its advantages in daily practice are still subject of discussion. In laparoscopic operations, the procedure has same technical difficulties, although provides definite advan­tages in staging and estimating the extent of lymph dissection.MATERIALS AND METHODS: We present techniques for intraoperative sentinel lymph nodes mapping in colorectal cancer and their detection with surgical gamma probe in laparoscopic resection, which are used in our clinic, and the initial results from them.RESULTS: The initial results show that sentinel lymph nodes mapping with radionuclides and their detec­tion with surgical gamma probe are technically feasible in laparoscopic resections for colorectal cancer. The method has additional possibilities for the surgeon for estimating of the lymph drainage and precise stag­ing in laparoscopic operation.CONCLUSION: Nevertheless the contradictory opinions for application of sentinel lymph nodes mapping in colorectal cancer, the method provides certain advantages in improving staging. In laparoscopic opera­tions, although having some difficulties, it could be used, as it offers additional facilitation for the surgeon in estimating the lymph drainage in condition of decreased tactile sensation. Scr Sci Med 2017; 49(3):19-2

Phosphorylation of phosducin-like protein BDM-1 by protein kinase 2 (CK2) is required for virulence and Gβ subunit stability in the fungal plant pathogen Cryphonectria parasitica

Phosducin-like proteins are conserved regulatory components of G-protein signalling pathways, which mediate many physiological processes. Identified throughout eukaryotic genomes, they are thought to serve as regulators of Gβγ assembly. Cryphonectria parasitica, a plant pathogen and causative agent of chestnut blight, contains three Gα, one Gβ, one Gγ subunits and phosducin-like protein BDM-1 that have important roles in pigmentation, sporulation and virulence. Deletion of either Gβ subunit or BDM-1 produces identical phenotypes. Additionally, we report that the Gβ subunit is not detectable in absence of BDM-1. Given that the regulatory role of phosducin-like proteins may be influenced by protein kinase 2 (CK2), we confirmed that BDM-1 is a phosphoprotein that can be targeted by CK2 in vitro. Mutagenesis of the five putative CK2 sites revealed that native phosphorylation likely occurs at two locations. Strains bearing a single or double serine to alanine substitutions at those sites were significantly less virulent with only minor phenotypic changes from vegetative colonies. Therefore, CK2 activity appears to mediate key signals that are required for virulence, but not for vegetative growth. Expression of selected CK2 mutants resulted in reduced accumulation of the Gβ subunit, suggesting that phosphorylation of BDM-1 influences Gβ stability