Chloroplast proteomics: potentials and challenges

With the available Arabidopsis genome and near-completion of the rice genome sequencing project, large-scale analysis of plant proteins with mass spectrometry has now become possible. Determining the proteome of a cell is a challenging task, which is complicated by proteome dynamics and complexity. The biochemical heterogeneity of proteins constrains the use of standardized analytical procedures and requires demanding techniques for proteome analysis. Several proteome studies of plant cell organelles have been reported, including chloroplasts and mitochondria. Chloroplasts are of particular interest for plant biologists because of their complex biochemical pathways for essential metabolic functions. Information from the chloroplast proteome will therefore provide new insights into pathway compartmentalization and protein sorting. Some approaches for the analysis of the chloroplast proteome and future prospects of plastid proteome research are discussed here.     

Increased leaf mesophyll porosity following transient retinoblastoma‐related protein silencing is revealed by microcomputed tomography imaging and leads to a system‐level physiological response to the altered cell division pattern

The causal relationship between cell division and growth in plants is complex. Although altered expression of cell‐cycle genes frequently leads to altered organ growth, there are many examples where manipulation of the division machinery leads to a limited outcome at the level of organ form, despite changes in constituent cell size. One possibility, which has been under‐explored, is that altered division patterns resulting from manipulation of cell‐cycle gene expression alter the physiology of the organ, and that this has an effect on growth. We performed a series of experiments on retinoblastoma‐related protein (RBR), a well characterized regulator of the cell cycle, to investigate the outcome of altered cell division on leaf physiology. Our approach involved combination of high‐resolution microCT imaging and physiological analysis with a transient gene induction system, providing a powerful approach for the study of developmental physiology. Our investigation identifies a new role for RBR in mesophyll differentiation that affects tissue porosity and the distribution of air space within the leaf. The data demonstrate the importance of RBR in early leaf development and the extent to which physiology adapts to modified cellular architecture resulting from altered cell‐cycle gene expression.     

Severity of COVID-19 among solid organ transplant recipients in Canada, 2020–2021: a prospective,multicentre cohort study

Background:Severe COVID-19 appears to disproportionately affect people who are immunocompromised, although Canadian data in this context are limited. We sought to determine factors associated with severe COVID-19 outcomes among recipients of organ transplants across Canada.Methods:We performed a multicentre, prospective cohort study of all recipients of solid organ transplants from 9 transplant programs in Canada who received a diagnosis of COVID-19 from March 2020 to November 2021. Data were analyzed to determine risk factors for oxygen requirement and other metrics of disease severity. We compared outcomes by organ transplant type and examined changes in outcomes over time. We performed a multivariable analysis to determine variables associated with need for supplemental oxygen.Results:A total of 509 patients with solid organ transplants had confirmed COVID-19 during the study period. Risk factors associated with needing (n = 190), compared with not needing (n = 319), supplemental oxygen included age (median 62.6 yr, interquartile range [IQR] 52.5–69.5 yr v. median 55.5 yr, IQR 47.5–66.5; p < 0.001) and number of comorbidities (median 3, IQR 2–3 v. median 2, IQR 1–3; p < 0.001), as well as parameters associated with immunosuppression. Recipients of lung transplants (n = 48) were more likely to have severe disease with a high mortality rate (n = 15, 31.3%) compared with recipients of other organ transplants, including kidney (n = 48, 14.8%), heart (n = 1, 4.4%), liver (n = 9, 11.4%) and kidney–pancreas (n = 3, 12.0%) transplants (p = 0.02). Protective factors against needing supplemental oxygen included having had a liver transplant and receiving azathioprine. Having had 2 doses of SARS-CoV-2 vaccine did not have an appreciable influence on oxygen requirement. Multivariable analysis showed that older age (odds ratio [OR] 1.04, 95% confidence interval [CI] 1.02–1.07) and number of comorbidities (OR 1.63, 95% CI 1.30–2.04), among other factors, were associated with the need for supplemental oxygen. Over time, disease severity did not decline significantly.Interpretation:Despite therapeutic advances and vaccination of recipients of solid organ transplants, evidence of increased severity of COVID-19, in particular among those with lung transplants, supports ongoing public health measures to protect these at-risk people, and early use of COVID-19 therapies for recipients of solid organ transplants.

Recipients of solid organ transplants take life-long immunosuppressive agents to prevent rejection. In Canada, an estimated 3000 transplant procedures are performed annually and 40 000 people are living with a transplant. Early studies from Europe and the United States suggested that transplant recipients were at greater risk of severe COVID-19, with a two- to fivefold greater mortality than the general population.^1–3 It is unclear whether the increased risk is owing to multiple comorbidities, immunosuppression or a combination of both factors.Initial trials of therapeutics for SARS-CoV-2, including remdesivir, dexamethasone and tocilizumab, did not formally include transplant recipients.^4–6 Similarly, pivotal studies of the SARS-CoV-2 vaccines did not include immunocompromised populations.^7,8 Therefore, the use of COVID-19 therapeutics and SARS-CoV-2 vaccines in the transplant population has been extrapolated from the general population. Commonly used COVID-19 therapies such as dexamethasone and tocilizumab may place transplant recipients at risk of over-immunosuppression, which may result in secondary infections. In addition, withdrawal of standard immunosuppression may result in organ rejection.Previous cohort studies of transplant recipients with COVID-19 have primarily focused on the early phase of the pandemic, when therapeutics and vaccinations were limited.^2,9,10 These have generally been single-centre studies with short-term follow-up. Canadian data may differ from that of other countries owing to differences in timing and strategy of vaccine rollouts, as well as use and availability of certain therapeutics. Moreover, current data are limited with regard to longer-term outcomes of COVID-19 in transplant recipients up to 90 days postinfection, especially for the development of graft rejection.We sought to determine factors associated with severe COVID-19 outcomes, to estimate the impact of available therapeutics on COVID-19 severity and to determine whether disease severity changed over the course of the pandemic among recipients of solid organ transplants from 9 centres in Canada.     

A simple method to evaluate biofilm formation in exopolysaccharide-producing strains of Sinorhizobium meliloti

ABSTRACT

Sinorhizobium meliloti

is a bacterium of great agroeconomic importance because of its ability to fix atmospheric nitrogen in symbiotic association with alfalfa (Medicago sativa) roots, and it is often used in model studies. We investigated the effects of exopolysaccharides (EPSs) in cell-to-cell and cell-to-surface interactions in S. meliloti. The microtiter plate assay, a quantitative spectrophotometric method, is used to study bio?lm formation by bacterial adherence to an abiotic surface. It consists in staining biofilms grown in microtiter plates. Here, we describe two microbiology laboratory classes designed for undergraduate students of Experimental Biological Chemistry, in which they learn about biofilm forming capacity by observing the behavior of both wild-type and mutant strains of S. meliloti.     

Specific responses in rat small intestinal epithelial mRNA expression and protein levels during chemotherapeutic damage and regeneration.

The rapidly dividing small intestinal epithelium is very sensitive to the cytostatic drug methotrexate. We investigated the regulation of epithelial gene expression in rat jejunum during methotrexate-induced damage and regeneration. Ten differentiation markers were localized on tissue sections and quantified at mRNA and protein levels relative to control levels. We analyzed correlations in temporal expression patterns between markers. mRNA expression of enterocyte and goblet cell markers decreased significantly during damage for a specific period. Of these, sucrase-isomaltase (-62%) and CPS (-82%) were correlated. Correlations were also found between lactase (-76%) and SGLT1 (-77%) and between I-FABP (-52%) and L-FABP (-45%). Decreases in GLUT5 (-53%), MUC2 (-43%), and TFF3 (-54%) mRNAs occurred independently of any of the other markers. In contrast, lysozyme mRNA present in Paneth cells increased (+76%). At the protein level, qualitative and quantitative changes were in agreement with mRNA expression, except for Muc2 (+115%) and TFF3 (+81%), which increased significantly during damage, following independent patterns. During regeneration, expression of each marker returned to control levels. The enhanced expression of cytoprotective molecules (Muc2, TFF3, lysozyme) during damage represents maintenance of goblet cell and Paneth cell functions, most likely to protect the epithelium. Decreased expression of enterocyte-specific markers represents decreased enterocyte function, of which fatty acid transporters were least affected.     

DISCLOSE : DISsection of CLusters Obtained by SEries of transcriptome data using functional annotations and putative transcription factor binding sites

Background  

A typical step in the analysis of gene expression data is the determination of clusters of genes that exhibit similar expression patterns. Researchers are confronted with the seemingly arbitrary choice between numerous algorithms to perform cluster analysis.     

Anorexia Nervosa: The Diagnosis

This paper argues that there is a relationship between understandings of anorexia nervosa (AN) and how the ethical issues associated with involuntary treatment for AN are identified, framed, and addressed. By positioning AN as a construct/discourse (hereinafter “AN: the diagnosis”) several ethical issues are revealed. Firstly, “AN: the diagnosis” influences how the autonomy and competence of persons diagnosed with AN are understood by decision-makers in the treatment environment. Secondly, “AN: the diagnosis” impacts on how treatment and treatment efficacy are defined and the ethical justifiability of paternalism. Thirdly, “AN: the diagnosis” can limit the opportunity for persons with AN to construct an identity that casts them as a competent person. “AN: the diagnosis” can thus inherently affirm professional knowledge and values. Postmodern professional ethics can support professionals in managing these issues by highlighting the importance of taking responsibility for professional knowledge, values, and power and embracing moral uncertainty.