Predicting Functional Regions on Objects

2013 ◽  
Author(s):  
Chaitanya Desai ◽  
Deva Ramanan
Keyword(s):  
Functional Regions

HCVS: Pinpointing Chromatin States Through Hierarchical Clustering and Visualization Scheme

2019 ◽  
Vol 14 (2) ◽  
pp. 148-156
Author(s):  
Nighat Noureen ◽  
Sahar Fazal ◽  
Muhammad Abdul Qadir ◽  
Muhammad Tanvir Afzal
Keyword(s):  
Hierarchical Clustering ◽  
Real Data ◽  
Cell Types ◽  
Computational Scheme ◽  
Data Set ◽  
Chromatin States ◽  
Functional Regions ◽  
Visualization Strategy ◽  
Hidden States ◽  
Next Generation Sequencing Ngs

Background: Specific combinations of Histone Modifications (HMs) contributing towards histone code hypothesis lead to various biological functions. HMs combinations have been utilized by various studies to divide the genome into different regions. These study regions have been classified as chromatin states. Mostly Hidden Markov Model (HMM) based techniques have been utilized for this purpose. In case of chromatin studies, data from Next Generation Sequencing (NGS) platforms is being used. Chromatin states based on histone modification combinatorics are annotated by mapping them to functional regions of the genome. The number of states being predicted so far by the HMM tools have been justified biologically till now. Objective: The present study aimed at providing a computational scheme to identify the underlying hidden states in the data under consideration. </P><P> Methods: We proposed a computational scheme HCVS based on hierarchical clustering and visualization strategy in order to achieve the objective of study. Results: We tested our proposed scheme on a real data set of nine cell types comprising of nine chromatin marks. The approach successfully identified the state numbers for various possibilities. The results have been compared with one of the existing models as well which showed quite good correlation. Conclusion: The HCVS model not only helps in deciding the optimal state numbers for a particular data but it also justifies the results biologically thereby correlating the computational and biological aspects.

scholarly journals The C-terminal domain of feline and bovine SAMHD1 proteins has a crucial role in lentiviral restriction

2020 ◽  
Vol 295 (13) ◽  
pp. 4252-4264 ◽  
Author(s):  
Chu Wang ◽  
Kaikai Zhang ◽  
Lina Meng ◽  
Xin Zhang ◽  
Yanan Song ◽  
...  
Keyword(s):  
Proteasomal Degradation ◽  
Acid Sites ◽  
Accessory Protein ◽  
Restriction Profile ◽  
Biological Functions ◽  
Terminal Domain ◽  
Functional Regions ◽  
Viral Restriction ◽  
Primate Lentiviruses

SAM and HD domain-containing protein 1 (SAMHD1) is a host factor that restricts reverse transcription of lentiviruses such as HIV in myeloid cells and resting T cells through its dNTP triphosphohydrolase (dNTPase) activity. Lentiviruses counteract this restriction by expressing the accessory protein Vpx or Vpr, which targets SAMHD1 for proteasomal degradation. SAMHD1 is conserved among mammals, and the feline and bovine SAMHD1 proteins (fSAM and bSAM) restrict lentiviruses by reducing cellular dNTP concentrations. However, the functional regions of fSAM and bSAM that are required for their biological functions are not well-characterized. Here, to establish alternative models to investigate SAMHD1 in vivo, we studied the restriction profile of fSAM and bSAM against different primate lentiviruses. We found that both fSAM and bSAM strongly restrict primate lentiviruses and that Vpx induces the proteasomal degradation of both fSAM and bSAM. Further investigation identified one and five amino acid sites in the C-terminal domain (CTD) of fSAM and bSAM, respectively, that are required for Vpx-mediated degradation. We also found that the CTD of bSAM is directly involved in mediating bSAM's antiviral activity by regulating dNTPase activity, whereas the CTD of fSAM is not. Our results suggest that the CTDs of fSAM and bSAM have important roles in their antiviral functions. These findings advance our understanding of the mechanism of fSAM- and bSAM-mediated viral restriction and might inform strategies for improving HIV animal models.

scholarly journals Genome-Wide Mapping of Histone H3 Lysine 4 Trimethylation (H3K4me3) and Its Involvement in Fatty Acid Biosynthesis in Sunflower Developing Seeds

Plants ◽  
2021 ◽  
Vol 10 (4) ◽  
pp. 706
Author(s):  
Antonio J. Moreno-Pérez ◽  
Raquel Martins-Noguerol ◽  
Cristina DeAndrés-Gil ◽  
Mónica Venegas-Calerón ◽  
Rosario Sánchez ◽  
...  
Keyword(s):  
Fatty Acid ◽  
Chromatin Remodeling ◽  
Molecular Mechanisms ◽  
Acid Metabolism ◽  
Fatty Acid Biosynthesis ◽  
Acid Synthesis ◽  
Sunflower Seeds ◽  
Acid Biosynthesis ◽  
Functional Regions ◽  
Genome Wide

Histone modifications are of paramount importance during plant development. Investigating chromatin remodeling in developing oilseeds sheds light on the molecular mechanisms controlling fatty acid metabolism and facilitates the identification of new functional regions in oil crop genomes. The present study characterizes the epigenetic modifications H3K4me3 in relationship with the expression of fatty acid-related genes and transcription factors in developing sunflower seeds. Two master transcriptional regulators identified in this analysis, VIV1 (homologous to Arabidopsis ABI3) and FUS3, cooperate in the regulation of WRINKLED 1, a transcriptional factor regulating glycolysis, and fatty acid synthesis in developing oilseeds.

Exploring global interregional food system's sustainability using the functional regions typology

2021 ◽  
Vol 68 ◽  
pp. 102276
Author(s):  
Dor Fridman ◽  
Thomas Koellner ◽  
Meidad Kissinger
Keyword(s):  
Functional Regions

scholarly journals Intramax and other objective functions: The case of Slovenia

2016 ◽  
Vol 24 (2) ◽  
pp. 12-25 ◽  
Author(s):  
Samo Drobne ◽  
Mitja Lakner
Keyword(s):  
Objective Function ◽  
The Other ◽  
Objective Functions ◽  
Interaction Index ◽  
Functional Regions ◽  
Hierarchical Aggregation ◽  
Administrative Units

Abstract The use of different objective functions in hierarchical aggregation procedures is examined in this paper. Specifically, we analyse the use of the original Intramax objective function, the sum-of-flows objective function, the sum-of-proportions-to-intra-regional-flows objective function, Smart’s weighted interaction index, the first and second CURDS weighted interaction indices, and Tolbert and Killian’s interaction index. The results of the functional regionalisation have been evaluated by self-containment statistics, and they show that the use of the original Intramax procedure tends to delineate operationally the most persuasive and balanced regions that, regarding the intra-regional flows, homogeneously cover the analysed territory. The other objective functions give statistically better but operationally less suitable results. Functional regions modelled using the original Intramax procedure were compared to the regions at NUTS 2 and NUTS 3 levels, as well as to administrative units in Slovenia. We conclude that there are some promising directions for further research on functional regionalisation using hierarchical aggregation procedures.

Functional regions in the essential light chain of smooth muscle myosin as revealed by the mutagenesis approach

2000 ◽  
Vol 267 (20) ◽  
pp. 6151-6157 ◽  
Author(s):  
Sophie Quevillon-Chéruel ◽  
Chantal Janmot ◽  
Muriel Nozais ◽  
Anne-Marie Lompré ◽  
Jean-Jacques Béchet
Keyword(s):  
Smooth Muscle ◽  
Light Chain ◽  
Smooth Muscle Myosin ◽  
Essential Light Chain ◽  
Functional Regions ◽  
Muscle Myosin

Location of functional regions of acetylcholine receptor α-subunit by site-directed mutagenesis

Nature ◽  
1985 ◽  
Vol 313 (6001) ◽  
pp. 364-369 ◽  
Author(s):  
Masayoshi Mishina ◽  
Takamasa Tobimatsu ◽  
Keiji Imoto ◽  
Ken-ichi Tanaka ◽  
Yoshihiko Fujita ◽  
...  
Keyword(s):  
Acetylcholine Receptor ◽  
Site Directed Mutagenesis ◽  
Directed Mutagenesis ◽  
Α Subunit ◽  
Functional Regions

scholarly journals The Unique Structure of Haemophilus influenzae Protein E Reveals Multiple Binding Sites for Host Factors

2012 ◽  
Vol 81 (3) ◽  
pp. 801-814 ◽  
Author(s):  
Birendra Singh ◽  
Tamim Al-Jubair ◽  
Matthias Mörgelin ◽  
Marjolein M. Thunnissen ◽  
Kristian Riesbeck
Keyword(s):  
Haemophilus Influenzae ◽  
Disulfide Bridge ◽  
Lung Epithelial Cells ◽  
Binding Region ◽  
Content Type ◽  
Bacterial Surface ◽  
Hydrogen Bonding Pattern ◽  
Functional Regions ◽  
C Terminus ◽  
Α Helix

ABSTRACTHaemophilus influenzaeprotein E (PE) is a multifunctional adhesin involved in direct interactions with lung epithelial cells and host proteins, including plasminogen and the extracellular matrix proteins vitronectin and laminin. We recently crystallized PE and successfully collected X-ray diffraction data at 1.8 Å. Here, we solved the structure of a recombinant version of PE and analyzed different functional regions. It is a dimer in solution and in the asymmetric unit of the crystals. The dimer has a structure that resembles a flattened β-barrel. It is, however, not a true β-barrel, as there are differences in both the hydrogen-bonding pattern and the shape. Each monomer consisted of a 6-stranded antiparallel β-sheet with a rigid α-helix at the C terminus tethered to the concave side of the sheet by a disulfide bridge. The laminin/plasminogen binding region (residues 41 to 68) is exposed, while the vitronectin binding region (residues 84 to 108) is partially accessible in the dimer. The dimerized PE explains the simultaneous interaction with laminin and vitronectin. In addition, we found this unique adhesin to be present in many bacterial genera of the familyPasteurellaceaeand also orthologues in other, unrelated species (Enterobacter cloacaeandListeria monocytogenes). Peptides corresponding to the surface-exposed regions PE 24 to 37, PE 74 to 89, and PE 134 to 156 were immunogenic in the mouse. Importantly, these peptide-based antibodies also recognized PE at the bacterial surface. Taken together, our detailed structure of PE explains how this important virulence factor ofH. influenzaesimultaneously interacts with host vitronectin, laminin, or plasminogen, promoting bacterial pathogenesis.

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