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Integrated metabolomics, transcriptional, and physicochemical analysis reveals key metabolites and genes associated with somatic embryogenesis in Phyllostachys pubescens.

Phyllostachys pubescens (Moso bamboo) is a significant perennial crop species that provides valuable nutritional and industrial uses, as well as carbon sequestration. Due to its remarkable growth rate, bamboo offers an ideal system for studying organogenesis, particularly in monocots. Somatic embryogenesis (SE) serves as a useful technique for crop breeding and improvement. SE in moso bamboo (Phyllostachys pubescens) remains challenging due to limited knowledge of its transcriptional and metabolomic reprogramming. To address this, we optimized callus initiation (MS + 18.1 µM 2,4-D + 8.5 µM picloram), callus proliferation (MS + 12.5 µM 2,4-D + 8.5 µM picloram), and somatic embryogenesis (MS + 1.1 µM 2,4-D + 3.3 µM metatopolin), using nodal segments as explants. UHPLC-Q-TOF-MS-based metabolite profiling revealed distinct biochemical trajectories across developmental stages of P. pubescens. NEC (non-embryogenic callus) was enriched in flavonoids, alkaloids, and saponins, while in-vitro shoots showed flavonoids and glycosides enrichment, and ex-vitro shoots showed high accumulation of glycosides and terpenoids. In contrast, EC (embryogenic callus) showed elevated levels of fatty acid derivatives (α-ESA, 26-Methyl Nigranoate), phytoalexins (Wyerone acid), sesquiterpene (Alpha-santalal, Beta-guaiene), flavonoid glycosides, and plant hormones (Cis-Zeatin, Gibberellin A45), indicating a metabolically active state supporting somatic embryogenesis. Similarly, genes and transcription factors controlling cell differentiation and embryogenesis were upregulated during SE. This study provides a comprehensive resource to facilitate future genomic and genetic investigations aimed at deciphering the molecular basis of organogenesis and advancing research on somatic embryogenesis in bamboo.

Plant Somatic Embryogenesis Techniques↗

Somatic hypermutation of Ig genes is affected differently by failures in apoptosis caused by disruption of Fas (lpr mutation) or by overexpression of Bcl-2.

The effects of the two main apoptotic pathways on the somatic hypermutation process were analysed. Transgenic mice carrying the V(kappa)Ox1-J(kappa)5 rat transgene were crossed with Fas-deficient lpr mice or with mice overexpressing the Bcl-2 protein. The transgenic V(kappa)Ox1 segment and the endogenous JH4-C(micro) Ig intron from Peyer's patches germinal centre B cells were sequenced to study the intrinsic somatic hypermutation process without the skewing effects of specific antigen selection. The lpr/ox mice displayed, in both regions, a high level of mutations with a normal pattern of substitutions. On the contrary, the bcl-2/ox mice displayed a lower level of mutations with an altered pattern, showing a decreased mutational rate in the intrinsic hotspots of the V(kappa)Ox1 gene. Our results suggest that the lpr mutation does not have a direct effect on the somatic hypermutation process, but rather on the negative selection of B cells in the germinal centres, leading to the accumulation of recurrent mutations. In contrast, Bcl-2 overexpression might influence the somatic hypermutational process either by altering the incorporation of mutations or by enhancing the repair mechanism(s). The present work supports the hypothesis that both apoptotic pathways, Fas and Bcl-2, play distinct roles in the germinal centre reactions.

Animals↗

Genetic dissection of lupus pathogenesis: Sle3/5 impacts IgH CDR3 sequences, somatic mutations, and receptor editing.

Sle3/5 is a lupus susceptibility locus identified on mouse chromosome 7 of the New Zealand Black/New Zealand White (NZB/NZW)-derived NZM2410 strain. Based on previous observations, this locus appears to contribute to lupus pathogenesis through its impact on diversification of immune responses. To understand how Sle3/5 affects somatic diversification of humoral responses, we analyzed IgH rearrangements preferentially encoding hapten-reactive IgG1 repertoires after immunization and assessed peripheral IgH VDJ recombination activities in C57BL/6 (B6) mice congenic for Sle3/5 (B6.Sle3/5). In addition to altered somatic V(H) mutation profiles, sequences from B6.Sle3/5 mice exhibited atypical IgH CDR3 structures characteristic of autoreactive B cells and consistent with peripheral B cells bearing putatively edited receptors. Significant expression of Rag genes and circular V(H)D gene excision products were detected in splenic mature B cells of B6.Sle3/5 but not B6 mice, showing that peripheral IgH rearrangements occurred beyond allelic exclusion. Taken together, on the nonautoimmune background, Sle3/5 affected V(H)DJ(H) junctional diversity and V(H) mutational diversity and led to recombinational activation of allelically excluded IgH genes in the periphery. Such impact on somatic IgH diversification may contribute to the development of autoreactive B cell repertoires. This is the first report to present evidence for significant association of a lupus susceptibility locus, which has been mapped to a chromosomal region in which no Ig genes have been identified, with somatic IgH sequence diversity and peripheral H chain receptor editing or revision without relying upon Ig transgene strategies.

Animals↗

The nucleotide targets of somatic mutation and the role of selection in immunoglobulin heavy chains of a teleost fish.

Sequence analysis of H chain cDNA derived from the spleen of an individual catfish has shown that somatic mutation occurs within both the VH- and JH-encoded regions. Somatic mutation preferentially targets G and C nucleotides with approximately balanced frequencies, resulting in the predominant accumulation of G-to-A and C-to-T substitutions that parallel the activation-induced cytidine deaminase nucleotide exchanges known in mammals. The overall mutation rate of A nucleotides is not significantly different from that expected by sequence-insensitive mutations, and a significant bias exists against mutations occurring in T. Targeting of mutations is dependent upon the sequence of neighboring nucleotides, allowing statistically significant hotspot motifs to be identified. Dinucleotide, trinucleotide, and RGYW analyses showed that mutational targets in catfish are restricted when compared with the spectrum of targets known in mammals. The preferential targets for G and C mutation are the central GC positions in both AGCT and AGCA. The WA motif, recognized as a mammalian hotspot for A mutations, was not a significant target for catfish mutations. The only significant target for A mutations was the terminal position in AGCA. Lastly, comparisons of mutations located in framework region and CDR codons coupled with multinomial distribution studies found no substantial evidence in either independent or clonally related VDJ rearrangements to indicate that somatic mutation coevolved with mechanisms that select B cells based upon nonsynonymous mutations within CDR-encoded regions. These results suggest that the principal role of somatic mutation early in phylogeny was to diversify the repertoire by targeting hotspot motifs preferentially located within CDR-encoded regions.

Amino Acid Motifs↗

The meaning of symptoms in 10 women with somatization disorder and a history of childhood abuse.

OBJECTIVE: To understand the associated experiences and illness behavior in patients with somatization disorder and a history of childhood abuse. DESIGN: In-depth interviews were conducted with patients who had somatization disorder and a history of childhood abuse; qualitative content analysis was then performed. SETTING: Patients were recruited from 2 primary care teaching practices. PARTICIPANTS: Physicians were asked to refer patients suspected of having both conditions, yielding 21 potential participants. Eight declined, and 3 did not meet standardized screening questionnaire criteria, yielding 10 women who participated in the study. Participants and nonparticipants had a similar range of socioeconomic variables. RESULTS: An analysis of the interviews yielded 22 themes. Seven themes relevant to understanding the link between illness behavior and abuse were the abuse experiences, emotional and behavioral reactions to the abuse, relationship of abuse to somatoform symptoms, relationship of abuse to health care use, attempts to tell about the abuse, relationships with physicians, and physician behavior. Childhood attempts to tell adults about the abuse resulted in threats of punishment, contributing to lifelong patterns of secrecy, even with physicians. Six women reported having childhood physicians who were family members, friends, or the abuser's physician, reinforcing their subsequent secrecy. The women reported that their current physicians denied their physical pain as adults, just as the abusers denied their emotional and physical pain in childhood. Seven women reported decreased health care use once they associated symptoms with abuse experiences. Nine women reported spousal abuse. CONCLUSIONS: Somatization and childhood abuse may involve a paradoxical pattern of hiding feelings and reality, while seeking acknowledgment of suffering. Patient insight may decrease health care use. Therefore, the exploration of patient experiences may be useful for women with somatization disorder and a history of childhood abuse. The risks of spousal abuse and denial and rejection in the physician-patient relationship could also be important.

Adolescent↗

Somatic gene therapy in otolaryngology-head and neck surgery.

The initial clinical trials of somatic gene therapy have demonstrated that gene transfer can be performed safely in a clinical setting and with public acceptance. These trials have focused attention on the broad applications of this technology in routine medical and surgical practice. This article reviews the reasons why somatic gene therapy could lead to significant improvements in clinical practice as well as specific therapies in otolaryngology-head and neck surgery. Early applications include the treatment of inherited diseases such as cystic fibrosis, new approaches for treating malignancies, new methods for enhancing tissue repair, and regeneration after plastic and reconstructive surgery, and the potential for using the thyroid as a target for somatic gene therapy. The following review will illustrate how somatic gene therapy may have a significant impact not only on the treatment of rare genetic diseases but on managing the common problems encountered by physicians and patients in daily practice.

Bone Transplantation↗

Somatic symptoms in primary affective disorder. Presence and relationship to the classification of depression.

The incidence and severity of somatic symptoms were determined in 132 patients with major depressive disorder and 80 normal controls. The role of somatic symptoms was analyzed in relation to the unipolar-bipolar division, Research Diagnostic Criteria (RDC) subtypes, hypersomnia, and appetite increase. The data suggest that the rate and level of somatic symptoms increased with the severity of depression and age, only appetite loss differentiated unipolar from bipolar patients, and the classic somatic symptoms of depression were present in most RDC subtypes and not exclusively associated with the "endogenous" subtype. Hypersomnia or increased appetite identified two overlapping depressive subgroups; patients in both groups were young and characterized by high interpersonal sensitivity. Hypersomniac depressed patients were less anxious and agitated; patients with increased appetite were more hostile and showed a greater decrease in libido than age-matched and sex-matched patients with neither symptom.

Adult↗

Hypochondriasis and somatization: two distinct aspects of somatoform disorders?

We investigated boundaries and overlap between somatization and hypochondriasis on different levels of psychopathology: (1) comorbidity between hypochondriasis and somatization on the level of diagnoses in the Diagnostic and Statistical Manual of Mental Disorders, Fourth Edition (DSM-IV; American Psychiatric Association, 1994): (2) comorbidity with other mental disorders; (3) differences in clinical characteristics: and (4) overlap on the level of psychometric measures. The sample consisted of 120 psycho somatic inpatients. Somatoform, hypochondriacal, and depressive symptomatology, cognitions about body and health, and further aspects of general symptomatology were investigated. Diagnoses of Axis I and II were based on DSM-IV Our results suggest a large overlap on the level of DSM-IV-diagnoses: only 3 of 31 hypochondriacal patients had no multiple somatoform symptoms, while 58 of 86 patients with multiple somatoform symptoms had no hypochondriasis. However, the overlap between hypochondriacal and somatization symptomatology on the level of psychometric measurement is only moderate, indicating that hypochondriasis is a markedly distinct aspect of somatoform disorders.

Adult↗

A comparison of self-devaluation and somatic suggestion content in depressive mood manipulation.

The Velten Mood Induction Procedure (VMIP), often used to manipulate depressive mood, has its effectiveness attributed to the self-devaluative content of its statements; this finding supports cognitive theories of depression. Recent research has suggested that somatic content is more important than self-devaluation content in producing depressive mood variations. To study this using the VMIP, a neutral condition and two modified depression conditions were used: Somatic and self-devaluation (N = 302). The results indicate that self-devaluative statements resulted in significantly more depressed affect than neutral Ss, but no more than somatic statements; this latter group, however, did not differ from neutral Ss. The results of the previous research indicating the importance of the somatic suggestion manipulations as having more influence than negative self-evaluative statements is questioned.

Adult↗

Cognitive and somatic item response pattern of pain patients, psychiatric patients, and hospital employees.

Standard psychological tests generally provide a single global score that reflects multidimensional constructs, such as depression and anxiety. This single score, however, integrates a range of item contents, including cognitive/affective, somatic, and behavioral characteristics of these multidimensional constructs. The present study was designed to compare the pattern of item endorsement among chronic pain patients (N = 50), psychiatric inpatients (N = 50), and hospital employees (N = 50) on the SCL-90-R (Derogatis, Rickels, & Rock, 1976). Pain patients reported the highest SCL-90 scale level of Somatization, while the psychiatric inpatients reported the highest level of Anxiety and Depression. Additionally, the within-scale pattern of item responses on the Anxiety and Depression scales differed among groups. Although psychiatric inpatients endorsed equivalent levels of somatic and cognitive items, the pain patients' reports of psychological distress were limited primarily to somatic signs of anxiety and depression. Thus, the interpretation of pain patients' psychological profiles and subsequent treatment recommendations may be inappropriate if based on normative data obtained from psychiatric and/or normal populations.

Anxiety↗

Somatization and malingering for workers' compensation applicants: a cross-cultural MMPI study.

A post hoc analysis was conducted of 60 Hispanics and 60 Caucasians who had filed claims under workers' compensation. The study examined cross-cultural differences of somatization and malingering as assessed by the MMPI. Somatization was assessed by analyzing two- and three-point code types based on scales 1 (Hs), 2 (D), and 3 (Hy) of the MMPI, using the cut-off criterion of T > or = 70. Malingering was determined by analysis of the dissimulation index from the MMPI (F-K > +9). Significant differences were found for somatization; Hispanics were more likely to somatize. Minimal differences were found between Hispanic and Caucasian subjects on the malingering scale.

Adolescent↗

Somatic Apc mutations are selected upon their capacity to inactivate the beta-catenin downregulating activity.

The APC gene, originally identified as the gene for familial adenomatous polyposis (FAP), is now considered as the true "gatekeeper" of colonic epithelial proliferation. Its main tumor suppressing activity seems to reside in the capacity to properly regulate intracellular beta-catenin signaling. Most somatic APC mutations are detected between codons 1286 and 1513, the mutation cluster region (MCR). This clustering can be explained either by the presence of mutation-prone sequences within the MCR, or by the selective advantage provided by the resulting truncated polypeptides. Here, a Msh2-deficient mouse model (Msh2(delta 7N) ) was generated and bred with Apc(1638N) and Apc(Min) that allowed the comparison of the somatic mutation spectra along the Apc gene in the different allelic combinations. Mutations identified in Msh2(delta 7N/delta 7N) tumors are predominantly dinucleotide deletions at simple sequence repeats leading to truncated Apc polypeptides that partially retain the 20 a.a. beta-catenin downregulating motifs. In contrast, the somatic mutations identified in the wild type Apc allele of Msh2(delta 7N/delta 7N) /Apc(+/1638N) and Msh2(delta 7N/delta 7N) /Apc(+/Min) tumors are clustered more to the 5' end, thereby completely inactivating the beta-catenin downregulating activity of APC. These results indicate that somatic Apc mutations are selected during intestinal tumorigenesis and that inactivation of the beta-catenin downregulating function of APC is likely to represent the main selective factor.

Adenomatous Polyposis Coli↗

Antigen persistence is required for somatic mutation and affinity maturation of immunoglobulin.

Whether germinal centers (GC) with follicular dendritic cell (FDC) clusters are the essential sites for affinity maturation of immunoglobulin is still controversial. To re-evaluate the role of GC / FDC in affinity maturation and somatic mutation in a defined antigen system, lymphotoxin-alpha(- / -) and TNF receptor I(- / -) mice, lacking GC / FDC, were immunized with (4-hydroxy-3-nitrophenyl) acetyl-sheep RBC (NP-SRBC). In contrast to soluble hapten-carrier systems, NP-SRBC allows us to compare affinity maturation in the presence or absence of adjuvant. These mice showed a dramatically impaired ability to generate high-affinity IgG to NP, but retained the ability to produce low-affinity anti-NP IgG when NP-SRBC was used in the absence of adjuvant. In contrast to wild-type mice, somatic mutation of the expressed IgG heavy chain gene was rarely detected in these GC / FDC-deficient mice. This suggests that GC / FDC are essential for affinity maturation. Trapping antigen-specific B cells inside the T cell zone of TNFRI(- / -) mice may prolong the interaction between T and B cells, which allows class switching but no further affinity maturation of IgG. Interestingly, GC / FDC-deficient mice could be induced to generate high-affinity, somatically mutated IgG antibodies by immunization with the same amount of NP-SRBC antigen emulsified in incomplete Freund's adjuvant or repeated immunization with the antigen alone. Thus, these data support a model in which prolonged availability of antigen is required for somatic mutation and affinity maturation, and FDC or adjuvants facilitate such processes by slowly releasing antigens.

Animals↗

Improvement in affinity and HIV-1 neutralization by somatic mutation in the heavy chain first complementarity-determining region of antibodies triggered by HIV-1 infection.

We assessed the impact of somatic hypermutation in the framework region 1 (FR1) and complementarity-determining region 1 (CDR1) of three clonally-related heavy chains from the human monovalent antigen-binding fragments Fab S19, S8 and S20 on gp120 binding and HIV-1 neutralization capacity. Nucleotide changes were introduced in the heavy chains to revert single and multiple amino acid residues, and two Fab libraries were constructed with the same light chain to express equivalent amounts of parental and reverted phage Fab. We studied the contribution of each amino acid replacement to antigen binding by calculating the frequency of phage Fab retrieval after competitive library selection on gp120. Whereas mutations in FR1 had no effect on antigen binding, somatic replacements in the CDR1 of the heavy chain (HCDR1) appeared to produce significant changes. In S19 HCDR1, somatic mutation of residue 32 reduced gp120 binding. In Fab S20, the Arg(30) and Asp(31) somatically replaced residues in HCDR1 improved antigen binding. Both of these residues are necessary to increase Fab binding to gp120; reversion of either residue alone results in a decrease in binding. The impact of these two replacements was confirmed by the greater neutralization capacity of S20 compared to the other Fab. Molecular modeling of S20 HCDR1 suggests that Arg(30) and Asp(31) are the main interaction sites for gp120, increasing antibody affinity and promoting the enhanced neutralization ability of S20. These findings are consistent with a gp120-driven process, supporting a role for affinity maturation and intraclonal evolution of HIV-1 neutralizing antibodies.

Amino Acid Sequence↗

Somatic control of protein synthesis in mammalian oocytes during maturation.

The extent to which signals from the follicular compartment regulate protein synthesis in sheep oocytes is considered. Evidence is derived from experiments on the control of actin synthesis and also from a quantitative analysis of protein synthesis in oocytes matured in follicles in which specific somatic signals have been altered. Actin represents about 10% of the total protein synthesized by oocytes enclosed by follicle cells but under 2% in denuded oocytes. Although follicle cells synthesize and release actin, no evidence of its uptake into oocytes has been obtained. Instead, the results suggest that regulatory signals of somatic origin are transmitted directly into the oocyte by intercellular transport. A variety of cell types in addition to those of follicular origin support actin synthesis in oocytes, provided only that functional communication between the somatic and germinal compartment is maintained. Finally, the results on precursor uptake, actin turnover and RNA inhibition, and those of Dawn Giebelhaus on actin mRNA measurements, indicate that the somatic signals act on post-transcriptional events, possibly by influencing the mobilization of stored actin message. The selective inhibition of 17 alpha-hydroxylase in follicles depresses oestrogen and androgen and enhances progesterone biosynthesis. These steroid alterations, if induced during the first 8 h of maturation, lead to developmental abnormalities at fertilization. In addition, these steroidogenic changes alter the synthesis of a small number of acidic proteins in the maturing oocyte. It is postulated that steroid signals regulate the synthesis of certain proteins associated specifically with maturation.

Actins↗

Somatic mosaicism in FSHD often goes undetected.

Autosomal dominant facioscapulohumeral muscular dystrophy (FSHD1A) is associated with contractions of the polymorphic D4Z4 repeat array on chromosome 4qter. The disease has a high frequency of new mutations of mitotic origin. Pulsed-field gel electrophoresis-based studies show that mitotic mutations leading to somatic mosaicism occur equally frequently in patients and parents. Nevertheless, somatic mosaicism in FSHD is mainly reported in asymptomatic parents by applying standard Southern analysis after linear gel electrophoresis. Explaining this apparent discrepancy, we here demonstrate that somatic mosaicism in FSHD patients goes largely undetected using the standard diagnostic technique, indicating that linear electrophoresis is unsuitable to identify mosaic patients. As a consequence, the phenotype of mosaic patient's offspring will be underestimated, whereas the recurrence risk in the symptomatic mosaic individuals will be overestimated. Moreover, somatic mosaicism may partly explain the observation of anticipation in de novo kindreds. Therefore, clinicians should always consider pulsed-field gel electrophoresis analysis in de novo FSHD families, in particular when the patient's phenotype is much milder than expected based on D4Z4 length proper.

Adult↗

Central projections of thoracic splanchnic and somatic nerves and the location of sympathetic preganglionic neurons in Xenopus laevis.

The central and peripheral organization of thoracic visceral and somatic nervous elements was studied by applying dextran amines to the proximal cut ends of the thoracic splanchnic and somatic nerves in Xenopus laevis. Many labeled dorsal root ganglion cells of visceral afferents, and all somatic afferents, were located in a single ganglion of one spinal segment, and the two types of cells were distributed topographically within the ganglion. The labeled sympathetic preganglionic neurons were located predominantly in the same area of the thoracic spinal gray as in other frogs and in mammals. The labeled visceral afferents projected to Lissauer's tract and the dorsal funiculus. The visceral fibers of the tract ascended to the level of the subcerebellar area, supplying collateral branches to the lateral one-third of the dorsal horn and to the area of brainstem nuclei, including lateral cervical and descending trigeminal nucleus, and descended to the filum terminale. The visceral fibers of the dorsal funiculus were distributed to the dorsal column nucleus and the solitary tract. A similar longitudinal projection was also seen in the somatic afferents. The dual central pathway of thoracic primary afferents in the anuran spinal cord is a property held in common with mammals, but the widespread rostrocaudal projection through Lissauer's tract may be a characteristic of the anuran central nervous system. In frogs, the direct transmission of primary afferent information to an extremely wide area of the central nervous system may be important for prompt assessment of environmental factors and control of body functions.

Afferent Pathways↗

The laminar distribution and ultrastructure of fibers projecting from three thalamic nuclei to the somatic sensory-motor cortex of the opossum.

The projections of the ventrobasal complex (VB), the ventrolateral complex (VL), and the central intralaminar nucleus (CIN) to the somatic sensory-motor (SSM) cortex of the Virginia opossum were studied with light and electron microscopic autoradiographic methods. VB, VL, and CIN have overlapping projections to SSM cortex and each one also projects to an additional cortical area. Unit responses to somatic sensory stimulation and the areal and laminar distribution of axons in cortex is different for VB, VL, and CIN, but the axons from each form similar round asymmetrical synapses, predominantly with dendritic spines. As in other mammals, VB units in the opossum have discrete, contralateral cutaneous receptive fields. VB projects somatotopically to SSM cortex and also projects to the second somatic sensory representation. Within the cortex, VB axons terminate densely in layer IV and the adjacent part of layer III. A few axons also terminate in the outermost part of layer I and the upper part of layer VI. Most VB axons terminate upon dendritic spines (86.6%), but they also contact dendritic shafts (10%) and neuronal cell bodies (3%). Neurons in VL have no reliable response to somatic stimulation under our recording conditions. VL projects to the SSM cortex and to the posterior parietal area. Throughout this entire projection field VL fibers terminate in layers I, III, and IV most densely, and sparsely in the other cortical layers. The density of termination in the mid-cortical laminae is quite sparse compared to VB, but the projection to layer I is considerably greater. Nearly all (93%) of VL axons contact dendritic spines, the remainder (7%) end on dendritic shafts. CIN is a thalamic target of ascending medial lemniscal, cerebellar, spinal, and reticular formation axons. Neurons in CIN respond to stimulation restricted to a particular body part, but typically responses may be evoked from larger areas and at longer latencies than neurons in VB that are related to the same body part. CIN neurons require a firm tap or electrical stimulation within their receptive field to elicit a response in the anesthetized preparation. CIN axons terminate throughout the entire parietal cortex, but unlike VB and VL, CIN fibers end almost exclusively in the outer part of layer I. Approximately 21% of CIN fibers contact dendritic shafts in layer I, which is twice the percentage of shafts contacted by VL or VB axons. All of the other CIN synapses are formed with dendritic spines. These experiments demonstrate three different pathways to SSM cortex. The results suggest that each projection has a unique role in controlling the patterns of activity of neurons within the SSM cortex.

Animals↗