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Advances in Infrared (IR) spectroscopies have entered a new era of research with applications in phytobiome, plant microbiome and health. Fusarium graminearum 3-ADON is the most aggressive mycotoxigenic chemotype causing Fusarium head blight (FHB) in cereals, while Sphaerodes mycoparasitica is the specific Fusarium mycoparasite with biotrophic lifestyle discovered in cereal seeds and roots. Fourier transform infrared (FTIR) spectroscopy analyses depicted shifts in the spectral peaks related to mycoparasitism mainly within the region of proteins, lipids, also indicating a link between carbohydrates and protein regions, involving potential phenolic compounds. Especially, S. mycoparasitica contributes to significant changes in lipid region 3050–2800 cm−1, while in the protein region, an increasing trend was observed for the peaks 1655–1638 cm−1 (amide I) and 1549–1548 cm−1 (amide II) with changes in indicative protein secondary structures. Besides, the peak extending on the region 1520–1500 cm−1 insinuates a presence of aromatic compounds in presence of mycoparasite on the F. graminearum root sample. Monitoring shift in improved seed germination, fungus-fungus interface through scanning electron microscopy (SEM) and confocal laser scanning microscopy (CLSM), and FTIR molecular signatures combined with principal component analysis (PCA) proved useful tools to detect an early mycoparasitism as a vital asset of the preventive biocontrol strategy against plant pathogens.

The objective of this study was to evaluate the prevalence, genotypic characterization, and determination of the patterns of shedding of human polyomavirus JC (JCPyV) and BK (BKPyV) in consecutive urine samples collected from healthy adults. Urine samples collected monthly over a 6 month period were screened by polymerase chain reaction (PCR) with two sets of primers complementary to the VP1 protein region specific for the JCPyV or BKPyV genome. The viral load of JCPyV and BKPyV in positive samples was determined by quantitative real time PCR. Seventy-one healthy individuals (ages between 18 and 65) were included in the study. Polyomavirus DNA urinary shedding was identified in 44 (62%) of the 71 individuals evaluated: BKPyV only in 16 (22.5%); JCPyV only in 19 (26.7%); and both in 9 (12.7%). Among the 28 individuals shedding JCPyV, the shedding was nearly continuous in 13 (46.4%) and sporadic in 15 (53.6%), whereas all BKPyV shedding was sporadic. A total of 45 (19 BKPyV and 26 JCPyV) strains were identified. Of the BKPyV strains, individuals were observed that excreted all genotypes except genotype 3 and the JCPyV strains, excretion of 5 different genotypes. Evaluating the age of individuals who excrete JCPyV and BKPyV, mostly are young adults, with a slight increase with increasing age and observing the viral load can not draw any parallel between the increase or decrease of age or excreted genotype as there was a wide variation both in the excretion of BKPyV and JCPyV. The high occurrence of isolated or simultaneous urinary shedding of JCPyV and BKPyV in healthy individuals merits further study. J. Med. Virol. 88:153–158, 2016. © 2015 Wiley Periodicals, Inc.

Wheat spindle streak mosaic virus is a Bymovirus transmitted by the plasmodiophorid Polymyxa graminis that infects small grains such as wheat, rye and triticale. Nucleotide sequences of WSSMV isolates from several locations in Germany used for virus resistance trials differ from the sequences of the isolates found in France, Denmark, and the USA by a nona-nucleotide insertion in the 14K protein region.

Bats have great potential as reservoirs for emerging viruses such as severe acute respiratory syndrome-coronavirus. In this study, bat coronaviruses (BtCoVs) were detected by RT-PCR from intestinal and fecal specimens of Miniopterus fuliginosus breeding colonies in Wakayama Prefecture caves, where we previously identified bat betaherpesvirus 2. Two primer sets were used for the detection of BtCoV: one was for the RNA-dependent RNA polymerase (RdRp) region and the other was for the spike (S) protein region. Eleven and 73% of intestinal and fecal specimens, respectively, were positive for RdRp region, and 2 and 40% of those were positive for S protein region. Sequencing and phylogenetic analysis showed that the detected BtCoV belonged to the group 1 (alpha) coronaviruses. These data suggest that BtCoV is endemic in M. fuliginosus in Japan.

The Melanophila acuminata beetle is attracted to forest fires via a pair of infrared sensory organs composed of sensilla. Our histological work showed that each sensillum contains lipid layers surrounding a protein layer and a unique polysaccharide base that is associated with a neuron to each sensillum. Infrared microscopy showed that the protein region maximally absorbs infrared radiation at 3 μm wavelength and at 10 μm, which corresponds to the known radiation produced by forest fires at 3 μm. Mathematical calculations showed that the physical properties of the sensilla are such that the expected temperature rise is insufficient for transduction of the infrared signal through mechanical means or as a thermal receptor as previously thought; hence the protein plays the pivotal role in perception of single photons and transmission of the signal within the sensilla.

Intrinsically disordered proteins (IDPs) constitute a recently recognized realm of atypical biologically active proteins that lack stable structure under physiological conditions, but are commonly involved in such crucial cellular processes as regulation, recognition, signaling and control. IDPs are very common among proteins associated with various diseases. Recently, we performed a systematic bioinformatics analysis of the human diseasome, a network that linked the human disease phenome (which includes all the human genetic diseases) with the human disease genome (which contains all the disease-related genes) (Goh, K. I., Cusick, M. E., Valle, D., Childs, B., Vidal, M., and Barabasi, A. L. (2007). The human disease network. Proc. Natl. Acad. Sci. U.S.A. 104, 8685-90). The analysis of this diseasome revealed that IDPs are abundant in proteins linked to human genetic diseases, and that different genetic disease classes varied dramatically in the IDP content (Midic U., Oldfield C.J., Dunker A.K., Obradovic Z., Uversky V.N. (2009) Protein disorder in the human diseasome: Unfoldomics of human genetic diseases. BMC Genomics. In press). Furthermore, many of the genetic disease- related proteins were shown to contain at least one molecular recognition feature, which is a relatively short loosely struc- tured protein region within a mostly disordered segment with the feature gaining structure upon binding to a partner. Fi- nally, alternative splicing was shown to be abundant among the diseasome genes. Based on these observations the human- genetic-disease-associated unfoldome was created. This minireview describes several illustrative examples of ordered and intrinsically disordered members of the human diseasome.

Black box modelling is used here to improve the performances of the PoPMuSiC program that predicts protein stability changes caused by single-site mutations. For that purpose previously developed statistical energy functions are exploited, which are based on a formalism that highlights the coupling between 4 different protein descriptors (sequence, distance, torsion angles and solvent-accessibility), as well as the volume variation of the mutated amino acid. As the importance of the different types of interactions may depend on the protein region, the stability change is expressed as a linear combination of these energetic functions, whose proportionality coefficients vary with the solvent-accessibility of the mutated residue. Two alternative structures are considered for these coefficients: a Radial Basis Function network, and a MultiLayer Perceptron with sigmoid nodes. These two structures are identified, leading to an improvement of the predictive capabilities of PoPMuSiC, and are discussed in terms of their biophysical interpretation.

Intrinsically disordered proteins (IDPs) are ubiquitously involved in cellular processes and often implicated in human pathological conditions. The critical biological roles of these proteins, despite not adopting a well-defined fold, encouraged structural biologists to revisit their views on the protein structure-function paradigm. Unfortunately, investigating the characteristics and describing the structural behavior of IDPs is far from trivial, and inferring the function(s) of a disordered protein region remains a major challenge. Computational methods have proven particularly relevant for studying IDPs: on the sequence level their dependence on distinct characteristics determined by the local amino acid context makes sequence-based prediction algorithms viable and reliable tools for large scale analyses, while on the structure level the in silico integration of fundamentally different experimental data types is essential to describe the behavior of a flexible protein chain. Here, we offer an overview of the latest developments and computational techniques that aim to uncover how protein function is connected to intrinsic disorder., SCOPUS: sh.j, info:eu-repo/semantics/published

Analysis of the intensely studied HIV-1 gp120 V3 protein region reveals that the among-population mean site-specific frequency of an amino acid is a measure of its relative marginal fitness. This surprising result may arise if populations are displaced from mutation–selection equilibrium by fluctuating selection and if the probability of fixation of a beneficial amino acid is proportional to its selection coefficient.

A series of glycosyl serines 1–6 which are located in the carbohydrate-protein linkage region of proteoglycans, including the chondrottin penta- and heptasaccharides GalNAcα(1–4)R (3), GalNAcs(1–4)R (4) and GalNAcs(1–4)GlcAs(1–3)GalNAc(1–4)R (6) as well as the heparin pentasaccharide GlcNAcα(1–4)R (5) [R = GlcAs(1–3)Gals(1–3)Gals(1–4)Xyls-Ser] were systematically synthesized as follows. Trisaccharide acceptor 27 having a Gal(1–3)Gals(1–4)Xyl sequence was glycosylated with di- and tetrasaccharide donors 16α, 16s, 22, and 26, which correspond to the non-reducing end sequences of 3–6, regio- and stereoselectively to afford penta- and heptasaccharides 30, 34, 36, and 39, respectively. After the conversion into the respective penta- and heptaosylimidates 42c-f as well as tri- and tetraosylimidates 42a and b, they were coupled with serine derivative 43 to give tri-, tetra-, penta-, and heptaosyl serines 44a-f. All the glycosyl serines were deprotected to 1–6.

Given the necessity for increased conservation of endangered birds such as the Crested ibis, it is crucial to identify the gender of individuals fro m species with similar external mo rphologies among females (ZW) and males(ZZ) to establish a self-sustainable population for restoration of the species. Moreover, raising young chicks during the juvenile period based on sex determination encourages familiarity, wh ich might increase mating success rates. Thus, this study was carried out to determine the sex of Crested ibis chicks using three primers designed to check their identity. A se t of poly- merase chain reaction(PCR) primers was used to amplify a 276 bp chro mo-helicase-DNA b inding protein region(CHD) on the Z chro mosome in both sexes, whereas the other set was used to amp lify a 169 bp female -specific CHD sequence on the W chromosome. The sequences have been submitted to NCBI(GenBank Accession Number: AB620020, AB620021). Th is method will enable researchers to determine the gender of Crested ibis more simp ly and quickly.

Over 500 researchers participated in a recent American Association for Cancer Research special conference, entitled “Apoptosis and Cancer: Basic Mechanisms and Therapeutic Opportunities in the Post-Genomic Era” (February 13–17, 2002) in sunny Hawaii (Hilton Waikoloa village, Kona, Hawaii). The meeting participants presented the most recent findings on the mechanisms regulating cell death in cancer. In the past decade, apoptosis research has undergone a quantum leap, metamorphosing from a descriptive, phenomenological discipline into a molecularly defined, highly complex signalling field. This transformation was highlighted in the conference's opening talk by meeting co-organizer, John Reed (The Burnham Institute, La Jolla, CA). Reed and colleagues used published protein functional information and bio-informatic mining of the available human genome databases to tabulate the number of human proteins predicted to be involved in regulating apoptosis. The list includes 11 catalytically active caspases, 26 CARD (caspase associated recruitment domain)-, 32 DD (death domain)-, 12 DED (death effector domain)-, 8 BIR (baculovirus inhibitor of apoptosis protein region)-, 24 BH (Bcl-2 homology)-, and 34 PAAD/PYD (pyrin/PAAD)-containing sequences.

Mitogenic activity and antitumor activity of Aloe arborescens Miller, Aloe barbadensis Miller and Aloe africana Miller, which have been used as traditional drugs and health food, were studied. The raw fresh aloe was divided into flesh and skins, and was lyophilized. Fraction were obtained by extraction with hot water, 0.1M NaOH and 0.5M NaOH. Mitogen assay was performed for all fraction using spleen cells from mice (_??_), C3H/HeN and C3H/HeJ. Six fractions showed mitogenic activity towards spleen cells of C3H/HeN. In addition, although the proteins were removed with actinase, the samples continued to show this activity. Among them, the non-dialyzable fraction of hot water extracts from a skin of Aloe arborescens Miller and the non-dialyzable fraction of hot water extracts from a skin of Aloe africana Miller showed strong mitogenic activity towards cells of C3H/HeJ, suggesting that it was free from bacterial endotoxic lipopolysaccharide. These results suggest that the activity components are not located in the protein region. No fraction showed antitumor activity against Sarcoma 180 ascites in mice.

In spite of the high similarity in amino acid sequence between rod visual pigment rhodopsin and gecko blue-sensitive pigment (gecko blue), not only the spectral sensitivities but also the thermal decay rates of the meta II- and III-intermediates are noticeably different from one another [Kojima et al. (1995) Biochemistry 34, 1096-1106]. In order to identify the protein region(s) that contain(s) key residue being responsible for the functional difference, we constructed six chimerical mutants derived from gecko blue and bovine rhodopsin, with the aid of protein production in a human embryonic kidney cell line (293S). While the absorption maximum of every mutant was located in between gecko blue (466 nm) and bovine rhodopsin (500 nm), a large blue-shift (18 nm) was observed when the helices I-III of rhodopsin were replaced with those of gecko blue. A time resolved spectroscopic study demonstrated that this replacement also accelerated the decay rate of the meta II-intermediate. The decay of the meta III-intermediate of the mutants became faster as the compartment of gecko blue was increased. Thus, the faster decay of the meta II-intermediate of gecko blue is largely attributed to residues within helices I-III, while the decay of the meta III-intermediate apparently depends on the overall structure of the protein.

55 accessions of wild peanuts (Arachis spp.) introduced from South America were analyzed for seed storage protein composition using SDS-PAGE electrophoresis. The objectives of the study were to evaluate variability within sect.Arachis and to classify taxa based on protein composition. 25 different band positions were resolved. Individual accessions had 11 to 18 bands which included the conarachin region (MW > 50 kD), two to five bands in the acidic arachin region (MW 38–49.9 kD), three to seven in the intermediate MW region (23 to 37.9 kD), two to five bands in the basic arachin region (18–22.9 kD), and one to three bands in the low MW protein region (14–17.9 kD). These data were utilized in a principal coordinate analysis based on the matrix of genetic distances between all pairs of the 55 accessions. Several groups of accessions conformed to expected species classification includingA. batizocoi, A. stenosperma, andA. monticola; whileA. duranensis, A. cardenasii, A. helodes, andA. correntina did not form good groups. The study showed that great diversity exists for protein profiles and seed storage proteins have potential for aiding species classification and for serving as markers for interspecific hybridization studies.

We identified two BRCA1 mutations in a high risk breast cancer family: the missense 1240 C>T (Thr>Ile) and the 1241delAC at codon 374, which results in a stop at codon 376. Both were contiguously located in the same BRCA1 gene, in a motif of 11 amino acids, which is highly conserved across human, canine and murine species. The presence of missense mutations in this motif in breast-cancer families suggests an important functional role for this protein region and a potential deleterious effect of the 1240C>T mutation.

Motivation: Protein–protein interactions are commonly mediated by the physical contact of distinct protein regions. Computational identification of interacting protein regions aids in the detailed understanding of protein networks and supports the prediction of novel protein interactions and the reconstruction of protein complexes. Results: We introduce an integrative approach for predicting protein region interactions using a probabilistic model fitted to an observed protein network. In particular, we consider globular domains, short linear motifs and coiled-coil regions as potential protein-binding regions. Possible cooperations between multiple regions within the same protein are taken into account. A finegrained confidence system allows for varying the impact of specific protein interactions and region annotations on the modeling process. We apply our prediction approach to a large training set using a maximum likelihood method, compare different scoring functions for region interactions and validate the predicted interactions against a collection of experimentally observed interactions. In addition, we analyze prediction performance with respect to the inclusion of different region types, the incorporation of confidence values for training data and the utilization of predicted protein interactions. Contact: mario.albrecht@mpi-inf.mpg.de Supplementary information: Supplementary data are available at Bioinformatics online.

The exon–junction complex (EJC) components hUpf3a and hUpf3b serve a dual function: They promote nonsense-mediated mRNA decay (NMD), and they also regulate translation efficiency. Whether these two functions are interdependent or independent of each other is unknown. We characterized the function of the hUpf3 proteins in a λN/boxB-based tethering system. Despite the high degree of sequence similarity between hUpf3b and hUpf3a, hUpf3a is much less active than hUpf3b to induce NMD and to stimulate translation. We show that induction of NMD by hUpf3 proteins requires interaction with Y14, Magoh, BTZ, and eIF4AIII. The protein region that mediates this interaction and discriminates between hUpf3a and hUpf3b in NMD function is located in the C-terminal domain and fully contained within a small sequence that is highly conserved in Upf3b but not Upf3a proteins. Stimulation of translation is independent of this interaction and is determined by other regions of the hUpf3 protein, indicating the presence of different downstream pathways of hUpf3 proteins either in NMD or in translation.

The foamy viral proteases (FV PRs) are set apart from other retroviral processing enzymes by unique features. The first remarkable property is that FV PRs are enzymatically active as high-molecular-mass Pro-Pol proteins. Hence there exist multiple forms of active FV PRs that likely contribute to cleavage site specificity. A FV PR of low molecular size is not detectable in purified virions, in contrast to PRs of other retroviruses that are found in virus particles. Because the major part of Pol remains attached to the amino-terminal enzymatically active PR protein region, the FV-specific way of expressing Pro-Pol polyproteins from a pol-specific transcript provides for the incorporation of Pro-Pol and IN into virus particles. Proteolytic processing of Gag and Pol proteins is incomplete and delayed. Another novel feature is that the catalytic center of the active dimers of cat FV PR consists of D-S/T-Q instead of D-S/T-G, an unprecedented feature of this enzyme. The temporal and spatial control and the factors that regulate FV PRs remain to be elucidated.

The epitopes recognized by 42 monoclonal antibodies directed against the human parainfluenza virus type 2 (hPIV-2) phosphoprotein (P) were mapped on the primary structure of the P protein by testing their reactivities with deletion mutants. By Western Immunoblotting with these monoclonal antibodies and P protein deletion mutants the region essential for P-P interactions was determined. The P protein region encompassing amino acids 211-248 was required for proper folding and oligomerization which is mediated by predicted coiled-coils in this region. The oligomer was shown to be a homotrimer by chemical cross-linking experiments.

Two different antigens of serotype 1 Chlamydia psittaci were localized using three immunoelectron microscopy techniques: non-embedding, pre-embedding and post-embedding. The antigens had previously been described as being of potential use in diagnosis (80-90 kDa protein region) and vaccine development (110 kDa protein). The results show a direct relationship between the protective capacity of the antigens and their surface localization on the elementary bodies, which are the infectious form of Chlamydia. The 80-90 kDa protein region is located on the surface of reticulate bodies but not of elementary bodies, where it was located periplasmically, while the 110 kDa protein occurs on the surface of both elementary and reticulate bodies.

Multiple-round in vitro transcription assays were performed using purified Escherichia coli RNA polymerase reconstituted with either wild-type or mutant final sigma70 proteins. These mutants, final sigma70(P504L) and final sigma70(S506F), bear single amino acid changes in conserved protein region 3. Behavior of the mutant enzymes on three test templates, bearing either the T7 A1, T5 N25, or T5 N25antiDSR promoter, were characterized. Transcription of all three promoter templates produced a pattern of specific abortive RNA species, which was qualitatively different for the mutants compared to the wild-type final sigma70 enzyme. Short abortive RNAs were produced at similar levels for mutant and wild-type enzymes. The production of longer abortive species was either reduced or increased by the mutant enzymes in a systematic manner that appears promoter-specific, and could be RNA length- or promoter distance-dependent. The process of abortive RNA transcription is thought to be tightly associated with that of promoter clearance. However, promoter clearance from these templates appears only slightly affected by the mutant enzymes. These mutants implicated region 3 of final sigma70 in the process of abortive transcription and suggest that the sequence of enzymatic events leading to the production of abortive or full-length RNA may be separable.

An evolutionary analysis of self peptides reported to be bound by HLA class I molecules showed that these peptides are largely derived from proteins that have been highly conserved in the history of mammals. These proteins also often have universal tissue expression and have a higher than average frequency of highly hydrophilic residues. The peptides themselves are generally still more highly conserved than the source proteins and have a higher frequency of highly hydrophobic residues, evidently often being derived from conserved hydrophobic cores of the source proteins. These results suggest that the mechanism by which peptides are derived for MHC presentation may preferentially select peptides from conserved protein regions. In the case of parasite-derived peptides, such a mechanism would be adaptive in that it would reduce the likelihood of escape mutants.

The wheat-grain proteome was investigated, as a basis for devising more efficient methods of cultivar identification or discrimination. Australian wheats (Halberd, Cranbrook, CD87 and Katepwa) were used as the basis of this study. These cultivars were selected on the basis of differences in the quality types represented, in terms of dough-processing attributes that can suit one cultivar better than another for specific types of industrial utilisation. Total wheat endosperm (flour) protein extracts were prepared from mature wheat for two-dimensional electrophoresis, across both acidic (pH 4-7) and basic (pH 6-11) pH ranges. Three particular regions of the proteome maps were chosen for close comparison, involving two sets of gluten proteins and a nongluten protein region (involving small heat shock proteins), based on previous protein characterisation. Differences in the nongluten protein regions (heat shock proteins and other unidentified polypeptides) are of particular interest as being possible targets for use in developing new approaches to cultivar discrimination, such as the development of simple immunoassays.

With the aid of gel filtration techniques (Sephadex G-200) the alkaline phosphatase (Bessey-Lowry-Brock) distribution patterns have been studied in the serum of control human subjects and of those with conditions known to affect total enzyme levels. Protein was scanned at 254 and 280 mμ and the 19S, 7S, and 4S peaks thus obtained were used as points of reference. The characteristic control serum revealed one sharp peak of enzyme activity in the 7S protein region. A similar but sharper peak was found in osteomalacia and Pagets' disease. In contrast, in malignant bone conditions 10.4%, in metastatic malignant liver disease 31.36% and in nonmalignant liver disease 12.7% of total enzyme moved with the 19S proteins. The patterns found in various conditions are reproducible, and that of metastatic malignant liver disease is particularly characteristic. The significance of the macromolecular-moving enzyme is discussed and is being investigated.

BamA is the main component of the beta-barrel assembly machinery (BAM) that folds and inserts outer membrane proteins in Gram-negative bacteria. Crystal structures have suggested that this process involves conformational changes in the transmembrane beta-barrel of BamA that allow for lateral opening, as well as large overall rearrangements of its periplasmic POTRA domains. Here, we identify local dynamics of the BamA POTRA 5 domain by solution and solid-state nuclear magnetic resonance. The protein region undergoing conformational exchange is highly conserved and contains residues critical for interaction with BamD and correct beta-barrel assembly in vivo. We show that mutations known to affect the latter processes influence the conformational equilibrium, suggesting that the plasticity of POTRA 5 is related to its interaction with BamD and possibly to substrate binding. Taken together, a view emerges in which local protein plasticity may be critically involved in the different stages of outer membrane protein folding and insertion.

The cytoplasmic concentration of Z protein (Mr approximately 12,000) was significantly reduced in a series of implanted Morris hepatomas with varying degrees of differentiation. Approximately half of the [14C]palmitoyl-CoA added to cytosol fractions from control or host livers was bound to the Z protein region whereas a much smaller proportion was bound to this region in the cytosol of nine Morris hepatomas studied. The possible implications of these findings are discussed in relation to the abnormal regulation of lipid metabolism in hepatomas.

Cowpea chlorotic mottle virus (CCMV) is a spherical plantvirus of the group of bromoviruses. An interesting feature of bromoviruses is the increase in hydrodynamic volume when the pH is raised from 5.0-7.5 at low ionic strength (