Top PDF Proteins of Novel Composition: Synthesis, Evolution, Dynamics

Proteins of Novel Composition: Synthesis, Evolution, Dynamics

Proteins of Novel Composition: Synthesis, Evolution, Dynamics

depolarization dynamics ......................................................................................84 4.1 Amino acid sequences of wtGFP, L024_3-3, GFPrm, and GFPrm_AM ..........112 4.2 Sequence changes of 10 randomly selected clones from M02c_2 ....................114 4.3 Yields of purified GFPrm_AM and mDHFR produced by E. coli strains outfitted with the mutant MetRS .....................................................................................115 4.4 Kinetic parameters for activation of Met and Tfn by the M02c_2-8 MetRS

14 Read more

Evolution and Dynamics of the Human Gut Virome

Evolution and Dynamics of the Human Gut Virome

The human body contains large numbers of viral particles (over 1012 per person), largely bacteriophage, but little is known of how these viral communities influence human health and disease. To study the viruses of the human gut (the so-called gut `virome') during a known environmental perturbation we collected stool samples from healthy individuals participating in a controlled diet study. Viral DNA was purified and deep- sequenced using 454 and Illumina technologies, yielding over 48 billion bases of viral sequence spread across 28 samples from 12 healthy individuals. Computational analysis of this unprecedentedly large database of viral sequences allowed us to characterize these communities on a genomic level. We found that the vast majority of viruses from the human gut were novel species of bacteriophage, and that only 1 of these 12 individuals contained a known eukaryotic DNA virus. Temporal changes in these viral communities were correlated with experimental manipulation of diet, and parallel deep sequencing of gut bacteria revealed co-variation between bacterial and viral communities, supporting the hypothesis of linked reproduction between these two groups. A large proportion of viral contigs have markers of temperate lifestyle, indicating that there is a significant role of lysogeny in the gut microbiome. Analysis of genetically variable elements within these viral genomes revealed novel classes of diversity-generating retroelements targeting immunoglobulin-superfamily proteins, suggesting a surprising example of convergent evolution with the vertebrate immune system. Optimization of assembly algorithms for these samples improved the recovery of complete and partial genome sequences. While the assembled genomes were highly dissimilar on the nucleotide level, analysis of syntenic protein- coding sequences revealed conserved gene cassettes that display an inferred structural and functional conservation despite a high degree of nucleotide substitution. Through high-throughput shotgun sequencing of viral DNA, we found that the healthy human gut contains a wide variety of extremely diverse
Show more

106 Read more

Investigating venom synthesis: exploring the composition, variation and gene expression dynamics of Bitis arietans venom

Investigating venom synthesis: exploring the composition, variation and gene expression dynamics of Bitis arietans venom

NaCl in 0.1% formic acid, pH 2.3) at a flow rate of 60µl/min using an Ultimate 3000 system (Dionex, UK). Following this, the fractions generated (20 per sample) were subjected to second dimension fractionation over a gradient (2-90% acetonitrile in 0.1% formic acid over 50 min) at a flow rate of 300nl/min using a 300μm I.D. x 15cm capillary LC ion exchange column packed with 3μm PepMap™ C 8 stationary phase. Eluted peptides were analysed on a LCQ Deca XP Plus Mass Spectrometer (ThermoFisher, UK), operating on a ‘triple play’ mode (zoom scan followed by MS/MS). Proteins were identified by screening LC-MS sequence data against Uniprot databases and a B. arietans venom gland EST database using Proteome Discoverer 1.0.0 (ThermoScientific) software incorporating both Sequest (ThermoScientific (Yates et al., 1996) and Mascot (Matrix Science Ltd, UK (Perkins et al., 1999) search algorithms. A parent mass tolerance of 1.5Da and fragment mass tolerance of 1Da were used, allowing for 1 missed cleavage. Carbamidomethylation of cysteine and oxidation of methionine were the fixed and variable modifications respectively. For Sequest, high confidence peptide matches were filtered with an XCorr cut-off (+1>1.5, +2>2 and +3>2.5) and for Mascot, an Exp value of less than 0.01 indicated a confident peptide match.
Show more

320 Read more

The MTA family proteins as novel histone H3 binding proteins

The MTA family proteins as novel histone H3 binding proteins

MTA family proteins as novel H3 binding proteins A surprising finding in our study is that the MTA family proteins in the NURD complex are novel H3 binding pro- teins that are likely to account for specific binding of H3 tail peptide in vitro by NURD. The MTA family proteins, especially MTA1, have been shown to play important roles in diverse processes including transcriptional regulation, DNA damage repair and cancer [27,29,46-48]. Interest- ingly, MTA1 seemed to differ from MTA2 in association with CHD3/CHD4 as reported in a previous study [28]. The ectopically expressed MTA2 was shown to assemble into the CHD3/4-containig NURD complex, whereas ectopically expressed MTA1 was shown to form the pro- tein complexes containing HDAC1/2 and RbAp46/48 but lacking CHD3/CHD4. In our effort to determining the protein subunit(s) responsible for H3 tail binding activity, we observed that the CHD3, MTA family proteins and RbAp48 all exhibited a H3 tail peptide binding specificity resembling to that of NURD (Figure 2A). However, our photo-induced cross-linking experiment pointed to the MTA family proteins rather than CHD3/CHD4 as the direct H3 tail peptide-binding proteins within the NURD complex (Figure 2B). Somewhat surprisingly, the H3 tail peptide binding activity was not mapped to the N-terminal regions containing SANT and zinc finger domains but to the C-terminal regions of MTA1 and MTA2 that are not known for any recognizable structural domain (Figure 3). We demonstrated that the purified re- combinant C-terminal regions of MTA1 and MTA2 are capable of binding H3 tail peptide (Figure 3C), and thus designated the C-terminal region of MTA proteins as a novel H3 binding domain (H3BD) (Figure 3C). Another compelling evidence supporting the MTA proteins as the H3 tail binding protein within the NURD complex came from our analysis of 293T expressed N-terminal and C-terminal fragments of MTA1 and MTA2 (Figure 4). The N-terminal fragments of MTA1(1–460) was found to asso- ciate with endogenous HDAC1/2 and RbAp48, whereas the N-terminal MTA2(1–434) fragment was found to be
Show more

14 Read more

Oxidative stress, thermogenesis and evolution of uncoupling proteins

Oxidative stress, thermogenesis and evolution of uncoupling proteins

To throw more light on the diversification of the UCP family and the evolution of the apparently unique function of UCP1 in thermogenesis, several recent phylogenetic analyses have focused on vertebrate UCP1-3 relationships [7-11]. The work of Hughes and Criscuolo published recently in BMC Evolutionary Biology [7] has confirmed previous studies indicating that the UCP family evolved through a series of gene duplications [8]. We have made a reconstructed phylogeny of vertebrate UCP1-3 using animal UCP4 as outgroup (Figure 2) that is in good agreement with those previously published [7,10,11]. As shown in the figure, UCP4 has been widely reported both in invertebrates and vertebrates, but apparently no duplications occurred during the evolution of this paralog. In contrast, vertebrate UCP1-3 acquired much of their diversity through two rounds of gene duplication [7,8,10]. The ancestor of vertebrate UCP1-3 first duplicated into UCP1 and the common ancestor of UCP2-3, which subsequently duplicated into UCP2 and UCP3. Each of the three paralogs is found in fish, amphibians, and mammals. Strikingly, UCP1 and UCP2 have not been reported in birds, nor UCP1 in sauropsids. These proteins have a single ortholog in invertebrates (it has been reported in, for example, a deuterostome (the sea urchin), but not in the fully sequenced protostome genomes of Drosophila and Caenorhabditis).
Show more

5 Read more

Dynamics of Changes in Microbiological Composition of Stored Sediments

Dynamics of Changes in Microbiological Composition of Stored Sediments

sediment storage [Statement of water manage- ment…2007, State of the environment 2011]. The parameters of all facilities are shown in Ta- ble 1. The samples of sediments were collected from the sedimentation tanks of the treatment facilities in the spring of 2015. The samples were taken in accordance with the recommended methodology [PN-EN ISO 5667–15:2009] using an Eijkelkamp sampler. Directly after collection, pH, dry residue, the content of organic compo- nents, and grain size composition of the samples were analysed. Additionally, the sediments were subjected to the microbiological analysis. In May 2016, the same tests were carried out on the same samples of sediments stored under variable temperature conditions (+4°C ÷ +25°C) to iden- tify the changes in microbiological composition. The parameters were determined in accordance with the current standards [PN-EN 12176:2004, PN-78/C-04541, Regulation of the Minister of Environment…2002].
Show more

6 Read more

Adaptive evolution of centromere proteins in plants and animals

Adaptive evolution of centromere proteins in plants and animals

Centromere drive may have important consequences for karyotypic evolution. Centromeres of two acrocentric chro- mosomes frequently fuse (Robertsonian translocations), and metacentrics often misdivide to yield two acrocentrics. In humans, there is a bias in favor of Robertsonian translocations over their homologous acrocentric pair when transmitted by females, and male carriers have reduced fer- tility [58]. This general sterility of Robertsonian males is consistent with centromere drive underlying post-zygotic reproductive isolation in emerging species [1]. Centromere drive provides a mechanism for the tendency of karyotypes to be either mostly metacentric or mostly acrocentric [59] and for the karyotype-specific accumulation of selfish B chromosomes in mammals [60]. Our finding that CENP-Cs, like CenH3s, evolve adaptively addresses a perceived short- coming of the centromere drive model for post-zygotic reproductive isolation: mutations that rescued hybrid steril- ity did not map to the Drosophila CenH3 gene [61,62]. The fact that CenH3 is not the only adaptively evolving centro- mere protein indicates that there are multiple candidate drive suppressors that might rescue hybrid sterility when in a mutant form.
Show more

17 Read more

Predicting the conformations of peptides and proteins in early evolution

Predicting the conformations of peptides and proteins in early evolution

In regularly-repeating polypeptides the main chain con- formations of successive amino acids are the same, or at least roughly so. Polypeptides can also fold to form a dif- ferent type of structure where the main chain conforma- tions of successive amino acids are enantiomers (mirror images). The φ, ψ values of one amino acid (the φ, ψ tor- sion angles, measuring rotation about the N 傼 Cα and Cα 傼C bonds, are major determinants of polypeptide con- formation) are equal to the φ, ψ values of its neighbour multiplied by -1. Such polypeptides [32,33] are achiral and without pitch, forming rings or chains, but not heli- ces, as in Figs 1d–g and 1j–l; they are expected to be favored by achiral or alternating racemic amino acids. This may be contrasted with the various chiral helices (strands of β-sheet are geometrically types of helix) observed in modern proteins with mainly chiral amino acids. Enantiomeric polypeptides occur as two kinds, nests and α-sheet, described below.
Show more

9 Read more

In vitro synthesis of barley storage proteins

In vitro synthesis of barley storage proteins

translation were processed to an identical size to polysome products both by barley stripped endoplasmic reticulum and by Xenopus oocytes, suggesting a simpler mechanism involving a sing[r]

238 Read more

Evolution of gap junction proteins – the pannexin alternative

Evolution of gap junction proteins – the pannexin alternative

We conclude that pannexins are ubiquitous metazoan proteins, whereas connexins appear to be chordate specific. As chordates apparently possess two distinct types of gap junction molecules it is important to understand what is the balance between them. Do pannexins duplicate GJ functions of connexins or does each play its own physiological role? Very little data are available on this subject, especially data describing pannexin function.

5 Read more

STATISTICAL ANALYSIS OF THE BASE COMPOSITION OF GENES USING DATA ON THE AMINO ACID COMPOSITION OF PROTEINS

STATISTICAL ANALYSIS OF THE BASE COMPOSITION OF GENES USING DATA ON THE AMINO ACID COMPOSITION OF PROTEINS

The difference between the result obtained by chemical analysis and those obtained by statistical analysis is probably due to the base composition at the third position, provided[r]

9 Read more

Synthesis and Cleavage of Influenza Virus Proteins

Synthesis and Cleavage of Influenza Virus Proteins

A, Comparison of proteins from 3H-labeled purified virions X, and of viral proteilns synthesized in infected cells labeled with '4C amino *acids between 8.0 and 9.0 hr afte infection 0..[r]

13 Read more

In Vitro Synthesis of Adenovirus Core Proteins

In Vitro Synthesis of Adenovirus Core Proteins

3 showed that in vitro synthesized polypeptides comigrating on SDS-polyacrylamide gel electrophoresis with the respective virion core polypeptide coeluted from hydroxyapatite with polype[r]

9 Read more

Contribution of Intra- and Interhost Dynamics to Norovirus Evolution

Contribution of Intra- and Interhost Dynamics to Norovirus Evolution

Of the 22 polymorphic positions identified in the P2 domain, 10 were found to contain substitutions that matched previously identified transitions between different GII.4 variants (residues 297, 298, 340, 341, 352, 356, 372, 393, 395, and 412). For example, at position 298, P2 domain variants with either aspartic acid or asparagine residues were identified. Most ancestral GII.4 variants (pre-2001), such as Bristol, Camberwell, and US-1995/96, have an aspartic acid at this position, while modern GII.4 variants, such as Hunter (2004), 2006b (2006 to 2007), Apeldoorn (2008), and New Orleans (2010), have an asparagine at this position. For the chron- ically infected subject, position 340 was another example where the P2 variants were toggling between residues that defined GII.4 variants, with the amino acids glycine, arginine, and threonine all being identified in the reconstructed P2 variants. Glycine was a defining residue of the Farmington Hills (2002), Asia 2003 (2003), 2006b (2006 to 2007), and Cairo (2007) GII.4 variants, while ar- ginine was present in the Hunter (2004) and 2006a (2006) GII.4 variants. Lastly, a threonine at position 340 defines the recent Apeldoorn (2008) and New Orleans (2010) GII.4 variants. This provides some evidence that individuals chronically infected with NoV may act as reservoirs for new variants, as a range of known antigenic variants was identified in the chronically infected sub- ject. However, toggling between these residues may also simply reflect the virus exploring its sequence space and functionally per- mitted changes. Due to the unavailability of serum samples, we were not able to investigate the driving force of the residue tog- gling in the subjects with chronic infection. The subject with chronic infection analyzed here was severely immunocompro- mised; therefore, the evolution in the P2 domain could be a con- sequence either of a weak humoral immune response or of a greater capacity of the specific virus to generate novel variants at these sites.
Show more

11 Read more

GREEN SYNTHESIS: A NOVEL APPROACH FOR NANOPARTICLES SYNTHESIS

GREEN SYNTHESIS: A NOVEL APPROACH FOR NANOPARTICLES SYNTHESIS

Biosynthesis of Nanoparticles: The synthesis of nanoparticles by green approach is an easy, reasonable and environmentally friendly method involved different types of natural sources like plants, fungi, algae, bacteria and yeast that have potential to produce nanoparticles at extracellular as well as intracellular level. In the biosynthesis of nanoparticles from microorganisms grow in a suitable growth medium. After a proper period of incubation mycelia of fungi wash with sterilized distilled water for 4 to 5 time to remove medium from biomass and transfer in sterilized distilled water and incubated for an appropriate period of incubation Fig. 3. After incubation flask contains fungal mat filter again and supernatant transfer in another sterilized flasks, add metal and incubated for a suitable duration or until the visual color is changed 25, 26 . There are different types of metal shows a variety of color change during nanoparticles synthesis like from pale yellow to pinkish indicate the formation of a gold nanoparticle, pale yellow to brownish color is the formation of silver nanoparticles and whitish yellow to yellow color result in the formation of manganese and zinc nanoparticles 27, 28 . The titanium dioxide nanoparticles indicated by a change in color from purple to white 29 .
Show more

13 Read more

Pathway mapping of proteins involved in multiple sclerosis and  identification of novel proteins

Pathway mapping of proteins involved in multiple sclerosis and identification of novel proteins

Three proteins (APBB2, APBB3 and MMP15) were identified having no information about their related pathway. New network was made for these proteins as shown in Figure 4 to identify pathways of these proteins .Figure 4 shows the network made in Cytoscape software in which all the three proteins, APBB2, APBB3 and MMP15, are connected linearly with LRP4 which is further connected to NCSTN, PSEN1, GSK3B, and MAPT and at the end, CAMK3B. Related pathways of the proteins are also mentioned in the figure.

6 Read more

The dynamics of norm change in the cultural evolution of language

The dynamics of norm change in the cultural evolution of language

In this work we have capitalized on a recently digitized corpus to analyze the process of norm change in the context of the cultural evolution of written English and Spanish. Through the analysis of 2, 541 cases of convention shifts occurring over the past two centuries, we identified three distinct mechanisms of norm change corresponding to the presence of an authority enforcing the adoption of a new norm, an informal institution recommending the normative update and a bottom-up process by which language speakers select a new norm. Each of these mechanisms displayed different stylized patterns in the data. We rationalized these findings by proposing a simple evolutionary model that describes the actions of the drivers of norm change previously identified in the literature, namely institutions and language users committed to the use of one of the two competing conventions. We showed that this single model captures the dynamics of norm change in each of the three cases described above, quantitatively matching the empirical data in all circumstances. In doing so, it differentiates the empirical curves in three classes according to the measured strength of the institutional intervention (fitted values of γ and single curve evaluation, see SI Sec. 8), thus confirming a posteriori the validity of our approach. Finally, through numerical simulations we were also able to reproduce the observed microscopic dynamics of norm adoption.
Show more

22 Read more

Supraorbital morphology and social dynamics in human evolution

Supraorbital morphology and social dynamics in human evolution

The resulting deformations of the 321 finite element models were compared through 1 visual assessment of strain magnitudes and 322 directions of maximum 1 and minimum 3 principal strai[r]

34 Read more

The Evolution. to Microsoft Dynamics CRM 4.0.

The Evolution. to Microsoft Dynamics CRM 4.0.

T hat Microsoft Dynamics CRM is arguably one of the easiest-to-use CRM applications on the market should come as no surprise to anyone. Combined with the need for most businesses to have a CRM solution and the market domi- nance of Windows (and, specifically, Outlook), this gives Microsoft a significant edge on integration and ease of use. Although Microsoft Dynamics CRM is designed around Outlook, initial versions suffered problems with installation and compatibility/functionality. Thus, the road to

13 Read more

Structural Motifs of Novel Metallothionein Proteins

Structural Motifs of Novel Metallothionein Proteins

This question also has practical implications since MT overexpression is thought to be a mechanism that allows cancer cells to overcome metal based chemotherapeuti[r]

189 Read more

Show all 10000 documents...