Codon Usage Heterogeneity in the Multipartite Prokaryote Genome: Selection-Based Coding Bias Associated with Gene Location, Expression Level, and Ancestry.

Prokaryotes represent an ancestral lineage in the tree of life and constitute optimal resources for investigating the evolution of genomes in unicellular organisms. Many bacterial species possess multipartite genomes offering opportunities to study functional variations among replicons, how and where new genes integrate into a genome, and how genetic information within a lineage becomes encoded and evolves. To analyze these issues, we focused on the model soil bacterium Sinorhizobium meliloti, which harbors a chromosome, a chromid (pSymB), a megaplasmid (pSymA), and, in many strains, one or more accessory plasmids. The analysis of several genomes, together with 1.4 Mb of accessory plasmid DNA that we purified and sequenced, revealed clearly different functional profiles associated with each genomic entity. pSymA, in particular, exhibited remarkable interstrain variation and a high density of singletons (unique, exclusive genes) featuring functionalities and modal codon usages that were very similar to those of the plasmidome. All this evidence reinforces the idea of a close relationship between pSymA and the plasmidome. Correspondence analyses revealed that adaptation of codon usages to the translational machinery increased from plasmidome to pSymA to pSymB to chromosome, corresponding as such to the ancestry of each replicon in the lineage. We demonstrated that chromosomal core genes gradually adapted to the translational machinery, reminiscent of observations in several bacterial taxa for genes with high expression levels. Such findings indicate a previously undiscovered codon usage adaptation associated with the chromosomal core information that likely operates to improve bacterial fitness. We present a comprehensive model illustrating the central findings described here, discussed in the context of the changes occurring during the evolution of a multipartite prokaryote genome.IMPORTANCE Bacterial genomes usually include many thousands of genes which are expressed with diverse spatial-temporal patterns and intensities. A well-known evidence is that highly expressed genes, such as the ribosomal and other translation-related proteins (RTRPs), have accommodated their codon usage to optimize translation efficiency and accuracy. Using a bioinformatic approach, we identify core-genes sets with different ancestries, and demonstrate that selection processes that optimize codon usage are not restricted to RTRPs but extended at a genome-wide scale. Such findings highlight, for the first time, a previously undiscovered adaptation strategy associated with the chromosomal-core information. Contrasted with the translationally more adapted genes, singletons (i.e., exclusive genes, including those of the plasmidome) appear as the gene pool with the less-ameliorated codon usage in the lineage. A comprehensive summary describing the inter- and intra-replicon heterogeneity of codon usages in a complex prokaryote genome is presented.

Psychological and Emotional Aspects in Living Donor Kidney Transplantation.

BACKGROUND: The decision to resort to living donor transplantation determines a particular condition characterized by a strong mental and emotional anguish, both for the patients and their families. The purpose of the study was to correlate the relational dynamics between donor-recipient, donor/recipient couple with the health team, and the family support perceived by the couple with the quality of life 6 months before transplant and 12 months after transplant and compare the data between the 2 time points after participating in the psychotherapy program of counseling about behavioral change. PATIENTS AND METHODS: Twenty-seven donor and recipient pairs consented to participate. The quality of life was studied through the Complete Form Health Survey (SF-36). All subjects completed a questionnaire that investigated the 3 types of fundamental relationships (donor-recipient, donor/recipient with the health team, and family support perceived by the couple). All participants were involved in an 18-month psychotherapy program in the pre- and post-transplant phase. RESULTS: The quality of the donor-recipient relationship significantly positively influences the subjective perception of psychophysical well-being before and after transplant. Post-transplant family support is crucial in ensuring a good perception of psychological and emotional health in donors and recipients. The relationship with the health team is important in ensuring a good perception of psychophysical health only in recipients after transplant. CONCLUSIONS: This study suggests that patients should be assisted by a multidisciplinary health care team and receive continuous support from relatives during the post-transplant adaptation process. This facilitates the donor and recipient postoperative quality of life.

Return to Work and Quality of Life: A Psychosocial Survey After Kidney Transplant.

BACKGROUND: The main goals of kidney transplantation are to recreate a condition of psychophysical well-being and to improve the quality of life of the patient, including going back to work after transplant. Returning to work after a kidney transplant is an important health care indicator. The aim of the study was to assess the psychophysical well-being and work condition in kidney transplant recipients and to identify possible predictors of return to work. PATIENTS AND METHODS: A total of 81 patients (mean age, 46.3; SD, 11.47) were selected among patients undergoing 1 or more kidney transplants during follow-up 12 months after transplant. Pre- and post-transplant employment were evaluated using a sociodemographic schedule. Short Form Health Survey 36 was used for the quality of life study. RESULTS: Only 38.3% of patients were back to work 12 months after transplant compared with 67.90% of pretransplant patients (P = .004). The unemployment rate increased from 32.1% to 61.7% (P = .005) after kidney transplant. The reasons for not returning to work included the type of work (eg, factory) and the disability pension. The sociodemographic characteristics of the study population was significantly correlated with the dimensions of the Short Form Health Survey 36. CONCLUSIONS: Kidney transplant recipients should be encouraged to go back to work until it is a risk to physical health. In this regard, there is a need for multidisciplinary collaboration with the psychologist and the psychiatrist on the team, which provides psychological support and cures any psychological fragility in the post-transplant condition.

Mesorhizobium sanjuanii sp. nov., isolated from nodules of Lotus tenuis in the saline-alkaline lowlands of Flooding Pampa, Argentina.

Two rhizobial strains, BSA136T and BSA150, related to the genus Mesorhizobium were isolated from root nodules of Lotus tenuis grown in saline-alkaline lowlands soil from Argentina. These strains showed different repetitive element palindromic PCR fingerprinting patterns but shared more than 99 % sequence similarity for both 16S rRNA and recA genes. Despite the symbiotic nodC gene sequences of our strains being related to the canonical Lotus biovar species comprising Mesorhizobium loti and Mesorhizobium japonicum, the 16S rRNA phylogenetic marker suggests that their taxonomical identities are closely related to Mesorhizobium helmanticense, Mesorhizobium metallidurans, Mesorhizobium thianshanense, Mesorhizobium gobiense and Mesorhizobium tarimense. Multilocus sequence analysis performed with seven housekeeping genes confirmed that BSA136T belongs to a separate clade within the genus Mesorhizobium. The results of comparisons for in silico DNA-DNA hybridization and average nucleotide identity indexes between the genomes of BSA136T and closest-related Mesorhizobium species were below the threshold for species delineation. Phenotypic features differentiated BSA136T from its closest-related species. On the basis of our results, BSA136T and BSA150 can be considered to represent a novel species of the genus Mesorhizobium, for which the name Mesorhizobium sanjuanii sp. nov. is hereby proposed. The type strain of this species is BSA136T (=CECT 9305T=LMG 30060T), for which the draft genome sequence is available.

Nasal cytology: Methodology with application to clinical practice and research.

Nasal cytology is an easy, cheap, non-invasive and point-of-care method to assess nasal inflammation and disease-specific cellular features. By means of nasal cytology, it is possible to distinguish between different inflammatory patterns that are typically associated with specific diseases (ie, allergic and non-allergic rhinitis). Its use is particularly relevant when other clinical information, such as signs, symptoms, time-course and allergic sensitizations, is not enough to recognize which of the different rhinitis phenotypes is involved; for example, it is only by means of nasal cytology that it is possible to distinguish, among the non-allergic rhinitis, those characterized by eosinophilic (NARES), mast cellular (NARMA), mixed eosinophilic-mast cellular (NARESMA) or neutrophilic (NARNE) inflammation. Despite its clinical usefulness, cheapness, non-invasiveness and easiness, nasal cytology is still underused and this is at least partially due to the fact that, as far as now, there is not a consensus or an official recommendation on its methodological issues. We here review the scientific literature about nasal cytology, giving recommendations on how to perform and interpret nasal cytology.

Alexithymia in Kidney Transplantation Patients.

Alexithymia is a marked difficulty in recognizing, exploring, and expressing inner feelings. Studies have proven the presence of a significant proportion of patients with alexithymia in samples from the transplantation population. This study aims to analyze the presence of alexithymia in a sample of 32 kidney transplantation patients from a deceased donor and to compare this construct with the presence of psychological symptoms and the physical and mental state of health perceived by the patients. Alexithymia assessment was analyzed using the Toronto Alexithymia Scale. The psychological symptoms were studied through the Symptom Checklist-90-R. The quality of life was studied through The Complete Form Health Survey. The study showed a high percentage of the presence of alexithymia in the examined transplant recipients. The construct is more present where the perception of their quality of life is low and where there is a greater presence of psychosomatic symptoms.

A consolidated analysis of the physiologic and molecular responses induced under acid stress in the legume-symbiont model-soil bacterium Sinorhizobium meliloti.

Abiotic stresses in general and extracellular acidity in particular disturb and limit nitrogen-fixing symbioses between rhizobia and their host legumes. Except for valuable molecular-biological studies on different rhizobia, no consolidated models have been formulated to describe the central physiologic changes that occur in acid-stressed bacteria. We present here an integrated analysis entailing the main cultural, metabolic, and molecular responses of the model bacterium Sinorhizobium meliloti growing under controlled acid stress in a chemostat. A stepwise extracellular acidification of the culture medium had indicated that S. meliloti stopped growing at ca. pH 6.0-6.1. Under such stress the rhizobia increased the O2 consumption per cell by more than 5-fold. This phenotype, together with an increase in the transcripts for several membrane cytochromes, entails a higher aerobic-respiration rate in the acid-stressed rhizobia. Multivariate analysis of global metabolome data served to unequivocally correlate specific-metabolite profiles with the extracellular pH, showing that at low pH the pentose-phosphate pathway exhibited increases in several transcripts, enzymes, and metabolites. Further analyses should be focused on the time course of the observed changes, its associated intracellular signaling, and on the comparison with the changes that operate during the sub lethal acid-adaptive response (ATR) in rhizobia.

Patterns of Personality in Living Kidney Donors.

BACKGROUND: The decision to undergo living donor transplantation determines a particular condition characterized by strong mental and emotional anguish, both for the patient and his family. Many recent studies showed the concern of living donors who, rather than being driven by altruistic reasons, meet the decision to donate with ambivalence, liabilities, and/or in response to family pressures. The aim of this study was to analyze the more frequently encountered personality variables in a sample of potential kidney living donors, together with any psychological variables that can express possible risks of an impulsive decision and/or poorly processed from a cognitive and emotional point of view. METHODS: We examined 32 potential kidney donors. The personality study was performed using The Millon Clinical Multiaxial Inventory-III. The psychic symptoms were studied through the Symptom Checklist-90-R. The quality of life was studied through the Complete Form Health Survey (SF-36). RESULTS: The study showed that the ability to express free and therefore invalid consent, in the role of donor, is an expression of specific personality patterns, cognitive, emotional aspects and interpersonal experiences. CONCLUSIONS: The psychological-psychiatric evaluation of potential donors is fundamental to certify the state of mental health and psychological well-being, an indispensable prerequisite for the donation.

A Study on Emotional-Affective Aspects and the Perception of General Health in Kidney Transplant Subjects.

BACKGROUND: Transplantation has profound psychological implications. Psychodiagnostic assessments with structured instruments (scales, questionnaires) may be insufficient for bringing out the deeper aspects of the personality. PATIENTS AND METHODS: Thirty kidney transplant recipients underwent the Thematic Apperception Test to detect significant variables hypothetically related to characteristics of the study sample and the SF-36 to assess quality of life. RESULTS: The variable of Thematic Apperception Test (TAT) "communication difficulties" was significantly correlated with the dimensions of the SF-36 "emotional role functioning," "social activities," and "mental health." The dimension of SF-36 "general health" did not interfere with the variable of TAT "constricted effect." CONCLUSIONS: This study is considered to be particularly useful in detecting the emergence of "removed difficulties" that transplanted subjects are not inclined to recognize. The analysis of these aspects is necessary to plan individualized psychotherapy pathways.

Somatopsychic correlates and quality of life of the dialyzed patient: a cross-sectional study.

BACKGROUND: The dialysis delivered after a chronic kidney disease (CDK) or any otherwise severe end-stage renal failure is a complex medical task, leading to major medical and psychopathological distress for the patient. The aim of the present study was to analyze the impact of the dialysis experience on the nephrologic patient's global quality of life. METHODS: In the present cross-sectional study, involving 96 patients with end-stage renal disease receiving hemodialysis, demographic, medical, and psychological differential features across different CDK diagnoses were accounted and were then correlated each other. RESULTS: Among other differential features, the "acknowledgement of dependence" (from the medical device delivering the dialysis) emerged as a factor correlated to "self-sufficiency" in CDK patients receiving hemodialysis. CONCLUSIONS: Although further, larger-sampled studies on the topic are needed, medical and psychological interventions are useful to ensure a better global quality of life and good therapeutic adherence in dialysis patients.

Role of "self-efficacy" in the process of long-term care in kidney transplant recipients.

OBJECTIVE: This study investigated the relationship between self-efficacy, quality of life, and psychic dimensions of patients with kidney transplants. Given the considerable emotional implications and the risk of psychopathology after transplantation, a protective role is assumed of the sense of self-efficacy, both from any psychopathologic disorders and from a precarious quality of life. METHODS: One hundred twenty recipients of kidney transplants from deceased donors were included in the study. The self-efficacy study was performed with the use of the General Self-Efficacy Scale. The quality of life of the subjects was studied with the use of the Short-Form Health Survey; The psychic symptoms of patients were performed using the Revised Symptom Checklist 90 (SCL-90R). RESULTS: Self-efficacy is positively correlated with both physical role limitations and mental health. With increasing self-efficacy there was a decrease of psychic symptoms as investigated with the use of the SCL-90R test. CONCLUSIONS: This study demonstrated the "protective" function of the sense of self-efficacy in the psychic sphere and its positive effect on quality of life, in the sense that an appropriate problem-solving strategy helps the transplant patient to maintain good mental and physical health.

The concept of self and emotional involvement in living kidney donation: a psychometric investigation.

OBJECTIVE: The aim of our study was to analyze, from a psychological point of view, living kidney donor personality, examining a sample of 18 living kidney donors. PATIENTS AND METHODS: The personality study was performed using The Millon Clinical Multiaxial Inventory-III in 18 potential kidney donors, 6 of whom were genetically and 12 emotionally related individuals. RESULTS: Our study showed the presence of narcissistic, histrionic, and obsessive-compulsive personality traits in living kidney donors. CONCLUSIONS: It is necessary to explore the development of motivation for living donation in order to achieve and maintain a harmonious relationship with the recipient while respecting their individuality.

The study of personality in renal transplant patients: possible predictor of an adequate social adaptation?

BACKGROUND: This study explored the personality characteristic traits within a sample of renal transplant patients, seeking to obtain predictive index for likely clinical impacts. PATIENTS AND METHODS: The personality study was performed using the Structured Clinical Interview Axis II Personality Disorders for Diagnostic and Statistical Manual of Mental Disorders fourth edition, text revision in 60 recipients of kidney transplantations from deceased donors. RESULTS: The personality trait that prevailed in the female gender was borderline, while in the male gender it appeared to be predominantly obsessive-compulsive personality trait. CONCLUSIONS: The personality study proved to be a good index to predict effects on the level of social adjustment. In this way, patients who have shown pathologic personality traits can be identified early to provide adequate psychologic-psychiatric support and follow-up.

Correlational study between psychic symptoms and quality of life among hemodialysis patients older than 55 years of age.

BACKGROUND: The loss of renal function and urination with dialysis can produce a strong emotional crisis in a patient. This study explored the correlation between psychic symptoms and quality of life among hemodialysis patients who were older than 55 years of age in relation to demographic characteristics of age, time on dialysis, and education. PATIENTS AND METHODS: Twenty patients undergoing hemodialysis were included in the study. The psychic symptoms were studied using the Symptom Checklist-90. Revised (SCL-90 R) and the quality of life was studied using the Complete Form Health Survey (SF 36). RESULTS: The high correlation between psychological sizes investigated through the SCL-90 R test and those for the SF-36 test confirmed the close relationship between physical disorders and mental suffering, and reduced vitality, and lack of socialization. CONCLUSION: The psychiatrist and psychologist may help hemodialysis patients to improve their quality of life by providing new coping strategies for each of the family, occupational, and social network.

Development of new positive-selection RIVET tools: detection of induced promoters by the excision-based transcriptional activation of an aacCI (GmR)-gfp fusion.

RIVET (Recombination Based in vivo Expression Technology) is a powerful genetic tool originally conceived for the identification of genes induced in complex biological niches where conventional transcriptomics is difficult to use. With a broader application, genetic recombination-based technologies have also been used, in combination with regulatory proteins and specific transcriptional regulators, for the development of highly sensitive biosensor systems. RIVET systems generally comprise two modules: a promoter-trap cassette generating genomic transcriptional fusions to the tnpR gene encoding the Tn-γδ TnpR resolvase, and a reporter cassette carrying res-flanked selection markers that are excised upon expression of tnpR to produce an irreversible, inheritable phenotypic change. We report here the construction and validation of a new set of positive-selection RIVET systems that, upon induction of the promoter-trap module, generate the transcriptional activation of an antibiotic-resistant and a green-fluorescent phenotype. Two classes of promoter-trap tools were constructed to generate transcriptional fusions to tnpR: one based on the use of a narrow-host-range plasmid (pRIVET-I), integrative in several Gram-negative bacteria, and the other based on the use of a broad-host-range plasmid (pRIVET-R). The system was evaluated in the model soil bacterium Sinorhizobium meliloti, where a clear-cut phenotypic transition from Nm(R)-Gm(S)-GFP(-) to Nm(S)-Gm(R)-GFP(+) occurred upon expression of tnpR. A S. meliloti integrative RIVET library was constructed in pRIVET-I and, as expected, changes in the extracellular conditions (e.g., salt stress) triggered a significant increase in the appearance of Gm(R)-GFP(+) (excised) clones. The sacB-independent positive-selection RIVET systems here described provide suitable basic tools both for the construction of new recombination-based biosensors and for the search of bacterial markers induced when microorganisms colonize and invade complex environments and eukaryotic hosts.

Quality of life in kidney transplantation from marginal donors.

OBJECTIVE: Enhancement of the subjective components, recognition of overall needs, and careful consideration of subjectively perceived quality of life among dialysis and/or transplanted patients appear to be key objectives to promote optimized adherence to treatment and active cooperation of the patient. This study explores the relationship between self-rated health among recipients of kidney transplantations from deceased marginal donors (age older than 55 years) in relation to gender, age, time on dialysis, years after transplantation, and donor age. PATIENTS AND METHODS: Posttransplant quality of life was assessed with the Complete Form Health Survey (SF-36) in 70 recipients of kidney transplantations from marginal deceased donors. RESULTS: Donor age did not negatively influence health status perceived by the subjects. The vitality and mental health seemed to increase with greater donor ages, but the status of perceived health, vitality, social activities, and mental health were negatively influenced by the age of the transplant. CONCLUSIONS: Our study shows that good general health and social well-functioning can be achieved also among recipients of organs from older donors. Thus, age alone should not be a barrier to organ donation, providing that the organ function is normal and that specific disease is absent in the organ.

Body image in kidney transplantation.

INTRODUCTION: Psychologic disturbances are becoming more common in kidney transplantation, owing to effects of immunosuppressive therapy. In this study, we explored the incidence and specifity of psychopathology among kidney transplant patients. Twenty kidney transplant recipients underwent the Machover Draw-A-person test to detect significant variables (V1=V6) hypothetically related to chronologic age, education, years from transplantation, and gender differences. Emotional coarctation (V1) in the sense of "mental rigidity," "egocentrism," and "hypercontrol" were present in all transplant recipients (100%), followed by difficulty in interpersonal relationships (V3; 70%) and anxiety (V5; 70%). This research confirmed the hypothesis that transplantation can display a potential risk to the psychologic balance of the patient. Psychologic evaluation may be a fundamental step together with surgical aspects and management of immunosuppression to achieve well-being of kidney transplant recipients.

Identification and characterization of a nodH ortholog from the alfalfa-nodulating Or191-like rhizobia.

Nodulation of Medicago sativa (alfalfa) is known to be restricted to Sinorhizobium meliloti and a few other rhizobia that include the poorly characterized isolates related to Rhizobium sp. strain Or191. Distinctive features of the symbiosis between alfalfa and S. meliloti are the marked specificity from the plant to the bacteria and the strict requirement for the presence of sulfated lipochitooligosaccharides (Nod factors [NFs]) at its reducing end. Here, we present evidence of the presence of a functional nodH-encoded NF sulfotransferase in the Or191-like rhizobia. The nodH gene, present in single copy, maps to a high molecular weight megaplasmid. As in S. meliloti, a nodF homolog was identified immediately upstream of nodH that was transcribed in the opposite direction (local synteny). This novel nodH ortholog was cloned and shown to restore both NF sulfation and the Nif+Fix+ phenotypes when introduced into an S. meliloti nodH mutant. Unexpectedly, however, nodH disruption in the Or191-like bacteria did not abolish their ability to nodulate alfalfa, resulting instead in a severely delayed nodulation. In agreement with evidence from other authors, the nodH sequence analysis strongly supports the idea that the Or191-like rhizobia most likely represent a genetic mosaic resulting from the horizontal transfer of symbiotic genes from a sinorhizobial megaplasmid to a not yet clearly identified ancestor.

Intranasal steroid reduces exhaled bronchial cysteinyl leukotrienes in allergic patients.

BACKGROUND: Allergic rhinitis (AR) precedes and is often associated with bronchial asthma. Indeed, local and systemic inflammations in both conditions are very similar. Cysteinyl-leukotrienes (cys-LTs) are generated during early- and late-phase allergic reactions and induce smooth-muscle contraction, microvascular leakage, and mucous hypersecretion. Cys-LTs are detected in exhaled breath condensate (EBC) of asthmatics and regardless of bronchial symptoms, they are also found in EBC of rhinitic patients. OBJECTIVE: To evaluate cys-LTs in EBC of allergic patients and to assess the activity of nasal fluticasone propionate (FP) on EBC cys-LTs levels. METHODS: Cys-LTs coefficient of variation (CV) was evaluated from different EBC in 5 healthy volunteers. Cys-LTs levels from EBCs in 13 healthy controls and 56 allergic rhinitic (n=31) and rhinitic/asthmatic (n=25) patients were also evaluated at baseline. Subsequently patients were randomized to receive either FP 100 microg/day per nostril or placebo for 2 weeks and then re-evaluated for EBC cys-LTs. RESULTS: The CV was 14.12%. EBC cys-LTs in allergic patients were significantly higher than in healthy subjects (70.9 vs. 20.6 pg/mL (median), P<0.05), while it did not differ between asthmatic/rhinitic and purely rhinitic patients. Treatment significantly reduced cys-LTs (from 93.6 to 19.9 pg/mL, P<0.001). This effect was evident both in asthmatic/rhinitic and in rhinitic patients. CONCLUSION: Treatment of AR with FP significantly reduces the levels of cys-LTs, major noninvasive markers of lower airway inflammation, suggesting that upper and lower airway inflammation is present and should be thus treated as a whole in subjects with AR with and without asthma.