Terms Of Domain Structure Research Articles

The DSM should replace maladaptive traits with the five-factor model: Comment on Clark and Watson (2022).

In their target article, Watson and Clark made a number of useful suggestions for improving Criterion B of the Diagnostic and Statistical Manual of Mental Disorders, Fifth Edition, alternative model of personality disorders, all of which assume that personality variation will be represented in the next iteration of the Diagnostic and Statistical Manual of Mental Disorders as a maladaptive trait variation diagnostic of personality disorders (PDs). I describe how maladaptive traits are not equivalent to normal-range five-factor model traits in terms of domain structure, range, and stability, and I conclude that rather than making subtle changes to the existing maladaptive trait model for PDs, it would be better to replace it with a genuine five-factor model that could be used to conceptualize all patients, whether or not they are diagnosed with a PD. (PsycInfo Database Record (c) 2022 APA, all rights reserved).

Genome-Wide Characterization and Expression Profiling of GASA Genes during Different Stages of Seed Development in Grapevine (Vitis vinifera L.) Predict Their Involvement in Seed Development.

Members of the plant-specific GASA (gibberellic acid-stimulated Arabidopsis) gene family have multiple potential roles in plant growth and development, particularly in flower induction and seed development. However, limited information is available about the functions of these genes in fruit plants, particularly in grapes. We identified 14 GASA genes in grapevine (Vitis vinifera L.) and performed comprehensive bioinformatics and expression analyses. In the bioinformatics analysis, the locations of genes on chromosomes, physiochemical properties of proteins, protein structure, and subcellular positions were described. We evaluated GASA proteins in terms of domain structure, exon-intron distribution, motif arrangements, promoter analysis, phylogenetic, and evolutionary history. According to the results, the GASA domain is conserved in all proteins and the proteins are divided into three well-conserved subgroups. Synteny analysis proposed that segmental and tandem duplication have played a role in the expansion of the GASA gene family in grapes, and duplicated gene pairs have negative selection pressure. Most of the proteins were predicted to be in the extracellular region, chloroplasts, and the vacuole. In silico promoter analysis suggested that the GASA genes may influence different hormone signaling pathways and stress-related mechanisms. Additionally, we performed a comparison of the expression between seedless (Thompson seedless) and seeded (Red globe) cultivars in different plant parts, including the ovule during different stages of development. Furthermore, some genes were differentially expressed in different tissues, signifying their role in grapevine growth and development. Several genes (VvGASA2 and 7) showed different expression levels in later phases of seed development in Red globe and Thompson seedless, suggesting their involvement in seed development. Our study presents the first genome-wide identification and expression profiling of grapevine GASA genes and provides the basis for functional characterization of GASA genes in grapes. We surmise that this information may provide new potential resources for the molecular breeding of grapes.

Genomic Organization of the B3-Domain Transcription Factor Family in Grapevine (Vitis vinifera L.) and Expression during Seed Development in Seedless and Seeded Cultivars.

Members of the plant-specific B3-domain transcription factor family have important and varied functions, especially with respect to vegetative and reproductive growth. Although B3 genes have been studied in many other plants, there is limited information on the genomic organization and expression of B3 genes in grapevine (Vitis vinifera L.). In this study, we identified 50 B3 genes in the grapevine genome and analyzed these genes in terms of chromosomal location and syntenic relationships, intron–exon organization, and promoter cis-element content. We also analyzed the presumed proteins in terms of domain structure and phylogenetic relationships. Based on the results, we classified these genes into five subfamilies. The syntenic relationships suggest that approximately half of the genes resulted from genome duplication, contributing to the expansion of the B3 family in grapevine. The analysis of cis-element composition suggested that most of these genes may function in response to hormones, light, and stress. We also analyzed expression of members of the B3 family in various structures of grapevine plants, including the seed during seed development. Many B3 genes were expressed preferentially in one or more structures of the developed plant, suggesting specific roles in growth and development. Furthermore, several of the genes were expressed differentially in early developing seeds from representative seeded and seedless cultivars, suggesting a role in seed development or abortion. The results of this study provide a foundation for functional analysis of B3 genes and new resources for future molecular breeding of grapevine.

Oestrogen-related receptor reduces vitellogenin expression by crosstalk with the ecdysone receptor pathway in female silkworm, Bombyx mori.

Oestrogen-related receptor (ERR) is involved in oestrogen receptor (ER) signalling pathways owing to its similarity to ER in terms of domain structure and co-activator and response elements. Although insects lack ER, they harbour an ERR gene that is thought to modulate metabolism and energy conversion via an unknown mechanism. The present study investigated the function of ERR in insects using female silkworm (Bombyx mori, Bm). We found that the expression of B.mori vitellogenin (BmVg) and B.mori ERR (BmERR) in the fat bodies of female silkworms at different stages of development exhibited alternating patterns, and RNA interference of BmERR in females induced BmVg transcription, resulting in an increase in egg weight relative to the control. Furthermore, BmERR was found to be involved in regulating the transcription of BmVg through an oestrogen-related receptor response element (ERRE) in the promoter of the BmVg gene, as demonstrated by electrophoretic mobility shift assay, cell transfection assay and chromatin immunoprecipitation. In summary, our results indicate that BmERR bound to the ERRE motif in the BmVg promoter reducing the expression of BmVg in the fat body of the female silkworm. To our surprise, the ERRE also showed the ability to bind the ecdysone receptor (BmEcR) and ultraspiracle complex. Thus, we surmise that ERR participates in steroid hormone signalling by engaging in crosstalk with the ER pathway in vertebrates and with the EcR pathway in insects.

Influence of thin platinum layer on the magnetic properties of multiple layers of CVD cobalt thin films

This paper presents the results obtained on the multiple layers of cobalt (Co)/platinum (Pt) and cobalt (Co)/platinum (Pt)/cobalt (Co) on the oxidised silicon substrate. The cobalt layers were deposited by metal-organic chemical vapour deposition on oxidised-silicon substrates at 450 °C, in H2 ambient with 2-torr processing pressure. The platinum layers were deposited by E-beam evaporation in a separate vacuum system. The magnetic properties of Co/Pt/Co and Co/Pt multilayer were compared with the single cobalt layers of similar thicknesses on the oxidised silicon substrate. From the hysteresis loops it was observed that thin cobalt layers on oxidised-silicon substrate shows hard magnetic property with coercivity H c values of 360 Oe and 500 Oe respectively for the 30- and 15-nm cobalt layers. The multiple layers of Co/Pt/Co and Co/Pt of cobalt thickness 15- and 30-nm with platinum 1.5-nm spacer-layer show significant change in magnetic properties (i.e. coercivity H c and magnetisation M s ) and, gave soft magnetic properties with H c values 51 and 49 Oe respectively, which are significantly less than the H c values of single cobalt layers on oxidised silicon. Also, single and multiple layers cobalt with platinum were annealed and compared with the as-deposited layer structures. From the microstructure analysis by SEM, and AFM it was found that the single and multilayer had similar roughness. Magnetic images were observed by MFM and analyzed in terms of domain structure.

Magnetic spectra of Fe-based nanocrystalline wires with axial or transverse domains

The circular permeability μ′= μ′− jμ″ of two Fe-based soft magnetic wires with axial and transverse domains, has been determined from the measurements of impedance Z= R+ jX as functions of frequency ( f=10–10 5 Hz) and AC current amplitude ( I=0.1–100 mA). From the magnetic spectra of μ′− f and μ″− f for a few circular fields ( H φ =0.4, 1.2, 4, 12, 40 A/m), we found that the sample with axial domain structure exhibits a relaxational feature, while for the one with transverse domain resonance-like spectra were observed when the circular field H φ ≥4 A/m. These results have been discussed in terms of domain structure and circular magnetization processes.

Identification of Neutral Cholesterol Ester Hydrolase, a Key Enzyme Removing Cholesterol from Macrophages

Unstable lipid-rich plaques in atherosclerosis are characterized by the accumulation of macrophage foam cells loaded with cholesterol ester (CE). Although hormone-sensitive lipase and cholesteryl ester hydrolase (CEH) have been proposed to mediate the hydrolysis of CE in macrophages, circumstantial evidence suggests the presence of other enzymes with neutral cholesterol ester hydrolase (nCEH) activity. Here we show that the murine orthologue of KIAA1363, designated as neutral cholesterol ester hydrolase (NCEH), is a microsomal nCEH with high expression in murine and human macrophages. The effect of various concentrations of NaCl on its nCEH activity resembles that on endogenous nCEH activity of macrophages. RNA silencing of NCEH decreases nCEH activity at least by 50%; conversely, its overexpression inhibits the CE formation in macrophages. Immunohistochemistry reveals that NCEH is expressed in macrophage foam cells in atherosclerotic lesions. These data indicate that NCEH is responsible for a major part of nCEH activity in macrophages and may be a potential therapeutic target for the prevention of atherosclerosis.

Study of magnetic properties of thin cobalt films deposited by chemical vapour deposition

Chemical Vapour Deposition (CVD) of cobalt was deposited from a liquid source precursor of cobalt tricarbonyl nitrosyl (Co(CO)3NO) on to oxidised silicon wafers. The cobalt layers were deposited at 450∘C at 1.5 torr chamber pressure of hydrogen for 15 min processing time with various precursor flow rates. X-ray diffraction studies of the cobalt films reveal both hcp and fcc peaks. The vibrating sample magnetometer (VSM) yields coercivity (Hc) 167 Oe and 364 Oe for 46 nm and 30 nm thickness layers respectively at room temperature and squareness (S) M r /M s (remanence/saturation of magnetisation) value of ∼ 1. The study of magnetic properties of the cobalt suggests that magnetisation is dependent on grain size and therefore thickness. The grain size was observed by atomic force microscopy (AFM). Magnetic images were observed by magnetic force microscopy (MFM) and analyzed in terms of domain structure. The surface domain structure was recorded with the tip lift height 100 nm so that the magnetic interactions arising produced the topography effect. Where there is repulsive interaction the intensity is recorded as a bright region and where the interaction is attractive the intensity is recorded as a dark region.

Gelatinase B functions as regulator and effector in leukocyte biology

Matrix metalloproteinases (MMPs) form a family of enzymes with major actions in the remodeling of extracellular matrix (ECM) components. Gelatinase B (MMP-9) is the most complex family member in terms of domain structure and regulation of its activity. Gelatinase B activity is under strict control at various levels: transcription of the gene by cytokines and cellular interactions; activation of the pro-enzyme by a cascade of enzymes comprising serine proteases and other MMPs; and regulation by specific tissue inhibitors of MMPs (TIMPs) or by unspecific inhibitors, such as alpha2-macroglobulin. Thus, remodeling ECM is the result of the local protease load, i.e., the net balance between enzymes and inhibitors. Glycosylation has a limited effect on the net activity of gelatinase B, and in contrast to the all-or-none effect of enzyme activation or inhibition, it results in a higher-level, fine-tuning effect on the ECM catalysis by proteases in mammalian species. Fast degranulation of considerable amounts of intracellularly stored gelatinase B from neutrophils, induced by various types of chemotactic factors, is another level of control of activity. Neutrophils are first-line defense leukocytes and do not produce gelatinase A or TIMP. Thus, neutrophils contrast sharply with mononuclear leukocytes, which produce gelatinase A constitutively, synthesize gelatinase B de novo after adequate triggering, and overproduce TIMP-1. Gelatinase B is also endowed with functions other than cleaving the ECM. It has been shown to generate autoimmune neo-epitopes and to activate pro-IL-1beta into active IL-1beta. Gelatinase B ablation in the mouse leads to altered bone remodeling and subfertility, results in resistance to several induced inflammatory or autoimmune pathologies, and indicates that the enzyme plays a crucial role in development and angiogenesis. The major human neutrophil chemoattractant, IL-8, stimulates fast degranulation of gelatinase B from neutrophils. Gelatinase B is also found to function as a regulator of neutrophil biology and to truncate IL-8 at the amino terminus into a tenfold more potent chemokine, resulting in an important positive feedback loop for neutrophil activation and chemotaxis. The CXC chemokines GRO-alpha, CTAP-III, and PF-4 are degraded by gelatinase B, whereas the CC chemokines MCP-2 and RANTES are not cleaved.

A Reference of the GOLD Classification of Monoclonal Antibodies against Carcinoembryonic Antigen to the Domain Structure of the Carcinoembryonic Antigen Molecule

The epitopes of 42 well-characterized monoclonal antibodies (MAbs) against carcinoembryonic antigen (CEA) from 10 different research groups were mapped in terms of domain structure (domains N, A1-B1, A2-B2, and A3-B3) of the CEA molecule on the basis of the reactivities with recombinant CEA proteins expressed in Chinese hamster ovary cells. Thirty-six of the 42 MAbs tested have previously been classified into 5 essentially nonoverlapping epitope groups (GOLD 1-5) by cross-competition assays among MAbs for CEA binding (Hammarström S, et al.: Cancer Res. 1989; 49:4852-4858). The epitopes recognized by GOLD 2 MAbs were all present on domain A2-B2, those for GOLD 5 MAbs were all on domain N, and those for GOLD 4 were mapped around domains A1-B1 and A2-B2. On the other hand, the epitopes for GOLD 1 MAbs were distributed into domains N, A2-B2, and A3-B3, and those for GOLD 3 MAbs were separated into domains N and A3-B3. Although the exact reasons for the dispersed patterns of GOLD 1 and 3 MAbs on the domain structure of the CEA molecule are unclear at present, several factors, such as a spatial relation or a close proximity of epitopes, conformation dependency, and repetitivity of epitopes, may be considered as possible explanations. The epitope mapping reported here helps form the basis for understanding the relation between the chemical structure and antigenic activities of the CEA molecule and may be useful to study the functions of the CEA molecule, especially those of the respective domains.

Biochemical characterization of 25 distinct carcinoembryonic antigen (CEA) epitopes recognized by 57 monoclonal antibodies and categorized into seven groups in terms of domain structure of the CEA molecule.

The chemical nature of 25 distinct carcinoembryonic antigen (CEA) epitopes, which were recognized by 57 different monoclonal antibodies and categorized into 7 groups (Groups A to G) in terms of domain structure of the CEA molecule, was analyzed and the findings obtained were compared with the results of our previous studies using recombinant CEA proteins. All 21 epitopes of Groups A to F defined by 48 MAbs were resistant to periodate oxidation and were to a greater or lesser extent retained after deglycosylation of CEA, indicating that they are all protein in nature. The 21 epitopes were detected in recombinant CEA proteins expressed in Chinese hamster ovary (CHO) cells. Seven of the 21 epitopes of protein nature were partially or completely sensitive to reduction and alkylation of CEA and not detected or only slightly revealed in the recombinant CEA proteins expressed in E. coli, indicating that those epitopes are dependent on the tertiary structure of the peptide chain, which is formed by disulfide bonds. All 4 epitopes of Group G defined by 9 MAbs were sensitive to mild periodate oxidation and deglycosylation, but resistant to reduction and alkylation and to digestion with pepsin or pronase, indicating that those 4 epitopes are carbohydrate in nature. Although none of the 4 epitopes of Group G were detected in the recombinant CEA proteins expressed in E. coli, two were detected in those expressed in CHO cells. The biochemical studies reported here thus provide information as to the nature of the epitopes on the CEA molecule and help form the basis for selecting the anti-CEA MAbs for use in biological study and potential clinical applications of CEA.

Kinetics of formation of hydrophobic regions during refolding of bovine serum albumin.

The rate of formation of hydrophobic regions during refolding of bovine serum albumin was studied using 1-anilinonaphthalene-8-sulfonate as the hydrophobic fluorescent probe. The refolding of serum albumin exhibited a sigmoidal behavior. The exhibition of a lag phase followed by a faster kinetic phase suggested that the refolding is a cooperative, sequential process. Refolding under reducing conditions almost completely inhibited the regeneration of hydrophobic binding regions, suggesting that the formation of disulfide bonds plays an important role in the refolding of serum albumin. The rate and the extent of refolding was apparently maximum at about 20 degrees; at 37 degrees the extent of refolding was very low compared to that at the other temperatures studied. Based on the results, the mechanism of albumin refolding is interpreted in terms of domain structures and interdomain interactions.

Crystallographic structural studies of a human Fc-fragment. I. An electron-density map at 4 A resolution and a partial model.

The crystal structure of a human Fc fragment was analysed at 4 A resolution. A partial interpretation of the electron-density map in terms of domain structure was possible. The molecule has the shape of a mickey mouse. The spherical domain was interpreted visually and by domain Patterson function interpretation as the CH3 dimer. This dimer resembles closely the CH1-CL dimer found in Fab structures. The ellipsoidal "ears" of the molecule represent the CH2 domains. They are widely separated from each other, but closely connected to CH3. Their tertiary structure must be different from CH1, as Patterson domain interpretations were unsuccessful. A chain tracing in CH2 was not yet possible.